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Magnesium in PDB 5vs0: Human Dna Polymerase Beta 8-Oxog:Dc Extension with Dttp After 80 S

Enzymatic activity of Human Dna Polymerase Beta 8-Oxog:Dc Extension with Dttp After 80 S

All present enzymatic activity of Human Dna Polymerase Beta 8-Oxog:Dc Extension with Dttp After 80 S:
2.7.7.7;

Protein crystallography data

The structure of Human Dna Polymerase Beta 8-Oxog:Dc Extension with Dttp After 80 S, PDB code: 5vs0 was solved by A.J.Reed, Z.Suo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 52.81 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.600, 80.300, 55.400, 90.00, 107.60, 90.00
R / Rfree (%) 20.2 / 26.2

Other elements in 5vs0:

The structure of Human Dna Polymerase Beta 8-Oxog:Dc Extension with Dttp After 80 S also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Human Dna Polymerase Beta 8-Oxog:Dc Extension with Dttp After 80 S (pdb code 5vs0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Human Dna Polymerase Beta 8-Oxog:Dc Extension with Dttp After 80 S, PDB code: 5vs0:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 5vs0

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Magnesium binding site 1 out of 6 in the Human Dna Polymerase Beta 8-Oxog:Dc Extension with Dttp After 80 S


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Dna Polymerase Beta 8-Oxog:Dc Extension with Dttp After 80 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:19.6
occ:1.00
 OD1 A:ASP190 2.0 28.5 1.0
O11 A:PPV408 2.1 23.3 1.0
O A:HOH558 2.1 16.1 1.0
OP1 P:DT11 2.1 20.2 1.0
OD2 A:ASP192 2.2 22.5 1.0
O12 A:PPV408 2.4 34.3 1.0
CG A:ASP190 3.1 24.3 1.0
P1 A:PPV408 3.2 21.9 1.0
CG A:ASP192 3.2 20.9 1.0
O21 A:PPV408 3.4 22.7 1.0
OD1 A:ASP192 3.5 21.2 1.0
OD2 A:ASP190 3.6 29.0 1.0
P P:DT11 3.6 23.0 1.0
MG A:MG402 3.7 19.0 1.0
P2 A:PPV408 3.8 32.5 1.0
OPP A:PPV408 3.9 28.2 1.0
O A:ASP190 4.0 20.0 1.0
O P:HOH203 4.1 32.5 1.0
O A:HOH582 4.2 21.7 1.0
O5' P:DT11 4.2 19.7 1.0
C5' P:DT11 4.2 19.5 1.0
N A:ASP190 4.3 21.9 1.0
C A:ASP190 4.3 21.7 1.0
CA A:GLY179 4.3 19.8 1.0
CB A:ASP190 4.4 22.9 1.0
OP2 P:DT11 4.4 20.0 1.0
N A:SER180 4.4 20.6 1.0
O31 A:PPV408 4.5 21.9 1.0
CB A:ASP192 4.5 20.5 1.0
CA A:ASP190 4.5 22.0 1.0
O3' P:DC10 4.6 23.1 1.0
O22 A:PPV408 4.6 33.9 1.0
OG A:SER180 4.7 22.5 1.0
MG P:MG101 4.8 33.4 1.0
O32 A:PPV408 4.8 32.3 1.0
N A:ASP192 4.9 19.5 1.0
C A:GLY179 5.0 20.7 1.0

Magnesium binding site 2 out of 6 in 5vs0

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Magnesium binding site 2 out of 6 in the Human Dna Polymerase Beta 8-Oxog:Dc Extension with Dttp After 80 S


