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Sodium in PDB 4ku0: Enterobacteria Phage T4 GP5.4 Paar Repeat Protein in Complex with T4 GP5 Beta-Helix Fragment

Enzymatic activity of Enterobacteria Phage T4 GP5.4 Paar Repeat Protein in Complex with T4 GP5 Beta-Helix Fragment

All present enzymatic activity of Enterobacteria Phage T4 GP5.4 Paar Repeat Protein in Complex with T4 GP5 Beta-Helix Fragment:
3.2.1.17;

Protein crystallography data

The structure of Enterobacteria Phage T4 GP5.4 Paar Repeat Protein in Complex with T4 GP5 Beta-Helix Fragment, PDB code: 4ku0 was solved by S.A.Buth, P.G.Leiman, M.M.Shneider, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.00 / 1.15
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 46.302, 49.327, 84.057, 90.00, 96.19, 90.00
R / Rfree (%) 12.7 / 17.1

Other elements in 4ku0:

The structure of Enterobacteria Phage T4 GP5.4 Paar Repeat Protein in Complex with T4 GP5 Beta-Helix Fragment also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Iron (Fe) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Enterobacteria Phage T4 GP5.4 Paar Repeat Protein in Complex with T4 GP5 Beta-Helix Fragment (pdb code 4ku0). 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 Enterobacteria Phage T4 GP5.4 Paar Repeat Protein in Complex with T4 GP5 Beta-Helix Fragment, PDB code: 4ku0:

Sodium binding site 1 out of 1 in 4ku0

Go back to Sodium Binding Sites List in 4ku0
Sodium binding site 1 out of 1 in the Enterobacteria Phage T4 GP5.4 Paar Repeat Protein in Complex with T4 GP5 Beta-Helix Fragment


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Enterobacteria Phage T4 GP5.4 Paar Repeat Protein in Complex with T4 GP5 Beta-Helix Fragment within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na102

b:21.0
occ:1.00
OD2 D:ASP41 2.7 14.5 1.0
N D:THR25 2.8 16.5 1.0
O D:VAL36 2.9 13.1 1.0
N D:GLN26 3.2 16.6 1.0
OG1 D:THR25 3.3 17.7 1.0
CA D:ALA24 3.5 16.0 1.0
CG D:ASP41 3.5 14.0 1.0
CG D:GLN26 3.5 14.6 1.0
CB D:ALA24 3.5 17.4 1.0
OD1 D:ASP41 3.6 15.9 1.0
C D:ALA24 3.6 16.5 1.0
N D:VAL38 3.8 12.2 1.0
CA D:THR25 3.8 16.9 1.0
CG2 D:VAL38 3.8 15.2 1.0
CA D:LEU37 3.9 12.0 1.0
C D:VAL36 3.9 12.1 1.0
C D:THR25 3.9 17.4 1.0
O D:GLN26 4.1 17.4 1.0
OE1 D:GLN26 4.2 15.1 1.0
CA D:GLN26 4.2 16.7 1.0
CB D:THR25 4.2 18.6 1.0
C D:LEU37 4.2 12.4 1.0
CB D:GLN26 4.2 15.6 1.0
CD D:GLN26 4.3 13.1 1.0
CG1 D:VAL38 4.4 13.8 1.0
N D:LEU37 4.4 12.2 1.0
CB D:VAL38 4.5 13.0 1.0
CD2 D:LEU37 4.6 15.5 1.0
C D:GLN26 4.7 16.7 1.0
CA D:VAL38 4.7 12.5 1.0
N D:ALA24 4.8 16.3 1.0
O D:ALA24 4.8 18.8 1.0
CB D:ASP41 4.9 14.6 1.0
CG2 D:THR25 4.9 19.6 1.0

Reference:

S.A.Buth, P.G.Leiman, M.M.Shneider. Crystall Structute of the Business End of the T4 Cell-Puncturing Device To Be Published.
Page generated: Tue Dec 15 06:50:35 2020

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