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Magnesium in PDB 5vrz: Human Dna Polymerase Beta 8-Oxog:Dc Extension with Dttp After 60 S

Enzymatic activity of Human Dna Polymerase Beta 8-Oxog:Dc Extension with Dttp After 60 S

All present enzymatic activity of Human Dna Polymerase Beta 8-Oxog:Dc Extension with Dttp After 60 S:
2.7.7.7;

Protein crystallography data

The structure of Human Dna Polymerase Beta 8-Oxog:Dc Extension with Dttp After 60 S, PDB code: 5vrz 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) 52.83 / 2.05
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.700, 79.800, 55.300, 90.00, 107.20, 90.00
R / Rfree (%) 19.7 / 24.2

Other elements in 5vrz:

The structure of Human Dna Polymerase Beta 8-Oxog:Dc Extension with Dttp After 60 S also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Sodium (Na) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Human Dna Polymerase Beta 8-Oxog:Dc Extension with Dttp After 60 S (pdb code 5vrz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Human Dna Polymerase Beta 8-Oxog:Dc Extension with Dttp After 60 S, PDB code: 5vrz:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 5vrz

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Magnesium binding site 1 out of 5 in the Human Dna Polymerase Beta 8-Oxog:Dc Extension with Dttp After 60 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 60 S within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mg102

b:39.7
occ:0.80
 O1A P:TTP101 1.9 10.7 0.2
O12 P:PPV107 2.2 25.8 0.8
O P:HOH513 2.2 39.6 1.0
OP2 P:DT11 2.4 22.1 0.8
O P:HOH501 2.7 51.8 1.0
PA P:TTP101 2.7 10.7 0.2
O3A P:TTP101 2.7 10.8 0.2
O P:HOH508 3.0 39.4 1.0
O3B P:TTP101 3.1 10.9 0.2
P P:DT11 3.4 22.6 0.8
O3G P:TTP101 3.5 10.7 0.2
O2A P:TTP101 3.6 10.9 0.2
P2 P:PPV107 3.6 25.1 0.8
O11 P:PPV107 3.6 29.8 0.8
PB P:TTP101 3.6 10.8 0.2
OP1 P:DT11 3.7 22.4 0.8
PG P:TTP101 3.7 11.3 0.2
O2G P:TTP101 3.8 10.7 0.2
OPP P:PPV107 3.8 28.0 0.8
O5' P:DT11 3.9 21.1 0.8
O5' P:TTP101 4.0 11.0 0.2
O21 P:PPV107 4.0 32.6 0.8
P1 P:PPV107 4.1 29.6 0.8
C5M P:TTP101 4.2 12.5 0.2
O P:HOH502 4.3 18.1 1.0
O22 P:PPV107 4.3 25.6 0.8
C7 P:DT11 4.4 21.4 0.8
O2B P:TTP101 4.6 10.9 0.2
O1B P:TTP101 4.6 10.9 0.2
O P:HOH504 4.7 37.6 1.0
O32 P:PPV107 4.7 24.8 0.8
O3' P:DC10 4.8 23.3 0.2
O3' P:DC10 4.8 24.8 0.8
MG P:MG105 4.9 13.6 1.0

Magnesium binding site 2 out of 5 in 5vrz

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Magnesium binding site 2 out of 5 in the Human Dna Polymerase Beta 8-Oxog:Dc Extension with Dttp After 60 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 60 S within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mg103

b:47.2
occ:1.00
 O P:HOH511 1.9 30.6 1.0
O P:HOH507 2.2 29.2 1.0
O T:HOH102 2.2 37.5 1.0
O T:HOH125 2.3 38.8 1.0
O P:HOH523 2.8 43.4 1.0
O6 T:DG8 3.9 24.7 1.0
O P:HOH521 4.1 41.5 1.0
O P:HOH516 4.2 38.1 1.0
N4 P:DC9 4.3 23.3 1.0
O T:HOH103 4.3 31.5 1.0
O T:HOH104 4.4 52.8 1.0
O6 P:DG8 4.4 21.0 1.0
N7 P:DG8 4.4 20.7 1.0
O P:HOH517 4.5 38.1 1.0
C5 P:DC7 4.7 22.7 1.0
O T:HOH118 4.7 48.6 1.0

