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Magnesium in PDB 5vs3: Human Dna Polymerase Beta 8-Oxog:Da Extension with Dttp After 90 S

Enzymatic activity of Human Dna Polymerase Beta 8-Oxog:Da Extension with Dttp After 90 S

All present enzymatic activity of Human Dna Polymerase Beta 8-Oxog:Da Extension with Dttp After 90 S:
2.7.7.7;

Protein crystallography data

The structure of Human Dna Polymerase Beta 8-Oxog:Da Extension with Dttp After 90 S, PDB code: 5vs3 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) 52.76 / 1.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.400, 79.600, 55.200, 90.00, 107.10, 90.00
R / Rfree (%) 20.6 / 24.9

Other elements in 5vs3:

The structure of Human Dna Polymerase Beta 8-Oxog:Da Extension with Dttp After 90 S also contains other interesting chemical elements:

Sodium (Na) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Human Dna Polymerase Beta 8-Oxog:Da Extension with Dttp After 90 S (pdb code 5vs3). 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 90 S, PDB code: 5vs3:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 5vs3

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Magnesium binding site 1 out of 6 in the Human Dna Polymerase Beta 8-Oxog:Da Extension with Dttp After 90 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 90 S within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Mg101

b:30.6
occ:1.00
 O T:HOH210 1.9 38.5 1.0
O A:HOH635 2.2 33.9 1.0
O T:HOH231 2.3 38.8 1.0
OP1 T:DC11 2.3 21.1 1.0
O T:HOH232 2.6 38.1 1.0
P T:DC11 3.5 22.1 1.0
OP2 T:DC11 4.0 21.7 1.0
O5' T:DC11 4.2 20.7 1.0
O A:HOH764 4.2 38.9 1.0
O A:LYS230 4.3 22.0 1.0
N A:LYS230 4.4 21.1 1.0
C5' T:DC11 4.5 25.6 1.0
O A:HOH588 4.8 41.5 1.0
O3' T:DG10 4.8 20.5 1.0
CA A:SER229 4.9 22.6 1.0

Magnesium binding site 2 out of 6 in 5vs3

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Magnesium binding site 2 out of 6 in the Human Dna Polymerase Beta 8-Oxog:Da Extension with Dttp After 90 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 90 S within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mg102

b:25.5
occ:0.80
 O1A P:TTP101 1.4 9.3 0.2
OP2 P:DT11 2.1 19.4 0.8
O11 P:PPV106 2.1 21.8 0.8
O P:HOH208 2.1 25.3 1.0
O P:HOH209 2.2 32.7 1.0
PA P:TTP101 2.2 9.2 0.2
O3A P:TTP101 2.3 9.6 0.2
O P:HOH206 2.4 33.0 1.0
O P:HOH202 2.4 34.9 1.0
P P:DT11 3.1 17.9 0.8
O2A P:TTP101 3.3 9.7 0.2
O5' P:TTP101 3.5 9.6 0.2
O3B P:TTP101 3.5 9.6 0.2
P1 P:PPV106 3.5 21.0 0.8
OP1 P:DT11 3.5 18.8 0.8
O2G P:TTP101 3.6 9.6 0.2
PB P:TTP101 3.6 9.5 0.2
O3G P:TTP101 3.6 9.3 0.2
O5' P:DT11 3.7 17.1 0.8
PG P:TTP101 3.8 9.9 0.2
O12 P:PPV106 3.9 27.8 0.8
O32 P:PPV106 3.9 24.4 0.8
OPP P:PPV106 4.1 23.3 0.8
O A:HOH539 4.2 33.5 1.0
O31 P:PPV106 4.2 21.0 0.8
C5M P:TTP101 4.2 10.6 0.2
O P:HOH204 4.2 25.6 1.0
P2 P:PPV106 4.3 25.8 0.8
C7 P:DT11 4.3 18.9 0.8
O2B P:TTP101 4.4 9.4 0.2
O1B P:TTP101 4.5 9.7 0.2
O3' P:DA10 4.5 20.2 1.0
O A:HOH501 4.5 31.3 1.0
O21 P:PPV106 4.6 18.6 0.8
MG P:MG104 4.6 12.8 1.0
C5' P:TTP101 4.7 9.9 0.2
C6 P:TTP101 4.8 10.3 0.2
C5' P:DT11 4.9 17.2 0.8
C5 P:TTP101 5.0 10.4 0.2

