1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Banci, L.
Bertini, I.
Del Conte, R.
Fadin, R.
Mangani, S.
Viezzoli, M.S.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
1
90.00
90.00
90.00
1.000
1.000
1.000
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
Cu 2
63.546
COPPER (II) ION
non-polymer
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
C6 H10 N3 O2 1
156.162
y
HISTIDINE
L-peptide linking
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
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
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
Zn 2
65.409
ZINC ION
non-polymer
GW
J.Biol.Inorg.Chem.
JJBCFA
2154
0949-8257
4
795
803
10.1007/s007750050353
10631612
The solution structure of a monomeric, reduced form of human copper,zinc superoxide dismutase bearing the same charge as the native protein.
1999
10.2210/pdb1dsw/pdb
pdb_00001dsw
ONE RESIDUE HAS INCORRECT CHIRALITY
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
COPPER, ZINC SUPEROXIDE DISMUTASE (SOD) IS AN ENZYME WHICH CATALYZES THE DISMUTATION OF SUPEROXIDE
15879.502
SUPEROXIDE DISMUTASE (CU-ZN)
1.15.1.1
M4SOD IS A MONOMERIC VARIANT OF HUMAN SOD. THE MUTANT IS STUDIED IN THE REDUCED FORM, EACH MOLECULE CONTAINS A CU(I) AND A ZN(II) IONS.
YES
1
man
polymer
63.546
COPPER (II) ION
1
syn
non-polymer
65.409
ZINC ION
1
syn
non-polymer
no
no
ATKAVAVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEEEDNTAGCTSAGPHFNPLSRKHGGPKDEERH
VGDLGNVTADKDGVADVSIEDSVISLSGDHSIIGRTLVVHEKADDLGKGGNEESTKTGNAGSRLACGKIGKAQ
ATKAVAVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEEEDNTAGCTSAGPHFNPLSRKHGGPKDEERH
VGDLGNVTADKDGVADVSIEDSVISLSGDHSIIGRTLVVHEKADDLGKGGNEESTKTGNAGSRLACGKIGKAQ
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
human
Homo
Escherichia
sample
9606
Homo sapiens
562
Escherichia coli
PLASMID
PBR322
database_2
pdbx_nmr_software
pdbx_nmr_spectrometer
pdbx_struct_assembly
pdbx_struct_oper_list
struct_site
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
1
0
2000-03-22
1
1
2007-10-21
1
2
2011-07-13
1
3
2022-02-16
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_software.name
_pdbx_nmr_spectrometer.model
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
RCSB
Y
RCSB
2000-01-10
REL
CU
COPPER (II) ION
ZN
ZINC ION
1
3D 15N NOESY-HSQC
3D HNHA
2D NOESY
5.00
ATMOSPHERIC
atm
298.00
K
INTENSITIES OF DIPOLAR CONNECTIVITIES IN 3D NOESY-HSQC, 3D HNHA AND 2D NOESY WERE MEASURED WITH THE INTEGRATION ROUTINES OF THE PROGRAM XEASY. PEAK VOLUMES WERE CONVERTED INTO UPPER DISTANCE LIMITS BY FOLLOWING THE METHODOLOGY OF THE PROGRAM CALIBA. 3JHNHA COUPLING CONSTANTS WERE OBTAINED FROM THE RATIO BETWEEN THE INTENSITY OF THE DIAGONAL PEAK AND THAT OF THE CROSS PEAK OF THE 3D HNHA EXPERIMENT. THE 3D STRUCTURE WAS CALCULATED WITH THE PROGRAM DYANA; THE FINAL DYANA FAMILY WAS FORMED BY THE 36 CONFORMERS WITH THE LOWEST TARGET FUNCTION. REFINEMENT WAS PERFORMED THROUGH RESTRAINED ENERGY MINIMIZATION WITH THE SANDER MODULE OF THE PROGRAM AMBER. NOESY CROSS PEAKS WERE BACK -CALCULATED ON THE FINAL STRUCTURE WITH THE PROGRAM CORMA.
THE NMR STRUCTURE CALCULATION PROGRAM USED DYANA THAT USES SIMULATED ANNEALING COMBINED WITH MOLECULAR DYNAMICS IN TORSION ANGLE SPACE (TORSION ANGLE DYNAMICS)
1
2MM M4SOD FULLY ENRICHED IN 15N; 20MM PHOSPHATE BUFFER PH 5.0; 90% H2O, 10% D2O. THE PROTEIN WAS REDUCED WITH SODIUM ISOASCORBATE UNDER UNAEROBIC CONDITIONS.
PEALRMAN, DA, ET AL. (1991)
refinement
Amber
4.0
structure solution
XwinNMR
2.1
structure solution
CALIBA
1.5
structure solution
DYANA
1.4
structure solution
CORMA
800
Bruker
AVANCE
600
Bruker
AVANCE
CU
154
2
CU
CU
154
A
ZN
155
3
ZN
ZN
155
A
ALA
1
n
1
ALA
1
A
THR
2
n
2
THR
2
A
LYS
3
n
3
LYS
3
A
ALA
4
n
4
ALA
4
A
VAL
5
n
5
VAL
5
A
ALA
6
n
6
ALA
6
A
VAL
7
n
7
VAL
7
A
LEU
8
n
8
LEU
8
A
LYS
9
n
9
LYS
9
A
GLY
10
n
10
GLY
10
A
ASP
11
n
11
ASP
11
A
GLY
12
n
12
GLY
12
A
PRO
13
n
13
PRO
13
A
VAL
14
n
14
VAL
14
A
GLN
15
n
15
GLN
15
A
GLY
16
n
16
GLY
16
A
ILE
17
n
17
ILE
17
A
ILE
18
n
18
ILE
18
A
ASN
19
n
19
ASN
19
A
PHE
20
n
20
PHE
20
A
GLU
21
n
21
GLU
21
A
GLN
22
n
22
GLN
22
A
LYS
23
n
23
LYS
23
A
GLU
24
n
24
GLU
24
A
SER
25
n
25
SER
25
A
ASN
26
n
26
ASN
26
A
GLY
27
n
27
GLY
27
A
PRO
28
n
28
PRO
28
A
VAL
29
n
29
VAL
29
A
LYS
30
n
30
LYS
30
A
VAL
31
n
31
VAL
31
A
TRP
32
n
32
TRP
32
A
GLY
33
n
33
GLY
33
A
SER
34
n
34
SER
34
A
ILE
35
n
35
ILE
35
A
LYS
36
n
36
LYS
36
A
GLY
37
n
37
GLY
37
A
LEU
38
n
38
LEU
38
A
THR
39
n
39
THR
39
A
GLU
40
n
40
GLU
40
A
GLY
41
n
41
GLY
41
A
LEU
42
n
42
LEU
42
A
HIS
43
n
43
HIS
43
A
GLY
44
n
44
GLY
44
A
PHE
45
n
45
PHE
45
A
HIS
46
n
46
HIS
46
A
VAL
47
n
47
VAL
47
A
HIS
48
n
48
HIS
48
A
GLU
49
n
49
GLU
49
A
GLU
50
n
50
GLU
50
A
GLU
51
n
51
GLU
51
A
ASP
52
n
52
ASP
52
A
ASN
53
n
53
ASN
53
A
THR
54
n
54
THR
54
A
ALA
55
n
55
ALA
55
A
GLY
56
n
56
GLY
56
A
CYS
57
n
57
CYS
57
A
THR
58
n
58
THR
58
A
SER
59
n
59
SER
59
A
ALA
60
n
60
ALA
60
A
GLY
61
n
61
GLY
61
A
PRO
62
n
62
PRO
62
A
HIS
63
n
63
HIS
63
A
PHE
64
n
64
PHE
64
A
ASN
65
n
65
ASN
65
A
PRO
66
n
66
PRO
66
A
LEU
67
n
67
LEU
67
A
SER
68
n
68
SER
68
A
ARG
69
n
69
ARG
69
A
LYS
70
n
70
LYS
70
A
HIS
71
n
71
HIS
71
A
GLY
72
n
72
GLY
72
A
GLY
73
n
73
GLY
73
A
PRO
74
n
74
PRO
74
A
LYS
75
n
75
LYS
75
A
ASP
76
n
76
ASP
76
A
GLU
77
n
77
GLU
77
A
GLU
78
n
78
GLU
78
A
ARG
79
n
79
ARG
79
A
HIS
80
n
80
HIS
80
A
VAL
81
n
81
VAL
81
A
GLY
82
n
82
GLY
82
A
ASP
83
n
83
ASP
83
A
LEU
84
n
84
LEU
84
A
GLY
85
n
85
GLY
85
A
ASN
86
n
86
ASN
86
A
VAL
87
n
87
VAL
87
A
THR
88
n
88
THR
88
A
ALA
89
n
89
ALA
89
A
ASP
90
n
90
ASP
90
A
LYS
91
n
91
LYS
91
A
ASP
92
n
92
ASP
92
A
GLY
93
n
93
GLY
93
A
VAL
94
n
94
VAL
94
A
ALA
95
n
95
ALA
95
A
ASP
96
n
96
ASP
96
A
VAL
97
n
97
VAL
97
A
SER
98
n
98
SER
98
A
ILE
99
n
99
ILE
99
A
GLU
100
n
100
GLU
100
A
ASP
101
n
101
ASP
101
A
SER
102
n
102
SER
102
A
VAL
103
n
103
VAL
103
A
ILE
104
n
104
ILE
104
A
SER
105
n
105
SER
105
A
LEU
106
n
106
LEU
106
A
SER
107
n
107
SER
107
A
GLY
108
n
108
GLY
108
A
ASP
109
n
109
ASP
109
A
HIS
110
n
110
HIS
110
A
SER
111
n
111
SER
111
A
ILE
112
n
112
ILE
112
A
ILE
113
n
113
ILE
113
A
GLY
114
n
114
GLY
114
A
ARG
115
n
115
ARG
115
A
THR
116
n
116
THR
116
A
LEU
117
n
117
LEU
117
A
VAL
118
n
118
VAL
118
A
VAL
119
n
119
VAL
119
A
HIS
120
n
120
HIS
120
A
GLU
121
n
121
GLU
121
A
LYS
122
n
122
LYS
122
A
ALA
123
n
123
ALA
123
A
ASP
124
n
124
ASP
124
A
ASP
125
n
125
ASP
125
A
LEU
126
n
126
LEU
126
A
GLY
127
n
127
GLY
127
A
LYS
128
n
128
LYS
128
A
GLY
129
n
129
GLY
129
A
GLY
130
n
130
GLY
130
A
ASN
131
n
131
ASN
131
A
GLU
132
n
132
GLU
132
A
GLU
133
n
133
GLU
133
A
SER
134
n
134
SER
134
A
THR
135
n
135
THR
135
A
LYS
136
n
136
LYS
136
A
THR
137
n
137
THR
137
A
GLY
138
n
138
GLY
138
A
ASN
139
n
139
ASN
139
A
ALA
140
n
140
ALA
140
A
GLY
141
n
141
GLY
141
A
SER
142
n
142
SER
142
A
ARG
143
n
143
ARG
143
A
LEU
144
n
144
LEU
144
A
ALA
145
n
145
ALA
145
A
CYS
146
n
146
CYS
146
A
GLY
147
n
147
GLY
147
A
LYS
148
n
148
LYS
148
A
ILE
149
n
149
ILE
149
A
GLY
150
n
150
GLY
150
A
LYS
151
n
151
LYS
151
A
ALA
152
n
152
ALA
152
A
GLN
153
n
153
GLN
153
A
author_defined_assembly
1
monomeric
A
HIS
46
A
ND1
HIS
46
1_555
A
CU
154
B
CU
CU
1_555
A
HIS
48
A
NE2
HIS
48
1_555
151.2
A
HIS
46
A
ND1
HIS
46
1_555
A
CU
154
B
CU
CU
1_555
A
HIS
120
A
NE2
HIS
120
1_555
81.4
A
HIS
48
A
NE2
HIS
48
1_555
A
CU
154
B
CU
CU
1_555
A
HIS
120
A
NE2
HIS
120
1_555
110.4
A
HIS
63
A
ND1
HIS
63
1_555
A
ZN
155
C
ZN
ZN
1_555
A
HIS
71
A
ND1
HIS
71
1_555
97.6
A
HIS
63
A
ND1
HIS
63
1_555
A
ZN
155
C
ZN
ZN
1_555
A
HIS
80
A
ND1
HIS
80
1_555
104.8
A
HIS
71
A
ND1
HIS
71
1_555
A
ZN
155
C
ZN
ZN
1_555
A
HIS
80
A
ND1
HIS
80
1_555
118.2
A
HIS
63
A
ND1
HIS
63
1_555
A
ZN
155
C
ZN
ZN
1_555
A
ASP
83
A
OD1
ASP
83
1_555
85.7
A
HIS
71
A
ND1
HIS
71
1_555
A
ZN
155
C
ZN
ZN
1_555
A
ASP
83
A
OD1
ASP
83
1_555
121.8
A
HIS
80
A
ND1
HIS
80
1_555
A
ZN
155
C
ZN
ZN
1_555
A
ASP
83
A
OD1
ASP
83
1_555
116.8
A
HIS
63
A
ND1
HIS
63
1_555
A
ZN
155
C
ZN
ZN
1_555
A
ASP
83
A
OD2
ASP
83
1_555
150.7
A
HIS
71
A
ND1
HIS
71
1_555
A
ZN
155
C
ZN
ZN
1_555
A
ASP
83
A
OD2
ASP
83
1_555
91.9
A
HIS
80
A
ND1
HIS
80
1_555
A
ZN
155
C
ZN
ZN
1_555
A
ASP
83
A
OD2
ASP
83
1_555
94.8
A
ASP
83
A
OD1
ASP
83
1_555
A
ZN
155
C
ZN
ZN
1_555
A
ASP
83
A
OD2
ASP
83
1_555
65.9
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
A
O
ASP
101
A
O
ASP
101
A
N
