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Magnesium in PDB 6bs1: 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: 6bs1 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) 41.27 / 3.15
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 63.800, 127.720, 168.140, 90.00, 90.00, 90.00
R / Rfree (%) 24.4 / 29.9

Other elements in 6bs1:

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:

Iodine (I) 9 atoms
Platinum (Pt) 2 atoms

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 6bs1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 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: 6bs1:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 6bs1

Go back to Magnesium Binding Sites List in 6bs1
Magnesium binding site 1 out of 6 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:67.3
occ:1.00
 O3G A:DZ4609 2.0 67.5 1.0
O1A A:DZ4609 2.2 68.6 1.0
O A:MET108 2.2 69.8 1.0
O1B A:DZ4609 2.2 69.7 1.0
OD1 A:ASP107 2.2 78.0 1.0
OD2 A:ASP198 2.2 68.3 1.0
PB A:DZ4609 3.1 68.4 1.0
CG A:ASP107 3.2 75.0 1.0
PG A:DZ4609 3.2 63.0 1.0
PA A:DZ4609 3.3 72.3 1.0
C A:MET108 3.3 69.2 1.0
O3B A:DZ4609 3.4 65.4 1.0
MG A:MG603 3.4 82.4 1.0
CG A:ASP198 3.4 69.9 1.0
N3A A:DZ4609 3.4 70.2 1.0
N A:MET108 3.8 72.0 1.0
O1G A:DZ4609 3.8 65.2 1.0
OD2 A:ASP107 3.8 81.0 1.0
C A:ASP107 3.9 70.3 1.0
CA A:MET108 4.0 70.0 1.0
OD1 A:ASP198 4.1 72.7 1.0
CB A:ASP107 4.2 69.7 1.0
O A:ASP107 4.2 75.0 1.0
O5' A:DZ4609 4.3 79.6 1.0
C5' A:DZ4609 4.3 82.2 1.0
N A:ASP109 4.4 64.6 1.0
O2A A:DZ4609 4.4 77.0 1.0
CA A:ASP107 4.4 67.3 1.0
CB A:ASP198 4.5 71.6 1.0
CB A:MET108 4.5 69.8 1.0
O2G A:DZ4609 4.5 66.0 1.0
O2B A:DZ4609 4.5 66.2 1.0
CA A:ASP109 4.6 62.2 1.0
N A:ALA110 4.7 61.6 1.0
O3' C:DC13 4.9 85.8 1.0
O A:ASP198 4.9 74.4 1.0
N A:PHE111 4.9 62.1 1.0
C A:ASP109 4.9 59.1 1.0
CB A:PHE111 5.0 58.8 1.0

Magnesium binding site 2 out of 6 in 6bs1

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Magnesium binding site 2 out of 6 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:80.5
occ:1.00
 O A:ILE357 2.2 68.6 1.0
OP1 C:DC12 2.2 70.0 1.0
O A:VAL354 2.2 69.1 1.0
O A:ARG352 2.4 87.4 1.0
O C:HOH101 2.9 50.6 1.0
C A:ILE357 3.2 65.1 1.0
C A:VAL354 3.3 70.7 1.0
C A:ARG352 3.6 85.5 1.0
P C:DC12 3.6 70.9 1.0
N A:ILE357 3.6 66.6 1.0
N A:GLY356 3.9 72.9 1.0
CA A:ILE357 3.9 65.5 1.0
CA A:SER355 4.0 75.3 1.0
N A:SER355 4.1 74.1 1.0
CD A:ARG352 4.1 89.5 1.0
N A:VAL354 4.1 74.3 1.0
CB A:ILE357 4.2 67.0 1.0
C A:LYS353 4.2 79.4 1.0
N A:GLY358 4.3 66.6 1.0
OP2 C:DC12 4.3 70.3 1.0
C A:SER355 4.3 75.1 1.0
CA A:VAL354 4.4 71.7 1.0
CA A:ARG352 4.4 86.0 1.0
O3' C:DA11 4.5 75.1 1.0
NH2 A:ARG352 4.5 86.0 1.0
CA A:GLY358 4.5 67.9 1.0
N A:LYS353 4.5 82.9 1.0
O5' C:DC12 4.6 74.7 1.0
C A:GLY356 4.6 68.5 1.0
O A:LYS353 4.6 78.3 1.0
CA A:LYS353 4.7 83.8 1.0
CA A:GLY356 4.8 72.0 1.0
O A:ILE351 4.8 91.5 1.0
CG A:ARG352 4.8 90.5 1.0