Magnesium binding site 3 out of 6 in 5vs3

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Magnesium binding site 3 out of 6 in the Human Dna Polymerase Beta 8-Oxog:Da Extension with Dttp After 90 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 90 S within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mg103

b:15.3
occ:1.00
 OD2 A:ASP190 2.0 26.8 1.0
OD2 A:ASP256 2.1 21.0 1.0
OD1 A:ASP192 2.2 17.4 1.0
OP1 P:DT11 2.3 18.8 0.8
O A:HOH501 2.4 31.3 1.0
O3' P:DA10 2.5 20.2 1.0
CG A:ASP190 2.8 21.9 1.0
OD1 A:ASP190 2.8 19.0 1.0
P P:DT11 3.0 17.9 0.8
O2A P:TTP101 3.0 9.7 0.2
CG A:ASP192 3.2 17.5 1.0
CG A:ASP256 3.3 19.5 1.0
MG P:MG104 3.6 12.8 1.0
OD2 A:ASP192 3.6 18.7 1.0
C3' P:DA10 3.8 20.5 1.0
PA P:TTP101 3.8 9.2 0.2
CB A:ASP256 3.9 17.9 1.0
C4' P:DA10 4.0 21.0 1.0
OP2 P:DT11 4.0 19.4 0.8
O5' P:TTP101 4.1 9.6 0.2
C5' P:DA10 4.2 20.3 1.0
O5' P:DT11 4.2 17.1 0.8
CB A:ASP190 4.2 19.5 1.0
OD1 A:ASP256 4.3 22.8 1.0
O1A P:TTP101 4.3 9.3 0.2
C5' P:TTP101 4.3 9.9 0.2
C5' P:DT11 4.4 17.2 0.8
O A:MET191 4.4 18.0 0.5
CB A:ASP192 4.5 16.9 1.0
O2G P:TTP101 4.6 9.6 0.2
O P:HOH206 4.6 33.0 1.0
O A:MET191 4.7 17.9 0.5
C A:MET191 4.8 17.2 0.5
C2' P:DA10 4.8 19.6 1.0
OP1 P:DA10 4.8 20.3 1.0
O5' P:DA10 4.8 20.1 1.0
NH2 A:ARG254 4.9 17.9 1.0
N A:ASP256 4.9 16.9 1.0
C A:MET191 4.9 17.1 0.5
CA A:ASP192 4.9 16.4 1.0

Magnesium binding site 4 out of 6 in 5vs3

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Magnesium binding site 4 out of 6 in the Human Dna Polymerase Beta 8-Oxog:Da Extension with Dttp After 90 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 90 S within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mg104

b:12.8
occ:1.00
 O2A P:TTP101 1.7 9.7 0.2
O2G P:TTP101 1.9 9.6 0.2
O2B P:TTP101 2.1 9.4 0.2
OD1 A:ASP190 2.1 19.0 1.0
OD2 A:ASP192 2.2 18.7 1.0
OP1 P:DT11 2.2 18.8 0.8
O21 P:PPV106 2.3 18.6 0.8
O A:HOH576 2.4 24.1 1.0
O12 P:PPV106 2.5 27.8 0.8
PA P:TTP101 3.1 9.2 0.2
O11 P:PPV106 3.2 21.8 0.8
PG P:TTP101 3.2 9.9 0.2
CG A:ASP192 3.2 17.5 1.0
PB P:TTP101 3.2 9.5 0.2
P1 P:PPV106 3.2 21.0 0.8
CG A:ASP190 3.3 21.9 1.0
OD1 A:ASP192 3.5 17.4 1.0
MG P:MG103 3.6 15.3 1.0
O3A P:TTP101 3.6 9.6 0.2
O3B P:TTP101 3.6 9.6 0.2
P P:DT11 3.7 17.9 0.8
O1G P:TTP101 3.7 9.2 0.2
O A:ASP190 3.7 18.8 1.0
P2 P:PPV106 3.8 25.8 0.8
OPP P:PPV106 3.9 23.3 0.8
C5' P:TTP101 3.9 9.9 0.2
O P:HOH206 4.0 33.0 1.0
OD2 A:ASP190 4.0 26.8 1.0
O5' P:TTP101 4.0 9.6 0.2
C A:ASP190 4.1 19.0 1.0
N A:ASP190 4.2 19.1 1.0
O1A P:TTP101 4.2 9.3 0.2
O5' P:DT11 4.3 17.1 0.8
C5' P:DT11 4.3 17.2 0.8
O A:HOH609 4.4 16.4 1.0
CB A:ASP190 4.4 19.5 1.0
O3G P:TTP101 4.4 9.3 0.2
CA A:ASP190 4.5 20.0 1.0
O22 P:PPV106 4.5 25.2 0.8
OP2 P:DT11 4.5 19.4 0.8
CB A:ASP192 4.5 16.9 1.0
O A:HOH501 4.6 31.3 1.0
OG A:SER180 4.6 18.5 1.0
N A:SER180 4.6 16.6 1.0
O31 P:PPV106 4.6 21.0 0.8
MG P:MG102 4.6 25.5 0.8
O1B P:TTP101 4.6 9.7 0.2
CA A:GLY179 4.6 15.6 1.0
O3' P:DA10 4.7 20.2 1.0
N A:MET191 4.8 18.3 0.5
O32 P:PPV106 4.9 24.4 0.8
N A:MET191 4.9 18.5 0.5
N A:ASP192 4.9 17.2 1.0

