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4DQQ
Biol. Unit 1
Info
Asym.Unit (663 KB)
Biol.Unit 1 (327 KB)
Biol.Unit 2 (330 KB)
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(1)
Title
:
TERNARY COMPLEX OF BACILLUS DNA POLYMERASE I LARGE FRAGMENT E658A, DNA DUPLEX, AND RCTP (PAIRED WITH DG OF TEMPLATE) IN PRESENCE OF MG2+
Authors
:
W. Wang, L. S. Beese
Date
:
16 Feb 12 (Deposition) - 06 Jun 12 (Release) - 21 Nov 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.59
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C (1x)
Biol. Unit 2: D,E,F (1x)
Keywords
:
Dna Polymerase I, Protein-Dna Complex, Rctp-Dg, Transferase-Dna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
W. Wang, E. Y. Wu, H. W. Hellinga, L. S. Beese
Structural Factors That Determine Selectivity Of A High Fidelity Dna Polymerase For Deoxy-, Dideoxy-, And Ribonucleotides.
J. Biol. Chem. V. 287 28215 2012
(for further references see the
PDB file header
)
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Hetero Components
(5, 6)
Info
All Hetero Components
1a: CYTIDINE-5'-TRIPHOSPHATE (CTPa)
1b: CYTIDINE-5'-TRIPHOSPHATE (CTPb)
2a: 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSP... (DOCa)
2b: 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSP... (DOCb)
3a: 2-(N-MORPHOLINO)-ETHANESULFONIC AC... (MESa)
4a: MAGNESIUM ION (MGa)
5a: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDa)
5b: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDb)
5c: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDc)
5d: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDd)
6a: SULFATE ION (SO4a)
6b: SULFATE ION (SO4b)
View:
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Label:
No.
Name
Count
Type
Full Name
1
CTP
1
Ligand/Ion
CYTIDINE-5'-TRIPHOSPHATE
2
DOC
1
Mod. Nucleotide
2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE
3
MES
1
Ligand/Ion
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
4
MG
-1
Ligand/Ion
MAGNESIUM ION
5
MPD
2
Ligand/Ion
(4S)-2-METHYL-2,4-PENTANEDIOL
6
SO4
1
Ligand/Ion
SULFATE ION
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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: AC9 (SOFTWARE)
7: BC1 (SOFTWARE)
View:
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLU A:469 , GLN A:470 , ASP A:471 , ARG A:472 , LEU A:473 , LEU A:767 , HIS A:768 , HOH A:1451
BINDING SITE FOR RESIDUE CTP A 901
2
AC2
SOFTWARE
ARG A:779 , ASN A:780 , HOH A:1132 , HOH A:1179 , HOH A:1318 , ARG D:423 , PRO D:424
BINDING SITE FOR RESIDUE SO4 A 902
3
AC3
SOFTWARE
HOH A:1027 , HOH A:1287 , LEU D:352 , LYS D:383 , HOH D:1037
BINDING SITE FOR RESIDUE MPD A 903
4
AC4
SOFTWARE
GLU A:321 , VAL A:322 , VAL A:323 , ASP A:425 , ARG A:435 , HOH A:1291
BINDING SITE FOR RESIDUE MPD A 904
5
AC5
SOFTWARE
ARG A:615 , ALA A:658 , PHE A:710 , VAL A:713 , TYR A:714 , ASN A:793 , ILE A:796 , GLN A:797 , HOH A:1398 , DOC B:29 , DG C:4
BINDING SITE FOR RESIDUE MES A 905
6
AC9
SOFTWARE
LEU A:352 , LYS A:383 , HOH D:1065 , HOH D:1099
BINDING SITE FOR RESIDUE MPD D 904
7
BC1
SOFTWARE
GLY A:504 , LYS A:505 , ALA D:353 , ASP D:354 , HOH D:1193 , HOH D:1313 , HOH D:1543
BINDING SITE FOR RESIDUE MPD D 905
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
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PROSITE Patterns/Profiles
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(2, 4)
Info
All SCOP Domains
1a: SCOP_d4dqqa1 (A:297-468)
1b: SCOP_d4dqqd1 (D:293-468)
2a: SCOP_d4dqqa2 (A:469-876)
2b: SCOP_d4dqqd2 (D:469-876)
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Protein Domains
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Organisms
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)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Ribonuclease H-like motif
(1424)
Superfamily
:
Ribonuclease H-like
(775)
Family
:
automated matches
(127)
Protein domain
:
automated matches
(127)
Geobacillus kaustophilus [TaxId: 235909]
(6)
1a
d4dqqa1
A:297-468
1b
d4dqqd1
D:293-468
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
:
automated matches
(26)
Geobacillus kaustophilus [TaxId: 235909]
(6)
2a
d4dqqa2
A:469-876
2b
d4dqqd2
D:469-876
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CATH Domains
(0, 0)
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all CATH domains
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Pfam Domains
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Asymmetric Unit 1
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Asym.Unit (663 KB)
Header - Asym.Unit
Biol.Unit 1 (327 KB)
Header - Biol.Unit 1
Biol.Unit 2 (330 KB)
Header - Biol.Unit 2
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