Magnesium binding site 3 out of 6 in 6bs1

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Magnesium binding site 3 out of 6 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:82.4
occ:1.00
 O1A A:DZ4609 2.2 68.6 1.0
OD2 A:ASP107 2.2 81.0 1.0
OD1 A:ASP107 2.2 78.0 1.0
O3' C:DC13 2.3 85.8 1.0
OE2 A:GLU199 2.5 89.4 1.0
CG A:ASP107 2.6 75.0 1.0
PA A:DZ4609 3.2 72.3 1.0
O2A A:DZ4609 3.2 77.0 1.0
OD1 A:ASP198 3.3 72.7 1.0
OD2 A:ASP198 3.4 68.3 1.0
MG A:MG601 3.4 67.3 1.0
C3' C:DC13 3.7 79.3 1.0
CD A:GLU199 3.7 81.5 1.0
CG A:ASP198 3.8 69.9 1.0
O5' A:DZ4609 4.0 79.6 1.0
CB A:GLU199 4.0 68.4 1.0
O3G A:DZ4609 4.0 67.5 1.0
CB A:ASP107 4.1 69.7 1.0
OP1 C:DC13 4.3 75.2 1.0
CG A:GLU199 4.3 74.9 1.0
C4' C:DC13 4.5 80.2 1.0
N3A A:DZ4609 4.5 70.2 1.0
C5' A:DZ4609 4.6 82.2 1.0
OE1 A:GLU199 4.6 85.2 1.0
C2' C:DC13 4.8 74.9 1.0
CA A:ASP107 4.8 67.3 1.0
C5' C:DC13 4.8 80.7 1.0
O1B A:DZ4609 4.9 69.7 1.0
O5' C:DC13 5.0 79.9 1.0

Magnesium binding site 4 out of 6 in 6bs1

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Magnesium binding site 4 out of 6 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:66.2
occ:1.00
 O B:ARG352 2.2 87.5 1.0
O B:ILE357 2.3 75.2 1.0
OP1 P:DC12 2.7 77.2 1.0
O B:VAL354 2.9 81.8 1.0
C B:ARG352 3.4 88.6 1.0
C B:ILE357 3.4 71.6 1.0
NH2 B:ARG352 3.5 84.4 1.0
P P:DC12 3.8 78.7 1.0
OP2 P:DC12 3.9 70.0 1.0
CD B:ARG352 4.0 89.9 1.0
C B:VAL354 4.0 81.6 1.0
CA B:ARG352 4.2 90.5 1.0
CG B:ARG352 4.3 94.8 1.0
N B:ILE357 4.3 68.1 1.0
CA B:ILE357 4.3 68.2 1.0
N B:GLY358 4.4 75.8 1.0
N B:LYS353 4.4 86.2 1.0
C B:LYS353 4.4 83.5 1.0
CA B:GLY358 4.5 78.7 1.0
N B:VAL354 4.5 80.0 1.0
CZ B:ARG352 4.5 81.5 1.0
CB B:ILE357 4.5 69.6 1.0
CA B:LYS353 4.5 88.3 1.0
NE B:ARG352 4.7 82.0 1.0
N B:GLY356 4.7 82.3 1.0
CA B:SER355 4.8 83.0 1.0
O B:LYS353 4.8 86.1 1.0
N B:SER355 4.8 80.7 1.0
CB B:ARG352 4.8 91.9 1.0
O5' P:DC12 4.9 75.0 1.0
O3' P:DA11 4.9 82.0 1.0
CA B:VAL354 4.9 82.9 1.0

