Atomistry » Sodium » PDB 6chk-6ctm » 6cly
Atomistry »
  Sodium »
    PDB 6chk-6ctm »
      6cly »

Sodium in PDB 6cly: Structure of Human Dna Polymerase Beta Complexed with 8-Clg As the Template Base in A 1-Nucleotide Gapped Dna

Enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with 8-Clg As the Template Base in A 1-Nucleotide Gapped Dna

All present enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with 8-Clg As the Template Base in A 1-Nucleotide Gapped Dna:
2.7.7.7;

Protein crystallography data

The structure of Structure of Human Dna Polymerase Beta Complexed with 8-Clg As the Template Base in A 1-Nucleotide Gapped Dna, PDB code: 6cly 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) 19.92 / 2.19
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.772, 79.668, 54.967, 90.00, 105.60, 90.00
R / Rfree (%) 21.9 / 26.8

Other elements in 6cly:

The structure of Structure of Human Dna Polymerase Beta Complexed with 8-Clg As the Template Base in A 1-Nucleotide Gapped Dna also contains other interesting chemical elements:

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 As the Template Base in A 1-Nucleotide Gapped Dna (pdb code 6cly). 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 As the Template Base in A 1-Nucleotide Gapped Dna, PDB code: 6cly:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 6cly

Go back to Sodium Binding Sites List in 6cly
Sodium binding site 1 out of 2 in the Structure of Human Dna Polymerase Beta Complexed with 8-Clg As the Template Base in A 1-Nucleotide Gapped Dna


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 As the Template Base in A 1-Nucleotide Gapped Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:21.9
occ:1.00
O A:THR101 2.3 25.4 1.0
OP1 P:DG9 2.4 20.9 1.0
O A:VAL103 2.4 21.4 1.0
O A:ILE106 2.4 22.4 1.0
O P:HOH111 2.7 24.4 1.0
C A:VAL103 3.3 25.1 1.0
C A:THR101 3.3 23.4 1.0
C A:ILE106 3.4 21.2 1.0
P P:DG9 3.5 21.3 1.0
O A:HOH508 3.5 27.6 1.0
N A:ILE106 3.7 18.3 1.0
OP2 P:DG9 3.8 21.8 1.0
CA A:SER104 3.9 19.1 1.0
CA A:THR101 3.9 20.1 1.0
N A:SER104 3.9 24.4 1.0
N A:GLY105 4.0 21.2 1.0
CA A:ILE106 4.0 17.1 1.0
N A:VAL103 4.1 20.1 1.0
C A:ARG102 4.3 27.1 1.0
C A:SER104 4.3 19.3 1.0
CA A:VAL103 4.3 20.8 1.0
N A:ARG102 4.3 23.2 1.0
N A:GLY107 4.4 22.7 1.0
CB A:ILE106 4.5 19.8 1.0
CB A:THR101 4.5 22.3 1.0
O3' P:DC8 4.6 23.2 1.0
CA A:ARG102 4.6 23.5 1.0
O5' P:DG9 4.6 20.0 1.0
C A:GLY105 4.6 19.8 1.0
CA A:GLY107 4.7 21.9 1.0
O A:ARG102 4.7 24.6 1.0
O A:LEU100 4.9 23.2 1.0
CA A:GLY105 4.9 18.8 1.0

Sodium binding site 2 out of 2 in 6cly

Go back to Sodium Binding Sites List in 6cly
Sodium binding site 2 out of 2 in the Structure of Human Dna Polymerase Beta Complexed with 8-Clg As the Template Base in A 1-Nucleotide Gapped Dna


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 As the Template Base in A 1-Nucleotide Gapped Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:36.0
occ:1.00
O D:HOH107 2.4 29.0 1.0
O A:LYS60 2.4 33.7 1.0
O A:VAL65 2.5 30.2 1.0
O A:HOH564 2.5 35.4 1.0
O A:LEU62 2.5 33.2 1.0
OP1 D:DC3 2.6 29.4 1.0
C A:LEU62 3.5 32.4 1.0
C A:VAL65 3.6 28.4 1.0
C A:LYS60 3.6 33.8 1.0
P D:DC3 3.8 30.2 1.0
N A:VAL65 3.9 24.0 1.0
OP2 D:DC3 4.0 26.1 1.0
CA A:PRO63 4.1 33.8 1.0
N A:GLY64 4.1 32.7 1.0
CA A:VAL65 4.2 25.9 1.0
N A:PRO63 4.2 31.5 1.0
C A:LYS61 4.2 35.0 1.0
O A:LYS61 4.3 37.6 1.0
N A:LEU62 4.3 34.9 1.0
CA A:LYS60 4.4 30.5 1.0
CB A:VAL65 4.5 28.8 1.0
CG A:LYS60 4.5 32.0 1.0
CA A:LEU62 4.5 33.7 1.0
C A:PRO63 4.6 32.0 1.0
N A:LYS61 4.6 34.9 1.0
N A:GLY66 4.6 25.6 1.0
CA A:LYS61 4.7 36.4 1.0
O3' D:DT2 4.7 24.2 1.0
C A:GLY64 4.8 28.4 1.0
CA A:GLY66 4.9 21.9 1.0
O5' D:DC3 4.9 25.9 1.0

Reference:

M.-C.Koag, S.Lee. Structure of Human Dna Polymerase Beta Complexed with 8-Clg As the Template Base in A 1-Nucleotide Gapped Dna To Be Published.
Page generated: Tue Dec 15 12:02:39 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