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Magnesium in PDB 6p20: Bacteriophage Phikz GP163.1 Paar Repeat Protein in Complex with A T4 GP5 Beta-Helix Fragment Modified to Mimic the Phikz Central Spike GP164

Enzymatic activity of Bacteriophage Phikz GP163.1 Paar Repeat Protein in Complex with A T4 GP5 Beta-Helix Fragment Modified to Mimic the Phikz Central Spike GP164

All present enzymatic activity of Bacteriophage Phikz GP163.1 Paar Repeat Protein in Complex with A T4 GP5 Beta-Helix Fragment Modified to Mimic the Phikz Central Spike GP164:
3.2.1.17;

Protein crystallography data

The structure of Bacteriophage Phikz GP163.1 Paar Repeat Protein in Complex with A T4 GP5 Beta-Helix Fragment Modified to Mimic the Phikz Central Spike GP164, PDB code: 6p20 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) 36.38 / 1.75
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 34.427, 66.597, 173.763, 90.00, 90.00, 90.00
R / Rfree (%) 14.8 / 19.1

Other elements in 6p20:

The structure of Bacteriophage Phikz GP163.1 Paar Repeat Protein in Complex with A T4 GP5 Beta-Helix Fragment Modified to Mimic the Phikz Central Spike GP164 also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Bacteriophage Phikz GP163.1 Paar Repeat Protein in Complex with A T4 GP5 Beta-Helix Fragment Modified to Mimic the Phikz Central Spike GP164 (pdb code 6p20). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Bacteriophage Phikz GP163.1 Paar Repeat Protein in Complex with A T4 GP5 Beta-Helix Fragment Modified to Mimic the Phikz Central Spike GP164, PDB code: 6p20:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 6p20

Go back to Magnesium Binding Sites List in 6p20
Magnesium binding site 1 out of 3 in the Bacteriophage Phikz GP163.1 Paar Repeat Protein in Complex with A T4 GP5 Beta-Helix Fragment Modified to Mimic the Phikz Central Spike GP164


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 A T4 GP5 Beta-Helix Fragment Modified to Mimic the Phikz Central Spike GP164 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:20.9
occ:1.00
 O B:HOH722 2.1 17.1 1.0
O B:HOH760 2.1 18.9 1.0
O C:HOH650 2.1 20.8 1.0
O C:HOH627 2.1 21.4 1.0
O A:HOH715 2.2 20.3 1.0
O A:HOH722 2.2 20.2 1.0
HE3 A:MET557 3.6 32.5 1.0
O A:HOH867 3.9 38.4 1.0
HE3 B:MET557 3.9 34.8 1.0
OE1 A:GLU552 4.1 19.1 1.0
OE2 B:GLU552 4.1 21.8 1.0
OE1 C:GLU552 4.1 21.0 1.0
O A:HOH855 4.2 37.4 1.0
OE2 A:GLU552 4.2 22.8 1.0
OE2 C:GLU552 4.2 19.8 1.0
OE1 B:GLU552 4.2 23.4 1.0
HE1 C:MET557 4.3 25.3 1.0
O A:HOH859 4.3 34.7 1.0
HE3 C:MET557 4.4 25.3 1.0
HZ2 B:TRP550 4.5 20.6 1.0
HZ2 C:TRP550 4.5 19.3 1.0
CD A:GLU552 4.6 21.1 1.0
HZ2 A:TRP550 4.6 25.8 1.0
CE A:MET557 4.6 27.1 1.0
CD B:GLU552 4.6 22.3 1.0
CD C:GLU552 4.6 21.8 1.0
CE B:MET557 4.8 29.0 1.0
CE C:MET557 4.8 21.1 1.0
HE1 B:MET557 4.8 34.8 1.0
CZ2 B:TRP550 4.8 17.2 1.0
CZ2 C:TRP550 4.8 16.1 1.0
HE1 B:TRP550 4.8 25.5 1.0
HE1 C:TRP550 4.9 19.2 1.0
HE1 A:MET557 4.9 32.5 1.0
CZ2 A:TRP550 5.0 21.5 1.0
HE2 A:MET557 5.0 32.5 1.0

Magnesium binding site 2 out of 3 in 6p20

Go back to Magnesium Binding Sites List in 6p20
Magnesium binding site 2 out of 3 in the Bacteriophage Phikz GP163.1 Paar Repeat Protein in Complex with A T4 GP5 Beta-Helix Fragment Modified to Mimic the Phikz Central Spike GP164


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 A T4 GP5 Beta-Helix Fragment Modified to Mimic the Phikz Central Spike GP164 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:30.6
occ:1.00
 O A:HOH724 2.1 29.4 1.0
O A:HOH822 2.1 26.8 1.0
O A:HOH750 2.1 30.1 1.0
OD1 A:ASP517 4.0 22.4 1.0
OD2 A:ASP517 4.0 26.1 1.0
O C:HOH630 4.0 27.0 1.0
O A:HOH755 4.0 27.3 1.0
O B:HOH829 4.3 30.8 1.0
CG A:ASP517 4.4 31.6 1.0
O B:HOH843 4.4 34.6 1.0
HA3 B:GLY524 4.7 32.1 1.0
HA2 B:GLY524 4.9 32.1 1.0

Magnesium binding site 3 out of 3 in 6p20

Go back to Magnesium Binding Sites List in 6p20
Magnesium binding site 3 out of 3 in the Bacteriophage Phikz GP163.1 Paar Repeat Protein in Complex with A T4 GP5 Beta-Helix Fragment Modified to Mimic the Phikz Central Spike GP164


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Bacteriophage Phikz GP163.1 Paar Repeat Protein in Complex with A T4 GP5 Beta-Helix Fragment Modified to Mimic the Phikz Central Spike GP164 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg601

b:25.7
occ:1.00
 O C:HOH731 2.1 25.3 1.0
O C:HOH607 2.1 24.7 1.0
O C:HOH612 2.1 26.1 1.0
O C:HOH745 2.2 24.9 1.0
HE3 B:LYS537 3.4 48.1 1.0
O B:HOH816 4.0 37.9 1.0
O C:HOH617 4.2 20.1 1.0
OD2 C:ASP543 4.2 27.3 1.0
CE B:LYS537 4.3 40.1 1.0
O C:HOH728 4.3 37.9 1.0
HB2 C:ASP545 4.4 21.7 1.0
OD2 C:ASP545 4.4 28.1 1.0
HZ2 B:LYS537 4.4 53.0 1.0
HD2 B:LYS537 4.5 41.1 1.0
HG2 B:LYS537 4.5 31.8 1.0
HZ1 B:LYS537 4.7 53.0 1.0
NZ B:LYS537 4.7 44.1 1.0
CD B:LYS537 4.8 34.3 1.0
HB3 C:ASP545 4.9 21.7 1.0
HE2 B:LYS537 4.9 48.1 1.0

Reference:

S.A.Buth, M.M.Shneider, P.G.Leiman. Bacteriophage Phikz GP163.1 Paar Repeat Protein in Complex with A T4 GP5 Beta-Helix Fragment Modified to Mimic the Phikz Central Spike GP164 To Be Published.
Page generated: Tue Oct 1 13:50:37 2024

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