1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Ikegami, T. Kuraoka, I. Saijo, M. Kodo, N. Kyogoku, Y. Morikawa, K. Tanaka, K. Shirakawa, M. 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 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 C5 H11 N O2 S 149.211 y METHIONINE 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 C9 H11 N O3 181.189 y TYROSINE L-peptide linking C5 H11 N O2 117.146 y VALINE L-peptide linking Zn 2 65.409 ZINC ION non-polymer US Nat.Struct.Biol. NSBIEW 2024 1072-8368 5 701 706 10.1038/1400 9699634 Solution structure of the DNA- and RPA-binding domain of the human repair factor XPA. 1998 10.2210/pdb1xpa/pdb pdb_00001xpa 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 14728.981 XPA MF122, RESIDUES 98-219 1 man polymer 65.409 ZINC ION 1 syn non-polymer no no MEFDYVICEECGKEFMDSYLMNHFDLPTCDNCRDADDKHKLITKTEAKQEYLLKDCDLEKREPPLKFIVKKNPHHSQWGD MKLYLKLQIVKRSLEVWGSQEALEEAKEVRQENREKMKQKKF MEFDYVICEECGKEFMDSYLMNHFDLPTCDNCRDADDKHKLITKTEAKQEYLLKDCDLEKREPPLKFIVKKNPHHSQWGD MKLYLKLQIVKRSLEVWGSQEALEEAKEVRQENREKMKQKKF 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 human Homo Escherichia Escherichia coli sample 9606 Homo sapiens HUMAN XPA CDNA 511693 Escherichia coli BL21 BL21 PET16B database_2 pdbx_database_status pdbx_struct_assembly pdbx_struct_conn_angle pdbx_struct_oper_list struct_conn struct_site repository Initial release Version format compliance Version format compliance Database references Derived calculations Other 1 0 1999-07-22 1 1 2008-03-24 1 2 2011-07-13 1 3 2022-03-02 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_database_status.process_site _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.value _struct_conn.pdbx_dist_value _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_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id Y BNL 1998-07-06 REL REL ZN ZINC ION THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 13C, 15N-LABELED XPA. THIS MODEL IS THE CLOSEST STRUCTURE TO THE MEAN. THE LOWEST ENERGY AND NO VIOLATION GREATER THAN 0.3A OR 5DEG 140 1 3D- 4D-MULTI-DIMENSIONAL EXPERIMENTS 150mM KCL 7.3 1 ATMOSPHERE 303 K distance geometry 50MM D-TRIS HCL structure solution X-PLOR 3.1 refinement X-PLOR 3.1 500 Bruker DMX500 800 Bruker DRX500 800 Bruker DRX800 ZN 220 2 ZN ZN 220 A MET 98 n 1 MET 98 A GLU 99 n 2 GLU 99 A PHE 100 n 3 PHE 100 A ASP 101 n 4 ASP 101 A TYR 102 n 5 TYR 102 A VAL 103 n 6 VAL 103 A ILE 104 n 7 ILE 104 A CYS 105 n 8 CYS 105 A GLU 106 n 9 GLU 106 A GLU 107 n 10 GLU 107 A CYS 108 n 11 CYS 108 A GLY 109 n 12 GLY 109 A LYS 110 n 13 LYS 110 A GLU 111 n 14 GLU 111 A PHE 112 n 15 PHE 112 A MET 113 n 16 MET 113 A ASP 114 n 17 ASP 114 A SER 115 n 18 SER 115 A TYR 116 n 19 TYR 116 A LEU 117 n 20 