4LND

Crystal structure of human apurinic/apyrimidinic endonuclease 1 with essential Mg2+ cofactor

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
C	0003677	molecular_function	DNA binding
C	0003824	molecular_function	catalytic activity
C	0004518	molecular_function	nuclease activity
C	0004519	molecular_function	endonuclease activity
C	0006281	biological_process	DNA repair

Functional Information from PDB Data

site_id	AC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG A 401

Chain	Residue
A	ASP70
A	GLU96
A	HOH501
A	HOH502
A	HOH503
A	HOH504

---

site_id	AC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG B 401

Chain	Residue
B	HOH502
B	HOH503
B	HOH504
B	ASP70
B	GLU96
B	HOH501

---

site_id	AC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG C 401

Chain	Residue
C	ASP70
C	GLU96
C	HOH501
C	HOH502
C	HOH503
C	HOH504

---

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

---

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

---

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

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	87
Details	Region: {"description":"Mitochondrial targeting sequence (MTS)"}

Chain

Residue

Details

---

site_id	SWS_FT_FI2
Number of Residues	48
Details	Motif: {"description":"Nuclear export signal (NES)"}

Chain

Residue

Details

---

site_id	SWS_FT_FI3
Number of Residues	3
Details	Active site: {"evidences":[{"source":"PubMed","id":"15380100","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI4
Number of Residues	3
Details	Active site: {"description":"Proton donor/acceptor","evidences":[{"source":"PubMed","id":"9351835","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1BIX","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI5
Number of Residues	3
Details	Active site: {"description":"Proton acceptor","evidences":[{"source":"PROSITE-ProRule","id":"PRU00764","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI6
Number of Residues	18
Details	Binding site: {"evidences":[{"source":"PROSITE-ProRule","id":"PRU00764","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI7
Number of Residues	3
Details	Site: {"description":"Transition state stabilizer","evidences":[{"source":"PubMed","id":"8932375","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI8
Number of Residues	3
Details	Site: {"description":"Important for catalytic activity","evidences":[{"source":"PubMed","id":"21762700","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"9804799","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI9
Number of Residues	3
Details	Site: {"description":"Interaction with DNA substrate"}

Chain

Residue

Details

---

site_id	SWS_FT_FI10
Number of Residues	3
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI11
Number of Residues	6
Details	Modified residue: {"description":"S-nitrosocysteine; alternate","evidences":[{"source":"PubMed","id":"17403694","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI12
Number of Residues	3
Details	Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"PubMed","id":"19608861","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI13
Number of Residues	3
Details	Modified residue: {"description":"Phosphothreonine; by CDK5","evidences":[{"source":"UniProtKB","id":"P28352","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI14
Number of Residues	3
Details	Modified residue: {"description":"S-nitrosocysteine","evidences":[{"source":"PubMed","id":"17403694","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

Catalytic Information from CSA

site_id	MCSA1
Number of Residues	8
Details	M-CSA 510

Chain	Residue	Details
A	ASP70	metal ligand
A	GLU96	metal ligand
A	TYR171	electrostatic stabiliser, metal ligand
A	ASP210	increase nucleophilicity, metal ligand, proton acceptor
A	ASN212
A	ASP283	electrostatic stabiliser
A	ASP308	metal ligand
A	HIS309	electrostatic stabiliser, metal ligand

---

site_id	MCSA2
Number of Residues	8
Details	M-CSA 510

Chain	Residue	Details
B	ASP70	metal ligand
B	GLU96	metal ligand
B	TYR171	electrostatic stabiliser, metal ligand
B	ASP210	increase nucleophilicity, metal ligand, proton acceptor
B	ASN212
B	ASP283	electrostatic stabiliser
B	ASP308	metal ligand
B	HIS309	electrostatic stabiliser, metal ligand

---

site_id	MCSA3
Number of Residues	8
Details	M-CSA 510

Chain	Residue	Details
C	ASP70	metal ligand
C	GLU96	metal ligand
C	TYR171	electrostatic stabiliser, metal ligand
C	ASP210	increase nucleophilicity, metal ligand, proton acceptor
C	ASN212
C	ASP283	electrostatic stabiliser
C	ASP308	metal ligand
C	HIS309	electrostatic stabiliser, metal ligand

---