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Sodium in PDB 4ymo: Structure of Human Dna Polymerase Beta Complexed with N7BG in the Template Opposite to Incoming Non-Hydrolyzable Ctp with Manganese in the Active Site

Enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with N7BG in the Template Opposite to Incoming Non-Hydrolyzable Ctp with Manganese in the Active Site

All present enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with N7BG in the Template Opposite to Incoming Non-Hydrolyzable Ctp with Manganese in the Active Site:
2.7.7.7;

Protein crystallography data

The structure of Structure of Human Dna Polymerase Beta Complexed with N7BG in the Template Opposite to Incoming Non-Hydrolyzable Ctp with Manganese in the Active Site, PDB code: 4ymo was solved by S.Lee, M.-C.Koag, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.93 / 2.15
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.728, 79.170, 55.634, 90.00, 107.23, 90.00
R / Rfree (%) 19.4 / 22.6

Other elements in 4ymo:

The structure of Structure of Human Dna Polymerase Beta Complexed with N7BG in the Template Opposite to Incoming Non-Hydrolyzable Ctp with Manganese in the Active Site also contains other interesting chemical elements:

Fluorine (F) 1 atom
Manganese (Mn) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Human Dna Polymerase Beta Complexed with N7BG in the Template Opposite to Incoming Non-Hydrolyzable Ctp with Manganese in the Active Site (pdb code 4ymo). 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 N7BG in the Template Opposite to Incoming Non-Hydrolyzable Ctp with Manganese in the Active Site, PDB code: 4ymo:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4ymo

Go back to Sodium Binding Sites List in 4ymo
Sodium binding site 1 out of 2 in the Structure of Human Dna Polymerase Beta Complexed with N7BG in the Template Opposite to Incoming Non-Hydrolyzable Ctp with Manganese in the Active Site


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 N7BG in the Template Opposite to Incoming Non-Hydrolyzable Ctp with Manganese in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:19.0
occ:1.00
 O A:THR101 2.3 19.6 1.0
O A:ILE106 2.4 16.5 1.0
OP1 P:DG9 2.4 14.7 1.0
O A:VAL103 2.4 17.4 1.0
O A:HOH560 2.7 24.3 1.0
C A:THR101 3.3 18.5 1.0
C A:VAL103 3.3 17.3 1.0
P P:DG9 3.4 19.0 1.0
C A:ILE106 3.4 18.9 1.0
OP2 P:DG9 3.5 21.0 1.0
N A:ILE106 3.7 18.6 1.0
O A:HOH620 3.8 34.9 1.0
CA A:SER104 3.9 21.2 1.0
N A:GLY105 3.9 14.8 1.0
CA A:THR101 3.9 21.8 1.0
N A:SER104 4.0 18.2 1.0
CA A:ILE106 4.0 19.5 1.0
N A:VAL103 4.1 15.1 1.0
C A:SER104 4.2 17.6 1.0
N A:ARG102 4.3 15.9 1.0
C A:ARG102 4.3 16.7 1.0
O3' P:DC8 4.3 19.8 1.0
CA A:VAL103 4.4 18.6 1.0
N A:GLY107 4.5 16.5 1.0
CB A:ILE106 4.5 19.5 1.0
CB A:THR101 4.5 17.3 1.0
CA A:ARG102 4.5 20.4 1.0
C A:GLY105 4.6 17.4 1.0
O5' P:DG9 4.7 17.7 1.0
O A:ARG102 4.7 18.6 1.0
CA A:GLY107 4.8 18.1 1.0
CA A:GLY105 4.8 16.6 1.0
O A:LEU100 4.9 16.7 1.0

Sodium binding site 2 out of 2 in 4ymo

Go back to Sodium Binding Sites List in 4ymo
Sodium binding site 2 out of 2 in the Structure of Human Dna Polymerase Beta Complexed with N7BG in the Template Opposite to Incoming Non-Hydrolyzable Ctp with Manganese in the Active Site


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 N7BG in the Template Opposite to Incoming Non-Hydrolyzable Ctp with Manganese in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:25.8
occ:1.00
 O A:VAL65 2.4 28.6 1.0
O A:HOH576 2.4 30.4 1.0
O A:LEU62 2.4 30.2 1.0
OP1 D:DC3 2.5 31.3 1.0
O A:LYS60 2.5 30.8 1.0
C A:VAL65 3.4 29.4 1.0
C A:LEU62 3.4 30.9 1.0
C A:LYS60 3.5 28.7 1.0
P D:DC3 3.6 31.8 1.0
OP2 D:DC3 3.8 36.6 1.0
N A:VAL65 3.8 26.4 1.0
CA A:VAL65 4.1 26.5 1.0
CA A:PRO63 4.1 29.7 1.0
C A:LYS61 4.2 29.9 1.0
N A:GLY64 4.2 29.0 1.0
N A:PRO63 4.2 28.5 1.0
N A:LEU62 4.2 27.6 1.0
CA A:LYS60 4.3 26.4 1.0
O A:LYS61 4.3 29.4 1.0
CB A:VAL65 4.4 27.4 1.0
CG A:LYS60 4.4 27.5 1.0
N A:GLY66 4.4 30.1 1.0
CA A:LEU62 4.4 26.9 1.0
C A:PRO63 4.5 32.3 1.0
N A:LYS61 4.5 26.7 1.0
O3' D:DT2 4.6 33.1 1.0
CA A:LYS61 4.7 28.3 1.0
O5' D:DC3 4.7 36.2 1.0
CA A:GLY66 4.7 31.6 1.0
NZ A:LYS60 4.7 34.1 1.0
C A:GLY64 4.8 28.3 1.0
CB A:LYS60 5.0 27.5 1.0
O A:ALA59 5.0 22.5 1.0

Reference:

Y.Kou, M.C.Koag, S.Lee. Structural and Kinetic Studies of the Effect of Guanine-N7 Alkylation and Metal Cofactors on Dna Replication. Biochemistry 2018.
ISSN: ISSN 1520-4995
PubMed: 29957995
DOI: 10.1021/ACS.BIOCHEM.8B00331
Page generated: Mon Oct 7 19:33:16 2024

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