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

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

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

Protein crystallography data

The structure of Structure of Human Dna Polymerase Beta Complexed with Nicked Dna Containing A Mismatched Template 8BRG and Incoming Gtp, PDB code: 4nlz 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) 52.84 / 2.68
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.414, 79.438, 54.798, 90.00, 105.37, 90.00
R / Rfree (%) 20 / 29.1

Other elements in 4nlz:

The structure of Structure of Human Dna Polymerase Beta Complexed with Nicked Dna Containing A Mismatched Template 8BRG and Incoming Gtp also contains other interesting chemical elements:

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

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Human Dna Polymerase Beta Complexed with Nicked Dna Containing A Mismatched Template 8BRG and Incoming Gtp (pdb code 4nlz). 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 Mismatched Template 8BRG and Incoming Gtp, PDB code: 4nlz:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4nlz

Go back to Sodium Binding Sites List in 4nlz
Sodium binding site 1 out of 2 in the Structure of Human Dna Polymerase Beta Complexed with Nicked Dna Containing A Mismatched Template 8BRG and Incoming Gtp


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 Mismatched Template 8BRG and Incoming Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:18.8
occ:1.00
 O4 A:PO4403 2.1 50.8 1.0
OP1 P:DG9 2.2 13.2 1.0
O A:ILE106 2.2 10.5 1.0
O A:THR101 2.4 12.8 1.0
O2 A:PO4403 2.5 48.6 1.0
O A:VAL103 2.6 10.5 1.0
P A:PO4403 2.8 55.0 1.0
P P:DG9 3.1 12.9 1.0
OP2 P:DG9 3.2 13.1 1.0
C A:ILE106 3.2 10.5 1.0
C A:THR101 3.5 11.6 1.0
C A:VAL103 3.6 10.5 1.0
N A:ILE106 3.7 9.9 1.0
O3 A:PO4403 3.9 49.4 1.0
N A:GLY105 3.9 9.6 1.0
O1 A:PO4403 3.9 52.5 1.0
CA A:SER104 3.9 9.9 1.0
CA A:ILE106 4.0 10.1 1.0
CA A:THR101 4.1 10.9 1.0
N A:SER104 4.1 10.2 1.0
N A:GLY107 4.1 11.0 1.0
O5' P:DG9 4.2 14.5 1.0
C A:SER104 4.3 9.6 1.0
CA A:GLY107 4.4 11.6 1.0
O3' P:DC8 4.4 13.5 1.0
N A:VAL103 4.4 11.0 1.0
CB A:ILE106 4.4 9.9 1.0
CB A:THR101 4.5 10.8 1.0
C A:ARG102 4.5 11.8 1.0
N A:ARG102 4.6 11.7 1.0
C A:GLY105 4.6 9.9 1.0
CA A:VAL103 4.7 10.6 1.0
CA A:ARG102 4.8 12.0 1.0
CA A:GLY105 4.8 9.8 1.0
O A:ARG102 4.9 11.2 1.0

Sodium binding site 2 out of 2 in 4nlz

Go back to Sodium Binding Sites List in 4nlz
Sodium binding site 2 out of 2 in the Structure of Human Dna Polymerase Beta Complexed with Nicked Dna Containing A Mismatched Template 8BRG and Incoming Gtp


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 Mismatched Template 8BRG and Incoming Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na101

b:17.5
occ:1.00
 O A:VAL65 2.7 18.3 1.0
O A:LYS60 2.8 22.2 1.0
OP2 D:DC3 3.0 15.4 1.0
OP1 D:DC3 3.0 16.2 1.0
P D:DC3 3.5 15.5 1.0
C A:VAL65 3.8 16.7 1.0
CG A:LYS60 3.9 22.3 1.0
C A:LYS60 4.0 21.4 1.0
O A:LEU62 4.0 24.1 1.0
NZ A:LYS60 4.1 25.6 1.0
CA A:GLY66 4.2 15.7 1.0
N A:GLY66 4.5 16.0 1.0
CA A:LYS60 4.6 20.9 1.0
O3' D:DT2 4.6 14.6 1.0
O5' D:DC3 4.7 15.8 1.0
CB A:LYS60 4.8 21.3 1.0
N A:VAL65 4.8 17.0 1.0
CE A:LYS60 4.9 24.3 1.0
CD A:LYS60 4.9 24.1 1.0
CA A:VAL65 4.9 16.4 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 17:15:56 2024

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