Atomistry » Sodium » PDB 6cto-6d4o » 6cua
Atomistry »
  Sodium »
    PDB 6cto-6d4o »
      6cua »

Sodium in PDB 6cua: Structure of Human Dna Polymerase Beta Complexed with 8-Clg in the Template Base Paired with Incoming Non-Hydrolyzable Gtp and Manganese

Enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with 8-Clg in the Template Base Paired with Incoming Non-Hydrolyzable Gtp and Manganese

All present enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with 8-Clg in the Template Base Paired with Incoming Non-Hydrolyzable Gtp and Manganese:
2.7.7.7;

Protein crystallography data

The structure of Structure of Human Dna Polymerase Beta Complexed with 8-Clg in the Template Base Paired with Incoming Non-Hydrolyzable Gtp and Manganese, PDB code: 6cua 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) 19.91 / 2.17
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.713, 79.620, 55.262, 90.00, 108.78, 90.00
R / Rfree (%) 20.9 / 25.9

Other elements in 6cua:

The structure of Structure of Human Dna Polymerase Beta Complexed with 8-Clg in the Template Base Paired with Incoming Non-Hydrolyzable Gtp and Manganese also contains other interesting chemical elements:

Manganese (Mn) 2 atoms
Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Human Dna Polymerase Beta Complexed with 8-Clg in the Template Base Paired with Incoming Non-Hydrolyzable Gtp and Manganese (pdb code 6cua). 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 8-Clg in the Template Base Paired with Incoming Non-Hydrolyzable Gtp and Manganese, PDB code: 6cua:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 6cua

Go back to Sodium Binding Sites List in 6cua
Sodium binding site 1 out of 2 in the Structure of Human Dna Polymerase Beta Complexed with 8-Clg in the Template Base Paired with Incoming Non-Hydrolyzable Gtp and Manganese


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

b:16.5
occ:1.00
OP1 P:DG9 2.3 19.8 1.0
O A:THR101 2.3 20.6 1.0
O A:ILE106 2.4 17.4 1.0
O A:VAL103 2.5 15.9 1.0
O P:HOH102 2.6 17.8 1.0
O A:HOH581 2.7 17.4 1.0
C A:THR101 3.3 19.6 1.0
C A:ILE106 3.4 14.7 1.0
C A:VAL103 3.4 19.4 1.0
P P:DG9 3.4 21.5 1.0
O A:HOH504 3.4 28.2 1.0
OP2 P:DG9 3.7 19.6 1.0
N A:ILE106 3.8 18.6 1.0
CA A:THR101 3.9 16.0 1.0
CA A:SER104 3.9 18.2 1.0
N A:GLY105 3.9 20.0 1.0
N A:SER104 4.0 19.7 1.0
CA A:ILE106 4.1 15.7 1.0
N A:VAL103 4.2 17.6 1.0
N A:ARG102 4.3 18.7 1.0
C A:ARG102 4.3 22.7 1.0
C A:SER104 4.3 17.9 1.0
N A:GLY107 4.3 19.5 1.0
CA A:VAL103 4.4 18.7 1.0
CB A:THR101 4.4 17.2 1.0
O5' P:DG9 4.5 21.0 1.0
CB A:ILE106 4.5 14.9 1.0
O3' P:DC8 4.5 19.9 1.0
CA A:ARG102 4.6 18.2 1.0
CA A:GLY107 4.6 15.2 1.0
C A:GLY105 4.6 17.4 1.0
O A:ARG102 4.7 24.4 1.0
CA A:GLY105 4.9 19.6 1.0
O A:LEU100 4.9 17.5 1.0

Sodium binding site 2 out of 2 in 6cua

Go back to Sodium Binding Sites List in 6cua
Sodium binding site 2 out of 2 in the Structure of Human Dna Polymerase Beta Complexed with 8-Clg in the Template Base Paired with Incoming Non-Hydrolyzable Gtp and Manganese


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

b:34.1
occ:1.00
O A:LYS60 2.4 27.8 1.0
O A:HOH556 2.5 30.7 1.0
O A:VAL65 2.5 25.3 1.0
OP1 D:DC3 2.7 26.1 1.0
O A:LEU62 2.9 23.5 1.0
C A:LYS60 3.6 27.1 1.0
C A:VAL65 3.6 25.9 1.0
P D:DC3 3.7 24.4 1.0
C A:LEU62 3.8 26.8 1.0
OP2 D:DC3 3.8 23.2 1.0
N A:VAL65 4.1 24.8 1.0
C A:LYS61 4.2 25.7 1.0
CG A:LYS60 4.3 25.9 1.0
CA A:VAL65 4.3 22.3 1.0
N A:LEU62 4.3 28.4 1.0
CA A:LYS60 4.3 25.5 1.0
O A:LYS61 4.3 29.8 1.0
CA A:PRO63 4.4 27.7 1.0
N A:PRO63 4.4 28.5 1.0
N A:GLY64 4.5 25.1 1.0
N A:LYS61 4.5 26.4 1.0
NZ A:LYS60 4.5 30.9 1.0
N A:GLY66 4.6 23.5 1.0
CB A:VAL65 4.6 25.7 1.0
CA A:LYS61 4.7 26.1 1.0
CA A:LEU62 4.7 26.0 1.0
O3' D:DT2 4.7 29.8 1.0
CA A:GLY66 4.8 20.0 1.0
C A:PRO63 4.8 29.0 1.0
O5' D:DC3 4.8 19.8 1.0
CB A:LYS60 4.9 27.9 1.0

Reference:

M.-C.Koag, S.Lee. Structure of Human Dna Polymerase Beta Complexed with 8-Clg in the Template Base Paired with Incoming Non-Hydrolyzable Gtp and Manganese To Be Published.
Page generated: Tue Oct 8 06:47:23 2024

Last articles

Mg in 6TR4
Mg in 6TR3
Mg in 6TMF
Mg in 6TQO
Mg in 6TQN
Mg in 6TQF
Mg in 6TQE
Mg in 6TQB
Mg in 6TQA
Mg in 6TPS
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy