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4BDP
Biol. Unit 1
Info
Asym.Unit (119 KB)
Biol.Unit 1 (115 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF BACILLUS DNA POLYMERASE I FRAGMENT COMPLEXED TO 11 BASE PAIRS OF DUPLEX DNA AFTER ADDITION OF TWO DATP RESIDUES
Authors
:
J. R. Kiefer, C. Mao, L. S. Beese
Date
:
17 Nov 97 (Deposition) - 13 Jan 99 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
Chains
:
Asym. Unit : A,P,T
Biol. Unit 1: A,P,T (1x)
Keywords
:
Bacillus Stearothermophilus Dna Polymerase, Bf Thermophilus Polymerase, Complex (Nucleotidyltransferase/Dna)
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. R. Kiefer, C. Mao, J. C. Braman, L. S. Beese
Visualizing Dna Replication In A Catalytically Active Bacillus Dna Polymerase Crystal.
Nature V. 391 304 1998
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(1, 3)
Info
All Hetero Components
1a: MAGNESIUM ION (MGa)
1b: MAGNESIUM ION (MGb)
2a: SULFATE ION (SO4a)
2b: SULFATE ION (SO4b)
2c: SULFATE ION (SO4c)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MG
-1
Ligand/Ion
MAGNESIUM ION
2
SO4
3
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(5, 5)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
HIS A:682 , ARG A:702 , LYS A:706 , HOH A:2611
BINDING SITE FOR RESIDUE SO4 A 910
2
AC2
SOFTWARE
ARG A:779 , ARG A:819 , MG A:952 , HOH A:2590
BINDING SITE FOR RESIDUE SO4 A 911
3
AC3
SOFTWARE
MET A:299 , ALA A:300 , ARG A:343 , ARG A:677
BINDING SITE FOR RESIDUE SO4 A 912
4
AC4
SOFTWARE
ASP A:653 , TYR A:654 , ASP A:830
BINDING SITE FOR RESIDUE MG A 950
5
AC5
SOFTWARE
GLU A:817 , SO4 A:911 , HOH A:2516
BINDING SITE FOR RESIDUE MG A 952
[
close Site info
]
SAPs(SNPs)/Variants
(48, 48)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
01: VAR_DPO1_GEOSE_001 (A298K, chain A, )
02: VAR_DPO1_GEOSE_002 (A300A, chain A, )
03: VAR_DPO1_GEOSE_003 (R306R, chain A, )
04: VAR_DPO1_GEOSE_004 (E309E, chain A, )
05: VAR_DPO1_GEOSE_005 (V320L, chain A, )
06: VAR_DPO1_GEOSE_006 (D329D, chain A, )
07: VAR_DPO1_GEOSE_007 (H341H, chain A, )
08: VAR_DPO1_GEOSE_008 (Q356Q, chain A, )
09: VAR_DPO1_GEOSE_009 (V358V, chain A, )
10: VAR_DPO1_GEOSE_010 (S369S, chain A, )
11: VAR_DPO1_GEOSE_011 (C388C, chain A, )
12: VAR_DPO1_GEOSE_012 (S391S, chain A, )
13: VAR_DPO1_GEOSE_013 (R411R, chain A, )
14: VAR_DPO1_GEOSE_014 (A413A, chain A, )
15: VAR_DPO1_GEOSE_015 (K417K, chain A, )
16: VAR_DPO1_GEOSE_016 (P424P, chain A, )
17: VAR_DPO1_GEOSE_017 (A436A, chain A, )
18: VAR_DPO1_GEOSE_018 (V442V, chain A, )
19: VAR_DPO1_GEOSE_019 (E456E, chain A, )
20: VAR_DPO1_GEOSE_020 (R459R, chain A, )
21: VAR_DPO1_GEOSE_021 (V475V, chain A, )
22: VAR_DPO1_GEOSE_022 (E487E, chain A, )
23: VAR_DPO1_GEOSE_023 (A491A, chain A, )
24: VAR_DPO1_GEOSE_024 (K505K, chain A, )
25: VAR_DPO1_GEOSE_025 (A508R, chain A, )
26: VAR_DPO1_GEOSE_026 (Q510K, chain A, )
27: VAR_DPO1_GEOSE_027 (Q516Q, chain A, )
28: VAR_DPO1_GEOSE_028 (E540E, chain A, )
29: VAR_DPO1_GEOSE_029 (Y567Y, chain A, )
30: VAR_DPO1_GEOSE_030 (N573N, chain A, )
31: VAR_DPO1_GEOSE_031 (R596R, chain A, )