LEU 117 A MET 118 n 21 MET 118 A ASN 119 n 22 ASN 119 A HIS 120 n 23 HIS 120 A PHE 121 n 24 PHE 121 A ASP 122 n 25 ASP 122 A LEU 123 n 26 LEU 123 A PRO 124 n 27 PRO 124 A THR 125 n 28 THR 125 A CYS 126 n 29 CYS 126 A ASP 127 n 30 ASP 127 A ASN 128 n 31 ASN 128 A CYS 129 n 32 CYS 129 A ARG 130 n 33 ARG 130 A ASP 131 n 34 ASP 131 A ALA 132 n 35 ALA 132 A ASP 133 n 36 ASP 133 A ASP 134 n 37 ASP 134 A LYS 135 n 38 LYS 135 A HIS 136 n 39 HIS 136 A LYS 137 n 40 LYS 137 A LEU 138 n 41 LEU 138 A ILE 139 n 42 ILE 139 A THR 140 n 43 THR 140 A LYS 141 n 44 LYS 141 A THR 142 n 45 THR 142 A GLU 143 n 46 GLU 143 A ALA 144 n 47 ALA 144 A LYS 145 n 48 LYS 145 A GLN 146 n 49 GLN 146 A GLU 147 n 50 GLU 147 A TYR 148 n 51 TYR 148 A LEU 149 n 52 LEU 149 A LEU 150 n 53 LEU 150 A LYS 151 n 54 LYS 151 A ASP 152 n 55 ASP 152 A CYS 153 n 56 CYS 153 A ASP 154 n 57 ASP 154 A LEU 155 n 58 LEU 155 A GLU 156 n 59 GLU 156 A LYS 157 n 60 LYS 157 A ARG 158 n 61 ARG 158 A GLU 159 n 62 GLU 159 A PRO 160 n 63 PRO 160 A PRO 161 n 64 PRO 161 A LEU 162 n 65 LEU 162 A LYS 163 n 66 LYS 163 A PHE 164 n 67 PHE 164 A ILE 165 n 68 ILE 165 A VAL 166 n 69 VAL 166 A LYS 167 n 70 LYS 167 A LYS 168 n 71 LYS 168 A ASN 169 n 72 ASN 169 A PRO 170 n 73 PRO 170 A HIS 171 n 74 HIS 171 A HIS 172 n 75 HIS 172 A SER 173 n 76 SER 173 A GLN 174 n 77 GLN 174 A TRP 175 n 78 TRP 175 A GLY 176 n 79 GLY 176 A ASP 177 n 80 ASP 177 A MET 178 n 81 MET 178 A LYS 179 n 82 LYS 179 A LEU 180 n 83 LEU 180 A TYR 181 n 84 TYR 181 A LEU 182 n 85 LEU 182 A LYS 183 n 86 LYS 183 A LEU 184 n 87 LEU 184 A GLN 185 n 88 GLN 185 A ILE 186 n 89 ILE 186 A VAL 187 n 90 VAL 187 A LYS 188 n 91 LYS 188 A ARG 189 n 92 ARG 189 A SER 190 n 93 SER 190 A LEU 191 n 94 LEU 191 A GLU 192 n 95 GLU 192 A VAL 193 n 96 VAL 193 A TRP 194 n 97 TRP 194 A GLY 195 n 98 GLY 195 A SER 196 n 99 SER 196 A GLN 197 n 100 GLN 197 A GLU 198 n 101 GLU 198 A ALA 199 n 102 ALA 199 A LEU 200 n 103 LEU 200 A GLU 201 n 104 GLU 201 A GLU 202 n 105 GLU 202 A ALA 203 n 106 ALA 203 A LYS 204 n 107 LYS 204 A GLU 205 n 108 GLU 205 A VAL 206 n 109 VAL 206 A ARG 207 n 110 ARG 207 A GLN 208 n 111 GLN 208 A GLU 209 n 112 GLU 209 A ASN 210 n 113 ASN 210 A n 114 211 A n 115 212 A n 116 213 A n 117 214 A n 118 215 A n 119 216 A n 120 217 A n 121 218 A n 122 219 A author_defined_assembly 1 monomeric A CYS 105 A SG CYS 8 1_555 A ZN 220 B ZN ZN 1_555 A CYS 108 A SG CYS 11 1_555 106.3 A CYS 105 A SG CYS 8 1_555 A ZN 220 B ZN ZN 1_555 A CYS 126 A SG CYS 29 1_555 112.1 A CYS 108 A SG CYS 11 1_555 A ZN 220 B ZN ZN 1_555 A CYS 126 A SG CYS 29 1_555 109.9 A CYS 105 A SG CYS 8 1_555 A ZN 220 B ZN ZN 1_555 A CYS 129 A SG CYS 32 1_555 106.8 A CYS 108 A SG CYS 11 1_555 A ZN 220 B ZN ZN 1_555 A CYS 129 A SG CYS 32 1_555 112.2 