Magnesium binding site 5 out of 6 in 5vs3

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Magnesium binding site 5 out of 6 in the Human Dna Polymerase Beta 8-Oxog:Da Extension with Dttp After 90 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 90 S within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mg105

b:24.5
occ:1.00
 O A:THR101 2.2 22.8 1.0
O A:ILE106 2.4 22.2 1.0
O A:VAL103 2.4 20.9 1.0
OP1 P:DC9 2.4 24.3 1.0
O A:HOH706 2.5 30.6 1.0
O P:HOH207 2.7 28.6 1.0
C A:THR101 3.3 21.1 1.0
P P:DC9 3.3 25.9 1.0
C A:VAL103 3.3 20.1 1.0
C A:ILE106 3.4 21.9 1.0
OP2 P:DC9 3.4 27.5 1.0
N A:ILE106 3.8 21.6 1.0
CA A:THR101 3.9 21.3 1.0
N A:GLY105 3.9 22.0 1.0
CA A:SER104 3.9 20.7 1.0
N A:VAL103 4.0 19.0 1.0
N A:SER104 4.0 20.9 1.0
CA A:ILE106 4.1 22.0 1.0
C A:ARG102 4.2 19.6 1.0
O3' P:DG8 4.2 25.7 1.0
N A:ARG102 4.3 20.5 1.0
CA A:VAL103 4.3 20.9 1.0
C A:SER104 4.3 20.9 1.0
N A:GLY107 4.4 21.3 1.0
CB A:ILE106 4.5 21.8 1.0
CB A:THR101 4.5 21.6 1.0
CA A:ARG102 4.5 20.8 1.0
O5' P:DC9 4.6 22.3 1.0
C A:GLY105 4.6 23.4 1.0
O P:HOH212 4.7 36.0 1.0
O A:ARG102 4.7 20.2 1.0
CA A:GLY107 4.7 22.3 1.0
O A:LEU100 4.8 20.8 1.0
CA A:GLY105 4.9 22.8 1.0

Magnesium binding site 6 out of 6 in 5vs3

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Magnesium binding site 6 out of 6 in the Human Dna Polymerase Beta 8-Oxog:Da Extension with Dttp After 90 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 90 S within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg101

b:28.6
occ:1.00
 O A:LYS60 2.3 30.8 1.0
O D:HOH202 2.3 35.5 1.0
O A:VAL65 2.3 28.4 1.0
O A:HOH700 2.4 34.5 1.0
O A:LEU62 2.4 26.2 1.0
OP1 D:DC3 2.7 31.4 1.0
C A:LYS60 3.4 31.7 1.0
C A:LEU62 3.4 25.7 1.0
C A:VAL65 3.5 27.6 1.0
P D:DC3 3.6 33.5 1.0
OP2 D:DC3 3.7 28.9 1.0
N A:VAL65 3.9 25.0 1.0
N A:LEU62 4.0 27.5 1.0
C A:LYS61 4.0 30.4 1.0
CA A:LYS60 4.1 30.9 1.0
CA A:VAL65 4.1 26.0 1.0
N A:PRO63 4.2 26.4 1.0
CA A:PRO63 4.2 27.1 1.0
O A:LYS61 4.3 30.6 1.0
CG A:LYS60 4.3 35.4 1.0
N A:GLY64 4.3 27.5 1.0
N A:LYS61 4.3 31.2 1.0
CA A:LEU62 4.3 27.3 1.0
CB A:VAL65 4.4 25.8 1.0
CA A:LYS61 4.4 30.7 1.0
O3' D:DT2 4.5 28.2 1.0
N A:GLY66 4.5 26.6 1.0
C A:PRO63 4.6 25.9 1.0
CA A:GLY66 4.8 27.6 1.0
NZ A:LYS60 4.8 41.0 1.0
O A:ALA59 4.8 25.7 1.0
CB A:LYS60 4.9 32.9 1.0
O5' D:DC3 4.9 34.4 1.0
C A:GLY64 4.9 26.9 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 06:17:33 2024

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