3NDK

RB69 DNA Polymerase (Y567A) Ternary Complex with dCTP Opposite dG

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000166	molecular_function	nucleotide binding
A	0003676	molecular_function	nucleic acid binding
A	0003677	molecular_function	DNA binding
A	0003887	molecular_function	DNA-directed DNA polymerase activity
A	0004527	molecular_function	exonuclease activity
A	0006260	biological_process	DNA replication
A	0006261	biological_process	DNA-templated DNA replication
A	0008408	molecular_function	3'-5' exonuclease activity
A	0039686	biological_process	bidirectional double-stranded viral DNA replication
A	0039693	biological_process	viral DNA genome replication
A	0046872	molecular_function	metal ion binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	21
Details	BINDING SITE FOR RESIDUE DCP A 904

Chain	Residue
A	ASP411
A	ASP623
A	CA905
A	CA906
A	CA908
A	HOH992
A	HOH1070
A	HOH1194
A	HOH1283
A	HOH1319
P	DOC115
A	LEU412
T	DG4
T	DG5
A	SER414
A	LEU415
A	TYR416
A	ARG482
A	LYS560
A	ASN564
A	THR622

---

site_id	AC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE CA A 905

Chain	Residue
A	ASP411
A	LEU412
A	ASP623
A	DCP904

---

site_id	AC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE CA A 906

Chain	Residue
A	ASP411
A	ASP623
A	DCP904
A	HOH1281
A	HOH1282

---

site_id	AC4
Number of Residues	7
Details	BINDING SITE FOR RESIDUE CA A 907

Chain	Residue
A	ASN505
A	ASN507
A	LYS531
A	HOH1014
A	HOH1015
A	HOH1258
A	HOH1476

---

site_id	AC5
Number of Residues	7
Details	BINDING SITE FOR RESIDUE CA A 908

Chain	Residue
A	ASP411
A	GLU686
A	GLU716
A	DCP904
A	HOH1164
A	HOH1283
A	HOH1284

---

site_id	AC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE CA A 909

Chain	Residue
A	GLU116
A	HOH947
A	HOH1083
A	HOH1232
A	HOH1276

---

site_id	AC7
Number of Residues	6
Details	BINDING SITE FOR RESIDUE CA A 910

Chain	Residue
A	GLU612
A	ASP792
A	HOH1370
A	HOH1371
A	HOH1372
A	HOH1373

---

site_id	AC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE CA A 911

Chain	Residue
A	ASP144
A	LYS185
A	HOH1007
A	HOH1102

---

Functional Information from PROSITE/UniProt

site_id	PS00116
Number of Residues	9
Details	DNA_POLYMERASE_B DNA polymerase family B signature. YGDTDSIYV

Chain	Residue	Details
A	TYR619-VAL627

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	2
Details	BINDING: BINDING => ECO:0000255|HAMAP-Rule:MF_04100

Chain	Residue	Details
A	ASP114
A	GLU116

---

site_id	SWS_FT_FI2
Number of Residues	2
Details	BINDING: BINDING => ECO:0000255|HAMAP-Rule:MF_04100, ECO:0000305|PubMed:23214497

Chain	Residue	Details
A	ALA222
A	ALA327

---

site_id	SWS_FT_FI3
Number of Residues	1
Details	BINDING: BINDING => ECO:0000255|HAMAP-Rule:MF_04100, ECO:0000269|PubMed:15057283, ECO:0000269|PubMed:17718515, ECO:0000269|PubMed:21566148, ECO:0000269|PubMed:21923197, ECO:0000269|PubMed:22026756, ECO:0000305|PubMed:11389835, ECO:0000305|PubMed:15057282, ECO:0000305|PubMed:18503083, ECO:0000305|PubMed:20166748, ECO:0000305|PubMed:21158418, ECO:0000305|PubMed:22571765, ECO:0000305|PubMed:23214497, ECO:0000305|PubMed:23921641, ECO:0000305|PubMed:24116139, ECO:0007744|PDB:2OZM, ECO:0007744|PDB:2OZS, ECO:0007744|PDB:3KD5, ECO:0007744|PDB:3SI6, ECO:0007744|PDB:3SNN, ECO:0007744|PDB:3SPY

Chain	Residue	Details
A	ASP411

---

site_id	SWS_FT_FI4
Number of Residues	1
Details	BINDING: BINDING => ECO:0000255|HAMAP-Rule:MF_04100, ECO:0000269|PubMed:17718515, ECO:0000269|PubMed:21566148, ECO:0000269|PubMed:21923197, ECO:0000305|PubMed:18503083, ECO:0000305|PubMed:23214497, ECO:0000305|PubMed:23921641, ECO:0007744|PDB:2OZM, ECO:0007744|PDB:2OZS, ECO:0007744|PDB:3KD5, ECO:0007744|PDB:3SI6, ECO:0007744|PDB:3SNN, ECO:0007744|PDB:3SPY

Chain	Residue	Details
A	LEU412

---

site_id	SWS_FT_FI5
Number of Residues	2
Details	BINDING: BINDING => ECO:0000255|HAMAP-Rule:MF_04100, ECO:0007744|PDB:1IG9, ECO:0007744|PDB:3CFP, ECO:0007744|PDB:3CFR, ECO:0007744|PDB:3CQ8, ECO:0007744|PDB:3LZJ, ECO:0007744|PDB:3NGI, ECO:0007744|PDB:3NHG, ECO:0007744|PDB:3QEP, ECO:0007744|PDB:3QET, ECO:0007744|PDB:3QNO, ECO:0007744|PDB:3RWU, ECO:0007744|PDB:3SQ2, ECO:0007744|PDB:3SQ4, ECO:0007744|PDB:3SUN, ECO:0007744|PDB:3SUO, ECO:0007744|PDB:4DTJ, ECO:0007744|PDB:4DTX, ECO:0007744|PDB:4FJ9, ECO:0007744|PDB:4FJJ, ECO:0007744|PDB:4FJN, ECO:0007744|PDB:4FK2, ECO:0007744|PDB:4J2A, ECO:0007744|PDB:4J2B, ECO:0007744|PDB:4J2D, ECO:0007744|PDB:4J2E, ECO:0007744|PDB:4KHS, ECO:0007744|PDB:4KHU, ECO:0007744|PDB:4KHW, ECO:0007744|PDB:4KHY, ECO:0007744|PDB:4KI4, ECO:0007744|PDB:4KI6, ECO:0007744|PDB:4M3R, ECO:0007744|PDB:4M3T, ECO:0007744|PDB:4M3U, ECO:0007744|PDB:4M3W, ECO:0007744|PDB:4M3X, ECO:0007744|PDB:4M3Y, ECO:0007744|PDB:4M3Z, ECO:0007744|PDB:4M41, ECO:0007744|PDB:4M42, ECO:0007744|PDB:4M45

Chain	Residue	Details
A	SER414
A	ARG482

---

site_id	SWS_FT_FI6
Number of Residues	1
Details	BINDING: BINDING => ECO:0000255|HAMAP-Rule:MF_04100, ECO:0007744|PDB:1IG9, ECO:0007744|PDB:3CFP, ECO:0007744|PDB:3CFR, ECO:0007744|PDB:3CQ8, ECO:0007744|PDB:3LZJ, ECO:0007744|PDB:3NGI, ECO:0007744|PDB:3NHG, ECO:0007744|PDB:3QEP, ECO:0007744|PDB:3QET, ECO:0007744|PDB:3QNO, ECO:0007744|PDB:3RWU, ECO:0007744|PDB:3SQ2, ECO:0007744|PDB:3SQ4, ECO:0007744|PDB:3SUN, ECO:0007744|PDB:3SUO, ECO:0007744|PDB:4DTJ, ECO:0007744|PDB:4DTX, ECO:0007744|PDB:4FJJ, ECO:0007744|PDB:4FJN, ECO:0007744|PDB:4FK2, ECO:0007744|PDB:4J2A, ECO:0007744|PDB:4J2B, ECO:0007744|PDB:4J2D, ECO:0007744|PDB:4J2E, ECO:0007744|PDB:4KHS, ECO:0007744|PDB:4KHU, ECO:0007744|PDB:4KHW, ECO:0007744|PDB:4KHY, ECO:0007744|PDB:4KI4, ECO:0007744|PDB:4KI6, ECO:0007744|PDB:4M3R, ECO:0007744|PDB:4M3T, ECO:0007744|PDB:4M3U, ECO:0007744|PDB:4M3W, ECO:0007744|PDB:4M3X, ECO:0007744|PDB:4M3Y, ECO:0007744|PDB:4M3Z, ECO:0007744|PDB:4M41, ECO:0007744|PDB:4M42, ECO:0007744|PDB:4M45

Chain	Residue	Details
A	LYS560

---

site_id	SWS_FT_FI7
Number of Residues	1
Details	BINDING: BINDING => ECO:0000255|HAMAP-Rule:MF_04100, ECO:0000269|PubMed:15057283, ECO:0000269|PubMed:17718515, ECO:0000269|PubMed:20166748, ECO:0000269|PubMed:20166752, ECO:0000269|PubMed:21566148, ECO:0000269|PubMed:21923197, ECO:0000269|PubMed:22026756, ECO:0000305|PubMed:11389835, ECO:0000305|PubMed:15057282, ECO:0000305|PubMed:18503083, ECO:0000305|PubMed:21158418, ECO:0000305|PubMed:22571765, ECO:0000305|PubMed:23214497, ECO:0000305|PubMed:23921641, ECO:0000305|PubMed:24116139, ECO:0007744|PDB:2OZM, ECO:0007744|PDB:2OZS, ECO:0007744|PDB:3KD5, ECO:0007744|PDB:3SI6, ECO:0007744|PDB:3SNN, ECO:0007744|PDB:3SPY

Chain	Residue	Details
A	ASP623

---

site_id	SWS_FT_FI8
Number of Residues	1
Details	SITE: Optimization of metal coordination by the polymerase active site => ECO:0000255|HAMAP-Rule:MF_04100, ECO:0000305|PubMed:15057283, ECO:0000305|PubMed:20166752, ECO:0000305|PubMed:22571765, ECO:0000305|PubMed:24116139

Chain	Residue	Details
A	ASP621

---

site_id	SWS_FT_FI9
Number of Residues	1
Details	SITE: Optimization of metal coordination by the polymerase active site => ECO:0000255|HAMAP-Rule:MF_04100, ECO:0000269|PubMed:15057283, ECO:0000269|PubMed:22571765

Chain	Residue	Details
A	LYS706

---

site_id	SWS_FT_FI10
Number of Residues	1
Details	SITE: Essential for viral replication => ECO:0000255|HAMAP-Rule:MF_04100, ECO:0000269|PubMed:24116139

Chain	Residue	Details
A	ASP714

---