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Sodium in PDB 4m2y: Structure of Human Dna Polymerase Beta Complexed with 8-Brg As the Template Base in A 1-Nucleotide Gapped Dna

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

All present enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with 8-Brg 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-Brg As the Template Base in A 1-Nucleotide Gapped Dna, PDB code: 4m2y 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) 19.83 / 2.27
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.554, 79.271, 54.915, 90.00, 105.48, 90.00
R / Rfree (%) 21.2 / 26.9

Other elements in 4m2y:

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

Bromine (Br) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Human Dna Polymerase Beta Complexed with 8-Brg As the Template Base in A 1-Nucleotide Gapped Dna (pdb code 4m2y). 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-Brg As the Template Base in A 1-Nucleotide Gapped Dna, PDB code: 4m2y:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4m2y

Go back to Sodium Binding Sites List in 4m2y
Sodium binding site 1 out of 2 in the Structure of Human Dna Polymerase Beta Complexed with 8-Brg 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-Brg As the Template Base in A 1-Nucleotide Gapped Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:13.6
occ:1.00
 O A:THR101 2.3 16.6 1.0
O A:ILE106 2.3 15.0 1.0
O A:VAL103 2.3 20.6 1.0
OP1 P:DG9 2.3 14.7 1.0
O P:HOH101 2.5 17.2 1.0
C A:VAL103 3.2 19.3 1.0
C A:THR101 3.3 17.8 1.0
C A:ILE106 3.3 15.6 1.0
P P:DG9 3.5 15.7 1.0
OP2 P:DG9 3.8 16.5 1.0
N A:ILE106 3.8 16.0 1.0
N A:SER104 3.9 17.3 1.0
CA A:SER104 3.9 16.1 1.0
CA A:THR101 3.9 16.8 1.0
N A:VAL103 4.0 19.2 1.0
N A:GLY105 4.1 15.0 1.0
CA A:ILE106 4.1 15.2 1.0
CA A:VAL103 4.3 19.0 1.0
C A:ARG102 4.3 19.3 1.0
N A:GLY107 4.3 15.7 1.0
N A:ARG102 4.3 18.9 1.0
C A:SER104 4.3 15.3 1.0
CB A:THR101 4.4 16.5 1.0
CB A:ILE106 4.4 16.8 1.0
O3' P:DC8 4.5 15.8 1.0
CA A:GLY107 4.6 16.0 1.0
CA A:ARG102 4.6 18.9 1.0
C A:GLY105 4.7 15.6 1.0
O5' P:DG9 4.7 15.5 1.0
O A:ARG102 4.7 17.9 1.0
O A:LEU100 4.8 17.3 1.0
CA A:GLY105 4.9 15.5 1.0

Sodium binding site 2 out of 2 in 4m2y

Go back to Sodium Binding Sites List in 4m2y
Sodium binding site 2 out of 2 in the Structure of Human Dna Polymerase Beta Complexed with 8-Brg 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-Brg As the Template Base in A 1-Nucleotide Gapped Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:29.3
occ:1.00
 O A:LYS60 2.3 34.1 1.0
O A:VAL65 2.4 27.4 1.0
OP1 D:DC3 2.6 22.7 1.0
O A:LEU62 2.7 29.9 1.0
C A:LYS60 3.5 34.9 1.0
C A:VAL65 3.5 21.9 1.0
C A:LEU62 3.7 28.7 1.0
P D:DC3 3.7 19.7 1.0
OP2 D:DC3 3.9 21.1 1.0
N A:VAL65 4.1 21.3 1.0
N A:LEU62 4.1 30.3 1.0
C A:LYS61 4.1 33.1 1.0
CA A:VAL65 4.2 21.5 1.0
CA A:LYS60 4.3 31.7 1.0
CA A:PRO63 4.3 27.2 1.0
N A:LYS61 4.4 35.7 1.0
N A:PRO63 4.5 27.5 1.0
O A:LYS61 4.5 35.9 1.0
N A:GLY64 4.5 25.5 1.0
CB A:VAL65 4.5 22.1 1.0
CA A:LYS61 4.5 36.7 1.0
N A:GLY66 4.5 20.8 1.0
CG A:LYS60 4.6 35.9 1.0
CA A:LEU62 4.6 30.4 1.0
O3' D:DT2 4.6 19.8 1.0
CA A:GLY66 4.8 20.2 1.0
C A:PRO63 4.9 25.6 1.0
O5' D:DC3 4.9 21.4 1.0
O A:ALA59 5.0 29.4 1.0

Reference:

M.C.Koag, K.Min, S.Lee. Structural Basis For Promutagenicity of 8-Halogenated Guanine. J.Biol.Chem. V. 289 6289 2014.
ISSN: ISSN 0021-9258
PubMed: 24425881
DOI: 10.1074/JBC.M113.537803
Page generated: Mon Oct 7 16:54:43 2024

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