Magnesium binding site 5 out of 6 in 6bs1

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Magnesium binding site 5 out of 6 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
B:Mg602

b:78.8
occ:1.00
 O3G B:DZ4607 2.0 86.5 1.0
O2A B:DZ4607 2.2 76.5 1.0
O B:MET108 2.2 81.8 1.0
OD1 B:ASP107 2.2 79.1 1.0
OD1 B:ASP198 2.2 82.4 1.0
O2B B:DZ4607 2.2 81.5 1.0
PB B:DZ4607 3.2 79.1 1.0
PG B:DZ4607 3.2 89.0 1.0
C B:MET108 3.3 80.1 1.0
MG B:MG608 3.4 88.8 1.0
PA B:DZ4607 3.4 75.9 1.0
CG B:ASP107 3.4 80.3 1.0
CG B:ASP198 3.4 87.8 1.0
O3B B:DZ4607 3.5 81.3 1.0
N3A B:DZ4607 3.6 77.3 1.0
O2G B:DZ4607 3.8 92.3 1.0
N B:MET108 3.8 75.4 1.0
OD2 B:ASP107 4.0 82.0 1.0
CA B:MET108 4.1 78.0 1.0
C B:ASP107 4.1 72.4 1.0
CB B:ASP198 4.3 88.0 1.0
OD2 B:ASP198 4.3 94.0 1.0
C5' B:DZ4607 4.3 77.4 1.0
O5' B:DZ4607 4.3 76.1 1.0
N B:ASP109 4.4 82.0 1.0
O1A B:DZ4607 4.4 75.1 1.0
O B:ASP107 4.5 68.5 1.0
CB B:ASP107 4.5 78.2 1.0
O1G B:DZ4607 4.5 89.9 1.0
CB B:MET108 4.5 84.3 1.0
CA B:ASP109 4.6 83.0 1.0
O1B B:DZ4607 4.6 72.5 1.0
CA B:ASP107 4.6 75.1 1.0
N B:ALA110 4.6 88.3 1.0
N B:PHE111 4.8 77.0 1.0
CB B:PHE111 4.8 73.6 1.0
C B:ASP109 4.8 83.5 1.0

Magnesium binding site 6 out of 6 in 6bs1

Go back to Magnesium Binding Sites List in 6bs1
Magnesium binding site 6 out of 6 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 6 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:Mg608

b:88.8
occ:1.00
 O2A B:DZ4607 2.1 76.5 1.0
OD2 B:ASP198 2.2 94.0 1.0
O3' P:DC13 2.2 86.8 1.0
OE2 B:GLU199 2.2 97.9 1.0
OD1 B:ASP198 2.2 82.4 1.0
CG B:ASP198 2.5 87.8 1.0
CD B:GLU199 3.0 95.2 1.0
PA B:DZ4607 3.1 75.9 1.0
CG B:GLU199 3.2 92.3 1.0
OD1 B:ASP107 3.2 79.1 1.0
MG B:MG602 3.4 78.8 1.0
O5' B:DZ4607 3.5 76.1 1.0
C3' P:DC13 3.5 86.3 1.0
OD2 B:ASP107 3.5 82.0 1.0
O1A B:DZ4607 3.5 75.1 1.0
CG B:ASP107 3.6 80.3 1.0
C5' B:DZ4607 3.7 77.4 1.0
CB B:ASP198 4.0 88.0 1.0
CB B:GLU199 4.1 88.9 1.0
OE1 B:GLU199 4.1 91.7 1.0
C4' P:DC13 4.4 87.0 1.0
OG B:SER196 4.5 89.6 1.0
C B:ASP198 4.5 91.2 1.0
C2' P:DC13 4.5 84.8 1.0
N3A B:DZ4607 4.6 77.3 1.0
N B:GLU199 4.6 87.3 1.0
O2B B:DZ4607 4.6 81.5 1.0
O3G B:DZ4607 4.6 86.5 1.0
CA B:GLU199 4.7 86.3 1.0
C5' P:DC13 4.7 86.9 1.0
O B:ASP198 4.8 88.8 1.0
CB B:ASP107 4.8 78.2 1.0
CA B:ASP198 4.8 94.1 1.0
CA B:ASP107 5.0 75.1 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 19:58:17 2024

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