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Zinc in PDB 6p1z: Bacteriophage Phikz GP163.1 Paar Repeat Protein in Complex with the C- Terminal Part of the T4 GP5 Beta-Helical Domain

Enzymatic activity of Bacteriophage Phikz GP163.1 Paar Repeat Protein in Complex with the C- Terminal Part of the T4 GP5 Beta-Helical Domain

All present enzymatic activity of Bacteriophage Phikz GP163.1 Paar Repeat Protein in Complex with the C- Terminal Part of the T4 GP5 Beta-Helical Domain:
3.2.1.17;

Protein crystallography data

The structure of Bacteriophage Phikz GP163.1 Paar Repeat Protein in Complex with the C- Terminal Part of the T4 GP5 Beta-Helical Domain, PDB code: 6p1z was solved by S.A.Buth, M.M.Shneider, P.G.Leiman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.60 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 72.275, 69.123, 77.802, 90.00, 102.48, 90.00
R / Rfree (%) 18.8 / 25.1

Other elements in 6p1z:

The structure of Bacteriophage Phikz GP163.1 Paar Repeat Protein in Complex with the C- Terminal Part of the T4 GP5 Beta-Helical Domain also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Bacteriophage Phikz GP163.1 Paar Repeat Protein in Complex with the C- Terminal Part of the T4 GP5 Beta-Helical Domain (pdb code 6p1z). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Bacteriophage Phikz GP163.1 Paar Repeat Protein in Complex with the C- Terminal Part of the T4 GP5 Beta-Helical Domain, PDB code: 6p1z:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6p1z

Go back to Zinc Binding Sites List in 6p1z
Zinc binding site 1 out of 2 in the Bacteriophage Phikz GP163.1 Paar Repeat Protein in Complex with the C- Terminal Part of the T4 GP5 Beta-Helical Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Bacteriophage Phikz GP163.1 Paar Repeat Protein in Complex with the C- Terminal Part of the T4 GP5 Beta-Helical Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn101

b:14.8
occ:1.00
 ND1 D:HIS76 2.0 27.7 1.0
NE2 D:HIS41 2.0 10.5 1.0
ND1 D:HIS46 2.0 13.3 1.0
SG D:CYS74 2.2 21.5 1.0
CE1 D:HIS76 2.8 30.6 1.0
HB2 D:CYS74 2.8 21.4 1.0
CE1 D:HIS46 2.9 23.0 1.0
HE1 D:HIS76 2.9 36.7 1.0
CD2 D:HIS41 3.0 10.6 1.0
CE1 D:HIS41 3.0 10.8 1.0
HE1 D:HIS46 3.1 27.6 1.0
HB2 D:HIS76 3.1 20.7 1.0
CG D:HIS76 3.1 23.2 1.0
CG D:HIS46 3.1 31.2 1.0
HB3 D:HIS46 3.1 17.4 1.0
CB D:CYS74 3.1 17.9 1.0
HD2 D:HIS41 3.2 12.7 1.0
HE1 D:HIS41 3.2 12.9 1.0
HA D:HIS46 3.4 17.0 1.0
H D:HIS76 3.5 24.8 1.0
CB D:HIS46 3.5 14.5 1.0
HA3 D:GLY13 3.5 20.4 1.0
CB D:HIS76 3.6 17.3 1.0
HB3 D:CYS74 3.6 21.4 1.0
NE2 D:HIS76 4.0 24.5 1.0
CA D:HIS46 4.0 14.2 1.0
NE2 D:HIS46 4.1 28.4 1.0
ND1 D:HIS41 4.1 10.9 1.0
CD2 D:HIS76 4.1 34.0 1.0
CG D:HIS41 4.1 14.9 1.0
O D:ALA12 4.2 20.5 1.0
CD2 D:HIS46 4.2 26.3 1.0
N D:HIS76 4.2 20.6 1.0
HB3 D:HIS76 4.3 20.7 1.0
O D:CYS74 4.3 25.0 1.0
CA D:CYS74 4.4 19.9 1.0
C D:CYS74 4.4 31.9 1.0
HB2 D:HIS46 4.4 17.4 1.0
CA D:GLY13 4.5 17.0 1.0
CA D:HIS76 4.5 21.1 1.0
HE2 D:HIS76 4.7 29.5 1.0
HB2 D:ALA49 4.8 31.9 1.0
O D:HOH269 4.8 30.0 1.0
HA2 D:GLY13 4.8 20.4 1.0
HE2 D:HIS46 4.8 34.0 1.0
H D:CYS74 4.9 23.8 1.0
N D:HIS46 4.9 19.9 1.0
HD1 D:HIS41 4.9 13.1 1.0
N D:GLY75 5.0 20.0 1.0
HA D:HIS76 5.0 25.3 1.0
HD2 D:HIS76 5.0 40.9 1.0

