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2KZM
Asym. Unit
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Asym.Unit (106 KB)
Biol.Unit 1 (101 KB)
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(1)
Title
:
KLENOW FRAGMENT WITH NORMAL SUBSTRATE AND ZINC AND MANGANESE
Authors
:
C. A. Brautigam, S. Sun, J. A. Piccirilli, T. A. Steitz
Date
:
03 Jul 98 (Deposition) - 16 Feb 99 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.60
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Polymerase, Exonuclease, Two Metal Ion, Nucleotidyltransferase/Dna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. A. Brautigam, S. Sun, J. A. Piccirilli, T. A. Steitz
Structures Of Normal Single-Stranded Dna And Deoxyribo-3'-S-Phosphorothiolates Bound To The 3'-5' Exonucleolytic Active Site Of Dna Polymerase I From Escherichia Coli.
Biochemistry V. 38 696 1999
(for further references see the
PDB file header
)
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Hetero Components
(2, 2)
Info
All Hetero Components
1a: MANGANESE (II) ION (MNa)
2a: ZINC ION (ZNa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MN
1
Ligand/Ion
MANGANESE (II) ION
2
ZN
1
Ligand/Ion
ZINC ION
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Sites
(3, 3)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: EXO (UNKNOWN)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP A:355 , GLU A:357 , ASP A:501 , MN B:2 , DC B:1008
BINDING SITE FOR RESIDUE ZN A 1
2
AC2
SOFTWARE
ZN A:1 , ASP A:355 , DG B:1007 , DC B:1008
BINDING SITE FOR RESIDUE MN B 2
3
EXO
UNKNOWN
ASP A:355
EXONUCLEASE ACTIVE SITE.
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: DNA_POLYMERASE_A (A:754-773)
;
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
DNA_POLYMERASE_A
PS00447
DNA polymerase family A signature.
DPO1_ECOLI
754-773
1
A:754-773
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Exons
(0, 0)
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(2, 2)
Info
All SCOP Domains
1a: SCOP_d2kzma1 (A:324-518)
2a: SCOP_d2kzma2 (A:519-928)
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Classes
(
)
(
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)
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)
(
)
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Ribonuclease H-like motif
(1424)
Superfamily
:
Ribonuclease H-like
(775)
Family
:
DnaQ-like 3'-5' exonuclease
(253)
Protein domain
:
Exonuclease domain of prokaryotic DNA polymerase
(81)
Escherichia coli [TaxId: 562]
(14)
1a
d2kzma1
A:324-518
Class
:
Multi-domain proteins (alpha and beta)
(2421)
Fold
:
DNA/RNA polymerases
(850)
Superfamily
:
DNA/RNA polymerases
(850)
Family
:
DNA polymerase I
(233)
Protein domain
:
DNA polymerase I (Klenow fragment)
(82)
Escherichia coli [TaxId: 562]
(14)
2a
d2kzma2
A:519-928
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CATH Domains
(4, 4)
Info
all CATH domains
1a: CATH_2kzmA03 (A:659-708,A:853-927)
2a: CATH_2kzmA01 (A:326-542)
3a: CATH_2kzmA04 (A:709-852)
4a: CATH_2kzmA02 (A:543-658)
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(
)
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)
Architectures
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)
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)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Alpha-Beta Plaits
(1688)
Homologous Superfamily
:
[code=3.30.70.370, no name defined]
(99)
[unclassified]
(84)
1a
2kzmA03
A:659-708,A:853-927
Topology
:
Nucleotidyltransferase; domain 5
(788)
Homologous Superfamily
:
[code=3.30.420.10, no name defined]
(372)
[unclassified]
(102)
2a
2kzmA01
A:326-542
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
DNA polymerase; domain 1
(617)
Homologous Superfamily
:
5' to 3' exonuclease, C-terminal subdomain
(384)
[unclassified]
(230)
3a
2kzmA04
A:709-852
Architecture
:
Up-down Bundle
(3216)
Topology
:
Taq DNA Polymerase; Chain T, domain 4
(88)
Homologous Superfamily
:
Taq DNA Polymerase; Chain T, domain 4
(88)
[unclassified]
(77)
4a
2kzmA02
A:543-658
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Pfam Domains
(2, 2)
Info
all PFAM domains
1a: PFAM_DNA_pol_A_exo1_2kzmA01 (A:330-517)
2a: PFAM_DNA_pol_A_2kzmA02 (A:547-927)
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Clans
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)
(
)
Families
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)
(
)
Organisms
(
)
(
)
Clan
:
RNase_H
(288)
Family
:
DNA_pol_A_exo1
(16)
Escherichia coli (strain K12)
(11)
1a
DNA_pol_A_exo1-2kzmA01
A:330-517
Clan
:
no clan defined [family: DNA_pol_A]
(69)
Family
:
DNA_pol_A
(69)
Escherichia coli (strain K12)
(10)
2a
DNA_pol_A-2kzmA02
A:547-927
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