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Sodium in PDB 4o5k: Structure of Human Dna Polymerase Complexed with N7MG in the Template Base Paired with Incoming Non-Hydrolyzable Ctp

Enzymatic activity of Structure of Human Dna Polymerase Complexed with N7MG in the Template Base Paired with Incoming Non-Hydrolyzable Ctp

All present enzymatic activity of Structure of Human Dna Polymerase Complexed with N7MG 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 Complexed with N7MG in the Template Base Paired with Incoming Non-Hydrolyzable Ctp, PDB code: 4o5k was solved by M-.C.Koag, S.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.87 / 2.06
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.870, 79.568, 55.670, 90.00, 107.71, 90.00
R / Rfree (%) 20 / 25.2

Other elements in 4o5k:

The structure of Structure of Human Dna Polymerase Complexed with N7MG in the Template Base Paired with Incoming Non-Hydrolyzable Ctp also contains other interesting chemical elements:

Fluorine (F) 1 atom
Magnesium (Mg) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Human Dna Polymerase Complexed with N7MG in the Template Base Paired with Incoming Non-Hydrolyzable Ctp (pdb code 4o5k). 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 Complexed with N7MG in the Template Base Paired with Incoming Non-Hydrolyzable Ctp, PDB code: 4o5k:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4o5k

Go back to Sodium Binding Sites List in 4o5k
Sodium binding site 1 out of 2 in the Structure of Human Dna Polymerase Complexed with N7MG 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 Complexed with N7MG in the Template Base Paired with Incoming Non-Hydrolyzable Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:18.3
occ:1.00
 O A:THR101 2.3 21.3 1.0
OP1 P:DG9 2.4 18.9 1.0
O A:ILE106 2.4 17.1 1.0
O P:HOH103 2.5 21.8 1.0
O A:HOH503 2.6 18.3 1.0
O A:VAL103 2.6 14.3 1.0
C A:THR101 3.3 17.7 1.0
P P:DG9 3.4 25.9 1.0
C A:ILE106 3.4 22.3 1.0
OP2 P:DG9 3.5 21.7 1.0
C A:VAL103 3.5 17.9 1.0
N A:ILE106 3.8 18.8 1.0
CA A:THR101 3.9 18.5 1.0
N A:GLY105 4.0 20.9 1.0
CA A:SER104 4.1 19.5 1.0
CA A:ILE106 4.1 14.9 1.0
N A:SER104 4.2 13.8 1.0
N A:VAL103 4.3 14.6 1.0
O3' P:DC8 4.4 19.8 1.0
N A:ARG102 4.4 15.2 1.0
N A:GLY107 4.4 21.6 1.0
C A:SER104 4.4 16.6 1.0
CB A:THR101 4.4 18.1 1.0
C A:ARG102 4.4 19.4 1.0
CB A:ILE106 4.5 18.6 1.0
CA A:VAL103 4.5 17.3 1.0
O5' P:DG9 4.6 24.5 1.0
C A:GLY105 4.6 22.2 1.0
CA A:GLY107 4.6 15.2 1.0
CA A:ARG102 4.7 17.4 1.0
CA A:GLY105 4.9 21.1 1.0
O A:LEU100 4.9 17.1 1.0
O A:ARG102 4.9 22.2 1.0

Sodium binding site 2 out of 2 in 4o5k

Go back to Sodium Binding Sites List in 4o5k
Sodium binding site 2 out of 2 in the Structure of Human Dna Polymerase Complexed with N7MG 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 Complexed with N7MG in the Template Base Paired with Incoming Non-Hydrolyzable Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:31.7
occ:1.00
 O A:VAL65 2.4 26.0 1.0
O A:LYS60 2.4 29.1 1.0
O A:HOH509 2.5 27.8 1.0
O A:LEU62 2.5 27.9 1.0
OP1 D:DC3 2.5 22.9 1.0
C A:LEU62 3.4 25.9 1.0
C A:VAL65 3.4 26.9 1.0
P D:DC3 3.5 30.0 1.0
C A:LYS60 3.6 27.1 1.0
OP2 D:DC3 3.6 27.4 1.0
N A:VAL65 3.9 24.6 1.0
CA A:PRO63 4.0 26.3 1.0
N A:PRO63 4.1 27.3 1.0
CA A:VAL65 4.1 24.7 1.0
N A:GLY64 4.1 27.7 1.0
C A:LYS61 4.2 28.8 1.0
N A:LEU62 4.2 24.7 1.0
O A:LYS61 4.3 29.4 1.0
CA A:LYS60 4.4 23.0 1.0
CA A:LEU62 4.4 25.4 1.0
CB A:VAL65 4.5 27.1 1.0
N A:GLY66 4.5 26.8 1.0
C A:PRO63 4.5 29.2 1.0
O3' D:DT2 4.5 32.1 1.0
N A:LYS61 4.5 24.3 1.0
CG A:LYS60 4.6 29.3 1.0
CA A:LYS61 4.7 25.3 1.0
CA A:GLY66 4.7 27.1 1.0
O5' D:DC3 4.7 31.3 1.0
C A:GLY64 4.8 29.2 1.0

Reference:

M.C.Koag, Y.Kou, H.Ouzon-Shubeita, S.Lee. Transition-State Destabilization Reveals How Human Dna Polymerase Beta Proceeds Across the Chemically Unstable Lesion N7-Methylguanine. Nucleic Acids Res. V. 42 8755 2014.
ISSN: ISSN 0305-1048
PubMed: 24966350
DOI: 10.1093/NAR/GKU554
Page generated: Mon Oct 7 17:25:19 2024

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