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Sodium in PDB 4mf2: Structure of Human Dna Polymerase Beta Complexed with O6MG As the Template Base in A 1-Nucleotide Gapped Dna

Enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with O6MG As the Template Base in A 1-Nucleotide Gapped Dna

All present enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with O6MG 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 O6MG As the Template Base in A 1-Nucleotide Gapped Dna, PDB code: 4mf2 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) 19.82 / 2.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.438, 79.265, 54.789, 90.00, 105.66, 90.00
R / Rfree (%) 19.8 / 27.9

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Human Dna Polymerase Beta Complexed with O6MG As the Template Base in A 1-Nucleotide Gapped Dna (pdb code 4mf2). 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 As the Template Base in A 1-Nucleotide Gapped Dna, PDB code: 4mf2:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4mf2

Go back to Sodium Binding Sites List in 4mf2
Sodium binding site 1 out of 2 in the Structure of Human Dna Polymerase Beta Complexed with O6MG 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 O6MG As the Template Base in A 1-Nucleotide Gapped Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:25.9
occ:1.00
OP1 P:DG9 2.2 18.2 1.0
O A:ILE106 2.3 20.1 1.0
O A:THR101 2.4 23.0 1.0
O A:VAL103 2.5 22.8 1.0
O P:HOH101 2.5 17.8 1.0
C A:ILE106 3.3 19.4 1.0
P P:DG9 3.3 17.5 1.0
C A:VAL103 3.4 22.6 1.0
C A:THR101 3.4 21.1 1.0
O A:HOH508 3.5 24.1 1.0
OP2 P:DG9 3.6 18.4 1.0
N A:ILE106 3.7 18.9 1.0
CA A:SER104 3.7 19.2 1.0
N A:GLY105 3.9 19.3 1.0
N A:SER104 3.9 22.0 1.0
CA A:THR101 4.0 19.1 1.0
CA A:ILE106 4.0 18.5 1.0
C A:SER104 4.1 19.0 1.0
N A:GLY107 4.2 19.5 1.0
O3' P:DC8 4.3 18.7 1.0
N A:VAL103 4.4 21.8 1.0
C A:ARG102 4.4 23.0 1.0
CB A:THR101 4.4 18.7 1.0
CA A:GLY107 4.5 19.2 1.0
CA A:VAL103 4.5 22.1 1.0
O5' P:DG9 4.5 19.2 1.0
C A:GLY105 4.5 19.2 1.0
CB A:ILE106 4.5 18.7 1.0
O A:ARG102 4.5 26.5 1.0
N A:ARG102 4.5 21.6 1.0
CA A:GLY105 4.7 18.4 1.0
CA A:ARG102 4.8 22.0 1.0
O A:LEU100 4.9 22.7 1.0

Sodium binding site 2 out of 2 in 4mf2

Go back to Sodium Binding Sites List in 4mf2
Sodium binding site 2 out of 2 in the Structure of Human Dna Polymerase Beta Complexed with O6MG 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 O6MG As the Template Base in A 1-Nucleotide Gapped Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:43.1
occ:1.00
O A:LYS60 2.4 33.0 1.0
O A:VAL65 2.7 29.6 1.0
OP1 D:DC3 3.0 30.5 1.0
OP2 D:DC3 3.3 25.2 1.0
O A:LEU62 3.6 34.7 1.0
P D:DC3 3.6 26.5 1.0
C A:LYS60 3.6 33.4 1.0
C A:VAL65 3.8 26.5 1.0
CG A:LYS60 3.9 32.9 1.0
CA A:LYS60 4.4 30.0 1.0
NZ A:LYS60 4.5 33.2 1.0
C A:LEU62 4.5 33.3 1.0
N A:LYS61 4.6 35.3 1.0
C A:LYS61 4.6 36.4 1.0
N A:VAL65 4.6 25.7 1.0
CA A:GLY66 4.6 24.2 1.0
O3' D:DT2 4.7 27.4 1.0
N A:GLY66 4.7 25.1 1.0
CA A:VAL65 4.7 24.9 1.0
CA A:LYS61 4.8 37.2 1.0
CB A:LYS60 4.8 31.2 1.0
O5' D:DC3 4.8 26.9 1.0
N A:LEU62 4.8 37.0 1.0
O A:LYS61 4.9 41.5 1.0
N A:GLY64 4.9 31.1 1.0
CE A:LYS60 5.0 36.2 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: Tue Dec 15 06:54:07 2020

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