Atomistry » Sodium » PDB 4pd8-4pp4 » 4pha
Atomistry »
  Sodium »
    PDB 4pd8-4pp4 »
      4pha »

Sodium in PDB 4pha: Structure of Human Dna Polymerase Beta Complexed with A in the Template Base Paired with Incoming Non-Hydrolyzable Ctp

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

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

Protein crystallography data

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

Resolution Low / High (Å) 20.00 / 2.52
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.440, 80.710, 54.834, 90.00, 108.88, 90.00
R / Rfree (%) 21.6 / 27.8

Other elements in 4pha:

The structure of Structure of Human Dna Polymerase Beta Complexed with A in the Template Base Paired with Incoming Non-Hydrolyzable Ctp 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 A in the Template Base Paired with Incoming Non-Hydrolyzable Ctp (pdb code 4pha). 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 A in the Template Base Paired with Incoming Non-Hydrolyzable Ctp, PDB code: 4pha:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4pha

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


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 A in the Template Base Paired with Incoming Non-Hydrolyzable Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:20.0
occ:1.00
 OP1 P:DG9 2.3 18.8 1.0
O A:THR101 2.4 21.6 1.0
O A:VAL103 2.5 19.9 1.0
O P:HOH109 2.5 22.6 1.0
O A:ILE106 2.7 18.5 1.0
O A:HOH548 2.8 22.5 1.0
O A:HOH515 3.1 28.0 1.0
C A:VAL103 3.3 22.4 1.0
C A:THR101 3.4 21.0 1.0
P P:DG9 3.5 17.9 1.0
C A:ILE106 3.7 18.6 1.0
OP2 P:DG9 3.8 23.7 1.0
CA A:SER104 3.8 19.1 1.0
N A:SER104 3.9 21.6 1.0
N A:ILE106 4.0 21.4 1.0
N A:GLY105 4.1 20.5 1.0
N A:VAL103 4.1 14.6 1.0
CA A:THR101 4.1 22.3 1.0
C A:SER104 4.3 18.2 1.0
CA A:VAL103 4.3 16.4 1.0
CA A:ILE106 4.3 23.8 1.0
C A:ARG102 4.3 22.4 1.0
O5' P:DG9 4.4 18.4 1.0
N A:ARG102 4.4 18.5 1.0
N A:GLY107 4.6 17.9 1.0
CA A:ARG102 4.6 18.1 1.0
CB A:THR101 4.6 21.6 1.0
O3' P:DC8 4.7 21.5 1.0
CB A:ILE106 4.8 23.6 1.0
C A:GLY105 4.8 22.3 1.0
CA A:GLY107 4.8 19.6 1.0
O A:ARG102 4.9 16.1 1.0

Sodium binding site 2 out of 2 in 4pha

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


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 A in the Template Base Paired with Incoming Non-Hydrolyzable Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:39.1
occ:1.00
 O A:LYS60 2.6 35.4 1.0
O A:VAL65 2.6 30.2 1.0
OP1 D:DC3 2.9 31.8 1.0
O A:LEU62 3.0 31.8 1.0
OP2 D:DC3 3.5 30.4 1.0
P D:DC3 3.7 36.3 1.0
C A:LYS60 3.8 33.4 1.0
C A:VAL65 3.8 29.2 1.0
C A:LEU62 3.9 28.1 1.0
O A:LYS61 4.3 34.4 1.0
C A:LYS61 4.3 28.0 1.0
CA A:PRO63 4.4 26.9 1.0
N A:VAL65 4.5 31.1 1.0
N A:PRO63 4.5 25.7 1.0
N A:LEU62 4.6 29.1 1.0
CG A:LYS60 4.6 33.4 1.0
N A:GLY64 4.6 30.4 1.0
CA A:VAL65 4.7 26.8 1.0
CA A:LYS60 4.7 27.7 1.0
N A:LYS61 4.7 34.6 1.0
O5' D:DC3 4.7 27.1 1.0
N A:GLY66 4.7 26.4 1.0
CA A:LYS61 4.8 27.2 1.0
CA A:GLY66 4.8 23.9 1.0
CA A:LEU62 4.9 24.5 1.0
C A:PRO63 4.9 30.9 1.0
O3' D:DT2 4.9 33.5 1.0

Reference:

M.C.Koag, K.Nam, S.Lee. The Spontaneous Replication Error and the Mismatch Discrimination Mechanisms of Human Dna Polymerase Beta. Nucleic Acids Res. V. 42 11233 2015.
ISSN: ESSN 1362-4962
PubMed: 25200079
DOI: 10.1093/NAR/GKU789
Page generated: Mon Oct 7 17:42:58 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy