0.013592
0.000000
0.000000
0.000000
0.013592
0.000000
0.000000
0.000000
0.009456
0.00000
0.00000
0.00000
Wallden, K.
Ruzzenente, B.
Rinaldo-Matthis, A.
Bianchi, V.
Nordlund, P.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
73.572
73.572
105.748
C3 H7 N O2
89.093
y
ALANINE
L-peptide linking
C6 H15 N4 O2 1
175.209
y
ARGININE
L-peptide linking
C4 H8 N2 O3
132.118
y
ASPARAGINE
L-peptide linking
C4 H7 N O4
133.103
y
ASPARTIC ACID
L-peptide linking
C3 H7 N O2 S
121.158
y
CYSTEINE
L-peptide linking
C5 H10 N2 O3
146.144
y
GLUTAMINE
L-peptide linking
C5 H9 N O4
147.129
y
GLUTAMIC ACID
L-peptide linking
C2 H5 N O2
75.067
y
GLYCINE
peptide linking
C3 H8 O3
92.094
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
non-polymer
C6 H10 N3 O2 1
156.162
y
HISTIDINE
L-peptide linking
H2 O
18.015
WATER
non-polymer
C6 H13 N O2
131.173
y
ISOLEUCINE
L-peptide linking
C6 H13 N O2
131.173
y
LEUCINE
L-peptide linking
C6 H15 N2 O2 1
147.195
y
LYSINE
L-peptide linking
C5 H11 N O2 S
149.211
y
METHIONINE
L-peptide linking
Mg 2
24.305
MAGNESIUM ION
non-polymer
C9 H11 N O2
165.189
y
PHENYLALANINE
L-peptide linking
C5 H9 N O2
115.130
y
PROLINE
L-peptide linking
C3 H7 N O3
105.093
y
SERINE
L-peptide linking
C4 H9 N O3
119.119
y
THREONINE
L-peptide linking
C11 H12 N2 O2
204.225
y
TRYPTOPHAN
L-peptide linking
C9 H11 N O3
181.189
y
TYROSINE
L-peptide linking
C9 H13 N2 O9 P
324.181
URIDINE-5'-MONOPHOSPHATE
non-polymer
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
UK
STRUCTURE
STRUE6
2005
0969-2126
13
1081
1088
10.1016/j.str.2005.04.023
16004879
Structural basis for substrate specificity of the human mitochondrial deoxyribonucleotidase
2005
10.2210/pdb1z4m/pdb
pdb_00001z4m
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
1
CCD
2004-01-27
SINGLE WAVELENGTH
M
x-ray
1
1.0
X11
EMBL/DESY, HAMBURG
SYNCHROTRON
EMBL/DESY, HAMBURG BEAMLINE X11
22840.135
5'(3')-deoxyribonucleotidase
3.1.3.-
D41N
1
man
polymer
24.305
MAGNESIUM ION
1
syn
non-polymer
324.181
URIDINE-5'-MONOPHOSPHATE
1
syn
non-polymer
92.094
GLYCEROL
1
syn
non-polymer
18.015
water
163
nat
water
Mitochondrial deoxyribonucleotidase, 5',3'-nucleotidase, mitochondrial, Deoxy-5'-nucleotidase 2, dNT-2
no
no
GGRALRVLVNMDGVLADFEGGFLRKFRARFPDQPFIALEDRRGFWVSEQYGRLRPGLSEKAISIWESKNFFFELEPLPGA
VEAVKEMASLQNTDVFICTSPIKMFKYCPYEKYAWVEKYFGPDFLEQIVLTRDKTVVSADLLIDDRPDITGAEPTPSWEH
VLFTACHNQHLQLQPPRRRLHSWADDWKAILDSKRPC
GGRALRVLVNMDGVLADFEGGFLRKFRARFPDQPFIALEDRRGFWVSEQYGRLRPGLSEKAISIWESKNFFFELEPLPGA
