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Sodium in PDB 7kt3: Dna Polymerase Mu, 8-Oxodgtp:at Pre-Catalytic Ground State Ternary Complex, 20 Mm CA2+ (120MIN)

Enzymatic activity of Dna Polymerase Mu, 8-Oxodgtp:at Pre-Catalytic Ground State Ternary Complex, 20 Mm CA2+ (120MIN)

All present enzymatic activity of Dna Polymerase Mu, 8-Oxodgtp:at Pre-Catalytic Ground State Ternary Complex, 20 Mm CA2+ (120MIN):
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Mu, 8-Oxodgtp:at Pre-Catalytic Ground State Ternary Complex, 20 Mm CA2+ (120MIN), PDB code: 7kt3 was solved by J.A.Jamsen, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.54 / 1.88
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.804, 68.579, 110.149, 90, 90, 90
R / Rfree (%) 16 / 18.8

Other elements in 7kt3:

The structure of Dna Polymerase Mu, 8-Oxodgtp:at Pre-Catalytic Ground State Ternary Complex, 20 Mm CA2+ (120MIN) also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms
Calcium (Ca) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Dna Polymerase Mu, 8-Oxodgtp:at Pre-Catalytic Ground State Ternary Complex, 20 Mm CA2+ (120MIN) (pdb code 7kt3). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Dna Polymerase Mu, 8-Oxodgtp:at Pre-Catalytic Ground State Ternary Complex, 20 Mm CA2+ (120MIN), PDB code: 7kt3:

Sodium binding site 1 out of 1 in 7kt3

Go back to Sodium Binding Sites List in 7kt3
Sodium binding site 1 out of 1 in the Dna Polymerase Mu, 8-Oxodgtp:at Pre-Catalytic Ground State Ternary Complex, 20 Mm CA2+ (120MIN)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Dna Polymerase Mu, 8-Oxodgtp:at Pre-Catalytic Ground State Ternary Complex, 20 Mm CA2+ (120MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na505

b:16.1
occ:1.00
 O A:THR241 2.3 19.6 1.0
O A:VAL246 2.3 17.4 1.0
O P:HOH114 2.3 21.2 1.0
O A:HOH840 2.4 23.0 1.0
O A:ILE243 2.4 16.6 1.0
OP1 P:DT3 2.7 15.7 1.0
C A:VAL246 3.4 17.9 1.0
C A:THR241 3.4 21.2 1.0
C A:ILE243 3.4 16.0 1.0
O P:HOH113 3.6 26.8 1.0
P P:DT3 3.7 16.4 1.0
N A:VAL246 3.8 18.0 1.0
OP2 P:DT3 3.9 15.3 1.0
CA A:VAL246 4.0 16.9 1.0
N A:ILE243 4.1 20.4 1.0
O A:HOH794 4.1 37.3 1.0
C A:GLN242 4.2 23.6 1.0
CA A:THR241 4.2 19.1 1.0
N A:PHE244 4.2 15.9 1.0
N A:GLY245 4.3 17.1 1.0
CA A:PHE244 4.3 16.5 1.0
N A:GLN242 4.3 17.3 1.0
CA A:ILE243 4.4 16.2 1.0
CB A:VAL246 4.4 16.7 1.0
N A:GLY247 4.4 16.7 1.0
O A:HOH852 4.4 33.6 1.0
CA A:GLN242 4.5 20.1 1.0
O A:GLN242 4.5 20.3 1.0
C A:PHE244 4.6 17.3 1.0
O A:PHE240 4.7 18.0 1.0
O3' P:DG2 4.7 17.3 1.0
CA A:GLY247 4.7 19.8 1.0
C A:GLY245 4.8 20.2 1.0
CB A:THR241 4.9 17.6 1.0
O5' P:DT3 5.0 15.7 1.0

Reference:

J.A.Jamsen, A.Sassa, D.D.Shock, W.A.Beard, S.H.Wilson. Dna Polymerase Mu, 8-Oxodgtp:at Pre-Catalytic Ground State Ternary Complex, 20 Mm CA2+ (120MIN) To Be Published.
Page generated: Tue Oct 8 17:28:01 2024

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