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Sodium in PDB 6nky: Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with "Hot-Spot Sequence" with Beta-Gamma Chf Analogue of Dgtp

Enzymatic activity of Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with "Hot-Spot Sequence" with Beta-Gamma Chf Analogue of Dgtp

All present enzymatic activity of Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with "Hot-Spot Sequence" with Beta-Gamma Chf Analogue of Dgtp:
2.7.7.7;

Protein crystallography data

The structure of Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with "Hot-Spot Sequence" with Beta-Gamma Chf Analogue of Dgtp, PDB code: 6nky 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) 21.98 / 2.09
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.643, 80.158, 55.251, 90.00, 107.89, 90.00
R / Rfree (%) 19.9 / 25.6

Other elements in 6nky:

The structure of Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with "Hot-Spot Sequence" with Beta-Gamma Chf Analogue 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 "Hot-Spot Sequence" with Beta-Gamma Chf Analogue of Dgtp (pdb code 6nky). 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 "Hot-Spot Sequence" with Beta-Gamma Chf Analogue of Dgtp, PDB code: 6nky:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 6nky

Go back to Sodium Binding Sites List in 6nky
Sodium binding site 1 out of 3 in the Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with "Hot-Spot Sequence" with Beta-Gamma Chf Analogue 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 "Hot-Spot Sequence" with Beta-Gamma Chf Analogue of Dgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:31.2
occ:1.00
 OD2 A:ASP190 2.1 34.5 1.0
OD1 A:ASP192 2.2 32.6 1.0
OD2 A:ASP256 2.2 34.5 1.0
O A:HOH537 2.4 41.6 1.0
O1A A:GFH408 2.5 27.9 1.0
CG A:ASP190 3.1 30.6 1.0
CG A:ASP192 3.2 27.5 1.0
C3' P:2DT10 3.4 41.3 1.0
CG A:ASP256 3.4 33.5 1.0
PA A:GFH408 3.5 31.1 1.0
OD1 A:ASP190 3.5 31.4 1.0
OD2 A:ASP192 3.6 26.7 1.0
O5' A:GFH408 3.6 30.9 1.0
MG A:MG401 3.6 26.5 1.0
O2A A:GFH408 3.8 28.7 1.0
C5' A:GFH408 3.9 31.2 1.0
CB A:ASP256 4.0 34.7 1.0
C4' P:2DT10 4.1 41.2 1.0
C5' P:2DT10 4.3 39.8 1.0
OD1 A:ASP256 4.4 33.0 1.0
CB A:ASP190 4.4 29.0 1.0
CB A:ASP192 4.5 30.5 1.0
O5' P:2DT10 4.6 37.9 1.0
O1G A:GFH408 4.6 25.8 1.0
C2' P:2DT10 4.6 37.3 1.0
OP1 P:2DT10 4.7 37.8 1.0
NH2 A:ARG254 4.8 34.9 1.0
O A:MET191 4.9 29.4 1.0
O3A A:GFH408 4.9 30.0 1.0

Sodium binding site 2 out of 3 in 6nky

Go back to Sodium Binding Sites List in 6nky
Sodium binding site 2 out of 3 in the Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with "Hot-Spot Sequence" with Beta-Gamma Chf Analogue 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 "Hot-Spot Sequence" with Beta-Gamma Chf Analogue of Dgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:29.5
occ:1.00
 O A:THR101 2.3 32.8 1.0
OP1 P:DT9 2.4 29.4 1.0
O A:ILE106 2.4 27.6 1.0
O A:VAL103 2.5 28.9 1.0
O P:HOH101 2.5 31.0 1.0
O A:HOH666 3.2 43.3 1.0
C A:THR101 3.3 35.3 1.0
C A:VAL103 3.4 32.0 1.0
P P:DT9 3.5 33.8 1.0
C A:ILE106 3.5 28.6 1.0
OP2 P:DT9 3.6 28.8 1.0
N A:ILE106 3.8 31.4 1.0
CA A:SER104 3.9 31.8 1.0
O A:HOH662 4.0 42.8 1.0
N A:GLY105 4.0 29.8 1.0
N A:SER104 4.0 29.2 1.0
CA A:THR101 4.1 31.4 1.0
N A:VAL103 4.1 30.0 1.0
CA A:ILE106 4.1 28.8 1.0
C A:ARG102 4.2 29.5 1.0
C A:SER104 4.3 31.8 1.0
N A:ARG102 4.3 29.4 1.0
O3' P:DC8 4.4 29.1 1.0
CA A:VAL103 4.4 30.9 1.0
CA A:ARG102 4.5 33.1 1.0
N A:GLY107 4.5 32.9 1.0
CB A:ILE106 4.5 32.0 1.0
CB A:THR101 4.6 34.8 1.0
O A:ARG102 4.6 32.5 1.0
C A:GLY105 4.6 33.8 1.0
O5' P:DT9 4.7 33.5 1.0
CA A:GLY107 4.8 32.9 1.0
CA A:GLY105 4.9 32.5 1.0
O A:LEU100 4.9 28.2 1.0

Sodium binding site 3 out of 3 in 6nky

Go back to Sodium Binding Sites List in 6nky
Sodium binding site 3 out of 3 in the Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with "Hot-Spot Sequence" with Beta-Gamma Chf Analogue 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 "Hot-Spot Sequence" with Beta-Gamma Chf Analogue of Dgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:40.4
occ:1.00
 O A:LYS60 2.3 38.4 1.0
O A:LEU62 2.3 41.5 1.0
O A:VAL65 2.4 41.0 1.0
OP1 D:DC3 2.7 42.0 1.0
O D:HOH102 3.1 41.9 1.0
C A:LEU62 3.4 40.8 1.0
C A:LYS60 3.4 41.7 1.0
C A:VAL65 3.5 36.2 1.0
P D:DC3 3.8 42.3 1.0
CA A:PRO63 4.0 42.5 1.0
OP2 D:DC3 4.0 35.9 1.0
N A:VAL65 4.0 36.6 1.0
N A:PRO63 4.0 44.0 1.0
N A:LEU62 4.1 41.6 1.0
C A:LYS61 4.1 44.0 1.0
CA A:LYS60 4.1 40.0 1.0
CA A:VAL65 4.2 38.4 1.0
CG A:LYS60 4.3 37.4 1.0
N A:GLY64 4.3 39.2 1.0
O A:LYS61 4.3 41.1 1.0
CA A:LEU62 4.3 43.0 1.0
N A:LYS61 4.4 42.0 1.0
CB A:VAL65 4.5 39.0 1.0
C A:PRO63 4.5 45.5 1.0
CA A:LYS61 4.6 41.8 1.0
N A:GLY66 4.6 35.5 1.0
O3' D:DT2 4.7 39.4 1.0
CB A:LYS60 4.8 36.3 1.0
CA A:GLY66 4.9 39.1 1.0
O A:ALA59 4.9 39.8 1.0
CD A:LYS60 4.9 42.0 1.0
C A:GLY64 5.0 38.4 1.0
O5' D:DC3 5.0 45.8 1.0

Reference:

V.K.Batra, S.H.Wilson. Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with "Hot-Spot Sequence" with Beta-Gamma Chf Analogue of Dgtp To Be Published.
Page generated: Tue Oct 8 12:18:14 2024

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