Atomistry » Sodium » PDB 1m90-1nji » 1mq2
Atomistry »
  Sodium »
    PDB 1m90-1nji »
      1mq2 »

Sodium in PDB 1mq2: Human Dna Polymerase Beta Complexed with Gapped Dna Containing An 8-Oxo-7,8-Dihydro-Guanine and Damp

Enzymatic activity of Human Dna Polymerase Beta Complexed with Gapped Dna Containing An 8-Oxo-7,8-Dihydro-Guanine and Damp

All present enzymatic activity of Human Dna Polymerase Beta Complexed with Gapped Dna Containing An 8-Oxo-7,8-Dihydro-Guanine and Damp:
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 and Damp, PDB code: 1mq2 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 / 3.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 55.200, 81.000, 55.600, 90.00, 106.10, 90.00
R / Rfree (%) 25.7 / 31.7

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 and Damp (pdb code 1mq2). 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 and Damp, PDB code: 1mq2:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 1mq2

Go back to Sodium Binding Sites List in 1mq2
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 and Damp


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 and Damp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na341

b:22.6
occ:1.00
O A:THR101 2.0 22.0 1.0
O A:HOH344 2.2 23.2 1.0
O A:ILE106 2.3 21.1 1.0
OP1 P:DG9 2.4 21.8 1.0
O A:VAL103 2.5 21.1 1.0
O A:HOH345 2.7 21.9 1.0
C A:THR101 3.1 23.7 1.0
C A:VAL103 3.4 19.4 1.0
C A:ILE106 3.5 18.2 1.0
P P:DG9 3.5 21.7 1.0
OP2 P:DG9 3.8 21.8 1.0
CA A:THR101 3.8 24.6 1.0
N A:ILE106 3.9 14.7 1.0
N A:GLY105 3.9 16.7 1.0
CA A:SER104 4.1 17.8 1.0
N A:VAL103 4.1 20.5 1.0
N A:SER104 4.1 19.6 1.0
C A:ARG102 4.1 21.1 1.0
N A:ARG102 4.2 20.8 1.0
CA A:ILE106 4.2 16.1 1.0
CB A:THR101 4.4 24.3 1.0
O3' P:DC8 4.4 20.9 1.0
CA A:VAL103 4.4 19.4 1.0
N A:GLY107 4.4 18.3 1.0
O A:ARG102 4.4 21.9 1.0
C A:SER104 4.5 17.2 1.0
CA A:ARG102 4.5 21.6 1.0
CA A:GLY107 4.6 18.4 1.0
C A:GLY105 4.6 15.6 1.0
CB A:ILE106 4.7 17.2 1.0
O5' P:DG9 4.7 25.5 1.0
O A:LEU100 4.8 26.2 1.0
CA A:GLY105 4.9 15.9 1.0

Sodium binding site 2 out of 2 in 1mq2

Go back to Sodium Binding Sites List in 1mq2
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 and Damp


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 and Damp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na342

b:37.6
occ:1.00
O A:LYS60 2.3 37.2 1.0
O D:HOH346 2.4 37.1 1.0
O A:VAL65 2.4 36.2 1.0
OP1 D:DC3 2.4 36.1 1.0
O A:HOH347 2.5 37.3 1.0
O A:LEU62 2.6 37.2 1.0
C A:VAL65 3.5 35.2 1.0
C A:LYS60 3.5 38.9 1.0
C A:LEU62 3.6 36.7 1.0
P D:DC3 3.7 34.0 1.0
N A:VAL65 3.8 34.6 1.0
OP2 D:DC3 4.0 34.0 1.0
CA A:VAL65 4.1 34.5 1.0
N A:GLY64 4.1 37.3 1.0
CA A:PRO63 4.2 36.9 1.0
C A:LYS61 4.2 39.0 1.0
CA A:LYS60 4.3 39.2 1.0
CG A:LYS60 4.3 38.8 1.0
N A:PRO63 4.3 36.2 1.0
O A:LYS61 4.3 38.6 1.0
N A:LEU62 4.3 37.6 1.0
CB A:VAL65 4.4 33.1 1.0
N A:LYS61 4.5 39.4 1.0
N A:GLY66 4.6 35.8 1.0
O3' D:DT2 4.6 32.2 1.0
C A:PRO63 4.6 37.3 1.0
CA A:LEU62 4.6 37.5 1.0
CA A:LYS61 4.7 39.9 1.0
O5' D:DC3 4.8 33.3 1.0
C A:GLY64 4.8 35.5 1.0
CA A:GLY66 4.9 36.0 1.0
CB A:LYS60 4.9 39.4 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: Tue Dec 15 05:30:37 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy