Atomistry » Magnesium » PDB 5vp0-5vw8 » 5vs3
Atomistry »
  Magnesium »
    PDB 5vp0-5vw8 »
      5vs3 »

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

Go back to Magnesium Binding Sites List in 5vs3
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

Go back to Magnesium Binding Sites List in 5vs3
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

Go back to Magnesium Binding Sites List in 5vs3
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

Go back to Magnesium Binding Sites List in 5vs3
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

Go back to Magnesium Binding Sites List in 5vs3
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

Go back to Magnesium Binding Sites List in 5vs3
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy