Atomistry » Sodium » PDB 4mfc-4mzx » 4mff
Atomistry »
  Sodium »
    PDB 4mfc-4mzx »
      4mff »

Sodium in PDB 4mff: Structure of Human Dna Polymerase Beta Complexed with O6MG in the Template Base Paired with Incoming Non-Hydrolyzable Ttp

Enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with O6MG in the Template Base Paired with Incoming Non-Hydrolyzable Ttp

All present enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with O6MG in the Template Base Paired with Incoming Non-Hydrolyzable Ttp:
2.7.7.7;

Protein crystallography data

The structure of Structure of Human Dna Polymerase Beta Complexed with O6MG in the Template Base Paired with Incoming Non-Hydrolyzable Ttp, PDB code: 4mff was solved by M.C.Koag, K.Min, A.F.Monzingo, S.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.55
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.546, 78.839, 54.751, 90.00, 105.95, 90.00
R / Rfree (%) 22.2 / 29.4

Other elements in 4mff:

The structure of Structure of Human Dna Polymerase Beta Complexed with O6MG in the Template Base Paired with Incoming Non-Hydrolyzable Ttp also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Human Dna Polymerase Beta Complexed with O6MG in the Template Base Paired with Incoming Non-Hydrolyzable Ttp (pdb code 4mff). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of Human Dna Polymerase Beta Complexed with O6MG in the Template Base Paired with Incoming Non-Hydrolyzable Ttp, PDB code: 4mff:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4mff

Go back to Sodium Binding Sites List in 4mff
Sodium binding site 1 out of 2 in the Structure of Human Dna Polymerase Beta Complexed with O6MG in the Template Base Paired with Incoming Non-Hydrolyzable Ttp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Human Dna Polymerase Beta Complexed with O6MG in the Template Base Paired with Incoming Non-Hydrolyzable Ttp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:12.0
occ:1.00
O A:ILE106 2.0 8.8 1.0
O A:THR101 2.3 10.5 1.0
O A:VAL103 2.3 8.8 1.0
OP1 P:DG9 2.4 11.7 1.0
O P:HOH101 3.0 4.1 1.0
C A:ILE106 3.1 8.9 1.0
C A:VAL103 3.3 9.0 1.0
C A:THR101 3.3 10.3 1.0
P P:DG9 3.4 11.7 1.0
N A:ILE106 3.5 8.2 1.0
OP2 P:DG9 3.6 12.3 1.0
CA A:SER104 3.8 8.2 1.0
N A:GLY105 3.8 7.9 1.0
CA A:THR101 3.8 10.2 1.0
N A:SER104 3.8 8.7 1.0
CA A:ILE106 3.9 8.6 1.0
N A:VAL103 4.1 9.5 1.0
C A:SER104 4.1 7.9 1.0
N A:GLY107 4.1 9.1 1.0
C A:ARG102 4.3 10.0 1.0
CB A:ILE106 4.3 8.7 1.0
CA A:VAL103 4.3 9.1 1.0
O3' P:DC8 4.4 11.9 1.0
C A:GLY105 4.4 8.0 1.0
N A:ARG102 4.4 10.1 1.0
CB A:THR101 4.4 10.2 1.0
CA A:GLY107 4.4 9.6 1.0
CA A:GLY105 4.6 7.9 1.0
O A:ARG102 4.6 10.0 1.0
CA A:ARG102 4.6 9.9 1.0
O5' P:DG9 4.7 11.9 1.0
O A:LEU100 4.7 10.8 1.0

Sodium binding site 2 out of 2 in 4mff

Go back to Sodium Binding Sites List in 4mff
Sodium binding site 2 out of 2 in the Structure of Human Dna Polymerase Beta Complexed with O6MG in the Template Base Paired with Incoming Non-Hydrolyzable Ttp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Human Dna Polymerase Beta Complexed with O6MG in the Template Base Paired with Incoming Non-Hydrolyzable Ttp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na101

b:16.5
occ:1.00
O A:LYS60 2.7 22.1 1.0
O A:VAL65 2.9 14.7 1.0
OP1 D:DC3 2.9 12.0 1.0
OP2 D:DC3 3.0 11.4 1.0
P D:DC3 3.4 11.0 1.0
NZ A:LYS60 3.8 21.6 1.0
C A:LYS60 3.9 20.6 1.0
C A:VAL65 3.9 13.8 1.0
O A:LEU62 4.0 21.4 1.0
CG A:LYS60 4.0 19.8 1.0
CA A:GLY66 4.3 13.6 1.0
N A:GLY66 4.5 13.3 1.0
CA A:LYS60 4.6 19.6 1.0
O5' D:DC3 4.6 11.2 1.0
O3' D:DT2 4.6 11.2 1.0
N A:VAL65 4.8 13.8 1.0
CB A:LYS60 4.8 19.5 1.0
N A:LYS61 4.9 21.0 1.0
CE A:LYS60 5.0 20.0 1.0
C A:LEU62 5.0 19.5 1.0
C A:LYS61 5.0 21.8 1.0
CA A:VAL65 5.0 13.5 1.0

Reference:

M.C.Koag, S.Lee. Metal-Dependent Conformational Activation Explains Highly Promutagenic Replication Across O6-Methylguanine By Human Dna Polymerase Beta. J.Am.Chem.Soc. V. 136 5709 2014.
ISSN: ISSN 0002-7863
PubMed: 24694247
DOI: 10.1021/JA500172D
Page generated: Mon Oct 7 17:00:22 2024

Last articles

Zn in 9FS1
Zn in 9FS3
Zn in 9FS2
Zn in 9H3H
Zn in 9F29
Zn in 9F2A
Zn in 9EY2
Zn in 9F26
Zn in 9E8J
Zn in 9E8N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy