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Magnesium 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:

Zinc (Zn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium 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 Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6p1z

Go back to Magnesium Binding Sites List in 6p1z
Magnesium 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 Magnesium with other atoms in the Mg 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
A:Mg601

b:15.9
occ:1.00
 O C:HOH729 2.1 16.9 1.0
O B:HOH709 2.1 15.3 1.0
O A:HOH719 2.1 11.6 1.0
O B:HOH714 2.1 17.3 1.0
O A:HOH726 2.1 17.1 1.0
O C:HOH703 2.2 17.2 1.0
OE2 B:GLU552 4.0 17.2 1.0
OE2 A:GLU552 4.0 21.0 1.0
OE1 B:GLU552 4.0 18.2 1.0
OE1 C:GLU552 4.1 16.1 1.0
OE2 C:GLU552 4.1 19.3 1.0
OE1 A:GLU552 4.2 15.5 1.0
O A:HOH730 4.3 24.9 1.0
HE3 A:MET557 4.4 23.8 1.0
HZ2 B:TRP550 4.4 19.6 1.0
O C:HOH726 4.4 25.2 1.0
HZ2 C:TRP550 4.5 19.7 1.0
CD B:GLU552 4.5 25.4 1.0
HE3 C:MET557 4.5 23.9 1.0
HE3 B:MET557 4.5 29.7 1.0
CD C:GLU552 4.5 28.5 1.0
CD A:GLU552 4.5 25.4 1.0
HZ2 A:TRP550 4.6 17.9 1.0
HE1 A:MET557 4.6 23.8 1.0
HE1 B:MET557 4.6 29.7 1.0
HE1 C:MET557 4.6 23.9 1.0
CZ2 B:TRP550 4.8 16.4 1.0
CZ2 C:TRP550 4.8 16.4 1.0
CZ2 A:TRP550 4.9 14.9 1.0
CE A:MET557 4.9 19.9 1.0
HE1 C:TRP550 4.9 29.5 1.0

Magnesium binding site 2 out of 2 in 6p1z

Go back to Magnesium Binding Sites List in 6p1z
Magnesium 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 Magnesium with other atoms in the Mg 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
E:Mg601

b:18.2
occ:1.00
 O G:HOH713 2.1 20.9 1.0
O F:HOH613 2.1 16.8 1.0
O G:HOH715 2.1 16.8 1.0
O F:HOH616 2.1 18.9 1.0
O E:HOH714 2.2 21.9 1.0
O E:HOH713 2.2 13.6 1.0
OE2 E:GLU552 4.0 17.1 1.0
OE1 G:GLU552 4.1 25.1 1.0
OE2 G:GLU552 4.1 22.6 1.0
OE1 E:GLU552 4.1 21.1 1.0
OE2 F:GLU552 4.1 23.6 1.0
OE1 F:GLU552 4.2 23.7 1.0
HE3 E:MET557 4.2 28.1 1.0
HE1 E:MET557 4.3 28.1 1.0
O G:HOH732 4.4 37.1 1.0
HZ2 G:TRP550 4.4 31.9 1.0
O E:HOH734 4.5 23.2 1.0
CD E:GLU552 4.5 44.1 1.0
CD G:GLU552 4.5 28.3 1.0
HE3 G:MET557 4.5 37.6 1.0
HZ2 E:TRP550 4.6 17.3 1.0
CD F:GLU552 4.6 29.6 1.0
HZ2 F:TRP550 4.6 29.1 1.0
HE3 F:MET557 4.6 30.6 1.0
HE1 G:MET557 4.7 37.6 1.0
CE E:MET557 4.7 23.4 1.0
CZ2 G:TRP550 4.8 26.6 1.0
HE1 F:MET557 4.8 30.6 1.0
HE1 G:TRP550 4.9 25.0 1.0
CZ2 F:TRP550 4.9 24.3 1.0
CZ2 E:TRP550 5.0 14.4 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: Wed Aug 13 13:34:02 2025

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