4IEM - Sequence, Chains, Asymmetric and Biological Units

• Title: HUMAN APURINIC/APYRIMIDINIC ENDONUCLEASE (APE1) WITH PRODUCT MG2+
• Keywords: METALLOPROTEIN, DNA DAMAGE, DNA REPAIR, BASE EXCISION REPAIR PROTEIN-DNA, REF1, NUCLEASE, HYDROLASE, LYASE-DNA COMPLEX
• Experiment: X-ray diffraction
• Number of Models: 1

Database	ID code	Status	Coordinate files
			Header	Asymmetric unit	Biological unit
PDB	4IEM	released	available	available	Quaternary Structure Server

Asymmetric unit from PDB

Unit	Type	Name	Chain ID	Residues	Atoms	Hetatoms
1	Protein	DNA-(APURINIC OR APYRIMIDINIC SITE) LYASE	A	278	4399	0
2	Other macromolecule	DNA (5'-D(*GP*CP*TP*AP*C)-3')	E	5	155	0
3	Other macromolecule	DNA (5'-D(P*(3DR)P*GP*AP*TP*CP*G)-3')	F	6	161	20
4	Other macromolecule	DNA (5'-D(*CP*GP*AP*TP*CP*GP*GP*TP*AP*GP*C)-3')	G	11	349	0
5	Protein	DNA-(APURINIC OR APYRIMIDINIC SITE) LYASE	B	275	4368	0
6	Other macromolecule	DNA (5'-D(*GP*CP*TP*AP*C)-3')	H	5	155	0
7	Other macromolecule	DNA (5'-D(P*(3DR)P*GP*AP*TP*CP*G)-3')	I	5	101	20
8	Other macromolecule	DNA (5'-D(*CP*GP*AP*TP*CP*GP*GP*TP*AP*GP*C)-3')	J	11	349	0
9	Protein	DNA-(APURINIC OR APYRIMIDINIC SITE) LYASE	C	278	4399	0
10	Other macromolecule	DNA (5'-D(*GP*CP*TP*AP*C)-3')	K	5	155	0
11	Other macromolecule	DNA (5'-D(P*(3DR)P*GP*AP*TP*CP*G)-3')	L	6	161	20
12	Other macromolecule	DNA (5'-D(*CP*GP*AP*TP*CP*GP*GP*TP*AP*GP*C)-3')	M	11	349	0
13	Protein	DNA-(APURINIC OR APYRIMIDINIC SITE) LYASE	D	276	4378	0
14	Other macromolecule	DNA (5'-D(*GP*CP*TP*AP*C)-3')	N	5	155	0
15	Other macromolecule	DNA (5'-D(P*(3DR)P*GP*AP*TP*CP*G)-3')	O	6	131	20
16	Other macromolecule	DNA (5'-D(*CP*GP*AP*TP*CP*GP*GP*TP*AP*GP*C)-3')	P	11	349	0
17	Ligand	DNA-(APURINIC OR APYRIMIDINIC SITE) LYASE	A	5	0	5
18	Ligand	DNA (5'-D(*GP*CP*TP*AP*C)-3')	E	1	0	1
19	Ligand	DNA (5'-D(P*(3DR)P*GP*AP*TP*CP*G)-3')	F	1	0	1
20	Ligand	DNA-(APURINIC OR APYRIMIDINIC SITE) LYASE	B	4	0	4
21	Ligand	DNA-(APURINIC OR APYRIMIDINIC SITE) LYASE	C	2	0	2
22	Ligand	DNA-(APURINIC OR APYRIMIDINIC SITE) LYASE	D	2	0	2
23	Ligand	DNA (5'-D(*GP*CP*TP*AP*C)-3')	N	1	0	1
24	Water			272	0	272
total				1482	20114	368

Proteins

Unit 1	GLY 41 PRO 42 ALA 43 LEU 44 TYR 45 GLU 46 ASP 47 PRO 48 PRO 49 ASP 50 GLN 51 LYS 52 THR 53 SER 54 PRO 55 SER 56 GLY 57 LYS 58 PRO 59 ALA 60 THR 61 LEU 62 LYS 63 ILE 64 CYS 65 SER 66 TRP 67 ASN 68 VAL 69 ASP 70 GLY 71 LEU 72 ARG 73 ALA 74 TRP 75 ILE 76 LYS 77 LYS 78 LYS 79 GLY 80 LEU 81 ASP 82 TRP 83 VAL 84 LYS 85 GLU 86 GLU 87 ALA 88 PRO 89 ASP 90 ILE 91 LEU 92 CYS 93 LEU 94 GLN 95 GLU 96 THR 97 LYS 98 CYS 99 SER 100 GLU 101 ASN 102 LYS 103 LEU 104 PRO 105 ALA 106 GLU 107 LEU 108 GLN 109 GLU 110 LEU 111 PRO 112 GLY 113 LEU 114 SER 115 HIS 116 GLN 117 TYR 118 TRP 119 SER 120 ALA 121 PRO 122 SER 123 ASP 124 LYS 125 GLU 126 GLY 127 TYR 128 SER 129 GLY 130 VAL 131 GLY 132 LEU 133 LEU 134 SER 135 ARG 136 GLN 137 CYS 138 PRO 139 LEU 140 LYS 141 VAL 142 SER 143 TYR 144 GLY 145 ILE 146 GLY 147 ASP 148 GLU 149 GLU 150 HIS 151 ASP 152 GLN 153 GLU 154 GLY 155 ARG 156 VAL 157 ILE 158 VAL 159 ALA 160 GLU 161 PHE 162 ASP 163 SER 164 PHE 165 VAL 166 LEU 167 VAL 168 THR 169 ALA 170 TYR 171 VAL 172 PRO 173 ASN 174 ALA 175 GLY 176 ARG 177 GLY 178 LEU 179 VAL 180 ARG 181 LEU 182 GLU 183 TYR 184 ARG 185 GLN 186 ARG 187 TRP 188 ASP 189 GLU 190 ALA 191 PHE 192 ARG 193 LYS 194 PHE 195 LEU 196 LYS 197 GLY 198 LEU 199 ALA 200 SER 201 ARG 202 LYS 203 PRO 204 LEU 205 VAL 206 LEU 207 CYS 208 GLY 209 ASP 210 LEU 211 ASN 212 VAL 213 ALA 214 HIS 215 GLU 216 GLU 217 ILE 218 ASP 219 LEU 220 ARG 221 ASN 222 PRO 223 LYS 224 GLY 225 ASN 226 LYS 227 LYS 228 ASN 229 ALA 230 GLY 231 PHE 232 THR 233 PRO 234 GLN 235 GLU 236 ARG 237 GLN 238 GLY 239 PHE 240 GLY 241 GLU 242 LEU 243 LEU 244 GLN 245 ALA 246 VAL 247 PRO 248 LEU 249 ALA 250 ASP 251 SER 252 PHE 253 ARG 254 HIS 255 LEU 256 TYR 257 PRO 258 ASN 259 THR 260 PRO 261 TYR 262 ALA 263 TYR 264 THR 265 PHE 266 TRP 267 THR 268 TYR 269 MET 270 MET 271 ASN 272 ALA 273 ARG 274 SER 275 LYS 276 ASN 277 VAL 278 GLY 279 TRP 280 ARG 281 LEU 282 ASP 283 TYR 284 PHE 285 LEU 286 LEU 287 SER 288 HIS 289 SER 290 LEU 291 LEU 292 PRO 293 ALA 294 LEU 295 CYS 296 ASP 297 SER 298 LYS 299 ILE 300 ARG 301 SER 302 LYS 303 ALA 304 LEU 305 GLY 306 SER 307 ASP 308 HIS 309 CYS 310 PRO 311 ILE 312 THR 313 LEU 314 TYR 315 LEU 316 ALA 317 LEU 318
Unit 5	LEU 44 TYR 45 GLU 46 ASP 47 PRO 48 PRO 49 ASP 50 GLN 51 LYS 52 THR 53 SER 54 PRO 55 SER 56 GLY 57 LYS 58 PRO 59 ALA 60 THR 61 LEU 62 LYS 63 ILE 64 CYS 65 SER 66 TRP 67 ASN 68 VAL 69 ASP 70 GLY 71 LEU 72 ARG 73 ALA 74 TRP 75 ILE 76 LYS 77 LYS 78 LYS 79 GLY 80 LEU 81 ASP 82 TRP 83 VAL 84 LYS 85 GLU 86 GLU 87 ALA 88 PRO 89 ASP 90 ILE 91 LEU 92 CYS 93 LEU 94 GLN 95 GLU 96 THR 97 LYS 98 CYS 99 SER 100 GLU 101 ASN 102 LYS 103 LEU 104 PRO 105 ALA 106 GLU 107 LEU 108 GLN 109 GLU 110 LEU 111 PRO 112 GLY 113 LEU 114 SER 115 HIS 116 GLN 117 TYR 118 TRP 119 SER 120 ALA 121 PRO 122 SER 123 ASP 124 LYS 125 GLU 126 GLY 127 TYR 128 SER 129 GLY 130 VAL 131 GLY 132 LEU 133 LEU 134 SER 135 ARG 136 GLN 137 CYS 