Magnesium in PDB 6brx: Crystal Structure of Human Dna Polymerase Kappa in Complex with Dna Containing the Major Cisplatin Lesion
Enzymatic activity of Crystal Structure of Human Dna Polymerase Kappa in Complex with Dna Containing the Major Cisplatin Lesion
All present enzymatic activity of Crystal Structure of Human Dna Polymerase Kappa in Complex with Dna Containing the Major Cisplatin Lesion:
2.7.7.7;
Protein crystallography data
The structure of Crystal Structure of Human Dna Polymerase Kappa in Complex with Dna Containing the Major Cisplatin Lesion, PDB code: 6brx
was solved by
V.K.Jha,
H.Ling,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
48.47 /
2.80
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
66.690,
129.060,
168.088,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
21.4 /
26.9
|
Other elements in 6brx:
The structure of Crystal Structure of Human Dna Polymerase Kappa in Complex with Dna Containing the Major Cisplatin Lesion also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of Human Dna Polymerase Kappa in Complex with Dna Containing the Major Cisplatin Lesion
(pdb code 6brx). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the
Crystal Structure of Human Dna Polymerase Kappa in Complex with Dna Containing the Major Cisplatin Lesion, PDB code: 6brx:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
Magnesium binding site 1 out
of 5 in 6brx
Go back to
Magnesium Binding Sites List in 6brx
Magnesium binding site 1 out
of 5 in the Crystal Structure of Human Dna Polymerase Kappa in Complex with Dna Containing the Major Cisplatin Lesion
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Crystal Structure of Human Dna Polymerase Kappa in Complex with Dna Containing the Major Cisplatin Lesion within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg601
b:52.0
occ:1.00
|
O2B
|
A:0KX604
|
2.2
|
60.9
|
1.0
|
OD1
|
A:ASP107
|
2.2
|
52.2
|
1.0
|
O3G
|
A:0KX604
|
2.2
|
56.2
|
1.0
|
OD2
|
A:ASP198
|
2.2
|
59.3
|
1.0
|
O1A
|
A:0KX604
|
2.2
|
60.5
|
1.0
|
O
|
A:MET108
|
2.2
|
52.3
|
1.0
|
PB
|
A:0KX604
|
3.2
|
64.6
|
1.0
|
CG
|
A:ASP107
|
3.3
|
50.4
|
1.0
|
PA
|
A:0KX604
|
3.3
|
62.6
|
1.0
|
CG
|
A:ASP198
|
3.4
|
62.8
|
1.0
|
PG
|
A:0KX604
|
3.4
|
58.4
|
1.0
|
C
|
A:MET108
|
3.4
|
48.8
|
1.0
|
N3A
|
A:0KX604
|
3.5
|
64.2
|
1.0
|
O3B
|
A:0KX604
|
3.6
|
59.9
|
1.0
|
MG
|
A:MG603
|
3.8
|
66.1
|
1.0
|
N
|
A:MET108
|
3.9
|
50.0
|
1.0
|
OD2
|
A:ASP107
|
3.9
|
51.9
|
1.0
|
OD1
|
A:ASP198
|
3.9
|
69.4
|
1.0
|
NZ
|
A:LYS328
|
4.1
|
76.5
|
1.0
|
O2G
|
A:0KX604
|
4.1
|
56.9
|
