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Sodium in PDB 4nlk: Structure of Human Dna Polymerase Beta Complexed with 8BRG in the Template Base-Paired with Incoming Non-Hydrolyzable Ctp

Enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with 8BRG in the Template Base-Paired with Incoming Non-Hydrolyzable Ctp

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

Protein crystallography data

The structure of Structure of Human Dna Polymerase Beta Complexed with 8BRG in the Template Base-Paired with Incoming Non-Hydrolyzable Ctp, PDB code: 4nlk 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) 53.01 / 2.49
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.807, 79.706, 55.683, 90.00, 107.83, 90.00
R / Rfree (%) 19.4 / 27

Other elements in 4nlk:

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

Bromine (Br) 1 atom
Magnesium (Mg) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Human Dna Polymerase Beta Complexed with 8BRG in the Template Base-Paired with Incoming Non-Hydrolyzable Ctp (pdb code 4nlk). 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 8BRG in the Template Base-Paired with Incoming Non-Hydrolyzable Ctp, PDB code: 4nlk:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4nlk

Go back to Sodium Binding Sites List in 4nlk
Sodium binding site 1 out of 2 in the Structure of Human Dna Polymerase Beta Complexed with 8BRG in the Template Base-Paired with Incoming Non-Hydrolyzable Ctp


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

b:22.3
occ:1.00
 O A:THR101 2.2 29.0 1.0
OP1 P:DG9 2.4 28.2 1.0
O A:ILE106 2.4 26.8 1.0
O A:VAL103 2.9 26.8 1.0
OP2 P:DG9 3.2 33.3 1.0
P P:DG9 3.2 29.8 1.0
C A:THR101 3.3 27.7 1.0
C A:ILE106 3.6 25.1 1.0
C A:VAL103 3.8 24.5 1.0
CA A:THR101 4.0 25.7 1.0
CA A:SER104 4.0 23.2 1.0
N A:GLY105 4.2 21.6 1.0
N A:ILE106 4.2 21.4 1.0
O3' P:DC8 4.2 29.5 1.0
C A:ARG102 4.3 26.6 1.0
N A:SER104 4.3 23.4 1.0
N A:ARG102 4.3 27.5 1.0
CA A:ILE106 4.4 22.6 1.0
CB A:THR101 4.4 25.7 1.0
N A:GLY107 4.5 26.1 1.0
O A:ARG102 4.5 30.8 1.0
N A:VAL103 4.5 24.6 1.0
C A:SER104 4.5 22.2 1.0
O5' P:DG9 4.5 30.6 1.0
CA A:ARG102 4.6 27.0 1.0
CA A:GLY107 4.6 25.8 1.0
CA A:VAL103 4.8 24.7 1.0
CB A:ILE106 4.8 24.0 1.0
C A:GLY105 4.9 23.0 1.0

Sodium binding site 2 out of 2 in 4nlk

Go back to Sodium Binding Sites List in 4nlk
Sodium binding site 2 out of 2 in the Structure of Human Dna Polymerase Beta Complexed with 8BRG in the Template Base-Paired with Incoming Non-Hydrolyzable Ctp


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

b:36.8
occ:1.00
 OP1 D:DC3 2.3 45.5 1.0
O A:LYS60 2.4 35.8 1.0
O A:VAL65 2.6 37.1 1.0
O A:LEU62 2.8 40.8 1.0
C A:VAL65 3.4 37.7 1.0
P D:DC3 3.4 42.3 1.0
C A:LYS60 3.6 36.1 1.0
C A:LEU62 3.6 41.0 1.0
OP2 D:DC3 3.7 44.6 1.0
N A:VAL65 3.8 34.4 1.0
CA A:VAL65 4.1 36.5 1.0
C A:LYS61 4.1 34.6 1.0
CA A:PRO63 4.1 43.7 1.0
O A:LYS61 4.1 39.0 1.0
N A:GLY64 4.2 40.5 1.0
N A:LEU62 4.2 36.9 1.0
N A:PRO63 4.3 43.5 1.0
N A:GLY66 4.3 40.5 1.0
CA A:LYS60 4.5 36.0 1.0
N A:LYS61 4.5 33.1 1.0
C A:PRO63 4.5 44.2 1.0
O5' D:DC3 4.5 52.8 1.0
CA A:LEU62 4.5 37.8 1.0
CA A:LYS61 4.6 34.5 1.0
CB A:VAL65 4.6 35.3 1.0
O3' D:DT2 4.6 45.7 1.0
C A:GLY64 4.7 35.3 1.0
CA A:GLY66 4.7 42.2 1.0
CG A:LYS60 4.9 38.4 1.0
O A:ALA59 4.9 28.6 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: Sun Aug 17 20:48:51 2025

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