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2PFQ
Biol. Unit 1
Info
Asym.Unit (75 KB)
Biol.Unit 1 (69 KB)
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(1)
Title
:
MANGANESE PROMOTES CATALYSIS IN A DNA POLYMERASE LAMBDA-DNA CRYSTAL
Authors
:
M. Garcia-Diaz, K. Bebenek, J. M. Krahn, L. C. Pedersen, T. A. Kunkel
Date
:
05 Apr 07 (Deposition) - 15 May 07 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,D,P,T
Biol. Unit 1: A,D,P,T (1x)
Keywords
:
Dna Polymerase, Dna Repair, Phosphoryl Transfer Reaction, Manganese, Transferase, Lyase/Dna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Garcia-Diaz, K. Bebenek, J. M. Krahn, L. C. Pedersen, T. A. Kunkel
Role Of The Catalytic Metal During Polymerization By Dna Polymerase Lambda.
Dna Repair V. 6 1333 2007
(for further references see the
PDB file header
)
[
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Hetero Components
(2, 2)
Info
All Hetero Components
1a: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE (DCPa)
2a: MAGNESIUM ION (MGa)
3a: MANGANESE (II) ION (MNa)
3b: MANGANESE (II) ION (MNb)
4a: SODIUM ION (NAa)
4b: SODIUM ION (NAb)
5a: PYROPHOSPHATE (PPVa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
DCP
1
Ligand/Ion
2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
2
MG
-1
Ligand/Ion
MAGNESIUM ION
3
MN
-1
Ligand/Ion
MANGANESE (II) ION
4
NA
-1
Ligand/Ion
SODIUM ION
5
PPV
1
Ligand/Ion
PYROPHOSPHATE
[
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Sites
(7, 7)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP A:427 , ASP A:429 , NA A:1295 , MN A:1297 , DCP A:1438 , PPV A:1439 , HOH A:1602 , DC P:7
BINDING SITE FOR RESIDUE MG A 1294
2
AC2
SOFTWARE
ASP A:427 , ASP A:429 , ASP A:490 , MG A:1294 , MN A:1296 , DCP A:1438 , DC P:6 , DC P:7 , HOH P:299
BINDING SITE FOR RESIDUE NA A 1295
3
AC3
SOFTWARE
ASP A:427 , ASP A:429 , NA A:1295 , MN A:1297 , DCP A:1438 , PPV A:1439 , HOH A:1602 , DC P:7
BINDING SITE FOR RESIDUE MN A 1296
4
AC4
SOFTWARE
ASP A:427 , ASP A:429 , ASP A:490 , MG A:1294 , MN A:1296 , DCP A:1438 , DC P:6 , DC P:7 , HOH P:299
BINDING SITE FOR RESIDUE MN A 1297
5
AC5
SOFTWARE
SER A:339 , ILE A:341 , ALA A:344 , HOH A:1452 , DA P:5
BINDING SITE FOR RESIDUE NA A 1
6
AC6
SOFTWARE
ARG A:386 , GLY A:416 , SER A:417 , ARG A:420 , GLY A:426 , ASP A:427 , ASP A:429 , TYR A:505 , PHE A:506 , THR A:507 , GLY A:508 , ASN A:513 , MG A:1294 , NA A:1295 , MN A:1296 , MN A:1297 , HOH A:1449 , HOH A:1602 , DC P:6 , DC P:7 , HOH P:28 , HOH P:84 , DG T:5
BINDING SITE FOR RESIDUE DCP A 1438
7
AC7
SOFTWARE
ARG A:386 , GLY A:416 , SER A:417 , ARG A:420 , GLY A:426 , ASP A:427 , ASP A:429 , MG A:1294 , MN A:1296 , HOH A:1449 , HOH A:1602 , DC P:7
BINDING SITE FOR RESIDUE PPV A 1439
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SAPs(SNPs)/Variants
(1, 1)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_020269 (R438W, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_020269
R
438
W
DPOLL_HUMAN
Polymorphism
3730477
A
R
438
W
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: DNA_POLYMERASE_X (A:416-435)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
DNA_POLYMERASE_X
PS00522
DNA polymerase family X signature.
DPOLL_HUMAN
416-435
1
A:416-435
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
SCOP Domains
(3, 3)
Info
All SCOP Domains
1a: SCOP_d2pfqa1 (A:252-328)
2a: SCOP_d2pfqa2 (A:329-385)
3a: SCOP_d2pfqa3 (A:386-575)
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)
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)
(
)
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
SAM domain-like
(639)
Superfamily
:
DNA polymerase beta, N-terminal domain-like
(205)
Family
:
DNA polymerase beta, N-terminal domain-like
(183)
Protein domain
:
DNA polymerase lambda
(24)
Human (Homo sapiens) [TaxId: 9606]
(24)
1a
d2pfqa1
A:252-328
Superfamily
:
PsbU/PolX domain-like
(218)
Family
:
DNA polymerase beta-like, second domain
(190)
Protein domain
:
DNA polymerase lambda
(23)
Human (Homo sapiens) [TaxId: 9606]
(23)
2a
d2pfqa2
A:329-385
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Nucleotidyltransferase
(287)
Superfamily
:
Nucleotidyltransferase
(287)
Family
:
DNA polymerase beta-like
(218)
Protein domain
:
DNA polymerase lambda
(23)
Human (Homo sapiens) [TaxId: 9606]
(23)
3a
d2pfqa3
A:386-575
[
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]
CATH Domains
(4, 4)
Info
all CATH domains
1a: CATH_2pfqA03 (A:386-508)
2a: CATH_2pfqA04 (A:509-575)
3a: CATH_2pfqA01 (A:252-331)
4a: CATH_2pfqA02 (A:332-385)
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)
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)
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)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Beta Polymerase; domain 2
(187)
Homologous Superfamily
:
Beta Polymerase, domain 2
(183)
2. Synthetic: yes. Yes.
(3)
1a
2pfqA03
A:386-508
Topology
:
Beta Polymerase; domain 3
(161)
Homologous Superfamily
:
Beta Polymerase, domain 3
(161)
2. Synthetic: yes. Yes.
(3)
2a
2pfqA04
A:509-575
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
DNA polymerase; domain 1
(617)
Homologous Superfamily
:
[code=1.10.150.110, no name defined]
(150)
2. Synthetic: yes. Yes.
(3)
3a
2pfqA01
A:252-331
Homologous Superfamily
:
5' to 3' exonuclease, C-terminal subdomain
(384)
2. Synthetic: yes. Yes.
(3)
4a
2pfqA02
A:332-385
[
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Pfam Domains
(1, 1)
Info
all PFAM domains
1a: PFAM_DNA_pol_lambd_f_2pfqA01 (A:335-385)
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Clans
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)
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)
Families
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)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: DNA_pol_lambd_f]
(69)
Family
:
DNA_pol_lambd_f
(69)
Homo sapiens (Human)
(55)
1a
DNA_pol_lambd_f-2pfqA01
A:335-385
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]
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Chain P
Chain T
Asymmetric Unit 1
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select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
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