1.0
|
CA
|
A:MET108
|
4.1
|
50.5
|
1.0
|
C5'
|
A:0KX604
|
4.2
|
66.7
|
1.0
|
C
|
A:ASP107
|
4.3
|
47.9
|
1.0
|
O5'
|
A:0KX604
|
4.3
|
63.9
|
1.0
|
O2A
|
A:0KX604
|
4.4
|
61.1
|
1.0
|
N
|
A:ASP109
|
4.4
|
45.6
|
1.0
|
CB
|
A:ASP107
|
4.5
|
49.4
|
1.0
|
CB
|
A:ASP198
|
4.5
|
59.1
|
1.0
|
O1B
|
A:0KX604
|
4.5
|
62.0
|
1.0
|
O1G
|
A:0KX604
|
4.5
|
58.7
|
1.0
|
CB
|
A:MET108
|
4.6
|
52.4
|
1.0
|
CA
|
A:ASP107
|
4.7
|
47.9
|
1.0
|
CA
|
A:ASP109
|
4.7
|
45.4
|
1.0
|
N
|
A:ALA110
|
4.8
|
46.0
|
1.0
|
O
|
A:ASP107
|
4.8
|
48.6
|
1.0
|
N
|
A:PHE111
|
4.9
|
55.1
|
1.0
|
CB
|
A:PHE111
|
4.9
|
55.4
|
1.0
|
CE
|
A:LYS328
|
4.9
|
76.4
|
1.0
|
C
|
A:ASP109
|
5.0
|
44.5
|
1.0
|
|
Magnesium binding site 2 out
of 5 in 6brx
Go back to
Magnesium Binding Sites List in 6brx
Magnesium binding site 2 out
of 5 in the Crystal Structure of Human Dna Polymerase Kappa in Complex with Dna Containing the Major Cisplatin Lesion
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Crystal Structure of Human Dna Polymerase Kappa in Complex with Dna Containing the Major Cisplatin Lesion within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg602
b:66.5
occ:1.00
|
O
|
A:ILE357
|
2.2
|
61.9
|
1.0
|
O
|
A:VAL354
|
2.2
|
58.5
|
1.0
|
OP1
|
C:DA12
|
2.2
|
56.0
|
1.0
|
O
|
A:ARG352
|
2.2
|
72.9
|
1.0
|
C
|
A:ILE357
|
3.2
|
55.5
|
1.0
|
C
|
A:VAL354
|
3.4
|
56.5
|
1.0
|
O
|
C:HOH109
|
3.4
|
54.9
|
1.0
|
C
|
A:ARG352
|
3.5
|
65.3
|
1.0
|
P
|
C:DA12
|
3.7
|
53.3
|
1.0
|
N
|
A:ILE357
|
3.7
|
55.7
|
1.0
|
CA
|
A:ILE357
|
3.9
|
56.1
|
1.0
|
N
|
A:GLY356
|
4.0
|
60.3
|
1.0
|
NH2
|
A:ARG352
|
4.0
|
75.7
|
1.0
|
N
|
A:VAL354
|
4.2
|
53.8
|
1.0
|
CA
|
A:SER355
|
4.2
|
62.3
|
1.0
|
N
|
A:SER355
|
4.2
|
60.3
|
1.0
|
CB
|
A:ILE357
|
4.2
|
57.6
|
1.0
|
N
|
A:GLY358
|
4.3
|
55.0
|
1.0
|
C
|
A:LYS353
|
4.3
|
56.5
|
1.0
|
OP2
|
C:DA12
|
4.3
|
52.6
|
1.0
|
CA
|
A:ARG352
|
4.3
|
67.5
|
1.0
|
CA
|
A:VAL354
|
4.4
|
53.3
|
1.0
|
N
|
A:LYS353
|
4.5
|
59.5
|
1.0
|
C
|
A:SER355
|
4.5
|
62.3
|
1.0
|
CA
|
A:GLY358
|
4.5
|
56.3
|
1.0
|
O3'
|
C:DC11
|
4.6
|
55.3
|
1.0
|
CD
|
A:ARG352
|
4.6
|
69.6
|
1.0
|
C
|
A:GLY356
|
4.6
|
58.4
|
1.0
|
O5'
|
C:DA12
|
4.7
|
56.4
|
1.0
|
CA
|
A:LYS353
|
4.7
|
60.4
|
1.0
|
O
|
A:LYS353
|
4.7
|
58.3
|
1.0
|
CG
|
A:ARG352
|
4.8
|
69.1
|
1.0
|
O
|
A:ILE351
|
4.8
|
63.9
|
1.0
|
CA
|
A:GLY356
|
4.9
|
60.6
|
1.0
|
|
Magnesium binding site 3 out
of 5 in 6brx
Go back to
Magnesium Binding Sites List in 6brx
Magnesium binding site 3 out
of 5 in the Crystal Structure of Human Dna Polymerase Kappa in Complex with Dna Containing the Major Cisplatin Lesion