A CYS 126 A SG CYS 29 1_555 A ZN 220 B ZN ZN 1_555 A CYS 129 A SG CYS 32 1_555 109.4 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 VAL 103 A O VAL 6 A N PHE 112 A N PHE 15 A O ILE 139 A O ILE 42 A N TYR 181 A N TYR 84 A O LEU 180 A O LEU 83 A N ILE 165 A N ILE 68 1 A ARG 211 A ARG 114 1 Y 1 A GLU 212 A GLU 115 1 Y 1 A LYS 213 A LYS 116 1 Y 1 A MET 214 A MET 117 1 Y 1 A LYS 215 A LYS 118 1 Y 1 A GLN 216 A GLN 119 1 Y 1 A LYS 217 A LYS 120 1 Y 1 A LYS 218 A LYS 121 1 Y 1 A PHE 219 A PHE 122 1 Y 1 A ARG 130 0.281 SIDE CHAIN 1 A ARG 158 0.269 SIDE CHAIN 1 A ARG 189 0.317 SIDE CHAIN 1 A ARG 207 0.307 SIDE CHAIN 1 A TYR 102 -152.09 33.45 1 A GLU 107 -125.52 -50.88 1 A SER 115 -157.32 -147.12 1 A ASP 134 -160.23 -56.71 1 A LYS 135 -46.33 -74.72 1 A LYS 137 -48.69 93.46 1 A LEU 138 -41.88 163.89 1 A LEU 149 43.70 26.25 1 A LYS 151 -123.23 -140.44 1 A CYS 153 -127.97 -86.25 1 A LEU 155 -125.18 -51.30 1 A GLU 159 39.13 85.21 1 A LEU 162 22.23 99.96 1 A LYS 163 -28.73 128.72 1 A ILE 165 -153.15 -159.22 1 A LYS 167 -157.72 -144.64 1 A HIS 171 -92.58 -155.47 1 A ASP 177 -158.61 55.81 1 A LEU 182 -46.18 105.90 1 A SER 196 179.38 -147.95 model building X-PLOR 3.1 refinement X-PLOR 3.1 phasing X-PLOR 3.1 SOLUTION STRUCTURE OF THE DNA-AND RPA-BINDING DOMAIN OF THE HUMAN REPAIR FACTOR XPA, NMR, 1 STRUCTURE 1 Y N 2 N N A LYS 141 A LYS 44 HELX_P A GLU 147 A GLU 50 1 H1 7 A LYS 183 A LYS 86 HELX_P A TRP 194 A TRP 97 1 H2 12 A GLN 197 A GLN 100 HELX_P A GLU 209 A GLU 112 1 H3 13 metalc 2.257 A CYS 105 A SG CYS 8 1_555 A ZN 220 B ZN ZN 1_555 metalc 2.350 A CYS 108 A SG CYS 11 1_555 A ZN 220 B ZN ZN 1_555 metalc 2.436 A CYS 126 A SG CYS 29 1_555 A ZN 220 B ZN ZN 1_555 metalc 2.353 A CYS 129 A SG CYS 32 1_555 A ZN 220 B ZN ZN 1_555 DNA REPAIR DNA REPAIR, NUCLEOTIDE EXCISION REPAIR, ZINC-FINGER A GLU 159 A GLU 62 1 A PRO 160 A PRO 63 0.07 XPA_HUMAN UNP 1 1 P23025 MAAADGALPEAAALEQPAELPASVRASIERKRQRALMLRQARLAARPYSATAAAATGGMANVKAAPKIIDTGGGFILEEE EEEEQKIGKVVHQPGPVMEFDYVICEECGKEFMDSYLMNHFDLPTCDNCRDADDKHKLITKTEAKQEYLLKDCDLEKREP PLKFIVKKNPHHSQWGDMKLYLKLQIVKRSLEVWGSQEALEEAKEVRQENREKMKQKKFDKKVKELRRAVRSSVWKRETI VHQHEYGPEENLEDDMYRKTCTMCGHELTYEKM 98 219 1XPA 98 219 P23025 A 1 1 122 2 3 anti-parallel anti-parallel anti-parallel A VAL 103 A VAL 6 A ILE 104 A ILE 7 A GLU 111 A GLU 14 A PHE 112 A PHE 15 A ILE 139 A ILE 42 A THR 140 A THR 43 A LEU 180 A LEU 83 A TYR 181 A TYR 84 A PHE 164 A PHE 67 A ILE 165 A ILE 68 ZN BINDING SITE. Unknown 4 BINDING SITE FOR RESIDUE ZN A 220 A ZN 220 Software 4 A CYS 105 A CYS 8 4 1_555 A CYS 108 A CYS 11 4 1_555 A CYS 126 A CYS 29 4 1_555 A CYS 129 A CYS 32 4 1_555 A CYS 105 A CYS 8 4 1_555 A CYS 108 A CYS 11 4 1_555 A CYS 126 A CYS 29 4 1_555 A CYS 129 A CYS 32 4 1_555 1 P 1