VEAVKEMASLQNTDVFICTSPIKMFKYCPYEKYAWVEKYFGPDFLEQIVLTRDKTVVSADLLIDDRPDITGAEPTPSWEH
VLFTACHNQHLQLQPPRRRLHSWADDWKAILDSKRPC
A
polypeptide(L)
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
human
Homo
Escherichia
Escherichia coli
sample
9606
Homo sapiens
469008
Escherichia coli BL21(DE3)
BL21(DE3)
plasmid
plysS
1
2.8
55
4.5
pH 4.5
database_2
diffrn_source
pdbx_struct_conn_angle
struct_conn
struct_ref_seq_dif
struct_site
repository
Initial release
Version format compliance
Non-polymer description
Version format compliance
Data collection
Database references
Derived calculations
1
0
2005-07-26
1
1
2008-04-30
1
2
2011-07-13
1
3
2021-11-10
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_diffrn_source.pdbx_synchrotron_site
_pdbx_struct_conn_angle.ptnr1_auth_comp_id
_pdbx_struct_conn_angle.ptnr1_auth_seq_id
_pdbx_struct_conn_angle.ptnr1_label_alt_id
_pdbx_struct_conn_angle.ptnr1_label_asym_id
_pdbx_struct_conn_angle.ptnr1_label_atom_id
_pdbx_struct_conn_angle.ptnr1_label_comp_id
_pdbx_struct_conn_angle.ptnr1_label_seq_id
_pdbx_struct_conn_angle.ptnr3_auth_comp_id
_pdbx_struct_conn_angle.ptnr3_auth_seq_id
_pdbx_struct_conn_angle.ptnr3_label_alt_id
_pdbx_struct_conn_angle.ptnr3_label_asym_id
_pdbx_struct_conn_angle.ptnr3_label_atom_id
_pdbx_struct_conn_angle.ptnr3_label_comp_id
_pdbx_struct_conn_angle.ptnr3_label_seq_id
_pdbx_struct_conn_angle.value
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_ptnr1_label_alt_id
_struct_conn.pdbx_ptnr2_label_alt_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_ref_seq_dif.details
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
the same protein complexed with deoxyribouridine 5'-monophosphate
the same protein complexed with uridine 2'-monophosphate
the same protein complexed with thymidine 3'-monophosphate
the same protein complexed with thymidine 5'-monophosphate
the same protein complexed with deoxyriboguanosine 5'-monophosphate
the same protein complexed with 3'-deoxy 2'3'-didehydrothymidine 5'-monophosphate (d4T-MP)
RCSB
Y
PDBJ
2005-03-16
REL
REL
MG
MAGNESIUM ION
U5P
URIDINE-5'-MONOPHOSPHATE
GOL
GLYCEROL
HOH
water
MG
2001
2
MG
MG
2001
A
U5P
1001
3
U5P
U5P
1001
A
GOL
3001
4
GOL
GOL
3001
A
HOH
1
5
HOH
HOH
3002
A
HOH
2
5
HOH
HOH
3003
A
HOH
3
5
HOH
HOH
3004
A
HOH
4
5
HOH
HOH
3005
A
HOH
5
5
HOH
HOH
3006
A
HOH
6
5
HOH
HOH
3007
A
HOH
7
5
HOH
HOH
3008
A
HOH
8
5
HOH
HOH
3009
A
HOH
9
5
HOH
HOH
3010
A
HOH
10
5
