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Sodium in PDB 4jt4: Structure of Clostridium Thermocellum Polynucleotide Kinase Bound to Datp

Enzymatic activity of Structure of Clostridium Thermocellum Polynucleotide Kinase Bound to Datp

All present enzymatic activity of Structure of Clostridium Thermocellum Polynucleotide Kinase Bound to Datp:
2.7.1.78;

Protein crystallography data

The structure of Structure of Clostridium Thermocellum Polynucleotide Kinase Bound to Datp, PDB code: 4jt4 was solved by U.Das, L.K.Wang, P.Smith, S.Shuman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.54 / 2.01
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.306, 66.781, 119.546, 90.00, 90.00, 90.00
R / Rfree (%) 15.4 / 21.8

Other elements in 4jt4:

The structure of Structure of Clostridium Thermocellum Polynucleotide Kinase Bound to Datp also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Clostridium Thermocellum Polynucleotide Kinase Bound to Datp (pdb code 4jt4). 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 Structure of Clostridium Thermocellum Polynucleotide Kinase Bound to Datp, PDB code: 4jt4:

Sodium binding site 1 out of 1 in 4jt4

Go back to Sodium Binding Sites List in 4jt4
Sodium binding site 1 out of 1 in the Structure of Clostridium Thermocellum Polynucleotide Kinase Bound to Datp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Clostridium Thermocellum Polynucleotide Kinase Bound to Datp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na203

b:15.2
occ:1.00
 O B:HOH355 3.0 28.0 1.0
O B:HOH352 3.1 31.8 1.0
O B:HOH388 3.1 15.9 1.0
O B:HOH372 3.2 35.6 1.0
CA B:PHE24 3.7 12.2 1.0
CD B:LYS27 3.9 35.2 1.0
CB B:PHE24 4.0 16.0 1.0
CD2 B:PHE24 4.0 20.3 1.0
N B:PHE24 4.0 12.8 1.0
CG1 B:VAL161 4.1 14.1 1.0
CG2 B:THR23 4.3 19.9 1.0
CG B:PHE24 4.4 20.7 1.0
C B:THR23 4.5 21.0 1.0
O B:HOH368 4.5 38.2 1.0
O B:THR23 4.5 15.0 1.0
NZ B:LYS27 4.6 32.5 1.0
N6 B:DTP202 4.6 35.8 1.0
CB B:LYS27 4.6 21.3 1.0
CE B:LYS27 4.8 28.3 1.0
CG B:LYS27 4.8 22.1 1.0
NE2 B:HIS28 4.9 26.2 1.0
C B:PHE24 4.9 12.1 1.0

Reference:

U.Das, L.K.Wang, P.Smith, S.Shuman. Structural and Biochemical Analysis of the Phosphate Donor Specificity of the Polynucleotide Kinase Component of the Bacterial PNKPHEN1 Rna Repair System. Biochemistry V. 52 4734 2013.
ISSN: ISSN 0006-2960
PubMed: 23721485
DOI: 10.1021/BI400412X
Page generated: Mon Oct 7 16:22:00 2024

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