Magnesium binding site 3 out of 5 in 5vrz

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Magnesium binding site 3 out of 5 in the Human Dna Polymerase Beta 8-Oxog:Dc Extension with Dttp After 60 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 60 S within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mg104

b:19.0
occ:1.00
 OD2 A:ASP190 1.9 31.3 1.0
OD2 A:ASP256 2.1 24.6 1.0
OD1 A:ASP192 2.2 19.2 1.0
O3' P:DC10 2.4 23.3 0.2
O3' P:DC10 2.4 24.8 0.8
OP1 P:DT11 2.5 22.4 0.8
O P:HOH504 2.6 37.6 1.0
CG A:ASP190 2.8 23.7 1.0
OD1 A:ASP190 2.8 26.4 1.0
O2A P:TTP101 2.9 10.9 0.2
P P:DT11 3.0 22.6 0.8
CG A:ASP192 3.3 20.9 1.0
CG A:ASP256 3.3 23.0 1.0
C3' P:DC10 3.6 23.0 0.2
C3' P:DC10 3.7 22.6 0.8
OD2 A:ASP192 3.7 21.1 1.0
MG P:MG105 3.7 13.6 1.0
PA P:TTP101 3.8 10.7 0.2
O5' P:TTP101 3.9 11.0 0.2
C4' P:DC10 3.9 23.1 0.2
C4' P:DC10 3.9 22.4 0.8
CB A:ASP256 4.0 23.1 1.0
OP2 P:DT11 4.0 22.1 0.8
C5' P:TTP101 4.0 11.4 0.2
C5' P:DC10 4.1 23.3 0.2
C5' P:DC10 4.1 22.9 0.8
O5' P:DT11 4.2 21.1 0.8
CB A:ASP190 4.2 22.1 1.0
OD1 A:ASP256 4.3 23.9 1.0
O1A P:TTP101 4.3 10.7 0.2
C5' P:DT11 4.3 21.1 0.8
O P:HOH508 4.4 39.4 1.0
O A:MET191 4.5 21.1 1.0
CB A:ASP192 4.5 20.4 1.0
O2G P:TTP101 4.6 10.7 0.2
C2' P:DC10 4.7 23.0 0.2
C2' P:DC10 4.7 22.1 0.8
OP1 P:DC10 4.7 23.8 0.2
C A:MET191 4.8 20.7 1.0
O5' P:DC10 4.8 23.4 0.8
NH2 A:ARG254 4.9 20.1 1.0
O5' P:DC10 4.9 23.6 0.2
CA A:ASP192 4.9 19.4 1.0
N A:ASP256 4.9 20.6 1.0
OP1 P:DC10 4.9 24.4 0.8

Magnesium binding site 4 out of 5 in 5vrz

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Magnesium binding site 4 out of 5 in the Human Dna Polymerase Beta 8-Oxog:Dc Extension with Dttp After 60 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 60 S within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mg105

