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2OWO
Asym. Unit
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Asym.Unit (127 KB)
Biol.Unit 1 (121 KB)
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(1)
Title
:
LAST STOP ON THE ROAD TO REPAIR: STRUCTURE OF E.COLI DNA LIGASE BOUND TO NICKED DNA-ADENYLATE
Authors
:
S. Shuman, J. Nandakumar, P. A. Nair
Date
:
16 Feb 07 (Deposition) - 15 May 07 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Dna, Ligase, Protein-Dna Complex, Ligase-Dna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. Nandakumar, P. A. Nair, S. Shuman
Last Stop On The Road To Repair: Structure Of E. Coli Dna Ligase Bound To Nicked Dna-Adenylate.
Mol. Cell V. 26 257 2007
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Hetero Components
(4, 7)
Info
All Hetero Components
1a: ADENOSINE MONOPHOSPHATE (AMPa)
2a: O2'-METHYLYCYTIDINE-5'-MONOPHOSPHA... (OMCa)
3a: SULFATE ION (SO4a)
3b: SULFATE ION (SO4b)
3c: SULFATE ION (SO4c)
3d: SULFATE ION (SO4d)
4a: ZINC ION (ZNa)
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Label:
No.
Name
Count
Type
Full Name
1
AMP
1
Ligand/Ion
ADENOSINE MONOPHOSPHATE
2
OMC
1
Mod. Nucleotide
O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE
3
SO4
4
Ligand/Ion
SULFATE ION
4
ZN
1
Ligand/Ion
ZINC ION
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Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
CYS A:408 , CYS A:411 , CYS A:426 , CYS A:432
BINDING SITE FOR RESIDUE ZN A 672
2
AC2
SOFTWARE
ARG A:446 , ARG A:447 , HOH A:922 , HOH C:42 , DC D:40
BINDING SITE FOR RESIDUE SO4 A 673
3
AC3
SOFTWARE
ARG A:74 , ARG A:510 , HOH A:718 , HOH A:759
BINDING SITE FOR RESIDUE SO4 A 674
4
AC4
SOFTWARE
ASN A:95 , GLN A:99 , SER A:262 , ALA A:263 , HOH A:799
BINDING SITE FOR RESIDUE SO4 A 675
5
AC5
SOFTWARE
HIS A:559 , ASN A:562
BINDING SITE FOR RESIDUE SO4 A 676
6
AC6
SOFTWARE
SER A:81 , LEU A:82 , GLU A:113 , LYS A:115 , ALA A:120 , ARG A:136 , GLU A:173 , TYR A:225 , VAL A:288 , LYS A:290 , HOH A:752 , HOH C:137 , DC D:40
BINDING SITE FOR RESIDUE AMP D 53
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(2, 2)
Info
All PROSITE Patterns/Profiles
1: DNA_LIGASE_N1 (A:115-144)
2: DNA_LIGASE_N2 (A:331-346)
;
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
DNA_LIGASE_N1
PS01055
NAD-dependent DNA ligase signature 1.
DNLJ_ECOLI
115-144
1
A:115-144
2
DNA_LIGASE_N2
PS01056
NAD-dependent DNA ligase signature 2.
DNLJ_ECOLI
331-346
1
A:331-346
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Exons
(0, 0)
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Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(0, 0)
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CATH Domains
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Info
all CATH domains
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Pfam Domains
(3, 3)
Info
all PFAM domains
1a: PFAM_DNA_ligase_aden_2owoA01 (A:2-318)
2a: PFAM_DNA_ligase_OB_2owoA02 (A:320-401)
3a: PFAM_DNA_ligase_ZBD_2owoA03 (A:407-434)
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Clans
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Families
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Organisms
(
)
(
)
Clan
:
DNA_ligase
(17)
Family
:
DNA_ligase_aden
(7)
Escherichia coli (strain K12)
(1)
1a
DNA_ligase_aden-2owoA01
A:2-318
Clan
:
OB
(224)
Family
:
DNA_ligase_OB
(2)
Escherichia coli (strain K12)
(1)
2a
DNA_ligase_OB-2owoA02
A:320-401
Clan
:
no clan defined [family: DNA_ligase_ZBD]
(1)
Family
:
DNA_ligase_ZBD
(1)
Escherichia coli (strain K12)
(1)
3a
DNA_ligase_ZBD-2owoA03
A:407-434
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Asym.Unit (127 KB)
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