32: VAR_DPO1_GEOSE_032 (D598D, chain A, )
33: VAR_DPO1_GEOSE_033 (K600K, chain A, )
34: VAR_DPO1_GEOSE_034 (I605I, chain A, )
35: VAR_DPO1_GEOSE_035 (T619T, chain A, )
36: VAR_DPO1_GEOSE_036 (S645S, chain A, )
37: VAR_DPO1_GEOSE_037 (M672M, chain A, )
38: VAR_DPO1_GEOSE_038 (D678D, chain A, )
39: VAR_DPO1_GEOSE_039 (Q691Q, chain A, )
40: VAR_DPO1_GEOSE_040 (P699P, chain A, )
41: VAR_DPO1_GEOSE_041 (S728S, chain A, )
42: VAR_DPO1_GEOSE_042 (E741E, chain A, )
43: VAR_DPO1_GEOSE_043 (R748R, chain A, )
44: VAR_DPO1_GEOSE_044 (E751E, chain A, )
45: VAR_DPO1_GEOSE_045 (M790M, chain A, )
46: VAR_DPO1_GEOSE_046 (K816K, chain A, )
47: VAR_DPO1_GEOSE_047 (M841M, chain A, )
48: VAR_DPO1_GEOSE_048 (S870S, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_DPO1_GEOSE_001
*
G
298
K
DPO1_GEOSE
---
---
A
A
298
K
02
UniProt
VAR_DPO1_GEOSE_002
*
D
300
A
DPO1_GEOSE
---
---
A
A
300
A
03
UniProt
VAR_DPO1_GEOSE_003
*
S
306
R
DPO1_GEOSE
---
---
A
R
306
R
04
UniProt
VAR_DPO1_GEOSE_004
*
D
309
E
DPO1_GEOSE
---
---
A
E
309
E
05
UniProt
VAR_DPO1_GEOSE_005
*
V
320
L
DPO1_GEOSE
---
---
A
V
320
L
06
UniProt
VAR_DPO1_GEOSE_006
*
H
329
D
DPO1_GEOSE
---
---
A
D
329
D
07
UniProt
VAR_DPO1_GEOSE_007
*
R
341
H
DPO1_GEOSE
---
---
A
H
341
H
08
UniProt
VAR_DPO1_GEOSE_008
*
K
356
Q
DPO1_GEOSE
---
---
A
Q
356
Q
09
UniProt
VAR_DPO1_GEOSE_009
*
L
358
V
DPO1_GEOSE
---
---
A
V
358
V
10
UniProt
VAR_DPO1_GEOSE_010
*
T
369
S
DPO1_GEOSE
---
---
A
S
369
S
11
UniProt
VAR_DPO1_GEOSE_011
*
R
388
C
DPO1_GEOSE
---
---
A
C
388
C
12
UniProt
VAR_DPO1_GEOSE_012
*
V
391
S
DPO1_GEOSE
---
---
A
S
391
S
13
UniProt
VAR_DPO1_GEOSE_013
*
A
411
R
DPO1_GEOSE
---
---
A
R
411
R
14
UniProt
VAR_DPO1_GEOSE_014
*
V
413
A
DPO1_GEOSE
---
---
A
A
413
A
15
UniProt
VAR_DPO1_GEOSE_015
*
H
417
K
DPO1_GEOSE
---
---
A
K
417
K
16
UniProt
VAR_DPO1_GEOSE_016
*
S
424
P
DPO1_GEOSE
---
---
A
P
424
P
17
UniProt
VAR_DPO1_GEOSE_017
*
T
436
A
DPO1_GEOSE
---
---
A
A
436
A
18
UniProt
VAR_DPO1_GEOSE_018
*
T
442
V
DPO1_GEOSE
---
---
A
V
442
V
19
UniProt
VAR_DPO1_GEOSE_019
*
A
456
E
DPO1_GEOSE
---
---
A
E
456
E
20
UniProt
VAR_DPO1_GEOSE_020
*
E
459
R
DPO1_GEOSE
---
---
A
R
459
R
21
UniProt
VAR_DPO1_GEOSE_021
*
T
475
V
DPO1_GEOSE
---
---
A
V
475
V
22
UniProt
VAR_DPO1_GEOSE_022
*
N
487
E
DPO1_GEOSE
---
---
A
E
487
E
23
UniProt
VAR_DPO1_GEOSE_023
*
T
491
A
DPO1_GEOSE
---
---
A
A
491
A
24
UniProt
VAR_DPO1_GEOSE_024
*
A
505
K
DPO1_GEOSE
---
---
A
K
505
K
25
UniProt
VAR_DPO1_GEOSE_025
*
T
508
R
DPO1_GEOSE
---
---
A
A
508
R
26
UniProt
VAR_DPO1_GEOSE_026
*
Q
510
K
DPO1_GEOSE
---
---
A
Q
510
K
27
UniProt
VAR_DPO1_GEOSE_027
*
R
516
Q
DPO1_GEOSE
---
---
A
Q
516
Q
28
UniProt
VAR_DPO1_GEOSE_028
*
D
540
E
DPO1_GEOSE
---
---
A
E
540
E
29
UniProt
VAR_DPO1_GEOSE_029
*
H
567
Y
DPO1_GEOSE
---
---
A
Y
567
Y
30
UniProt
VAR_DPO1_GEOSE_030
*
H
573
N
DPO1_GEOSE
---
---
A
N
573
N
31
UniProt
VAR_DPO1_GEOSE_031
*
H
596
R
DPO1_GEOSE
---
---
A
R
596
R
32
UniProt
VAR_DPO1_GEOSE_032
*
V
598
D
DPO1_GEOSE
---
---
A
D
598
D
33
UniProt
VAR_DPO1_GEOSE_033
*
G
600
K
DPO1_GEOSE
---
---
A
K
600
K
34
UniProt