HOH
HOH
3011
A
HOH
11
5
HOH
HOH
3012
A
HOH
12
5
HOH
HOH
3013
A
HOH
13
5
HOH
HOH
3014
A
HOH
14
5
HOH
HOH
3015
A
HOH
15
5
HOH
HOH
3016
A
HOH
16
5
HOH
HOH
3017
A
HOH
17
5
HOH
HOH
3018
A
HOH
18
5
HOH
HOH
3019
A
HOH
19
5
HOH
HOH
3020
A
HOH
20
5
HOH
HOH
3021
A
HOH
21
5
HOH
HOH
3022
A
HOH
22
5
HOH
HOH
3023
A
HOH
23
5
HOH
HOH
3024
A
HOH
24
5
HOH
HOH
3025
A
HOH
25
5
HOH
HOH
3026
A
HOH
26
5
HOH
HOH
3027
A
HOH
27
5
HOH
HOH
3028
A
HOH
28
5
HOH
HOH
3029
A
HOH
29
5
HOH
HOH
3030
A
HOH
30
5
HOH
HOH
3031
A
HOH
31
5
HOH
HOH
3032
A
HOH
32
5
HOH
HOH
3033
A
HOH
33
5
HOH
HOH
3034
A
HOH
34
5
HOH
HOH
3035
A
HOH
35
5
HOH
HOH
3036
A
HOH
36
5
HOH
HOH
3037
A
HOH
37
5
HOH
HOH
3038
A
HOH
38
5
HOH
HOH
3039
A
HOH
39
5
HOH
HOH
3040
A
HOH
40
5
HOH
HOH
3041
A
HOH
41
5
HOH
HOH
3042
A
HOH
42
5
HOH
HOH
3043
A
HOH
43
5
HOH
HOH
3044
A
HOH
44
5
HOH
HOH
3045
A
HOH
45
5
HOH
HOH
3046
A
HOH
46
5
HOH
HOH
3047
A
HOH
47
5
HOH
HOH
3048
A
HOH
48
5
HOH
HOH
3049
A
HOH
49
5
HOH
HOH
3050
A
HOH
50
5
HOH
HOH
3051
A
HOH
51
5
HOH
HOH
3052
A
HOH
52
5
HOH
HOH
3053
A
HOH
53
5
HOH
HOH
3054
A
HOH
54
5
HOH
HOH
3055
A
HOH
55
5
HOH
HOH
3056
A
HOH
56
5
HOH
HOH
3057
A
HOH
57
5
HOH
HOH
3058
A
HOH
58
5
HOH
HOH
3059
A
HOH
59
5
HOH
HOH
3060
A
HOH
60
5
HOH
HOH
3061
A
HOH
61
5
HOH
HOH
3062
A
HOH
62
5
HOH
HOH
3063
A
HOH
63
5
HOH
HOH
3064
A
HOH
64
5
HOH
HOH
3065
A
HOH
65
5
HOH
HOH
3066
A
HOH
66
5
HOH
HOH
3067
A
HOH
67
5
HOH
HOH
3068
A
HOH
68
5
HOH
HOH
3069
A
HOH
69
5
HOH
HOH
3070
A
HOH
70
5
HOH
HOH
3071
A
HOH
71
5
HOH
HOH
3072
A
HOH
72
5
HOH
HOH
3073
A
HOH
73
5
HOH
HOH
3074
A
HOH
74
5
HOH
HOH
3075
A
HOH
75
5
HOH
HOH
3076
A
HOH
76
5
HOH
HOH
3077
A
HOH
77
5
HOH
HOH
3078
A
HOH
78
5
HOH
HOH
3079
A
HOH
79
5
HOH
HOH
3080
A
HOH
80
5
HOH
HOH
3081
A
HOH
81
5
HOH
HOH
3082
A
HOH
82
5
HOH
HOH
3083
A
HOH
83
5
HOH
HOH
3084
A
HOH
84
5
HOH
HOH
3085
A
HOH
85
5
HOH
HOH
3086
A
HOH
86
5
HOH
HOH
3087
A
HOH
87
5
HOH
HOH
3088
A
HOH
88
5
HOH
HOH
3089
A
HOH
89
5
HOH
HOH
3090
A
HOH
90
5
HOH
HOH
3091
A
HOH
91
5
HOH
HOH
3092
A
HOH
92
5
HOH
HOH
3093
A
HOH
93
5
HOH
HOH
3094
A
HOH
94
5
HOH
HOH
3095
A
HOH
95
5
HOH
HOH
3096
A
HOH
96
5
HOH
HOH
3097
A
HOH
97
5
HOH
HOH
3098
A
HOH
98
5
HOH
HOH
3099
A
HOH
99
5
HOH
HOH
3100
A
HOH
100
5
HOH
HOH
3101
A
HOH
101
5
HOH
HOH
3102
A
HOH
102
5
HOH
HOH
3103
A
HOH
103
5
HOH
HOH
3104
A
HOH
104
5
HOH
HOH
3105
A
HOH
105
5
HOH
HOH
3106
A
HOH
106
5
HOH
HOH
3107
A
HOH
107
5
HOH
HOH
3108
A
HOH
108
5
HOH
HOH
3109
A
HOH
109
5
HOH
HOH
3110
A
HOH
110
5
HOH
HOH
3111
A
