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Magnesium in PDB 5vry: Human Dna Polymerase Beta 8-Oxog:Dc Extension with Dttp After 20 S

Enzymatic activity of Human Dna Polymerase Beta 8-Oxog:Dc Extension with Dttp After 20 S

All present enzymatic activity of Human Dna Polymerase Beta 8-Oxog:Dc Extension with Dttp After 20 S:
2.7.7.7;

Protein crystallography data

The structure of Human Dna Polymerase Beta 8-Oxog:Dc Extension with Dttp After 20 S, PDB code: 5vry 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) 48.62 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.900, 80.100, 55.600, 90.00, 107.20, 90.00
R / Rfree (%) 20.3 / 24.4

Other elements in 5vry:

The structure of Human Dna Polymerase Beta 8-Oxog:Dc Extension with Dttp After 20 S also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Human Dna Polymerase Beta 8-Oxog:Dc Extension with Dttp After 20 S (pdb code 5vry). 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 20 S, PDB code: 5vry:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 5vry

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Magnesium binding site 1 out of 6 in the Human Dna Polymerase Beta 8-Oxog:Dc Extension with Dttp After 20 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 20 S within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Mg101

b:27.2
occ:1.00
 O T:HOH206 2.1 31.0 1.0
O T:HOH227 2.4 34.4 1.0
O T:HOH203 2.4 24.8 1.0
O6 T:DG8 2.5 19.4 1.0
O P:HOH210 2.5 25.3 1.0
O T:HOH231 2.6 32.9 1.0
O P:HOH224 2.6 39.3 1.0
C6 T:DG8 3.5 20.1 1.0
N7 T:DG8 4.0 20.5 1.0
C5 T:DG8 4.1 19.9 1.0
N4 P:DC9 4.2 18.0 1.0
O P:HOH216 4.2 29.6 1.0
N7 T:8OG7 4.2 18.6 1.0
O6 T:8OG7 4.4 17.5 1.0
O6 P:DG8 4.7 18.1 1.0
C5 T:8OG7 4.7 18.2 1.0
N1 T:DG8 4.7 19.8 1.0
C6 T:8OG7 4.8 18.1 1.0

Magnesium binding site 2 out of 6 in 5vry

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Magnesium binding site 2 out of 6 in the Human Dna Polymerase Beta 8-Oxog:Dc Extension with Dttp After 20 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 20 S within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mg102

b:5.7
occ:0.20
 O1A P:TTP101 1.9 17.7 0.8
O11 P:PPV106 2.2 16.2 0.1
O P:HOH220 2.3 32.8 1.0
O3A P:TTP101 2.5 18.4 0.8
PA P:TTP101 2.6 18.7 0.8
O P:HOH205 2.7 36.2 1.0
OP2 P:DT11 2.8 20.6 0.1
O P:HOH209 2.9 28.9 1.0
O12 P:PPV106 3.0 17.1 0.1
O P:HOH219 3.1 44.8 1.0
O3B P:TTP101 3.3 19.4 0.8
O3G P:TTP101 3.4 19.7 0.8
O2A P:TTP101 3.5 17.6 0.8
PB P:TTP101 3.6 17.4 0.8
P1 P:PPV106 3.7 16.1 0.1
PG P:TTP101 3.8 21.4 0.8
P P:DT11 3.9 20.4 0.1
O2G P:TTP101 3.9 19.5 0.8
O5' P:TTP101 3.9 16.7 0.8
P2 P:PPV106 4.0 17.0 0.1
O A:HOH579 4.1 38.2 1.0
OPP P:PPV106 4.1 16.6 0.1
O P:HOH227 4.2 31.4 1.0
OP1 P:DT11 4.2 20.5 0.1
O22 P:PPV106 4.2 17.2 0.1
O P:HOH201 4.2 28.6 1.0
O31 P:PPV106 4.4 16.2 0.1
O5' P:DT11 4.4 20.3 0.1
O P:HOH203 4.4 20.0 1.0
C7 P:DT11 4.5 19.3 0.1
O1B P:TTP101 4.5 18.2 0.8
O P:HOH214 4.5 40.1 1.0
C5M P:TTP101 4.5 14.6 0.8
O2B P:TTP101 4.6 18.0 0.8
O21 P:PPV106 4.7 16.1 0.1
MG P:MG104 4.9 5.8 1.0