138 PRO 139 LEU 140 LYS 141 VAL 142 SER 143 TYR 144 GLY 145 ILE 146 GLY 147 ASP 148 GLU 149 GLU 150 HIS 151 ASP 152 GLN 153 GLU 154 GLY 155 ARG 156 VAL 157 ILE 158 VAL 159 ALA 160 GLU 161 PHE 162 ASP 163 SER 164 PHE 165 VAL 166 LEU 167 VAL 168 THR 169 ALA 170 TYR 171 VAL 172 PRO 173 ASN 174 ALA 175 GLY 176 ARG 177 GLY 178 LEU 179 VAL 180 ARG 181 LEU 182 GLU 183 TYR 184 ARG 185 GLN 186 ARG 187 TRP 188 ASP 189 GLU 190 ALA 191 PHE 192 ARG 193 LYS 194 PHE 195 LEU 196 LYS 197 GLY 198 LEU 199 ALA 200 SER 201 ARG 202 LYS 203 PRO 204 LEU 205 VAL 206 LEU 207 CYS 208 GLY 209 ASP 210 LEU 211 ASN 212 VAL 213 ALA 214 HIS 215 GLU 216 GLU 217 ILE 218 ASP 219 LEU 220 ARG 221 ASN 222 PRO 223 LYS 224 GLY 225 ASN 226 LYS 227 LYS 228 ASN 229 ALA 230 GLY 231 PHE 232 THR 233 PRO 234 GLN 235 GLU 236 ARG 237 GLN 238 GLY 239 PHE 240 GLY 241 GLU 242 LEU 243 LEU 244 GLN 245 ALA 246 VAL 247 PRO 248 LEU 249 ALA 250 ASP 251 SER 252 PHE 253 ARG 254 HIS 255 LEU 256 TYR 257 PRO 258 ASN 259 THR 260 PRO 261 TYR 262 ALA 263 TYR 264 THR 265 PHE 266 TRP 267 THR 268 TYR 269 MET 270 MET 271 ASN 272 ALA 273 ARG 274 SER 275 LYS 276 ASN 277 VAL 278 GLY 279 TRP 280 ARG 281 LEU 282 ASP 283 TYR 284 PHE 285 LEU 286 LEU 287 SER 288 HIS 289 SER 290 LEU 291 LEU 292 PRO 293 ALA 294 LEU 295 CYS 296 ASP 297 SER 298 LYS 299 ILE 300 ARG 301 SER 302 LYS 303 ALA 304 LEU 305 GLY 306 SER 307 ASP 308 HIS 309 CYS 310 PRO 311 ILE 312 THR 313 LEU 314 TYR 315 LEU 316 ALA 317 LEU 318
Unit 9	GLY 41 PRO 42 ALA 43 LEU 44 TYR 45 GLU 46 ASP 47 PRO 48 PRO 49 ASP 50 GLN 51 LYS 52 THR 53 SER 54 PRO 55 SER 56 GLY 57 LYS 58 PRO 59 ALA 60 THR 61 LEU 62 LYS 63 ILE 64 CYS 65 SER 66 TRP 67 ASN 68 VAL 69 ASP 70 GLY 71 LEU 72 ARG 73 ALA 74 TRP 75 ILE 76 LYS 77 LYS 78 LYS 79 GLY 80 LEU 81 ASP 82 TRP 83 VAL 84 LYS 85 GLU 86 GLU 87 ALA 88 PRO 89 ASP 90 ILE 91 LEU 92 CYS 93 LEU 94 GLN 95 GLU 96 THR 97 LYS 98 CYS 99 SER 100 GLU 101 ASN 102 LYS 103 LEU 104 PRO 105 ALA 106 GLU 107 LEU 108 GLN 109 GLU 110 LEU 111 PRO 112 GLY 113 LEU 114 SER 115 HIS 116 GLN 117 TYR 118 TRP 119 SER 120 ALA 121 PRO 122 SER 123 ASP 124 LYS 125 GLU 126 GLY 127 TYR 128 SER 129 GLY 130 VAL 131 GLY 132 LEU 133 LEU 134 SER 135 ARG 136 GLN 137 CYS 138 PRO 139 LEU 140 LYS 141 VAL 142 SER 143 TYR 144 GLY 145 ILE 146 GLY 147 ASP 148 GLU 149 GLU 150 HIS 151 ASP 152 GLN 153 GLU 154 GLY 155 ARG 156 VAL 157 ILE 158 VAL 159 ALA 160 GLU 161 PHE 162 ASP 163 SER 164 PHE 165 VAL 166 LEU 167 VAL 168 THR 169 ALA 170 TYR 171 VAL 172 PRO 173 ASN 174 ALA 175 GLY 176 ARG 177 GLY 178 LEU 179 VAL 180 ARG 181 LEU 182 GLU 183 TYR 184 ARG 185 GLN 186 ARG 187 TRP 188 ASP 189 GLU 190 ALA 191 PHE 192 ARG 193 LYS 194 PHE 195 LEU 196 LYS 197 GLY 198 LEU 199 ALA 200 SER 201 ARG 202 LYS 203 PRO 204 LEU 205 VAL 206 LEU 207 CYS 208 GLY 209 ASP 210 LEU 211 ASN 212 VAL 213 ALA 214 HIS 215 GLU 216 GLU 217 ILE 218 ASP 219 LEU 220 ARG 221 ASN 222 PRO 223 LYS 224 GLY 225 ASN 226 LYS 227 