1DE9

HUMAN APE1 ENDONUCLEASE WITH BOUND ABASIC DNA AND MN2+ ION

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0003677	molecular_function	DNA binding
A	0003824	molecular_function	catalytic activity
A	0004518	molecular_function	nuclease activity
A	0004519	molecular_function	endonuclease activity
A	0006281	biological_process	DNA repair
B	0003677	molecular_function	DNA binding
B	0003824	molecular_function	catalytic activity
B	0004518	molecular_function	nuclease activity
B	0004519	molecular_function	endonuclease activity
B	0006281	biological_process	DNA repair

Functional Information from PDB Data

site_id	AC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE MN A 1000

Chain	Residue
A	GLU96
A	ASP308
X	DC5
Y	3DR6

---

site_id	AC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE MN B 1001

Chain	Residue
B	GLU96
B	ASP308
U	DC5
V	3DR6

---

Functional Information from PROSITE/UniProt

site_id	PS00726
Number of Residues	10
Details	AP_NUCLEASE_F1_1 AP endonucleases family 1 signature 1. PDILCLQETK

Chain	Residue	Details
A	PRO89-LYS98

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site_id	PS00727
Number of Residues	17
Details	AP_NUCLEASE_F1_2 AP endonucleases family 1 signature 2. DSFRHlypntpyaYTFW

Chain	Residue	Details
A	ASP251-TRP267

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site_id	PS00728
Number of Residues	12
Details	AP_NUCLEASE_F1_3 AP endonucleases family 1 signature 3. NvGwRLDYfLlS

Chain	Residue	Details
A	ASN277-SER288

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Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	2
Details	ACT_SITE: ACT_SITE => ECO:0000269|PubMed:15380100

Chain	Residue	Details
A	VAL172
B	VAL172

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site_id	SWS_FT_FI2
Number of Residues	2
Details	ACT_SITE: Proton donor/acceptor => ECO:0000269|PubMed:9351835, ECO:0007744|PDB:1BIX

Chain	Residue	Details
A	LEU211
B	LEU211

---

site_id	SWS_FT_FI3
Number of Residues	2
Details	ACT_SITE: Proton acceptor => ECO:0000255|PROSITE-ProRule:PRU00764

Chain	Residue	Details
A	CYS310
B	CYS310

---

site_id	SWS_FT_FI4
Number of Residues	12
Details	BINDING: BINDING => ECO:0000255|PROSITE-ProRule:PRU00764

Chain	Residue	Details
A	VAL69
B	VAL213
B	HIS309
B	CYS310
A	THR97
A	LEU211
A	VAL213
A	HIS309
A	CYS310
B	VAL69
B	THR97
B	LEU211

---

site_id	SWS_FT_FI5
Number of Residues	2
Details	SITE: Transition state stabilizer => ECO:0000269|PubMed:8932375

Chain	Residue	Details
A	VAL213
B	VAL213

---

site_id	SWS_FT_FI6
Number of Residues	2
Details	SITE: Important for catalytic activity => ECO:0000269|PubMed:21762700, ECO:0000269|PubMed:9804799

Chain	Residue	Details
A	TYR284
B	TYR284

---

site_id	SWS_FT_FI7
Number of Residues	2
Details	SITE: Interaction with DNA substrate

Chain	Residue	Details
A	CYS310
B	CYS310

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site_id	SWS_FT_FI8
Number of Residues	2
Details	MOD_RES: Phosphoserine => ECO:0007744|PubMed:23186163

Chain	Residue	Details
A	PRO55
B	PRO55

---

site_id	SWS_FT_FI9
Number of Residues	4
Details	MOD_RES: S-nitrosocysteine; alternate => ECO:0000269|PubMed:17403694

Chain	Residue	Details
A	SER66
A	LEU94
B	SER66
B	LEU94

---

site_id	SWS_FT_FI10
Number of Residues	2
Details	MOD_RES: N6-acetyllysine => ECO:0007744|PubMed:19608861

Chain	Residue	Details
A	GLY198
B	GLY198

---

site_id	SWS_FT_FI11
Number of Residues	2
Details	MOD_RES: Phosphothreonine; by CDK5 => ECO:0000250|UniProtKB:P28352

Chain	Residue	Details
A	PRO234
B	PRO234

---

site_id	SWS_FT_FI12
Number of Residues	2
Details	MOD_RES: S-nitrosocysteine => ECO:0000269|PubMed:17403694

Chain	Residue	Details
A	PRO311
B	PRO311

---

Catalytic Information from CSA

site_id	CSA1
Number of Residues	5
Details	Annotated By Reference To The Literature 1ako

Chain	Residue	Details
A	ASN212
A	HIS309
A	ASN68
A	ASP283
A	ASP210

---

site_id	CSA2
Number of Residues	5
Details	Annotated By Reference To The Literature 1ako

Chain	Residue	Details
B	ASN212
B	HIS309
B	ASN68
B	ASP283
B	ASP210

---

site_id	MCSA1
Number of Residues	8
Details	M-CSA 510

Chain	Residue	Details
A	GLY71	metal ligand
A	THR97	metal ligand
A	VAL172	electrostatic stabiliser, metal ligand
A	LEU211	increase nucleophilicity, metal ligand, proton acceptor
A	VAL213
A	TYR284	electrostatic stabiliser
A	HIS309	metal ligand
A	CYS310	electrostatic stabiliser, metal ligand

---

site_id	MCSA2
Number of Residues	8
Details	M-CSA 510

Chain	Residue	Details
B	GLY71	metal ligand
B	THR97	metal ligand
B	VAL172	electrostatic stabiliser, metal ligand
B	LEU211	increase nucleophilicity, metal ligand, proton acceptor
B	VAL213
B	TYR284	electrostatic stabiliser
B	HIS309	metal ligand
B	CYS310	electrostatic stabiliser, metal ligand

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