HOH
111
5
HOH
HOH
3112
A
HOH
112
5
HOH
HOH
3113
A
HOH
113
5
HOH
HOH
3114
A
HOH
114
5
HOH
HOH
3115
A
HOH
115
5
HOH
HOH
3116
A
HOH
116
5
HOH
HOH
3117
A
HOH
117
5
HOH
HOH
3118
A
HOH
118
5
HOH
HOH
3119
A
HOH
119
5
HOH
HOH
3120
A
HOH
120
5
HOH
HOH
3121
A
HOH
121
5
HOH
HOH
3122
A
HOH
122
5
HOH
HOH
3123
A
HOH
123
5
HOH
HOH
3124
A
HOH
124
5
HOH
HOH
3125
A
HOH
125
5
HOH
HOH
3126
A
HOH
126
5
HOH
HOH
3127
A
HOH
127
5
HOH
HOH
3128
A
HOH
128
5
HOH
HOH
3129
A
HOH
129
5
HOH
HOH
3130
A
HOH
130
5
HOH
HOH
3131
A
HOH
131
5
HOH
HOH
3132
A
HOH
132
5
HOH
HOH
3133
A
HOH
133
5
HOH
HOH
3134
A
HOH
134
5
HOH
HOH
3135
A
HOH
135
5
HOH
HOH
3136
A
HOH
136
5
HOH
HOH
3137
A
HOH
137
5
HOH
HOH
3138
A
HOH
138
5
HOH
HOH
3139
A
HOH
139
5
HOH
HOH
3140
A
HOH
140
5
HOH
HOH
3141
A
HOH
141
5
HOH
HOH
3142
A
HOH
142
5
HOH
HOH
3143
A
HOH
143
5
HOH
HOH
3144
A
HOH
144
5
HOH
HOH
3145
A
HOH
145
5
HOH
HOH
3146
A
HOH
146
5
HOH
HOH
3147
A
HOH
147
5
HOH
HOH
3148
A
HOH
148
5
HOH
HOH
3149
A
HOH
149
5
HOH
HOH
3150
A
HOH
150
5
HOH
HOH
3151
A
HOH
151
5
HOH
HOH
3152
A
HOH
152
5
HOH
HOH
3153
A
HOH
153
5
HOH
HOH
3154
A
HOH
154
5
HOH
HOH
3155
A
HOH
155
5
HOH
HOH
3156
A
HOH
156
5
HOH
HOH
3157
A
HOH
157
5
HOH
HOH
3158
A
HOH
158
5
HOH
HOH
3159
A
HOH
159
5
HOH
HOH
3160
A
HOH
160
5
HOH
HOH
3161
A
HOH
161
5
HOH
HOH
3162
A
HOH
162
5
HOH
HOH
3163
A
HOH
163
5
HOH
HOH
3164
A
n
1
32
A
n
2
33
A
ARG
34
n
3
ARG
34
A
ALA
35
n
4
ALA
35
A
LEU
36
n
5
LEU
36
A
ARG
37
n
6
ARG
37
A
VAL
38
n
7
VAL
38
A
LEU
39
n
8
LEU
39
A
VAL
40
n
9
VAL
40
A
ASN
41
n
10
ASN
41
A
MET
42
n
11
MET
42
A
ASP
43
n
12
ASP
43
A
GLY
44
n
13
GLY
44
A
VAL
45
n
14
VAL
45
A
LEU
46
n
15
LEU
46
A
ALA
47
n
16
ALA
47
A
ASP
48
n
17
ASP
48
A
PHE
49
n
18
PHE
49
A
GLU
50
n
19
GLU
50
A
GLY
51
n
20
GLY
51
A
GLY
52
n
21
GLY
52
A
PHE
53
n
22
PHE
53
A
LEU
54
n
23
LEU
54
A
ARG
55
n
24
ARG
55
A
LYS
56
n
25
LYS
56
A
PHE
57
n
26
PHE
57
A
ARG
58
n
27
ARG
58
A
ALA
59
n
28
ALA
59
A
ARG
60
n
29
ARG
60
A
PHE
61
n
30
PHE
61
A
PRO
62
n
31
PRO
62
A
ASP
63
n
32
ASP
63
A
GLN
64
n
33
GLN
64
A
PRO
65
n
34
PRO
65
A
PHE
66
n
35
PHE
66
A
ILE
67
n
36
ILE
67
A
ALA
68
n
37
ALA
68
A
LEU
69
n
38
LEU
69
A
GLU
70
n
39
GLU
70
A
ASP
71
n
40
ASP
71
A
ARG
72
n
41
ARG
72
A
ARG
73
n
42
ARG
73
A
GLY
74
n
43
GLY
74
A
PHE
75
n
44
PHE
75
A
TRP
76
n
45
TRP
76
A
VAL
77
n
46
VAL
77
A
SER
78
n
47
SER
78
A
GLU
79
n
48
GLU
79
A
GLN
80
n
49
GLN
80
A
TYR
81
n
50
TYR
81
A
GLY
82
n
51
GLY
82
A
ARG
83
n
52
ARG
83
A
LEU
84
n
53
LEU
84
A
ARG
85
n
54
ARG
85
A
PRO
86
n
55
PRO
86
A
GLY
87
n
56
GLY
87
A
LEU
88
n
57
LEU
88
A
SER
89
n
58
SER
89
A
GLU
90
n
59
GLU
90
A
LYS
91
n
60
LYS
91
A
ALA
92
n
61
ALA
92
A
ILE
93
n
62
ILE
93
A
SER
94
n
63
SER
94
A
ILE
95
n
64
ILE
95
A
TRP
96
n
65
TRP
96
A
GLU
97
n
66
GLU
97
A
SER
98
n
67
SER
98
A
LYS
99
n
68
LYS
99
A
ASN
100
n
69
ASN
100
A
PHE
101
n
70
PHE
101
A
PHE
102
n
71
PHE
102
A
PHE
103
n
72
PHE
103
A
GLU
104
n
73
GLU
104
A
LEU
105
n
74
LEU
105
A
GLU
106
n
75
GLU
106
A
PRO
107
n
76
PRO
107
A
LEU
108
n
77
LEU
108
A
PRO
109
n
78
PRO
109
A
GLY
110
n
79
GLY
110
A
ALA
111
n
80
ALA
111
A
VAL
112
n
81
VAL
112
A
GLU
113
n
82
GLU
113
A
ALA
114
n
83
ALA
114
A
VAL
115
n
84
VAL
115
A
LYS
116
n
85
LYS
116
A
GLU
117
n
86
GLU
117
A
MET
118
n
87
MET
118
A
ALA
119
n
88
ALA
119
A
SER
120
n
89
SER
120
A
LEU
121
n
90
LEU
121
A
GLN
122
n
91
GLN
122
A
ASN
123
n
92
ASN
123
A
THR
124
n
93
THR
124
A
ASP
125
n
94
ASP
125
A
VAL
126
n
95
VAL
126
A
PHE
127
n
96
PHE
127
A
ILE
128
n
97
ILE
128
A
CYS
129
n
98
CYS
129
A
THR
130
n
99
THR
130
A
SER
131
n
100
SER
131
A
PRO
132
n
101
PRO
132
A
ILE
133
n
102
ILE
133
A
LYS
134
n
103
LYS
134
A
MET
135
n
104
MET
135
A
PHE
136
n
105
PHE
136
A
LYS
137
n
106
LYS
137
A
TYR
138
n
107
TYR
138
A
CYS
139
n
108
CYS
139
A
PRO
140
n
109
PRO
140
A
TYR
141
n
110
TYR
141
A
GLU
142
n
111
GLU
142
A
LYS
143
n
112
LYS
143
A
TYR
144
n
113
TYR
144
A
ALA
145
n
114
ALA
145
A
TRP
146
n
115
TRP
146
A
VAL
147
n
116
VAL
147
A
GLU
148
n
117
GLU
148
A
LYS
149
n
118
LYS
149
A
TYR
150
n
119
TYR
150
A
PHE
151
n
120
PHE
151
A
GLY
152
n
121
GLY
152
A
PRO
153
n
122
PRO
153
A
ASP
154
n
123
ASP
154
A
PHE
155
n
124
PHE
155
A
LEU
156
n
125
LEU
156
A
GLU
157
n
126
GLU
157
A
GLN
158
n
127
GLN
158
A
ILE
159
n
128
ILE
159
A
VAL
160
n
129
VAL
160
A
LEU
161
n
130
LEU
161
A
THR
162
n
131
THR
162
A
ARG
163
n
132
ARG
163
A
ASP
164
n
133
ASP
164
A
LYS
165
n
134
LYS
165
A
THR
166
n
135
THR
166
A
VAL
167
n
136
VAL
167
A
VAL
168
n
137
VAL
168
A
SER
169
n
138
SER
169
A
ALA
170
n
139
ALA
170
A
ASP
171
n
140
ASP
171
A
LEU
172
n
141
LEU
172
A
LEU
173
n
142
LEU
173
A
ILE
174
n
143
ILE
174
A
ASP
175
n
144
ASP
175
A
ASP
176
n
145
ASP
176
A
ARG
177
n
146
ARG
177
A
PRO
178
n
147
PRO
178
A
ASP
179
n
148
ASP
179
A
ILE
180
n
149
ILE
180
A
THR
181
n
150
THR
181
A
GLY
182
n
151
GLY
182
A
ALA
183
n
152
ALA
183
A
GLU
184
n
153
GLU
184
A
PRO
185
n
154
PRO
185
A
THR
186
n
155
THR
186
A
PRO
187
n
156
PRO
187
A
SER
188
n
157
SER
188
A
TRP
189
n
158
TRP
189
A
GLU
190
n
159
GLU
190
A
HIS
191
n
160
HIS
191
A
VAL
192
n
161
VAL
192
A
LEU
193
n
162
LEU
193
A
PHE
194
n
163
PHE
194
A
THR
195
n
164
THR
195
A
ALA
196
n
165
ALA
196
A
CYS
197
n
166
CYS
197
A
HIS
198
n
167
HIS
198
A
ASN
199
n
168
ASN
199
A
GLN
200
n
169
GLN
200
A
HIS
201
n
170
HIS
201
A
LEU
202
n
171
LEU
202
A
GLN
203
n
172
GLN
203
A
LEU
204
n
173
LEU
204
A
GLN
205
n
174
GLN
205
A
PRO
206
n
175
PRO
206
A
PRO
207
n
176
PRO
207
A
ARG
208
n
177
ARG
208
A
ARG
209
n
178
ARG
209
A
ARG
210
n
179
ARG
210
A
LEU
211
n
180
LEU
211
A
HIS
212
n
181
HIS
212
A
SER
213
n
182
SER
213
A
TRP
214
n
183
TRP
214
A
ALA
215
n
184
ALA
215
A
ASP
216
n
185
ASP
216
A
ASP
217
n
186
ASP
217
A
TRP
218
n
187
TRP
218
A
LYS
219
n
188
LYS
219
A
ALA
220
n
189
ALA
220
A
ILE
221
n
190
ILE
221
A
LEU
222
n
191
LEU
222
A
ASP
223
n
192
ASP
223
A
SER
224
n
193
SER
224
A
LYS
225
n
194
LYS
225
A
ARG
226
n
195
ARG
226
A
PRO
227
n
196
PRO
227
A
n
197
228
A
author_defined_assembly
2
dimeric
A
ASN
41
A
OD1
ASN
10
1_555
A
MG
2001
B
MG
MG
1_555
A
ASP
43
A
O
ASP
12
1_555
92.3
A
ASN
41
A
OD1
ASN
10
1_555
A
MG
2001
B
MG
MG
1_555
A
ASP
176
A
OD1
ASP
145
1_555
88.4
A
ASP
43
A
O
ASP
12
1_555
A
MG
2001
B
MG
MG
1_555
A
ASP
176
A
OD1
ASP
145
1_555
87.8
A
ASN
41
A
OD1
ASN
10
1_555
A
MG
2001
B
MG
MG
1_555
A
U5P
1001
B
C
O1P
U5P
1_555
101.8
A
ASP
43
A
O
ASP
12
1_555
A
MG
2001
B
MG
MG
1_555
A
U5P
1001
B
C
O1P
U5P
1_555
107.5
A
ASP
176
A
OD1
ASP
145
1_555
A
MG
2001
B
MG
MG
1_555
A
U5P
1001
B
C
O1P
U5P
1_555
161.0
A
ASN
41
A
OD1
ASN
10
1_555
A
MG
2001
B
MG
MG
1_555
A
U5P
1001
A
C
O3P
U5P
1_555
94.2
A
ASP
43
A
O
ASP
12
1_555
A
MG
2001
B
MG
MG
1_555
A
U5P
1001
A
C
O3P
U5P
1_555
86.9
A
ASP
176
A
OD1
ASP
145
1_555
A
MG
2001
B
MG
MG
1_555
A
U5P
1001
A
C
O3P
U5P
1_555
174.3
A
U5P
1001
B
C
O1P
U5P
1_555
A
MG
2001
B
MG
MG
1_555
A
U5P
1001
A
C
O3P
U5P
1_555
22.4
A
ASN
41
A
OD1
ASN
10
1_555
A
MG
2001
B
MG
MG
1_555
A
HOH
3050
E
O
HOH
1_555
88.2
A
ASP
43
A
O
ASP
12
1_555
A
MG
2001
B
MG
MG
1_555
A
HOH
3050
E
O
HOH
1_555
173.7
A
ASP
176
A
OD1
ASP
145
1_555
A
MG
2001
B
MG
MG
1_555
A
HOH
3050
E
O
HOH
1_555
85.9
A
U5P
1001
B
C
O1P
U5P
1_555
A
MG
2001
B
MG
MG
1_555
A
HOH
3050
E
O
HOH
1_555
78.6
A
U5P
1001
A
C
O3P
U5P
1_555
A
MG
2001
B
MG
MG
1_555
A
HOH
3050
E
O
HOH
1_555
99.3
A
ASN
41
A
OD1
ASN
10
1_555
A
MG
2001
B
MG
MG
1_555
A
HOH
3051
E
O
HOH
1_555
173.7
A
ASP
43
A
O
ASP
12
1_555
A
MG
2001
B
MG
MG
1_555
A
HOH
3051
E
O
HOH
1_555
83.1
A
ASP
176
A
OD1
ASP
145
1_555
A
MG
