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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 Oct 8 06:35:40 2024

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