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Dna Polymerase Beta 8-Oxog:Dc Extension with Dttp After 80 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:19.0
occ:1.00
 OD2 A:ASP190 1.9 29.0 1.0
OD2 A:ASP256 2.1 26.0 1.0
OD1 A:ASP192 2.2 21.2 1.0
O3' P:DC10 2.4 23.1 1.0
OP1 P:DT11 2.6 20.2 1.0
CG A:ASP190 2.9 24.3 1.0
P P:DT11 3.0 23.0 1.0
OD1 A:ASP190 3.1 28.5 1.0
CG A:ASP192 3.2 20.9 1.0
CG A:ASP256 3.2 23.3 1.0
C3' P:DC10 3.6 21.3 1.0
OD2 A:ASP192 3.6 22.5 1.0
MG A:MG401 3.7 19.6 1.0
C4' P:DC10 3.8 21.1 1.0
CB A:ASP256 3.8 22.4 1.0
C5' P:DC10 4.1 22.3 1.0
OP2 P:DT11 4.1 20.0 1.0
O5' P:DT11 4.1 19.7 1.0
C5' P:DT11 4.2 19.5 1.0
CB A:ASP190 4.3 22.9 1.0
OD1 A:ASP256 4.3 23.5 1.0
CB A:ASP192 4.5 20.5 1.0
C2' P:DC10 4.6 21.8 1.0
O A:MET191 4.6 22.0 1.0
CA A:ASP192 4.8 19.0 1.0
C A:MET191 4.9 19.3 1.0
O5' P:DC10 4.9 20.4 1.0
NH2 A:ARG254 4.9 20.8 1.0
N A:ASP256 5.0 22.2 1.0
N A:ASP192 5.0 19.5 1.0
OP1 P:DC10 5.0 21.3 1.0
O P:HOH203 5.0 32.5 1.0

Magnesium binding site 3 out of 6 in 5vs0

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Magnesium binding site 3 out of 6 in the Human Dna Polymerase Beta 8-Oxog:Dc Extension with Dttp After 80 S


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Human Dna Polymerase Beta 8-Oxog:Dc Extension with Dttp After 80 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:23.2
occ:1.00
 O A:THR101 2.2 26.2 1.0
OP1 P:DC9 2.3 21.1 1.0
O P:HOH201 2.4 27.2 1.0
O A:ILE106 2.4 21.5 1.0
O A:HOH589 2.4 32.0 1.0
O A:VAL103 2.4 19.6 1.0
C A:THR101 3.2 23.5 1.0
C A:VAL103 3.4 20.6 1.0
C A:ILE106 3.4 21.1 1.0
P P:DC9 3.4 21.2 1.0
OP2 P:DC9 3.6 20.0 1.0
N A:ILE106 3.7 19.9 1.0
CA A:THR101 3.8 23.1 1.0
N A:GLY105 3.9 18.1 1.0
CA A:SER104 3.9 18.0 1.0
N A:SER104 4.0 19.2 1.0
CA A:ILE106 4.0 20.0 1.0
O A:HOH586 4.1 38.0 1.0
N A:VAL103 4.1 22.9 1.0
C A:ARG102 4.1 24.8 1.0
N A:ARG102 4.2 23.9 1.0
C A:SER104 4.2 18.6 1.0
O3' P:DG8 4.4 24.4 1.0
N A:GLY107 4.4 21.5 1.0
CA A:VAL103 4.4 21.6 1.0
CB A:THR101 4.4 22.8 1.0
CB A:ILE106 4.5 19.8 1.0
CA A:ARG102 4.5 24.3 1.0
O A:ARG102 4.6 23.8 1.0
C A:GLY105 4.6 19.2 1.0
O5' P:DC9 4.6 21.9 1.0
CA A:GLY107 4.7 22.3 1.0
CA A:GLY105 4.8 19.4 1.0
O A:LEU100 4.8 19.2 1.0

Magnesium binding site 4 out of 6 in 5vs0

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Magnesium binding site 4 out of 6 in the Human Dna Polymerase Beta 8-Oxog:Dc Extension with Dttp After 80 S


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Human Dna Polymerase Beta 8-Oxog:Dc Extension with Dttp After 80 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:42.2
occ:1.00
 O A:LYS60 2.3 33.6 1.0
O A:VAL65 2.3 42.3 1.0
O A:LEU62 2.3 35.8 1.0
OP1 D:DC3 2.7 36.3 1.0
C A:LYS60 3.4 36.3 1.0
C A:LEU62 3.4 34.5 1.0
C A:VAL65 3.5 35.3 1.0
P D:DC3 3.6 39.7 1.0
OP2 D:DC3 3.6 37.1 1.0
C A:LYS61 4.0 39.2 1.0
N A:LEU62 4.0 34.3 1.0
N A:VAL65 4.0 33.3 1.0
CA A:VAL65 4.2 33.7 1.0
N A:PRO63 4.2 34.7 1.0
O A:LYS61 4.2 40.0 1.0
CA A:PRO63 4.2 35.8 1.0
CA A:LYS60 4.2 36.0 1.0
N A:LYS61 4.3 38.9 1.0
CA A:LEU62 4.4 34.5 1.0
CA A:LYS61 4.5 39.9 1.0
N A:GLY64 4.5 35.1 1.0
CB A:VAL65 4.5 34.4 1.0
N A:GLY66 4.5 32.0 1.0
CE A:LYS60 4.6 47.3 1.0
O3' D:DT2 4.7 38.1 1.0
C A:PRO63 4.7 36.4 1.0
CA A:GLY66 4.7 31.6 1.0
CG A:LYS60 4.7 42.9 1.0
O5' D:DC3 4.8 45.0 1.0
O A:ALA59 4.8 29.2 1.0
CD A:LYS60 4.9 43.8 1.0

Magnesium binding site 5 out of 6 in 5vs0

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Magnesium binding site 5 out of 6 in the Human Dna Polymerase Beta 8-Oxog:Dc Extension with Dttp After 80 S


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Human Dna Polymerase Beta 8-Oxog:Dc Extension with Dttp After 80 S within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mg101

b:33.4
occ:1.00
 O21 A:PPV408 2.0 22.7 1.0
O A:HOH501 2.1 31.7 1.0
O A:HOH564 2.2 28.8 1.0
O P:HOH203 2.3 32.5 1.0
OP2 P:DT11 2.3 20.0 1.0
P P:DT11 3.3 23.0 1.0
P1 A:PPV408 3.4 21.9 1.0
O32 A:PPV408 3.5 32.3 1.0
OP1 P:DT11 3.7 20.2 1.0
O5' P:DT11 3.8 19.7 1.0
OPP A:PPV408 3.8 28.2 1.0
O A:HOH512 4.0 18.5 1.0
O12 A:PPV408 4.0 34.3 1.0
P2 A:PPV408 4.1 32.5 1.0
O31 A:PPV408 4.2 21.9 1.0
C7 P:DT11 4.3 24.3 1.0
O11 A:PPV408 4.4 23.3 1.0
O3' P:DC10 4.7 23.1 1.0
MG A:MG401 4.8 19.6 1.0

Magnesium binding site 6 out of 6 in 5vs0

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Magnesium binding site 6 out of 6 in the Human Dna Polymerase Beta 8-Oxog:Dc Extension with Dttp After 80 S


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Human Dna Polymerase Beta 8-Oxog:Dc Extension with Dttp After 80 S within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mg102

b:42.0
occ:1.00
 O T:HOH120 1.8 43.1 1.0
O P:HOH204 1.9 32.1 1.0
O T:HOH119 2.1 33.8 1.0
O P:HOH202 2.2 27.1 1.0
O6 T:DG8 4.3 25.1 1.0
N7 P:DG8 4.4 23.9 1.0
O P:HOH205 4.4 36.4 1.0
C5 P:DC7 4.4 27.5 1.0
O6 P:DG8 4.4 22.1 1.0
N4 P:DC9 4.8 20.6 1.0

Reference:

A.J.Reed, Z.Suo. Time-Dependent Extension From An 8-Oxoguanine Lesion By Human Dna Polymerase Beta. J. Am. Chem. Soc. V. 139 9684 2017.
ISSN: ESSN 1520-5126
PubMed: 28682600
DOI: 10.1021/JACS.7B05048
Page generated: Mon Sep 30 06:17:30 2024

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