Magnesium binding site 3 out of 6 in 5vry

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Magnesium binding site 3 out of 6 in the Human Dna Polymerase Beta 8-Oxog:Dc Extension with Dttp After 20 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 20 S within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mg103

b:12.3
occ:1.00
 OP1 P:DT11 2.0 20.5 0.1
OD2 A:ASP256 2.2 19.3 1.0
OD2 A:ASP190 2.2 21.6 1.0
OD1 A:ASP192 2.2 15.2 1.0
O3' P:DC10 2.3 21.8 0.8
O3' P:DC10 2.3 20.8 0.1
P P:DT11 2.6 20.4 0.1
O P:HOH201 2.6 28.6 1.0
OD1 A:ASP190 2.7 18.5 1.0
O2A P:TTP101 2.7 17.6 0.8
CG A:ASP190 2.8 18.8 1.0
CG A:ASP192 3.3 16.1 1.0
CG A:ASP256 3.4 18.4 1.0
OP2 P:DT11 3.5 20.6 0.1
C3' P:DC10 3.6 20.4 0.8
C3' P:DC10 3.6 20.5 0.1
PA P:TTP101 3.7 18.7 0.8
MG P:MG104 3.7 5.8 1.0
OD2 A:ASP192 3.7 16.8 1.0
O5' P:DT11 3.9 20.3 0.1
O5' P:TTP101 4.0 16.7 0.8
C4' P:DC10 4.0 20.5 0.1
C4' P:DC10 4.0 20.4 0.8
CB A:ASP256 4.1 18.4 1.0
C5' P:DC10 4.1 20.0 0.8
C5' P:DC10 4.1 20.4 0.1
O1A P:TTP101 4.1 17.7 0.8
C5' P:TTP101 4.2 15.9 0.8
C5' P:DT11 4.3 19.9 0.1
CB A:ASP190 4.3 18.3 1.0
O P:HOH209 4.3 28.9 1.0
OD1 A:ASP256 4.4 19.5 1.0
O A:MET191 4.5 16.7 1.0
CB A:ASP192 4.6 15.7 1.0
C2' P:DC10 4.7 20.4 0.8
O5' P:DC10 4.7 20.3 0.1
C2' P:DC10 4.7 20.6 0.1
O5' P:DC10 4.8 20.0 0.8
OP1 P:DC10 4.8 20.1 0.1
C A:MET191 4.9 16.4 1.0
OP1 P:DC10 4.9 19.4 0.8
NH2 A:ARG254 4.9 18.0 1.0

Magnesium binding site 4 out of 6 in 5vry

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Magnesium binding site 4 out of 6 in the Human Dna Polymerase Beta 8-Oxog:Dc Extension with Dttp After 20 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 20 S within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mg104

b:5.8
occ:1.00
 O2A P:TTP101 2.1 17.6 0.8
O2G P:TTP101 2.2 19.5 0.8
OD1 A:ASP190 2.2 18.5 1.0
O2B P:TTP101 2.2 18.0 0.8
OD2 A:ASP192 2.3 16.8 1.0
O A:HOH574 2.3 15.7 1.0
O21 P:PPV106 2.4 16.1 0.1
OP1 P:DT11 2.5 20.5 0.1
CG A:ASP192 3.2 16.1 1.0
O12 P:PPV106 3.3 17.1 0.1
O A:ASP190 3.3 17.1 1.0
PB P:TTP101 3.3 17.4 0.8
P1 P:PPV106 3.4 16.1 0.1
O11 P:PPV106 3.4 16.2 0.1
CG A:ASP190 3.4 18.8 1.0
PA P:TTP101 3.5 18.7 0.8
PG P:TTP101 3.5 21.4 0.8
OD1 A:ASP192 3.5 15.2 1.0
O3A P:TTP101 3.7 18.4 0.8
MG P:MG103 3.7 12.3 1.0
O3B P:TTP101 3.8 19.4 0.8
C A:ASP190 3.8 17.6 1.0
P P:DT11 3.9 20.4 0.1
N A:ASP190 3.9 17.8 1.0
O P:HOH209 4.0 28.9 1.0
P2 P:PPV106 4.1 17.0 0.1
O32 P:PPV106 4.2 17.0 0.1
OPP P:PPV106 4.2 16.6 0.1
O1G P:TTP101 4.2 19.9 0.8
OD2 A:ASP190 4.2 21.6 1.0
O A:HOH617 4.2 15.5 1.0
CA A:ASP190 4.3 17.8 1.0
C5' P:TTP101 4.3 15.9 0.8
OG A:SER180 4.4 16.7 1.0
O5' P:TTP101 4.4 16.7 0.8
CB A:ASP190 4.4 18.3 1.0
O5' P:DT11 4.5 20.3 0.1
CB A:ASP192 4.6 15.7 1.0
N A:MET191 4.6 17.2 1.0
OP2 P:DT11 4.6 20.6 0.1
N A:SER180 4.6 16.3 1.0
O1A P:TTP101 4.6 17.7 0.8
CA A:GLY179 4.6 15.7 1.0
O3G P:TTP101 4.7 19.7 0.8
O1B P:TTP101 4.7 18.2 0.8
O31 P:PPV106 4.7 16.2 0.1
C5' P:DT11 4.8 19.9 0.1
N A:ASP192 4.8 15.7 1.0
MG P:MG102 4.9 5.7 0.2
O P:HOH201 4.9 28.6 1.0
C A:MET191 4.9 16.4 1.0
CA A:MET191 5.0 17.4 1.0
C A:GLY189 5.0 17.9 1.0
N A:GLY189 5.0 18.5 1.0