LYS 228 ASN 229 ALA 230 GLY 231 PHE 232 THR 233 PRO 234 GLN 235 GLU 236 ARG 237 GLN 238 GLY 239 PHE 240 GLY 241 GLU 242 LEU 243 LEU 244 GLN 245 ALA 246 VAL 247 PRO 248 LEU 249 ALA 250 ASP 251 SER 252 PHE 253 ARG 254 HIS 255 LEU 256 TYR 257 PRO 258 ASN 259 THR 260 PRO 261 TYR 262 ALA 263 TYR 264 THR 265 PHE 266 TRP 267 THR 268 TYR 269 MET 270 MET 271 ASN 272 ALA 273 ARG 274 SER 275 LYS 276 ASN 277 VAL 278 GLY 279 TRP 280 ARG 281 LEU 282 ASP 283 TYR 284 PHE 285 LEU 286 LEU 287 SER 288 HIS 289 SER 290 LEU 291 LEU 292 PRO 293 ALA 294 LEU 295 CYS 296 ASP 297 SER 298 LYS 299 ILE 300 ARG 301 SER 302 LYS 303 ALA 304 LEU 305 GLY 306 SER 307 ASP 308 HIS 309 CYS 310 PRO 311 ILE 312 THR 313 LEU 314 TYR 315 LEU 316 ALA 317 LEU 318
Unit 13	ALA 43 LEU 44 TYR 45 GLU 46 ASP 47 PRO 48 PRO 49 ASP 50 GLN 51 LYS 52 THR 53 SER 54 PRO 55 SER 56 GLY 57 LYS 58 PRO 59 ALA 60 THR 61 LEU 62 LYS 63 ILE 64 CYS 65 SER 66 TRP 67 ASN 68 VAL 69 ASP 70 GLY 71 LEU 72 ARG 73 ALA 74 TRP 75 ILE 76 LYS 77 LYS 78 LYS 79 GLY 80 LEU 81 ASP 82 TRP 83 VAL 84 LYS 85 GLU 86 GLU 87 ALA 88 PRO 89 ASP 90 ILE 91 LEU 92 CYS 93 LEU 94 GLN 95 GLU 96 THR 97 LYS 98 CYS 99 SER 100 GLU 101 ASN 102 LYS 103 LEU 104 PRO 105 ALA 106 GLU 107 LEU 108 GLN 109 GLU 110 LEU 111 PRO 112 GLY 113 LEU 114 SER 115 HIS 116 GLN 117 TYR 118 TRP 119 SER 120 ALA 121 PRO 122 SER 123 ASP 124 LYS 125 GLU 126 GLY 127 TYR 128 SER 129 GLY 130 VAL 131 GLY 132 LEU 133 LEU 134 SER 135 ARG 136 GLN 137 CYS 138 PRO 139 LEU 140 LYS 141 VAL 142 SER 143 TYR 144 GLY 145 ILE 146 GLY 147 ASP 148 GLU 149 GLU 150 HIS 151 ASP 152 GLN 153 GLU 154 GLY 155 ARG 156 VAL 157 ILE 158 VAL 159 ALA 160 GLU 161 PHE 162 ASP 163 SER 164 PHE 165 VAL 166 LEU 167 VAL 168 THR 169 ALA 170 TYR 171 VAL 172 PRO 173 ASN 174 ALA 175 GLY 176 ARG 177 GLY 178 LEU 179 VAL 180 ARG 181 LEU 182 GLU 183 TYR 184 ARG 185 GLN 186 ARG 187 TRP 188 ASP 189 GLU 190 ALA 191 PHE 192 ARG 193 LYS 194 PHE 195 LEU 196 LYS 197 GLY 198 LEU 199 ALA 200 SER 201 ARG 202 LYS 203 PRO 204 LEU 205 VAL 206 LEU 207 CYS 208 GLY 209 ASP 210 LEU 211 ASN 212 VAL 213 ALA 214 HIS 215 GLU 216 GLU 217 ILE 218 ASP 219 LEU 220 ARG 221 ASN 222 PRO 223 LYS 224 GLY 225 ASN 226 LYS 227 LYS 228 ASN 229 ALA 230 GLY 231 PHE 232 THR 233 PRO 234 GLN 235 GLU 236 ARG 237 GLN 238 GLY 239 PHE 240 GLY 241 GLU 242 LEU 243 LEU 244 GLN 245 ALA 246 VAL 247 PRO 248 LEU 249 ALA 250 ASP 251 SER 252 PHE 253 ARG 254 HIS 255 LEU 256 TYR 257 PRO 258 ASN 259 THR 260 PRO 261 TYR 262 ALA 263 TYR 264 THR 265 PHE 266 TRP 267 THR 268 TYR 269 MET 270 MET 271 ASN 272 ALA 273 ARG 274 SER 275 LYS 276 ASN 277 VAL 278 GLY 279 TRP 280 ARG 281 LEU 282 ASP 283 TYR 284 PHE 285 LEU 286 LEU 287 SER 288 HIS 289 SER 290 LEU 291 LEU 292 PRO 293 ALA 294 LEU 295 CYS 296 ASP 297 SER 298 LYS 299 ILE 300 ARG 301 SER 302 LYS 303 ALA 304 LEU 305 GLY 306 SER 307 ASP 308 HIS 309 CYS 310 PRO 311 ILE 312 THR 313 LEU 314 TYR 315 LEU 316 ALA 317 LEU 318