2001
B
MG
MG
1_555
A
HOH
3051
E
O
HOH
1_555
87.1
A
U5P
1001
B
C
O1P
U5P
1_555
A
MG
2001
B
MG
MG
1_555
A
HOH
3051
E
O
HOH
1_555
83.8
A
U5P
1001
A
C
O3P
U5P
1_555
A
MG
2001
B
MG
MG
1_555
A
HOH
3051
E
O
HOH
1_555
89.9
A
HOH
3050
E
O
HOH
1_555
A
MG
2001
B
MG
MG
1_555
A
HOH
3051
E
O
HOH
1_555
95.9
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_555
x,y,z
identity operation
0.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
8_665
-y+1,-x+1,-z+1/2
crystal symmetry operation
73.5720000000
73.5720000000
52.8740000000
A
O
VAL
160
A
O
VAL
129
A
N
ILE
128
A
N
ILE
97
A
O
PHE
127
A
O
PHE
96
A
N
VAL
40
A
N
VAL
9
A
N
LEU
39
A
N
LEU
8
A
O
LEU
172
A
O
LEU
141
A
N
LEU
173
A
N
LEU
142
A
O
VAL
192
A
O
VAL
161
A
N
LEU
193
A
N
LEU
162
A
O
ARG
209
A
O
ARG
178
1
A
O
PRO
227
A
O
PRO
196
1
Y
1
A
GLY
32
A
GLY
1
1
Y
1
A
GLY
33
A
GLY
2
1
Y
1
A
CYS
228
A
CYS
197
1
Y
1
4.54
0.50
120.30
124.84
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
37
37
37
N
1
-4.59
0.50
120.30
115.71
A
A
A
NE
CZ
NH2
ARG
ARG
ARG
37
37
37
N
1
A
MET
42
-95.06
-71.20
1
A
VAL
45
-129.00
-51.02
1
A
ARG
85
-172.10
146.82
1
A
ASN
100
79.07
-5.41
1
A
SER
213
177.84
171.56
24.348
-0.28
0.00
0.00
-0.28
0.00
0.56
0.960
0.947
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
0.21527
0.19291
0.19403
1.70
40.00
1624
30463
5.1
98.49
1.667
0.057
RANDOM
1
THROUGHOUT
MOLECULAR REPLACEMENT
0.094
0.092
0.80
0.80
1.20
MAXIMUM LIKELIHOOD
MASK
1.70
40.00
163
1788
28
0
1597
0.015
0.022
1707
1.631
1.984
2318
5.866
5.000
193
29.469
22.824
85
13.953
15.000
283
16.438
15.000
16
0.105
0.200
241
0.007
0.020
1308
0.212
0.200
796
0.316
0.200
1155
0.105
0.200
119
0.009
0.200
1
0.244
0.200
51
0.137
0.200
25
1.051
1.500
993
1.739
2.000
1579
2.554
3.000
817
3.935
4.500
739
0.312
0.253
1.745
118
2195
20
98.01
1.7
40
1Z4M
32144
0.047
1
24.5
5.0
98.5
1.70
1.76
3.7
0.334
1
98.3
refinement
REFMAC
5.2.0005
Structure of the D41N variant of the human mitochondrial deoxyribonucleotidase in complex with uridine 5'-monophosphate
1
N
N
2
N
N
3
N
N
4
N
N
5
N
N
A
ASP
48
A
ASP
17
HELX_P
A
PHE
61
A
PHE
30
1
1
14
A
ALA
68
A
ALA
37
HELX_P
A
ARG
72
A
ARG
41
5
2
5
A
TRP
76
A
TRP
45
HELX_P
A
ARG
85
A
ARG
54
1
3
10
A
GLY
87
A
GLY
56
HELX_P
A
GLU
97
A
GLU
66
1
4
11
A
GLY
110
A
GLY
79
HELX_P
A
LEU
121
A
LEU
90
1
5
12
A
TYR
138
A
TYR
107
HELX_P
A
GLY
152
A
GLY
121
1
6
15
A
PRO
153
A
PRO
122
HELX_P
A
GLU
157
A
GLU
126
5
7
5
A
ASP
217
A
ASP
186
HELX_P
A
SER
224
A
SER
193
1
8
8
metalc