VAL
29
A
N
VAL
29
A
N
LYS
36
A
N
LYS
36
A
O
GLN
15
A
O
GLN
15
A
N
PHE
20
A
N
PHE
20
A
O
ALA
4
A
O
ALA
4
A
O
VAL
5
A
O
VAL
5
A
N
GLY
150
A
N
GLY
150
A
O
ALA
89
A
O
ALA
89
A
N
GLY
41
A
N
GLY
41
A
N
HIS
48
A
N
HIS
48
A
O
THR
116
A
O
THR
116
A
N
VAL
119
A
N
VAL
119
A
O
ALA
145
A
O
ALA
145
1
A
CA
ALA
1
WRONG HAND
1
A
HIS
43
0.106
SIDE CHAIN
1
A
GLU
24
-174.91
-169.37
1
A
GLU
50
-163.69
-77.11
1
A
GLU
51
62.20
-44.96
1
A
ALA
55
-120.56
-50.48
1
A
THR
58
-79.06
-72.16
1
A
SER
59
-100.28
43.48
1
A
PRO
62
-65.14
-175.24
1
A
LEU
67
-144.16
-80.72
1
A
LYS
75
-146.35
-53.59
1
A
VAL
81
171.44
-49.87
1
A
SER
98
-166.31
95.23
1
A
ASP
109
-23.31
-67.48
1
A
SER
111
33.55
66.85
1
A
ARG
115
-35.83
142.67
1
A
ARG
143
52.99
70.72
THE SOLUTION STRUCTURE OF A MONOMERIC, REDUCED FORM OF HUMAN COPPER, ZINC SUPEROXIDE DISMUTASE BEARING THE SAME CHARGE AS THE NATIVE PROTEIN
1
N
N
2
N
N
3
N
N
A
ASN
131
A
ASN
131
HELX_P
A
GLY
138
A
GLY
138
1
1
8
disulf
2.052
A
CYS
57
A
SG
CYS
57
1_555
A
CYS
146
A
SG
CYS
146
1_555
metalc
2.128
A
HIS
46
A
ND1
HIS
46
1_555
A
CU
154
B
CU
CU
1_555
metalc
2.014
A
HIS
48
A
NE2
HIS
48
1_555
A
CU
154
B
CU
CU
1_555
metalc
2.095
A
HIS
63
A
ND1
HIS
63
1_555
A
ZN
155
C
ZN
ZN
1_555
metalc
2.097
A
HIS
71
A
ND1
HIS
71
1_555
A
ZN
155
C
ZN
ZN
1_555
metalc
2.141
A
HIS
80
A
ND1
HIS
80
1_555
A
ZN
155
C
ZN
ZN
1_555
metalc
2.028
A
ASP
83
A
OD1
ASP
83
1_555
A
ZN
155
C
ZN
ZN
1_555
metalc
1.991
A
ASP
83
A
OD2
ASP
83
1_555
A
ZN
155
C
ZN
ZN
1_555
metalc
2.180
A
HIS
120
A
NE2
HIS
120
1_555
A
CU
154
B
CU
CU
1_555
OXIDOREDUCTASE
REDUCED COPPER-ZINC-PROTEIN, BETA BARREL, SINGLE ALPHA HELIX, OXIDOREDUCTASE
SODC_HUMAN
UNP
1
P00441
2
154
1DSW
1
153
P00441
A
1
1
153
5
4
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
VAL
94
A
VAL
94
A
ASP
101
A
ASP
101
A
VAL
29
A
VAL
29
A
LYS
36
A
LYS
36
A
GLN
15
A
GLN
15
A
GLN
22
A
GLN
22
A
LYS
3
A
LYS
3
A
LYS
9
A
LYS
9
A
ILE
149
A
ILE
149
A
LYS
151
A
LYS
151
A
ASP
83
A
ASP
83
A
ALA
89
A
ALA
89
A
GLY
41
A
GLY
41
A
HIS
48
A
HIS
48
A
THR
116
A
THR
116
A
VAL
119
A
VAL
119
A
ALA
145
A
ALA
145
A
CYS
146
A
CYS
146
BINDING SITE FOR RESIDUE CU A 154
A
CU
154
Software
5
BINDING SITE FOR RESIDUE ZN A 155
A
ZN
155
Software
4
A
HIS
46
A
HIS
46
5
1_555
A
HIS
48
A
HIS
48
5
1_555
A
HIS
63
A
HIS
63
5
1_555
A
VAL
118
A
VAL
118
5
1_555
A
HIS
120
A
HIS
120
5
1_555
A
HIS
63
A
HIS
63
4
1_555
A
HIS
71
A
HIS
71
4
1_555
A
HIS
80
A
HIS
80
4
1_555
A
ASP
83
A
ASP
83
4
1_555
1
P 1