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Magnesium in PDB 5vs4: Human Dna Polymerase Beta 8-Oxog:Da Extension with Dttp After 120 S

Enzymatic activity of Human Dna Polymerase Beta 8-Oxog:Da Extension with Dttp After 120 S

All present enzymatic activity of Human Dna Polymerase Beta 8-Oxog:Da Extension with Dttp After 120 S:
2.7.7.7;

Protein crystallography data

The structure of Human Dna Polymerase Beta 8-Oxog:Da Extension with Dttp After 120 S, PDB code: 5vs4 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) 48.55 / 1.87
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.800, 79.700, 55.300, 90.00, 107.10, 90.00
R / Rfree (%) 19.9 / 25.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Human Dna Polymerase Beta 8-Oxog:Da Extension with Dttp After 120 S (pdb code 5vs4). 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:Da Extension with Dttp After 120 S, PDB code: 5vs4:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 5vs4

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Magnesium binding site 1 out of 6 in the Human Dna Polymerase Beta 8-Oxog:Da Extension with Dttp After 120 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:Da Extension with Dttp After 120 S within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mg101

b:24.7
occ:1.00
 O12 P:PPV102 2.3 20.2 1.0
O P:HOH521 2.3 25.4 1.0
OP2 P:DT11 2.4 20.2 1.0
O P:HOH514 2.4 30.7 1.0
O P:HOH515 3.1 35.9 1.0
O P:HOH501 3.1 39.7 1.0
P P:DT11 3.4 20.1 1.0
P2 P:PPV102 3.7 16.9 1.0
OP1 P:DT11 3.7 20.0 1.0
O11 P:PPV102 3.8 32.0 1.0
O21 P:PPV102 3.9 28.0 1.0
O5' P:DT11 4.0 16.7 1.0
OPP P:PPV102 4.0 22.2 1.0
P1 P:PPV102 4.1 29.0 1.0
O P:HOH508 4.4 19.7 1.0
O22 P:PPV102 4.4 17.2 1.0
MG P:MG104 4.5 7.2 1.0
C7 P:DT11 4.6 16.3 1.0
O32 P:PPV102 4.8 15.7 1.0
O3' P:DA10 4.8 20.8 1.0

Magnesium binding site 2 out of 6 in 5vs4

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Magnesium binding site 2 out of 6 in the Human Dna Polymerase Beta 8-Oxog:Da Extension with Dttp After 120 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:Da Extension with Dttp After 120 S within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mg103

b:9.2
occ:1.00
 OD1 A:ASP192 2.0 15.9 1.0
OD2 A:ASP190 2.0 23.2 1.0
OD2 A:ASP256 2.0 18.2 1.0
OP1 P:DT11 2.3 20.0 1.0
O3' P:DA10 2.7 20.8 1.0
CG A:ASP190 2.7 18.6 1.0
OD1 A:ASP190 2.8 17.5 1.0
CG A:ASP192 3.0 16.4 1.0
P P:DT11 3.1 20.1 1.0
CG A:ASP256 3.1 17.3 1.0
OD2 A:ASP192 3.4 18.0 1.0
MG P:MG104 3.6 7.2 1.0
CB A:ASP256 3.7 16.5 1.0
C3' P:DA10 4.0 19.6 1.0
OP2 P:DT11 4.2 20.2 1.0
CB A:ASP190 4.2 17.0 1.0
OD1 A:ASP256 4.2 18.7 1.0
O5' P:DT11 4.2 16.7 1.0
C4' P:DA10 4.2 19.6 1.0
O A:MET191 4.3 16.6 1.0
CB A:ASP192 4.3 15.8 1.0
C5' P:DT11 4.4 16.7 1.0
C5' P:DA10 4.5 19.0 1.0
C A:MET191 4.6 16.2 1.0
N A:ASP256 4.7 15.2 1.0
CA A:ASP192 4.7 15.7 1.0
O P:HOH514 4.7 30.7 1.0
N A:ASP192 4.8 16.9 1.0
CA A:ASP256 4.8 15.6 1.0
NH2 A:ARG254 4.9 16.9 1.0
N A:MET191 5.0 16.9 1.0
C2' P:DA10 5.0 19.5 1.0

Magnesium binding site 3 out of 6 in 5vs4

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Magnesium binding site 3 out of 6 in the Human Dna Polymerase Beta 8-Oxog:Da Extension with Dttp After 120 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:Da Extension with Dttp After 120 S within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mg104

b:7.2
occ:1.00
 OP1 P:DT11 2.2 20.0 1.0
OD1 A:ASP190 2.2 17.5 1.0
OD2 A:ASP192 2.2 18.0 1.0
O32 P:PPV102 2.3 15.7 1.0
O A:HOH634 2.4 20.9 1.0
O21 P:PPV102 2.6 28.0 1.0
O12 P:PPV102 3.0 20.2 1.0
P2 P:PPV102 3.1 16.9 1.0
CG A:ASP192 3.2 16.4 1.0
CG A:ASP190 3.3 18.6 1.0
OD1 A:ASP192 3.5 15.9 1.0
MG P:MG103 3.6 9.2 1.0
P P:DT11 3.6 20.1 1.0
O P:HOH514 3.7 30.7 1.0
P1 P:PPV102 3.8 29.0 1.0
OD2 A:ASP190 3.9 23.2 1.0
OPP P:PPV102 3.9 22.2 1.0
O5' P:DT11 4.1 16.7 1.0
C5' P:DT11 4.1 16.7 1.0
O A:ASP190 4.2 16.7 1.0
N A:ASP190 4.3 17.0 1.0
C A:ASP190 4.3 16.6 1.0
OP2 P:DT11 4.4 20.2 1.0
O22 P:PPV102 4.4 17.2 1.0
O31 P:PPV102 4.5 27.4 1.0
MG P:MG101 4.5 24.7 1.0
O A:HOH629 4.5 16.6 1.0
CB A:ASP190 4.5 17.0 1.0
CA A:GLY179 4.6 14.6 1.0
CB A:ASP192 4.6 15.8 1.0
CA A:ASP190 4.6 16.9 1.0
O3' P:DA10 4.7 20.8 1.0
N A:SER180 4.7 14.1 1.0
OG A:SER180 4.7 16.0 1.0
O11 P:PPV102 4.9 32.0 1.0
N A:MET191 5.0 16.9 1.0

Magnesium binding site 4 out of 6 in 5vs4

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Magnesium binding site 4 out of 6 in the Human Dna Polymerase Beta 8-Oxog:Da Extension with Dttp After 120 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:Da Extension with Dttp After 120 S within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mg105

b:19.6
occ:1.00
 O A:THR101 2.3 20.3 1.0
O A:ILE106 2.4 17.6 1.0
OP1 P:DC9 2.4 18.6 1.0
O A:VAL103 2.4 14.8 1.0
O P:HOH504 2.4 21.5 1.0
O A:HOH706 2.5 24.1 1.0
C A:THR101 3.2 18.6 1.0
C A:VAL103 3.4 15.2 1.0
P P:DC9 3.4 18.6 1.0
C A:ILE106 3.5 17.2 1.0
OP2 P:DC9 3.5 19.2 1.0
O A:HOH569 3.7 36.4 1.0
N A:ILE106 3.8 17.5 1.0
CA A:THR101 3.8 19.1 1.0
N A:GLY105 3.9 15.9 1.0
CA A:SER104 4.0 14.3 1.0
N A:SER104 4.0 15.0 1.0
N A:VAL103 4.1 17.0 1.0
CA A:ILE106 4.1 17.0 1.0
C A:ARG102 4.2 17.2 1.0
N A:ARG102 4.3 18.2 1.0
O3' P:DG8 4.3 20.2 1.0
C A:SER104 4.3 15.1 1.0
CA A:VAL103 4.4 16.4 1.0
CB A:THR101 4.4 19.2 1.0
N A:GLY107 4.5 17.7 1.0
CB A:ILE106 4.5 17.7 1.0
CA A:ARG102 4.5 18.6 1.0
O P:HOH519 4.5 42.6 1.0
O5' P:DC9 4.6 20.5 1.0
O A:ARG102 4.6 17.4 1.0
C A:GLY105 4.6 17.7 1.0
CA A:GLY107 4.7 17.8 1.0
O A:LEU100 4.8 18.2 1.0
CA A:GLY105 4.8 17.6 1.0

Magnesium binding site 5 out of 6 in 5vs4

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Magnesium binding site 5 out of 6 in the Human Dna Polymerase Beta 8-Oxog:Da Extension with Dttp After 120 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:Da Extension with Dttp After 120 S within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg101

b:31.4
occ:1.00
 O A:LYS60 2.4 31.5 1.0
O A:HOH715 2.4 38.4 1.0
O A:VAL65 2.4 25.9 1.0
O A:LEU62 2.4 27.0 1.0
O D:HOH204 2.5 31.9 1.0
OP1 D:DC3 2.6 27.7 1.0
C A:LEU62 3.4 26.9 1.0
C A:LYS60 3.5 31.6 1.0
C A:VAL65 3.5 26.2 1.0
P D:DC3 3.6 31.2 1.0
OP2 D:DC3 3.7 27.6 1.0
N A:VAL65 3.9 26.6 1.0
CA A:PRO63 4.0 27.6 1.0
N A:LEU62 4.1 28.4 1.0
N A:PRO63 4.1 27.9 1.0
C A:LYS61 4.1 31.1 1.0
CA A:VAL65 4.2 26.3 1.0
N A:GLY64 4.2 25.8 1.0
CA A:LYS60 4.3 30.8 1.0
N A:LYS61 4.4 30.4 1.0
CA A:LEU62 4.4 27.3 1.0
O A:LYS61 4.4 26.9 1.0
CB A:VAL65 4.4 27.7 1.0
CA A:LYS61 4.5 30.0 1.0
C A:PRO63 4.5 27.1 1.0
N A:GLY66 4.6 25.5 1.0
O3' D:DT2 4.6 27.8 1.0
CG A:LYS60 4.6 37.7 1.0
O5' D:DC3 4.8 30.6 1.0
CA A:GLY66 4.9 24.4 1.0
C A:GLY64 4.9 25.6 1.0
O A:ALA59 4.9 25.0 1.0

Magnesium binding site 6 out of 6 in 5vs4

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Magnesium binding site 6 out of 6 in the Human Dna Polymerase Beta 8-Oxog:Da Extension with Dttp After 120 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:Da Extension with Dttp After 120 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:27.7
occ:1.00
 O A:HOH666 2.3 37.5 1.0
O A:HOH657 2.3 40.4 1.0
OE2 A:GLU249 2.3 27.6 1.0
O A:HOH510 2.4 35.7 1.0
OE1 A:GLU249 2.5 27.6 1.0
O A:HOH747 2.5 48.0 1.0
CD A:GLU249 2.8 28.3 1.0
CG A:GLU249 4.3 26.0 1.0
OE1 A:GLN240 4.5 17.8 1.0
O A:HOH543 4.7 29.3 1.0
NE2 A:GLN240 4.8 15.9 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 06:17:50 2024

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