2.017
A
ASN
41
A
OD1
ASN
10
1_555
A
MG
2001
B
MG
MG
1_555
metalc
2.080
A
ASP
43
A
O
ASP
12
1_555
A
MG
2001
B
MG
MG
1_555
metalc
2.195
A
ASP
176
A
OD1
ASP
145
1_555
A
MG
2001
B
MG
MG
1_555
metalc
1.981
B
A
U5P
1001
C
O1P
U5P
1_555
A
MG
2001
B
MG
MG
1_555
metalc
2.078
A
A
U5P
1001
C
O3P
U5P
1_555
A
MG
2001
B
MG
MG
1_555
metalc
2.121
A
MG
2001
B
MG
MG
1_555
A
HOH
3050
E
O
HOH
1_555
metalc
2.222
A
MG
2001
B
MG
MG
1_555
A
HOH
3051
E
O
HOH
1_555
HYDROLASE
alfa beta fold, Hydrolase
A
PRO
206
A
PRO
175
1
A
PRO
207
A
PRO
176
6.53
NT5M_HUMAN
UNP
1
32
Q9NPB1
GGRALRVLVDMDGVLADFEGGFLRKFRARFPDQPFIALEDRRGFWVSEQYGRLRPGLSEKAISIWESKNFFFELEPLPGA
VEAVKEMASLQNTDVFICTSPIKMFKYCPYEKYAWVEKYFGPDFLEQIVLTRDKTVVSADLLIDDRPDITGAEPTPSWEH
VLFTACHNQHLQLQPPRRRLHSWADDWKAILDSKRPC
32
228
1Z4M
32
228
Q9NPB1
A
1
1
197
1
ASP
engineered mutation
ASN
41
1Z4M
A
Q9NPB1
UNP
41
10
6
parallel
parallel
parallel
parallel
parallel
A
ILE
159
A
ILE
128
A
LEU
161
A
LEU
130
A
THR
124
A
THR
93
A
THR
130
A
THR
99
A
LEU
36
A
LEU
5
A
ASN
41
A
ASN
10
A
LEU
172
A
LEU
141
A
ASP
175
A
ASP
144
A
GLU
190
A
GLU
159
A
PHE
194
A
PHE
163
A
ARG
209
A
ARG
178
A
LEU
211
A
LEU
180
BINDING SITE FOR RESIDUE MG A 2001
A
MG
2001
Software
6
BINDING SITE FOR RESIDUE U5P A 1001
A
U5P
1001
Software
27
BINDING SITE FOR RESIDUE GOL A 3001
A
GOL
3001
Software
7
A
ASN
41
A
ASN
10
6
1_555
A
ASP
43
A
ASP
12
6
1_555
A
ASP
176
A
ASP
145
6
1_555
A
U5P
1001
C
U5P
6
1_555
A
HOH
3050
E
HOH
6
1_555
A
HOH
3051
E
HOH
6
1_555
A
ASN
41
A
ASN
10
27
1_555
A
MET
42
A
MET
11
27
1_555
A
ASP
43
A
ASP
12
27
1_555
A
PHE
49
A
PHE
18
27
1_555
A
PHE
75
A
PHE
44
27
1_555
A
TRP
76
A
TRP
45
27
1_555
A
VAL
77
A
VAL
46
27
1_555
A
SER
78
A
SER
47
27
1_555
A
TRP
96
A
TRP
65
27
1_555
A
PHE
102
A
PHE
71
27
1_555
A
THR
130
A
THR
99
27
1_555
A
SER
131
A
SER
100
27
1_555
A
PRO
132
A
PRO
101
27
1_555
A
ILE
133
A
ILE
102
27
1_555
A
LYS
143
A
LYS
112
27
1_555
A
LYS
165
A
LYS
134
27
1_555
A
MG
2001
B
MG
27
1_555
A
GOL
3001
D
GOL
27
1_555
A
HOH
3025
E
HOH
27
1_555
A
HOH
3050
E
HOH
27
1_555
A
HOH
3051
E
HOH
27
1_555
A
HOH
3054
E
HOH
27
1_555
A
HOH
3150
E
HOH
27
1_555
A
HOH
3151
E
HOH
27
1_555
A
HOH
3152
E
HOH
27
1_555
A
HOH
3153
E
HOH
27
1_555
A
HOH
3161
E
HOH
27
1_555
A
TRP
96
A
TRP
65
7
1_555
A
GLU
97
A
GLU
66
7
1_555
A
ILE
133
A
ILE
102
7
1_555
A
LYS
134
A
LYS
103
7
1_555
A
MET
135
A
MET
104
7
1_555
A
U5P
1001
C
U5P
7
1_555
A
HOH
3154
E
HOH
7
1_555
96
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