b:13.6
occ:1.00
 O2G P:TTP101 1.8 10.7 0.2
O2A P:TTP101 1.9 10.9 0.2
O2B P:TTP101 2.0 10.9 0.2
O P:HOH506 2.0 21.9 1.0
OD1 A:ASP190 2.0 26.4 1.0
OD2 A:ASP192 2.2 21.1 1.0
OP1 P:DT11 2.3 22.4 0.8
O32 P:PPV107 2.4 24.8 0.8
O21 P:PPV107 2.7 32.6 0.8
PG P:TTP101 3.1 11.3 0.2
PB P:TTP101 3.2 10.8 0.2
CG A:ASP192 3.2 20.9 1.0
CG A:ASP190 3.2 23.7 1.0
PA P:TTP101 3.3 10.7 0.2
O12 P:PPV107 3.3 25.8 0.8
P2 P:PPV107 3.3 25.1 0.8
OD1 A:ASP192 3.5 19.2 1.0
O3B P:TTP101 3.6 10.9 0.2
O3A P:TTP101 3.6 10.8 0.2
MG P:MG104 3.7 19.0 1.0
P P:DT11 3.7 22.6 0.8
O1G P:TTP101 3.7 10.6 0.2
O A:ASP190 3.7 20.4 1.0
O P:HOH508 3.9 39.4 1.0
OD2 A:ASP190 3.9 31.3 1.0
P1 P:PPV107 4.0 29.6 0.8
OPP P:PPV107 4.0 28.0 0.8
C5' P:TTP101 4.1 11.4 0.2
C A:ASP190 4.1 21.3 1.0
N A:ASP190 4.1 20.1 1.0
O A:HOH609 4.1 18.1 1.0
O5' P:TTP101 4.2 11.0 0.2
O5' P:DT11 4.2 21.1 0.8
CB A:ASP190 4.3 22.1 1.0
O3G P:TTP101 4.4 10.7 0.2
CA A:ASP190 4.4 21.6 1.0
C5' P:DT11 4.4 21.1 0.8
O1A P:TTP101 4.4 10.7 0.2
O1B P:TTP101 4.5 10.9 0.2
CA A:GLY179 4.5 19.5 1.0
OG A:SER180 4.5 20.7 1.0
CB A:ASP192 4.5 20.4 1.0
N A:SER180 4.6 20.4 1.0
O22 P:PPV107 4.6 25.6 0.8
OP2 P:DT11 4.7 22.1 0.8
O3' P:DC10 4.7 23.3 0.2
O3' P:DC10 4.7 24.8 0.8
O31 P:PPV107 4.7 29.7 0.8
N A:MET191 4.8 20.2 1.0
O P:HOH504 4.8 37.6 1.0
N A:ASP192 4.9 19.6 1.0
MG P:MG102 4.9 39.7 0.8

Magnesium binding site 5 out of 5 in 5vrz

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Magnesium binding site 5 out of 5 in the Human Dna Polymerase Beta 8-Oxog:Dc Extension with Dttp After 60 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 60 S within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mg106

b:22.6
occ:1.00
 O A:THR101 2.1 21.2 1.0
O A:ILE106 2.3 22.3 1.0
O A:HOH628 2.3 32.0 1.0
OP1 P:DC9 2.4 20.6 1.0
O A:VAL103 2.4 20.8 1.0
O P:HOH503 2.5 29.1 1.0
C A:THR101 3.1 22.1 1.0
C A:ILE106 3.3 21.0 1.0
C A:VAL103 3.4 20.6 1.0
P P:DC9 3.4 21.4 1.0
OP2 P:DC9 3.6 19.7 1.0
N A:ILE106 3.7 19.3 1.0
CA A:THR101 3.8 23.6 1.0
O A:HOH598 3.8 36.9 1.0
CA A:ILE106 4.0 19.8 1.0
CA A:SER104 4.0 18.2 1.0
N A:GLY105 4.0 19.2 1.0
N A:VAL103 4.1 21.6 1.0
N A:SER104 4.1 18.9 1.0
C A:ARG102 4.2 22.3 1.0
N A:ARG102 4.2 21.9 1.0
CB A:THR101 4.3 24.6 1.0
N A:GLY107 4.3 19.7 1.0
C A:SER104 4.4 19.0 1.0
O3' P:DG8 4.4 24.2 1.0
CA A:VAL103 4.4 21.6 1.0
CB A:ILE106 4.4 20.1 1.0
O P:HOH518 4.5 41.3 1.0
CA A:ARG102 4.5 21.8 1.0
CA A:GLY107 4.6 21.3 1.0
O A:ARG102 4.6 21.8 1.0
C A:GLY105 4.6 19.4 1.0
O5' P:DC9 4.7 21.5 1.0
O A:LEU100 4.8 19.0 1.0
O A:HOH517 4.9 44.6 1.0
CA A:GLY105 4.9 20.1 1.0
O A:HOH595 4.9 31.8 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 06:17:18 2024

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