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Sodium in PDB 4nln: Structure of Human Dna Polymerase Beta Complexed with Nicked Dna Containing A Template 8BRG and Incoming Ctp

Enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with Nicked Dna Containing A Template 8BRG and Incoming Ctp

All present enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with Nicked Dna Containing A Template 8BRG and Incoming Ctp:
2.7.7.7;

Protein crystallography data

The structure of Structure of Human Dna Polymerase Beta Complexed with Nicked Dna Containing A Template 8BRG and Incoming Ctp, PDB code: 4nln 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) 52.67 / 2.26
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.955, 79.075, 54.912, 90.00, 106.59, 90.00
R / Rfree (%) 21 / 27.3

Other elements in 4nln:

The structure of Structure of Human Dna Polymerase Beta Complexed with Nicked Dna Containing A Template 8BRG and Incoming 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 Nicked Dna Containing A Template 8BRG and Incoming Ctp (pdb code 4nln). 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 Nicked Dna Containing A Template 8BRG and Incoming Ctp, PDB code: 4nln:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4nln

Go back to Sodium Binding Sites List in 4nln
Sodium binding site 1 out of 2 in the Structure of Human Dna Polymerase Beta Complexed with Nicked Dna Containing A Template 8BRG and Incoming 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 Nicked Dna Containing A Template 8BRG and Incoming Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:23.5
occ:1.00
 O A:THR101 2.2 27.2 1.0
OP1 P:DG9 2.4 24.7 1.0
O A:ILE106 2.4 19.8 1.0
O A:VAL103 2.6 24.1 1.0
C A:THR101 3.2 26.0 1.0
C A:VAL103 3.4 25.9 1.0
P P:DG9 3.5 28.3 1.0
C A:ILE106 3.5 21.7 1.0
OP2 P:DG9 3.6 26.1 1.0
N A:ILE106 3.8 22.4 1.0
CA A:THR101 3.9 24.6 1.0
N A:SER104 3.9 25.6 1.0
CA A:SER104 4.0 25.0 1.0
N A:GLY105 4.0 22.6 1.0
N A:VAL103 4.1 24.3 1.0
CA A:ILE106 4.2 20.0 1.0
N A:ARG102 4.3 24.6 1.0
C A:ARG102 4.3 26.4 1.0
CA A:VAL103 4.4 24.4 1.0
C A:SER104 4.4 22.4 1.0
N A:GLY107 4.4 25.4 1.0
CB A:THR101 4.4 24.4 1.0
O3' P:DC8 4.5 25.4 1.0
CA A:ARG102 4.5 25.3 1.0
CA A:GLY107 4.6 27.6 1.0
C A:GLY105 4.6 23.4 1.0
CB A:ILE106 4.7 20.0 1.0
O5' P:DG9 4.7 26.8 1.0
O A:ARG102 4.8 25.9 1.0
O A:LEU100 4.8 20.7 1.0
CA A:GLY105 4.9 23.0 1.0

Sodium binding site 2 out of 2 in 4nln

Go back to Sodium Binding Sites List in 4nln
Sodium binding site 2 out of 2 in the Structure of Human Dna Polymerase Beta Complexed with Nicked Dna Containing A Template 8BRG and Incoming 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 Nicked Dna Containing A Template 8BRG and Incoming Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:41.7
occ:1.00
 O A:LYS60 2.2 40.3 1.0
O A:LEU62 2.5 40.1 1.0
O A:VAL65 2.5 29.3 1.0
OP1 D:DC3 2.9 38.1 1.0
C A:LYS60 3.4 39.4 1.0
C A:LEU62 3.5 37.0 1.0
C A:VAL65 3.6 30.2 1.0
C A:LYS61 3.8 35.0 1.0
N A:LEU62 3.9 35.0 1.0
P D:DC3 3.9 30.7 1.0
OP2 D:DC3 3.9 27.5 1.0
N A:VAL65 3.9 33.3 1.0
O A:LYS61 4.1 38.8 1.0
CA A:VAL65 4.2 30.1 1.0
N A:GLY64 4.2 35.5 1.0
CA A:PRO63 4.2 37.2 1.0
N A:LYS61 4.3 39.2 1.0
N A:PRO63 4.3 35.1 1.0
CA A:LYS60 4.3 36.2 1.0
CA A:LYS61 4.3 37.0 1.0
CA A:LEU62 4.3 36.6 1.0
CB A:VAL65 4.5 32.0 1.0
C A:PRO63 4.7 38.6 1.0
CG A:LYS60 4.7 39.3 1.0
N A:GLY66 4.7 25.4 1.0
O3' D:DT2 4.8 28.9 1.0
NZ A:LYS60 4.8 29.1 1.0
O A:ALA59 4.9 37.0 1.0
C A:GLY64 4.9 35.8 1.0
CE A:LYS60 5.0 32.7 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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