Magnesium binding site 5 out of 6 in 5vry

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Magnesium binding site 5 out of 6 in the Human Dna Polymerase Beta 8-Oxog:Dc Extension with Dttp After 20 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 20 S within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mg105

b:19.2
occ:1.00
 O A:THR101 2.2 20.9 1.0
OP1 P:DC9 2.3 18.2 1.0
O A:HOH691 2.4 28.3 1.0
O P:HOH202 2.4 25.1 1.0
O A:ILE106 2.4 17.8 1.0
O A:VAL103 2.5 16.4 1.0
C A:THR101 3.2 19.9 1.0
P P:DC9 3.4 18.6 1.0
C A:VAL103 3.4 17.1 1.0
C A:ILE106 3.5 17.6 1.0
OP2 P:DC9 3.6 18.1 1.0
N A:ILE106 3.8 17.0 1.0
CA A:THR101 3.9 20.4 1.0
CA A:SER104 3.9 17.2 1.0
N A:GLY105 4.0 17.1 1.0
N A:SER104 4.0 17.1 1.0
N A:VAL103 4.1 17.9 1.0
CA A:ILE106 4.2 17.4 1.0
C A:ARG102 4.2 19.0 1.0
N A:ARG102 4.3 19.7 1.0
O3' P:DG8 4.3 18.6 1.0
C A:SER104 4.3 17.1 1.0
CA A:VAL103 4.4 17.7 1.0
CB A:THR101 4.4 20.9 1.0
N A:GLY107 4.5 17.6 1.0
CA A:ARG102 4.5 20.0 1.0
O P:HOH217 4.5 31.6 1.0
CB A:ILE106 4.6 17.6 1.0
O5' P:DC9 4.6 18.5 1.0
C A:GLY105 4.7 17.3 1.0
O A:ARG102 4.7 18.5 1.0
O A:LEU100 4.8 19.6 1.0
CA A:GLY107 4.8 18.1 1.0
CA A:GLY105 4.9 17.3 1.0
O A:HOH644 5.0 33.8 1.0

Magnesium binding site 6 out of 6 in 5vry

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Magnesium binding site 6 out of 6 in the Human Dna Polymerase Beta 8-Oxog:Dc Extension with Dttp After 20 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 20 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:28.8
occ:1.00
 O A:HOH662 2.3 35.9 1.0
O A:HOH506 2.4 34.9 1.0
OE2 A:GLU249 2.5 28.4 1.0
O A:HOH699 2.5 48.8 1.0
OE1 A:GLU249 2.6 28.4 1.0
CD A:GLU249 2.9 28.1 1.0
O A:HOH560 4.3 35.0 1.0
CG A:GLU249 4.4 26.2 1.0
OE1 A:GLN240 4.6 18.3 1.0
O A:HOH527 4.7 24.1 1.0
NE2 A:GLN240 4.8 18.2 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 06:17:16 2024

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