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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

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