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Crystal Structure of Human Dna Polymerase Kappa in Complex with Dna Containing the Major Cisplatin Lesion within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg603
b:66.1
occ:1.00
|
OE2
|
A:GLU199
|
2.2
|
69.6
|
1.0
|
O3'
|
C:DC13
|
2.2
|
66.3
|
1.0
|
O1A
|
A:0KX604
|
2.2
|
60.5
|
1.0
|
OD1
|
A:ASP198
|
2.7
|
69.4
|
1.0
|
PA
|
A:0KX604
|
3.0
|
62.6
|
1.0
|
O2A
|
A:0KX604
|
3.2
|
61.1
|
1.0
|
C3'
|
C:DC13
|
3.3
|
63.3
|
1.0
|
O5'
|
A:0KX604
|
3.4
|
63.9
|
1.0
|
CD
|
A:GLU199
|
3.4
|
70.3
|
1.0
|
CG
|
A:ASP198
|
3.5
|
62.8
|
1.0
|
OD2
|
A:ASP198
|
3.5
|
59.3
|
1.0
|
OD1
|
A:ASP107
|
3.6
|
52.2
|
1.0
|
OD2
|
A:ASP107
|
3.7
|
51.9
|
1.0
|
C5'
|
A:0KX604
|
3.8
|
66.7
|
1.0
|
MG
|
A:MG601
|
3.8
|
52.0
|
1.0
|
C4'
|
C:DC13
|
3.9
|
62.9
|
1.0
|
C5'
|
C:DC13
|
3.9
|
64.4
|
1.0
|
CG
|
A:ASP107
|
4.0
|
50.4
|
1.0
|
CB
|
A:GLU199
|
4.1
|
63.1
|
1.0
|
CG
|
A:GLU199
|
4.2
|
68.0
|
1.0
|
OE1
|
A:GLU199
|
4.2
|
71.4
|
1.0
|
OG
|
A:SER196
|
4.4
|
63.4
|
1.0
|
O5'
|
C:DC13
|
4.5
|
64.6
|
1.0
|
OP1
|
C:DC13
|
4.6
|
64.6
|
1.0
|
N3A
|
A:0KX604
|
4.6
|
64.2
|
1.0
|
C2'
|
C:DC13
|
4.6
|
63.2
|
1.0
|
CB
|
A:ASP198
|
4.9
|
59.1
|
1.0
|
|
Magnesium binding site 4 out
of 5 in 6brx
Go back to
Magnesium Binding Sites List in 6brx
Magnesium binding site 4 out
of 5 in the Crystal Structure of Human Dna Polymerase Kappa in Complex with Dna Containing the Major Cisplatin Lesion
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Crystal Structure of Human Dna Polymerase Kappa in Complex with Dna Containing the Major Cisplatin Lesion within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg601
b:66.8
occ:1.00
|
O1B
|
B:0KX602
|
2.1
|
73.2
|
1.0
|
O3G
|
B:0KX602
|
2.2
|
74.0
|
1.0
|
OD1
|
B:ASP198
|
2.2
|
69.7
|
1.0
|
OD1
|
B:ASP107
|
2.2
|
71.1
|
1.0
|
O
|
B:MET108
|
2.2
|
71.0
|
1.0
|
O2A
|
B:0KX602
|
2.2
|
77.9
|
1.0
|
PB
|
B:0KX602
|
3.2
|
80.8
|
1.0
|
PG
|
B:0KX602
|
3.4
|
79.1
|
1.0
|
CG
|
B:ASP107
|
3.4
|
75.2
|
1.0
|
C
|
B:MET108
|
3.4
|
70.2
|
1.0
|
PA
|
B:0KX602
|
3.4
|
77.9
|
1.0
|
CG
|
B:ASP198
|
3.4
|
72.8
|
1.0
|
O3B
|
B:0KX602
|
3.5
|
80.0
|
1.0
|
N3A
|
B:0KX602
|
3.5
|
79.2
|
1.0
|
N
|
B:MET108
|
3.9
|
70.6
|
1.0
|
OD2
|
B:ASP107
|
4.0
|
74.2
|
1.0
|
NZ
|
B:LYS328
|
4.1
|
93.2
|
1.0
|
OD2
|
B:ASP198
|
4.1
|
73.2
|
1.0
|
O1G
|
B:0KX602
|
4.1
|
78.9
|
1.0
|
CA
|
B:MET108
|
4.1
|
72.3
|
1.0
|
C
|
B:ASP107
|
4.3
|
72.3
|
1.0
|
C5'
|
B:0KX602
|
4.3
|
79.5
|
1.0
|
O5'
|
B:0KX602
|
4.4
|
79.3
|
1.0
|
CB
|
B:ASP198
|
4.4
|
75.5
|
1.0
|
N
|
B:ASP109
|
4.4
|
69.4
|
1.0
|
O2B
|
B:0KX602
|
4.4
|
79.6
|
1.0
|
O1A
|
B:0KX602
|
4.5
|
78.3
|
1.0
|
CB
|
B:ASP107
|
4.5
|
73.7
|
1.0
|
O2G
|
B:0KX602
|
4.5
|
81.7
|
1.0
|
CB
|
B:MET108
|
4.6
|
76.9
|
1.0
|
CA
|
B:ASP109
|
4.7
|
71.5
|
1.0
|
CA
|
B:ASP107
|
4.7
|
72.1
|
1.0
|
N
|
B:ALA110
|
4.7
|
67.1
|
1.0
|
O
|
B:ASP107
|
4.8
|
76.0
|
1.0
|
N
|
B:PHE111
|
4.8
|
71.8
|
1.0
|
CB
|
B:PHE111
|
4.9
|
70.1
|
1.0
|
CE
|
B:LYS328
|
5.0
|
97.3
|
1.0
|
C
|
B:ASP109
|
5.0
|
66.8
|
1.0
|
|
Magnesium binding site 5 out
of 5 in 6brx
Go back to
Magnesium Binding Sites List in 6brx
Magnesium binding site 5 out
of 5 in the Crystal Structure of Human Dna Polymerase Kappa in Complex with Dna Containing the Major Cisplatin Lesion
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Crystal Structure of Human Dna Polymerase Kappa in Complex with Dna Containing the Major Cisplatin Lesion within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
P:Mg101
b:79.7
occ:1.00
|
O
|
B:VAL354
|
2.2
|
70.8
|
1.0
|
O
|
B:ILE357
|
2.2
|
72.6
|
1.0
|
OP1
|
P:DA12
|
2.2
|
64.7
|
1.0
|
O
|
B:ARG352
|
2.2
|
90.0
|
1.0
|
O
|
B:HOH702
|
3.2
|
53.1
|
1.0
|
C
|
B:ILE357
|
3.2
|
64.5
|
1.0
|
C
|
B:VAL354
|
3.4
|
68.3
|
1.0
|
C
|
B:ARG352
|
3.5
|
84.1
|
1.0
|
O
|
P:HOH209
|
3.5
|
52.9
|
1.0
|
N
|
B:ILE357
|
3.6
|
64.1
|
1.0
|
P
|
P:DA12
|
3.7
|
62.4
|
1.0
|
CA
|
B:ILE357
|
3.8
|
65.4
|
1.0
|
N
|
B:GLY356
|
3.9
|
67.2
|
1.0
|
CB
|
B:ILE357
|
4.1
|
67.9
|
1.0
|
CA
|
B:SER355
|
4.2
|
70.0
|
1.0
|
NH2
|
B:ARG352
|
4.2
|
97.2
|
1.0
|
N
|
B:SER355
|
4.2
|
69.9
|
1.0
|
N
|
B:VAL354
|
4.2
|
67.4
|
1.0
|
N
|
B:GLY358
|
4.3
|
63.7
|
1.0
|
OP2
|
P:DA12
|
4.3
|
61.4
|
1.0
|
CA
|
B:ARG352
|
4.4
|
82.2
|
1.0
|
C
|
B:LYS353
|
4.4
|
71.0
|
1.0
|
CA
|
B:VAL354
|
4.4
|
67.7
|
1.0
|
C
|
B:SER355
|
4.5
|
69.0
|
1.0
|
N
|
B:LYS353
|
4.5
|
79.0
|
1.0
|
C
|
B:GLY356
|
4.6
|
64.5
|
1.0
|
O3'
|
P:DC11
|
4.6
|
63.9
|
1.0
|
CA
|
B:GLY358
|
4.6
|
66.7
|
1.0
|
CD
|
B:ARG352
|
4.6
|
93.7
|
1.0
|
O5'
|
P:DA12
|
4.7
|
65.8
|
1.0
|
CA
|
B:LYS353
|
4.7
|
74.8
|
1.0
|
O
|
B:LYS353
|
4.8
|
74.4
|
1.0
|
CA
|
B:GLY356
|
4.8
|
65.6
|
1.0
|
O
|
B:ILE351
|
4.8
|
65.8
|
1.0
|
CG
|
B:ARG352
|
4.9
|
92.2
|
1.0
|
|
Reference:
V.Jha,
H.Ling.
Structural Basis For Human Dna Polymerase Kappa to Bypass Cisplatin Intrastrand Cross-Link (Pt-Gg) Lesion As An Efficient and Accurate Extender. J. Mol. Biol. V. 430 1577 2018.
ISSN: ESSN 1089-8638
PubMed: 29715472
DOI: 10.1016/J.JMB.2018.04.023
Page generated: Mon Sep 30 19:57:40 2024
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