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Sodium in PDB 6nks: Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with Beta-Gamma Chf Analog of Dgtp

Enzymatic activity of Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with Beta-Gamma Chf Analog of Dgtp

All present enzymatic activity of Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with Beta-Gamma Chf Analog of Dgtp:
2.7.7.7;

Protein crystallography data

The structure of Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with Beta-Gamma Chf Analog of Dgtp, PDB code: 6nks was solved by V.K.Batra, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.27 / 2.35
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.607, 80.327, 55.391, 90.00, 108.13, 90.00
R / Rfree (%) 18.9 / 25.5

Other elements in 6nks:

The structure of Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with Beta-Gamma Chf Analog of Dgtp also contains other interesting chemical elements:

Fluorine (F) 1 atom
Magnesium (Mg) 1 atom
Chlorine (Cl) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with Beta-Gamma Chf Analog of Dgtp (pdb code 6nks). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with Beta-Gamma Chf Analog of Dgtp, PDB code: 6nks:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 6nks

Go back to Sodium Binding Sites List in 6nks
Sodium binding site 1 out of 3 in the Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with Beta-Gamma Chf Analog of Dgtp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with Beta-Gamma Chf Analog of Dgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:39.8
occ:1.00
OD1 A:ASP192 2.4 35.6 1.0
O1A A:GFH401 2.5 29.2 1.0
OD2 A:ASP190 2.6 37.5 1.0
OD2 A:ASP256 2.7 40.9 1.0
CG A:ASP190 3.3 33.8 1.0
OD1 A:ASP190 3.3 31.5 1.0
CG A:ASP192 3.4 31.5 1.0
PA A:GFH401 3.5 30.3 1.0
C3' P:DOC10 3.5 41.6 1.0
O5' A:GFH401 3.6 29.8 1.0
OD2 A:ASP192 3.7 32.5 1.0
MG A:MG402 3.7 29.2 1.0
CG A:ASP256 3.7 37.9 1.0
C5' P:DOC10 3.9 48.5 1.0
O2A A:GFH401 3.9 35.4 1.0
C5' A:GFH401 3.9 28.3 1.0
C4' P:DOC10 4.0 46.6 1.0
O5' P:DOC10 4.2 44.7 1.0
CB A:ASP256 4.4 35.5 1.0
OP1 P:DOC10 4.6 44.4 1.0
OD1 A:ASP256 4.6 32.7 1.0
CB A:ASP190 4.6 31.4 1.0
CB A:ASP192 4.7 26.9 1.0
O A:MET191 4.8 27.9 1.0
NH2 A:ARG254 4.8 36.9 1.0
C2' P:DOC10 4.8 37.5 1.0
O1G A:GFH401 4.8 36.6 1.0
O3A A:GFH401 4.9 25.7 1.0

Sodium binding site 2 out of 3 in 6nks

Go back to Sodium Binding Sites List in 6nks
Sodium binding site 2 out of 3 in the Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with Beta-Gamma Chf Analog of Dgtp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with Beta-Gamma Chf Analog of Dgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:33.1
occ:1.00
O A:THR101 2.3 32.8 1.0
O A:HOH528 2.3 34.7 1.0
OP1 P:DG9 2.5 31.9 1.0
O A:ILE106 2.5 30.4 1.0
O A:VAL103 2.7 31.1 1.0
O A:HOH554 3.0 35.6 1.0
C A:THR101 3.3 34.4 1.0
P P:DG9 3.5 31.9 1.0
C A:VAL103 3.5 32.7 1.0
C A:ILE106 3.5 32.5 1.0
OP2 P:DG9 3.6 36.8 1.0
N A:ILE106 3.9 33.7 1.0
CA A:SER104 4.0 27.1 1.0
CA A:THR101 4.0 31.3 1.0
N A:GLY105 4.1 31.4 1.0
N A:SER104 4.1 25.8 1.0
N A:VAL103 4.2 33.7 1.0
C A:ARG102 4.2 33.0 1.0
CA A:ILE106 4.3 30.6 1.0
N A:ARG102 4.3 33.6 1.0
C A:SER104 4.4 29.5 1.0
CA A:ARG102 4.5 32.0 1.0
O3' P:DC8 4.5 30.5 1.0
N A:GLY107 4.5 32.3 1.0
CA A:VAL103 4.5 32.8 1.0
CB A:THR101 4.6 29.8 1.0
O5' P:DG9 4.6 37.8 1.0
CB A:ILE106 4.7 32.7 1.0
O A:ARG102 4.7 35.8 1.0
CA A:GLY107 4.7 33.9 1.0
C A:GLY105 4.8 34.0 1.0
O A:LEU100 4.9 32.4 1.0
CA A:GLY105 5.0 34.9 1.0

Sodium binding site 3 out of 3 in 6nks

Go back to Sodium Binding Sites List in 6nks
Sodium binding site 3 out of 3 in the Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with Beta-Gamma Chf Analog of Dgtp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with Beta-Gamma Chf Analog of Dgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na405

b:54.6
occ:1.00
O A:LYS60 2.7 46.3 1.0
O A:LEU62 2.8 42.1 1.0
OP1 D:DC3 3.0 49.1 1.0
C A:LEU62 3.3 42.4 1.0
O A:VAL65 3.5 41.6 1.0
CA A:PRO63 3.6 44.1 1.0
N A:PRO63 3.7 44.0 1.0
C A:LYS60 3.8 44.7 1.0
C A:LYS61 3.9 45.4 1.0
N A:LEU62 4.0 45.8 1.0
O A:LYS61 4.0 51.1 1.0
CA A:LEU62 4.2 39.1 1.0
P D:DC3 4.2 49.4 1.0
N A:GLY64 4.4 43.2 1.0
CA A:LYS61 4.4 44.1 1.0
C A:PRO63 4.5 44.5 1.0
OP2 D:DC3 4.6 49.5 1.0
N A:LYS61 4.6 46.4 1.0
C A:VAL65 4.6 40.7 1.0
CB A:PRO63 4.7 41.2 1.0
N A:VAL65 4.8 37.6 1.0
CA A:LYS60 4.8 41.4 1.0
CG A:LYS60 4.9 45.5 1.0
CD A:PRO63 4.9 40.6 1.0

Reference:

V.K.Batra, S.H.Wilson. Ternary Complex Crystal Structure To Be Published.
Page generated: Tue Oct 8 12:16:45 2024

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