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Sodium in PDB 4gxk: R283K Dna Polymerase Beta Ternary Complex with A Templating 8OG and Incoming Datp Analog

Enzymatic activity of R283K Dna Polymerase Beta Ternary Complex with A Templating 8OG and Incoming Datp Analog

All present enzymatic activity of R283K Dna Polymerase Beta Ternary Complex with A Templating 8OG and Incoming Datp Analog:
2.7.7.7;

Protein crystallography data

The structure of R283K Dna Polymerase Beta Ternary Complex with A Templating 8OG and Incoming Datp Analog, PDB code: 4gxk was solved by B.D.Freudenthal, W.A.Beard, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 22.89 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.861, 78.791, 55.151, 90.00, 112.65, 90.00
R / Rfree (%) 21.9 / 27.8

Other elements in 4gxk:

The structure of R283K Dna Polymerase Beta Ternary Complex with A Templating 8OG and Incoming Datp Analog also contains other interesting chemical elements:

Manganese (Mn) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the R283K Dna Polymerase Beta Ternary Complex with A Templating 8OG and Incoming Datp Analog (pdb code 4gxk). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the R283K Dna Polymerase Beta Ternary Complex with A Templating 8OG and Incoming Datp Analog, PDB code: 4gxk:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 4gxk

Go back to Sodium Binding Sites List in 4gxk
Sodium binding site 1 out of 5 in the R283K Dna Polymerase Beta Ternary Complex with A Templating 8OG and Incoming Datp Analog


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of R283K Dna Polymerase Beta Ternary Complex with A Templating 8OG and Incoming Datp Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na405

b:30.0
occ:1.00
 OP1 P:DG9 2.2 22.8 1.0
O A:ILE106 2.4 18.6 1.0
O A:THR101 2.5 21.3 1.0
O A:HOH551 2.6 28.2 1.0
O A:VAL103 2.6 19.9 1.0
P P:DG9 3.4 23.2 1.0
C A:ILE106 3.4 22.2 1.0
C A:THR101 3.5 20.4 1.0
C A:VAL103 3.6 25.6 1.0
OP2 P:DG9 3.6 25.1 1.0
N A:ILE106 3.9 17.2 1.0
N A:GLY105 4.0 19.9 1.0
CA A:SER104 4.0 18.7 1.0
CA A:THR101 4.0 21.9 1.0
N A:SER104 4.2 18.4 1.0
CA A:ILE106 4.2 17.5 1.0
N A:VAL103 4.3 18.8 1.0
N A:GLY107 4.3 20.4 1.0
C A:SER104 4.4 21.4 1.0
O5' P:DG9 4.4 26.2 1.0
O3' P:DC8 4.5 26.6 1.0
C A:ARG102 4.5 22.8 1.0
CB A:THR101 4.5 24.7 1.0
N A:ARG102 4.5 22.7 1.0
CA A:GLY107 4.5 17.2 1.0
CA A:VAL103 4.6 22.1 1.0
CB A:ILE106 4.6 17.3 1.0
C A:GLY105 4.8 21.6 1.0
CA A:ARG102 4.8 27.1 1.0
O A:HOH579 4.8 32.5 1.0
O A:ARG102 4.9 21.9 1.0
CA A:GLY105 5.0 17.8 1.0

Sodium binding site 2 out of 5 in 4gxk

Go back to Sodium Binding Sites List in 4gxk
Sodium binding site 2 out of 5 in the R283K Dna Polymerase Beta Ternary Complex with A Templating 8OG and Incoming Datp Analog


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of R283K Dna Polymerase Beta Ternary Complex with A Templating 8OG and Incoming Datp Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na406

b:30.0
occ:1.00
 O A:HOH644 2.1 30.0 1.0
O A:HOH643 2.2 30.0 1.0
NE2 A:HIS51 2.3 46.7 1.0
CE1 A:HIS51 3.2 36.1 1.0
CD2 A:HIS51 3.3 33.7 1.0
ND1 A:HIS51 4.3 39.0 1.0
CG A:HIS51 4.4 44.3 1.0

Sodium binding site 3 out of 5 in 4gxk

Go back to Sodium Binding Sites List in 4gxk
Sodium binding site 3 out of 5 in the R283K Dna Polymerase Beta Ternary Complex with A Templating 8OG and Incoming Datp Analog


