Atomistry » Sodium » PDB 1m90-1nji » 1mq3
Atomistry »
  Sodium »
    PDB 1m90-1nji »
      1mq3 »

Sodium in PDB 1mq3: Human Dna Polymerase Beta Complexed with Gapped Dna Containing An 8-Oxo-7,8-Dihydro-Guanine Template Paired with Dctp

Enzymatic activity of Human Dna Polymerase Beta Complexed with Gapped Dna Containing An 8-Oxo-7,8-Dihydro-Guanine Template Paired with Dctp

All present enzymatic activity of Human Dna Polymerase Beta Complexed with Gapped Dna Containing An 8-Oxo-7,8-Dihydro-Guanine Template Paired with Dctp:
2.7.7.7;

Protein crystallography data

The structure of Human Dna Polymerase Beta Complexed with Gapped Dna Containing An 8-Oxo-7,8-Dihydro-Guanine Template Paired with Dctp, PDB code: 1mq3 was solved by J.M.Krahn, W.A.Beard, H.Miller, A.P.Grollman, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.500, 79.900, 55.600, 90.00, 107.90, 90.00
R / Rfree (%) 23.5 / 29.5

Other elements in 1mq3:

The structure of Human Dna Polymerase Beta Complexed with Gapped Dna Containing An 8-Oxo-7,8-Dihydro-Guanine Template Paired with Dctp also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Human Dna Polymerase Beta Complexed with Gapped Dna Containing An 8-Oxo-7,8-Dihydro-Guanine Template Paired with Dctp (pdb code 1mq3). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Human Dna Polymerase Beta Complexed with Gapped Dna Containing An 8-Oxo-7,8-Dihydro-Guanine Template Paired with Dctp, PDB code: 1mq3:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 1mq3

Go back to Sodium Binding Sites List in 1mq3
Sodium binding site 1 out of 2 in the Human Dna Polymerase Beta Complexed with Gapped Dna Containing An 8-Oxo-7,8-Dihydro-Guanine Template Paired with Dctp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Human Dna Polymerase Beta Complexed with Gapped Dna Containing An 8-Oxo-7,8-Dihydro-Guanine Template Paired with Dctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na341

b:8.3
occ:1.00
 O P:HOH344 2.2 10.4 1.0
OP1 P:DG9 2.2 9.8 1.0
O A:THR101 2.2 9.2 1.0
O A:VAL103 2.4 11.1 1.0
O A:ILE106 2.6 11.0 1.0
O A:HOH345 2.6 10.2 1.0
C A:THR101 3.2 9.7 1.0
C A:VAL103 3.2 9.4 1.0
P P:DG9 3.5 11.2 1.0
C A:ILE106 3.6 11.3 1.0
N A:VAL103 3.6 6.5 1.0
CA A:THR101 3.8 9.4 1.0
OP2 P:DG9 3.8 8.8 1.0
N A:ILE106 3.8 11.1 1.0
N A:SER104 3.9 9.6 1.0
CA A:SER104 4.0 8.8 1.0
CA A:VAL103 4.1 6.5 1.0
N A:GLY105 4.1 7.9 1.0
CA A:ILE106 4.1 10.9 1.0
N A:ARG102 4.2 9.0 1.0
O A:HOH363 4.3 16.3 1.0
C A:ARG102 4.3 8.3 1.0
O5' P:DG9 4.4 12.6 1.0
C A:SER104 4.4 7.7 1.0
CB A:THR101 4.4 8.7 1.0
CB A:ILE106 4.5 8.7 1.0
CA A:ARG102 4.6 7.1 1.0
N A:GLY107 4.6 10.8 1.0
O3' P:DC8 4.6 13.3 1.0
O A:LEU100 4.7 10.9 1.0
C A:GLY105 4.8 10.5 1.0
CA A:GLY107 4.9 10.8 1.0

Sodium binding site 2 out of 2 in 1mq3

Go back to Sodium Binding Sites List in 1mq3
Sodium binding site 2 out of 2 in the Human Dna Polymerase Beta Complexed with Gapped Dna Containing An 8-Oxo-7,8-Dihydro-Guanine Template Paired with Dctp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Human Dna Polymerase Beta Complexed with Gapped Dna Containing An 8-Oxo-7,8-Dihydro-Guanine Template Paired with Dctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na342

b:24.3
occ:1.00
 O A:LYS60 2.4 24.5 1.0
O D:HOH346 2.4 24.4 1.0
O A:LEU62 2.5 25.4 1.0
OP1 D:DC3 2.5 25.3 1.0
O A:VAL65 2.5 24.3 1.0
O A:HOH347 2.5 24.6 1.0
C A:VAL65 3.3 21.8 1.0
P D:DC3 3.5 26.1 1.0
C A:LEU62 3.5 25.5 1.0
C A:LYS60 3.6 23.8 1.0
OP2 D:DC3 3.6 24.8 1.0
N A:VAL65 3.7 21.4 1.0
CA A:VAL65 3.9 21.4 1.0
O A:LYS61 4.0 21.2 1.0
CA A:PRO63 4.0 27.0 1.0
C A:LYS61 4.1 21.4 1.0
CB A:VAL65 4.2 21.2 1.0
N A:PRO63 4.2 26.4 1.0
N A:GLY66 4.2 21.8 1.0
N A:GLY64 4.3 26.2 1.0
C A:PRO63 4.3 27.4 1.0
CA A:LYS60 4.4 22.8 1.0
N A:LEU62 4.4 22.5 1.0
CG A:LYS60 4.5 23.5 1.0
N A:LYS61 4.5 23.6 1.0
CA A:GLY66 4.6 20.6 1.0
O3' D:DT2 4.6 23.8 1.0
CA A:LEU62 4.6 24.0 1.0
O5' D:DC3 4.7 27.8 1.0
CA A:LYS61 4.7 21.6 1.0
C A:GLY64 4.8 23.7 1.0

Reference:

J.M.Krahn, W.A.Beard, H.Miller, A.P.Grollman, S.H.Wilson. Structure of Dna Polymerase Beta with the Mutagenic Dna Lesion 8-Oxodeoxyguanine Reveals Structural Insights Into Its Coding Potential Structure V. 11 121 2003.
ISSN: ISSN 0969-2126
PubMed: 12517346
DOI: 10.1016/S0969-2126(02)00930-9
Page generated: Sun Oct 6 20:34:20 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