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Sodium in PDB 4o5e: Structure of Human Dna Polymerase Complexed with N7MG in the Template Base Paired with Incoming Non-Hydrolyzable Ttp

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

All present enzymatic activity of Structure of Human Dna Polymerase Complexed with N7MG in the Template Base Paired with Incoming Non-Hydrolyzable Ttp:
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 Ttp, PDB code: 4o5e 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) 19.73 / 2.53
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.425, 78.920, 54.819, 90.00, 105.97, 90.00
R / Rfree (%) 20.5 / 27.3

Other elements in 4o5e:

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

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

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 Ttp (pdb code 4o5e). 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 Ttp, PDB code: 4o5e:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4o5e

Go back to Sodium Binding Sites List in 4o5e
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 Ttp


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 Ttp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:33.8
occ:1.00
 O A:VAL65 2.5 34.5 1.0
OP1 D:DC3 2.8 31.1 1.0
O A:LYS60 2.8 35.7 1.0
OP2 D:DC3 3.1 23.5 1.0
P D:DC3 3.4 28.0 1.0
O A:LEU62 3.4 32.0 1.0
C A:VAL65 3.6 28.9 1.0
C A:LYS60 3.9 33.5 1.0
CG A:LYS60 4.2 29.7 1.0
CA A:GLY66 4.3 22.2 1.0
N A:GLY66 4.3 31.4 1.0
O3' D:DT2 4.5 28.0 1.0
N A:VAL65 4.5 26.8 1.0
C A:LEU62 4.5 30.4 1.0
NZ A:LYS60 4.5 39.1 1.0
CA A:VAL65 4.6 22.3 1.0
CA A:LYS60 4.6 27.3 1.0
O5' D:DC3 4.6 32.3 1.0
N A:GLY64 4.9 28.6 1.0
CB A:LYS60 5.0 30.1 1.0
C A:LYS61 5.0 34.3 1.0

Sodium binding site 2 out of 2 in 4o5e

Go back to Sodium Binding Sites List in 4o5e
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 Ttp


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 Ttp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:28.9
occ:1.00
 OP1 P:DG9 2.3 22.4 1.0
O A:THR101 2.3 25.5 1.0
O A:VAL103 2.5 22.4 1.0
O A:ILE106 2.5 20.0 1.0
O A:HOH559 2.9 28.7 1.0
O A:HOH506 3.1 22.5 1.0
C A:THR101 3.4 25.6 1.0
P P:DG9 3.4 15.2 1.0
C A:VAL103 3.4 21.0 1.0
C A:ILE106 3.5 18.8 1.0
OP2 P:DG9 3.6 33.3 1.0
CA A:SER104 3.9 18.8 1.0
N A:SER104 3.9 23.9 1.0
N A:ILE106 4.0 18.3 1.0
N A:GLY105 4.0 18.3 1.0
CA A:THR101 4.0 23.2 1.0
N A:VAL103 4.2 20.0 1.0
C A:ARG102 4.3 25.4 1.0
CA A:ILE106 4.3 16.1 1.0
N A:ARG102 4.3 26.0 1.0
C A:SER104 4.4 20.4 1.0
O5' P:DG9 4.4 24.2 1.0
CA A:VAL103 4.4 17.4 1.0
N A:GLY107 4.5 21.1 1.0
O3' P:DC8 4.5 20.1 1.0
CA A:ARG102 4.6 23.3 1.0
CB A:THR101 4.6 23.4 1.0
O A:ARG102 4.7 27.3 1.0
CA A:GLY107 4.7 18.6 1.0
CB A:ILE106 4.7 18.3 1.0
C A:GLY105 4.8 18.9 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: Sun Aug 17 20:57:21 2025

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