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of R283K Dna Polymerase Beta Ternary Complex with A Templating 8OG and Incoming Datp Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na407

b:30.0
occ:1.00
 O A:LEU62 2.4 27.0 1.0
O A:VAL65 2.5 29.4 1.0
O A:HOH601 2.5 34.0 1.0
O A:HOH507 2.5 23.3 1.0
O A:LYS60 2.5 27.2 1.0
OP1 D:DC3 2.6 20.0 1.0
C A:LEU62 3.4 27.0 1.0
C A:VAL65 3.5 26.5 1.0
P D:DC3 3.7 20.0 1.0
C A:LYS60 3.7 29.1 1.0
N A:VAL65 3.9 24.8 1.0
OP2 D:DC3 3.9 20.0 1.0
CA A:PRO63 4.0 26.9 1.0
N A:PRO63 4.1 26.6 1.0
N A:LEU62 4.1 30.2 1.0
CA A:VAL65 4.2 23.5 1.0
C A:LYS61 4.2 30.0 1.0
N A:GLY64 4.2 27.6 1.0
CB A:VAL65 4.4 25.4 1.0
O A:LYS61 4.4 32.6 1.0
CA A:LEU62 4.4 27.3 1.0
C A:PRO63 4.5 28.7 1.0
CA A:LYS60 4.5 29.2 1.0
CD A:LYS60 4.5 28.8 1.0
N A:GLY66 4.6 28.2 1.0
O3' D:DT2 4.6 20.0 1.0
N A:LYS61 4.6 27.4 1.0
CA A:LYS61 4.8 31.6 1.0
CA A:GLY66 4.8 27.2 1.0
CG A:LYS60 4.8 31.8 1.0
C A:GLY64 4.9 25.7 1.0
O5' D:DC3 4.9 20.0 1.0
O A:ALA59 4.9 26.2 1.0
NZ A:LYS60 4.9 33.0 1.0

Sodium binding site 4 out of 5 in 4gxk

Go back to Sodium Binding Sites List in 4gxk
Sodium binding site 4 out of 5 in the R283K Dna Polymerase Beta Ternary Complex with A Templating 8OG and Incoming Datp Analog


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of R283K Dna Polymerase Beta Ternary Complex with A Templating 8OG and Incoming Datp Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Na102

b:30.0
occ:1.00
 O A:HOH645 2.3 30.0 1.0
O A:HOH580 2.4 29.0 1.0
O P:HOH204 3.9 31.1 1.0
OP2 P:DA10 4.3 32.2 1.0
O1G A:F2A404 4.5 27.8 0.9
O A:HOH514 4.5 29.2 1.0
OP1 P:DA10 4.6 31.6 1.0
O3G A:F2A404 4.7 24.3 0.9
OD2 A:ASP190 4.9 23.0 1.0
P P:DA10 5.0 34.7 1.0

Sodium binding site 5 out of 5 in 4gxk

Go back to Sodium Binding Sites List in 4gxk
Sodium binding site 5 out of 5 in the R283K Dna Polymerase Beta Ternary Complex with A Templating 8OG and Incoming Datp Analog


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of R283K Dna Polymerase Beta Ternary Complex with A Templating 8OG and Incoming Datp Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na101

b:30.0
occ:1.00
 N7 D:DG4 2.2 45.6 1.0
C8 D:DG4 3.2 41.9 1.0
C5 D:DG4 3.2 41.1 1.0
O6 D:DG4 3.5 45.7 1.0
C6 D:DG4 3.7 40.2 1.0
O6 D:DG5 3.8 52.4 1.0
C6 D:DC3 4.3 20.0 1.0
N9 D:DG4 4.3 42.1 1.0
C4 D:DG4 4.4 42.3 1.0
C2' D:DC3 4.4 20.0 1.0
C5 D:DC3 4.7 20.0 1.0
C6 D:DG5 4.7 43.9 1.0
OP2 D:DG4 4.7 45.1 1.0
N1 D:DC3 4.8 20.0 1.0
N7 D:DG5 5.0 48.8 1.0

Reference:

B.D.Freudenthal, W.A.Beard, S.H.Wilson. Dna Polymerase Minor Groove Interactions Modulate Mutagenic Bypass of A Templating 8-Oxoguanine Lesion. Nucleic Acids Res. V. 41 1848 2013.
ISSN: ISSN 0305-1048
PubMed: 23267011
DOI: 10.1093/NAR/GKS1276
Page generated: Tue Dec 15 06:42:25 2020

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