Zinc binding site 2 out of 2 in 6p1z

Go back to Zinc Binding Sites List in 6p1z
Zinc binding site 2 out of 2 in the Bacteriophage Phikz GP163.1 Paar Repeat Protein in Complex with the C- Terminal Part of the T4 GP5 Beta-Helical Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Bacteriophage Phikz GP163.1 Paar Repeat Protein in Complex with the C- Terminal Part of the T4 GP5 Beta-Helical Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn101

b:24.2
occ:1.00
 NE2 H:HIS41 2.0 27.0 1.0
ND1 H:HIS46 2.0 42.5 1.0
ND1 H:HIS76 2.0 41.2 1.0
SG H:CYS74 2.3 26.4 1.0
HB2 H:CYS74 2.8 32.4 1.0
CE1 H:HIS76 2.8 21.7 1.0
CE1 H:HIS46 2.9 31.3 1.0
HE1 H:HIS76 2.9 26.0 1.0
CE1 H:HIS41 3.0 31.7 1.0
HE1 H:HIS46 3.0 37.6 1.0
CD2 H:HIS41 3.1 33.4 1.0
HB2 H:HIS76 3.1 30.9 1.0
CB H:CYS74 3.1 27.0 1.0
CG H:HIS76 3.1 37.3 1.0
CG H:HIS46 3.1 46.1 1.0
HE1 H:HIS41 3.1 38.0 1.0
HB3 H:HIS46 3.2 35.0 1.0
HD2 H:HIS41 3.3 40.0 1.0
HA H:HIS46 3.4 48.0 1.0
H H:HIS76 3.6 24.9 1.0
CB H:HIS46 3.6 29.2 1.0
HB3 H:CYS74 3.6 32.4 1.0
CB H:HIS76 3.6 25.7 1.0
HA3 H:GLY13 3.7 31.7 1.0
NE2 H:HIS76 4.0 53.1 1.0
CA H:HIS46 4.0 40.0 1.0
NE2 H:HIS46 4.1 36.4 1.0
ND1 H:HIS41 4.1 27.7 1.0
CD2 H:HIS76 4.1 29.9 1.0
CG H:HIS41 4.2 28.1 1.0
CD2 H:HIS46 4.2 35.8 1.0
O H:ALA12 4.2 41.5 1.0
N H:HIS76 4.3 20.8 1.0
O H:CYS74 4.3 20.8 1.0
HB3 H:HIS76 4.3 30.9 1.0
CA H:CYS74 4.3 26.3 1.0
C H:CYS74 4.4 28.5 1.0
HB2 H:HIS46 4.5 35.0 1.0
CA H:HIS76 4.6 30.1 1.0
CA H:GLY13 4.6 26.4 1.0
O H:HOH275 4.7 41.5 1.0
HE2 H:HIS76 4.7 63.8 1.0
HE2 H:HIS46 4.8 43.6 1.0
O H:HOH225 4.8 34.2 1.0
HB2 H:ALA49 4.8 32.2 1.0
H H:CYS74 4.9 27.8 1.0
HD1 H:HIS41 4.9 33.2 1.0
N H:HIS46 4.9 37.0 1.0
HA2 H:GLY13 5.0 31.7 1.0
HA H:CYS74 5.0 31.5 1.0

Reference:

S.A.Buth, M.M.Shneider, P.G.Leiman. Bacteriophage Phikz GP163.1 Paar Repeat Protein in Complex with the C-Terminal Part of the T4 GP5 Beta-Helical Domain To Be Published.
Page generated: Tue Oct 29 04:46:17 2024

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