Other macromolecules

Unit 2	DG 501 DC 502 DT 503 DA 504 DC 505
Unit 3	3DR 506 DG 507 DA 508 DT 509 DC 510 DG 511
Unit 4	DC 512 DG 513 DA 514 DT 515 DC 516 DG 517 DG 518 DT 519 DA 520 DG 521 DC 522
Unit 6	DG 501 DC 502 DT 503 DA 504 DC 505
Unit 7	3DR 506 DG 507 DA 508 DT 509 DC 510
Unit 8	DC 512 DG 513 DA 514 DT 515 DC 516 DG 517 DG 518 DT 519 DA 520 DG 521 DC 522
Unit 10	DG 501 DC 502 DT 503 DA 504 DC 505
Unit 11	3DR 506 DG 507 DA 508 DT 509 DC 510 DG 511
Unit 12	DC 512 DG 513 DA 514 DT 515 DC 516 DG 517 DG 518 DT 519 DA 520 DG 521 DC 522
Unit 14	DG 501 DC 502 DT 503 DA 504 DC 505
Unit 15	3DR 506 DG 507 DA 508 DT 509 DC 510 DG 511
Unit 16	DC 512 DG 513 DA 514 DT 515 DC 516 DG 517 DG 518 DT 519 DA 520 DG 521 DC 522

Ligands

Unit 17	MG 501 MG 502 MG 503 NA 504 NA 505
Unit 18	NA 601
Unit 19	NA 601
Unit 20	MG 401 NA 402 NA 403 NA 404
Unit 21	MG 401 MG 402
Unit 22	MG 401 NA 402
Unit 23	NA 601