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 P 43 21 2