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4KHN
Asym. Unit
Info
Asym.Unit (663 KB)
Biol.Unit 1 (337 KB)
Biol.Unit 2 (321 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE TERNARY COMPLEX OF THE D714A MUTANT OF RB69 DNA POLYMERASE
Authors
:
K. E. Guja, A. Jacewicz, A. Trzemecka, D. Plochocka, E. Yakubovskaya, A M. Garcia-Diaz
Date
:
30 Apr 13 (Deposition) - 09 Oct 13 (Release) - 23 Oct 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.55
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,C,D (1x)
Biol. Unit 2: B,E,F (1x)
Keywords
:
Palm Subdomain, Hydrolase, Transferase, Transferase-Dna Complex
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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)
Reference
:
A. Jacewicz, A. Trzemecka, K. E. Guja, D. Plochocka, E. Yakubovskaya, A. Bebenek, M. Garcia-Diaz
A Remote Palm Domain Residue Of Rb69 Dna Polymerase Is Critical For Enzyme Activity And Influences The Conformatio Of The Active Site.
Plos One V. 8 76700 2013
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Hetero Components
(5, 15)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
3a: SODIUM ION (NAa)
4a: SULFATE ION (SO4a)
4b: SULFATE ION (SO4b)
4c: SULFATE ION (SO4c)
4d: SULFATE ION (SO4d)
4e: SULFATE ION (SO4e)
4f: SULFATE ION (SO4f)
5a: 2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HY... (XG4a)
5b: 2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HY... (XG4b)
5c: 2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HY... (XG4c)
5d: 2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HY... (XG4d)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
2
Ligand/Ion
CALCIUM ION
2
GOL
2
Ligand/Ion
GLYCEROL
3
NA
1
Ligand/Ion
SODIUM ION
4
SO4
6
Ligand/Ion
SULFATE ION
5
XG4
4
Ligand/Ion
2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]GUANOSINE
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Sites
(15, 15)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
SER A:36 , PHE A:38 , LYS A:48 , TYR A:49 , ARG A:59 , GLY A:84 , MET A:85 , ASP A:95 , PHE A:370 , LYS A:374 , LYS A:378 , VAL A:379 , ILE A:380
BINDING SITE FOR RESIDUE XG4 A 1001
02
AC2
SOFTWARE
ASP A:623 , HOH A:1126 , HOH A:1317 , XG4 C:101
BINDING SITE FOR RESIDUE CA A 1002
03
AC3
SOFTWARE
THR A:413 , SER A:414 , ARG A:482 , LYS A:486 , LYS A:560 , HOH A:1126
BINDING SITE FOR RESIDUE SO4 A 1003
04
AC4
SOFTWARE
TRP A:216 , ASN A:217 , SER A:289 , LEU A:290
BINDING SITE FOR RESIDUE SO4 A 1004
05
AC5
SOFTWARE
GLY A:637 , GLU A:638 , SER A:639
BINDING SITE FOR RESIDUE SO4 A 1005
06
AC6
SOFTWARE
TYR A:49 , ARG A:59 , HOH A:1151
BINDING SITE FOR RESIDUE SO4 A 1006
07
AC7
SOFTWARE
HIS A:105 , VAL A:110
BINDING SITE FOR RESIDUE SO4 A 1007
08
AC8
SOFTWARE
ILE A:557 , LEU A:561 , ASN A:564 , XG4 C:101
BINDING SITE FOR RESIDUE GOL A 1008
09
AC9
SOFTWARE
PHE A:650 , LYS A:653 , PHE A:654 , ARG A:658
BINDING SITE FOR RESIDUE GOL A 1009
10
BC1
SOFTWARE
TYR A:619 , ASP A:621 , LYS A:706 , DA D:114 , DC D:115
BINDING SITE FOR RESIDUE NA A 1010
11
BC2
SOFTWARE
LEU A:415 , TYR A:416 , LYS A:560 , ASN A:564 , THR A:622 , ASP A:623 , CA A:1002 , GOL A:1008 , HOH A:1114 , HOH A:1317 , DC C:4 , DG C:5 , HOH C:201 , DC D:115
BINDING SITE FOR RESIDUE XG4 C 101
12
BC3
SOFTWARE
SER B:36 , PHE B:38 , TYR B:49 , GLY B:84 , MET B:85 , ASP B:95 , PHE B:370 , LYS B:374 , ASN B:377 , LYS B:378 , VAL B:379 , ILE B:380 , HOH B:1101
BINDING SITE FOR RESIDUE XG4 B 1001
13
BC4
SOFTWARE
LEU B:415 , TYR B:416 , LYS B:560 , ASN B:564 , THR B:622 , ASP B:623 , SO4 B:1003 , CA B:1004 , DC E:4 , DG E:5 , DC F:115
BINDING SITE FOR RESIDUE XG4 B 1002
14
BC5
SOFTWARE
THR B:413 , SER B:414 , ARG B:482 , LYS B:560 , XG4 B:1002
BINDING SITE FOR RESIDUE SO4 B 1003
15
BC6
SOFTWARE
ASP B:623 , XG4 B:1002
BINDING SITE FOR RESIDUE CA B 1004
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
Info
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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, 4)
Info
All SCOP Domains
1a: SCOP_d4khna1 (A:1-375)
1b: SCOP_d4khnb1 (B:1-375)
2a: SCOP_d4khna2 (A:376-901)
2b: SCOP_d4khnb2 (B:376-901)
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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
:
DnaQ-like 3'-5' exonuclease
(253)
Protein domain
:
Exonuclease domain of family B DNA polymerases
(102)
Bacteriophage RB69 [TaxId: 12353]
(92)
1a
d4khna1
A:1-375
1b
d4khnb1
B:1-375
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
:
Family B DNA polymerase
(100)
Bacteriophage RB69 [TaxId: 12353]
(92)
2a
d4khna2
A:376-901
2b
d4khnb2
B:376-901
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CATH Domains
(0, 0)
Info
all CATH domains
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Pfam Domains
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Asymmetric Unit 1
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select all 'ALA' residues (Alanines) in chain 'A'
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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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Asym.Unit (663 KB)
Header - Asym.Unit
Biol.Unit 1 (337 KB)
Header - Biol.Unit 1
Biol.Unit 2 (321 KB)
Header - Biol.Unit 2
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