VAR_DPO1_GEOSE_034
*
M
605
I
DPO1_GEOSE
---
---
A
I
605
I
35
UniProt
VAR_DPO1_GEOSE_035
*
V
619
T
DPO1_GEOSE
---
---
A
T
619
T
36
UniProt
VAR_DPO1_GEOSE_036
*
P
645
S
DPO1_GEOSE
---
---
A
S
645
S
37
UniProt
VAR_DPO1_GEOSE_037
*
I
672
M
DPO1_GEOSE
---
---
A
M
672
M
38
UniProt
VAR_DPO1_GEOSE_038
*
G
678
D
DPO1_GEOSE
---
---
A
D
678
D
39
UniProt
VAR_DPO1_GEOSE_039
*
H
691
Q
DPO1_GEOSE
---
---
A
Q
691
Q
40
UniProt
VAR_DPO1_GEOSE_040
*
A
699
P
DPO1_GEOSE
---
---
A
P
699
P
41
UniProt
VAR_DPO1_GEOSE_041
*
T
728
S
DPO1_GEOSE
---
---
A
S
728
S
42
UniProt
VAR_DPO1_GEOSE_042
*
A
741
E
DPO1_GEOSE
---
---
A
E
741
E
43
UniProt
VAR_DPO1_GEOSE_043
*
Q
748
R
DPO1_GEOSE
---
---
A
R
748
R
44
UniProt
VAR_DPO1_GEOSE_044
*
D
751
E
DPO1_GEOSE
---
---
A
E
751
E
45
UniProt
VAR_DPO1_GEOSE_045
*
T
790
M
DPO1_GEOSE
---
---
A
M
790
M
46
UniProt
VAR_DPO1_GEOSE_046
*
R
816
K
DPO1_GEOSE
---
---
A
K
816
K
47
UniProt
VAR_DPO1_GEOSE_047
*
I
841
M
DPO1_GEOSE
---
---
A
M
841
M
48
UniProt
VAR_DPO1_GEOSE_048
*
P
870
S
DPO1_GEOSE
---
---
A
S
870
S
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: DNA_POLYMERASE_A (A:702-721)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
DNA_POLYMERASE_A
PS00447
DNA polymerase family A signature.
DPO1_GEOSE
702-721
1
A:702-721
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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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
(2, 2)
Info
All SCOP Domains
1a: SCOP_d4bdpa1 (A:297-468)
2a: SCOP_d4bdpa2 (A:469-876)
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Classes
(
)
(
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Folds
(
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(
)
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(
)
(
)
Families
(
)
(
)
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)
Bacillus stearothermophilus, newly identified strain as yet unnamed [TaxId: 1422]
(43)
1a
d4bdpa1
A:297-468
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
:
DNA polymerase I (Klenow fragment)
(82)
Bacillus stearothermophilus, newly identified strain as yet unnamed [TaxId: 1422]
(44)
2a
d4bdpa2
A:469-876
[
close SCOP info
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CATH Domains
(4, 4)
Info
all CATH domains
1a: CATH_4bdpA03 (A:606-656,A:801-875)
2a: CATH_4bdpA01 (A:297-490)
3a: CATH_4bdpA04 (A:657-800)
4a: CATH_4bdpA02 (A:491-605)
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)
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)
Architectures
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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
4bdpA03
A:606-656,A:801-875
Topology
:
Nucleotidyltransferase; domain 5
(788)
Homologous Superfamily
:
[code=3.30.420.10, no name defined]
(372)
[unclassified]
(102)
2a
4bdpA01
A:297-490
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
4bdpA04
A:657-800
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
4bdpA02
A:491-605
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
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