Atomistry » Magnesium » PDB 4ohf-4osl » 4osd
Atomistry »
  Magnesium »
    PDB 4ohf-4osl »
      4osd »

Magnesium in PDB 4osd: Dimer of A C-Terminal Fragment of Phage T4 GP5 Beta-Helix

Enzymatic activity of Dimer of A C-Terminal Fragment of Phage T4 GP5 Beta-Helix

All present enzymatic activity of Dimer of A C-Terminal Fragment of Phage T4 GP5 Beta-Helix:
3.2.1.17;

Protein crystallography data

The structure of Dimer of A C-Terminal Fragment of Phage T4 GP5 Beta-Helix, PDB code: 4osd 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) 59.87 / 1.96
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 110.288, 73.786, 111.602, 90.00, 113.39, 90.00
R / Rfree (%) 21.9 / 27.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Dimer of A C-Terminal Fragment of Phage T4 GP5 Beta-Helix (pdb code 4osd). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Dimer of A C-Terminal Fragment of Phage T4 GP5 Beta-Helix, PDB code: 4osd:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 4osd

Go back to Magnesium Binding Sites List in 4osd
Magnesium binding site 1 out of 6 in the Dimer of A C-Terminal Fragment of Phage T4 GP5 Beta-Helix


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Dimer of A C-Terminal Fragment of Phage T4 GP5 Beta-Helix within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg601

b:41.7
occ:1.00
O B:HOH738 2.0 36.9 1.0
O C:HOH740 2.0 27.6 1.0
O C:HOH741 2.1 44.6 1.0
O A:HOH735 2.1 39.8 1.0
O A:HOH736 2.2 32.7 1.0
O B:HOH737 2.3 40.7 1.0
OE2 C:GLU552 3.8 34.6 1.0
OE2 B:GLU552 3.9 24.1 1.0
OE1 C:GLU552 4.0 33.6 1.0
O B:HOH729 4.0 40.1 1.0
O A:HOH723 4.1 52.8 1.0
OE1 B:GLU552 4.1 23.5 1.0
CD C:GLU552 4.3 32.1 1.0
OE2 A:GLU552 4.3 29.3 1.0
O C:HOH718 4.4 40.6 1.0
CD B:GLU552 4.4 22.5 1.0
OE1 A:GLU552 4.5 27.1 1.0
CE C:MET557 4.6 30.5 1.0
CD A:GLU552 4.8 28.1 1.0
CE B:MET557 4.8 34.2 1.0
CZ2 B:TRP550 4.9 28.8 1.0
CZ2 C:TRP550 4.9 30.4 1.0

Magnesium binding site 2 out of 6 in 4osd

Go back to Magnesium Binding Sites List in 4osd
Magnesium binding site 2 out of 6 in the Dimer of A C-Terminal Fragment of Phage T4 GP5 Beta-Helix


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Dimer of A C-Terminal Fragment of Phage T4 GP5 Beta-Helix within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg601

b:40.3
occ:1.00
O F:HOH742 1.9 37.7 1.0
O F:HOH741 2.0 34.2 1.0
O E:HOH636 2.1 36.5 1.0
O D:HOH738 2.1 43.1 1.0
O E:HOH635 2.2 25.0 1.0
O D:HOH737 2.3 30.1 1.0
OE1 F:GLU552 3.9 31.5 1.0
OE2 F:GLU552 3.9 29.7 1.0
OE2 E:GLU552 4.0 28.1 1.0
OE1 E:GLU552 4.1 24.6 1.0
O E:HOH614 4.3 40.8 1.0
CD F:GLU552 4.3 29.1 1.0
OE2 D:GLU552 4.3 31.0 1.0
O D:HOH727 4.3 44.1 1.0
OE1 D:GLU552 4.3 30.5 1.0
CD E:GLU552 4.5 25.4 1.0
O F:HOH732 4.5 39.8 1.0
CZ2 E:TRP550 4.7 27.9 1.0
CD D:GLU552 4.7 29.0 1.0
CZ2 F:TRP550 4.7 29.5 1.0
CE F:MET557 4.8 32.7 1.0
CE E:MET557 4.9 27.8 1.0
CE D:MET557 4.9 27.7 1.0
NE1 F:TRP550 4.9 29.8 1.0
CZ2 D:TRP550 5.0 30.0 1.0
CE2 F:TRP550 5.0 28.9 1.0

Magnesium binding site 3 out of 6 in 4osd

Go back to Magnesium Binding Sites List in 4osd
Magnesium binding site 3 out of 6 in the Dimer of A C-Terminal Fragment of Phage T4 GP5 Beta-Helix


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Dimer of A C-Terminal Fragment of Phage T4 GP5 Beta-Helix within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg601

b:46.6
occ:1.00
O I:HOH620 2.0 37.0 1.0
O G:HOH727 2.0 40.2 1.0
O H:HOH721 2.1 39.1 1.0
O G:HOH728 2.1 37.3 1.0
O H:HOH720 2.1 37.8 1.0
O I:HOH619 2.3 31.9 1.0
O G:HOH723 3.6 49.4 1.0
O I:HOH617 3.9 52.9 1.0
OE2 G:GLU552 3.9 33.7 1.0
OE2 I:GLU552 3.9 35.8 1.0
O H:HOH706 4.0 33.8 1.0
OE1 I:GLU552 4.1 32.6 1.0
OE2 H:GLU552 4.1 34.0 1.0
OE1 H:GLU552 4.3 30.8 1.0
OE1 G:GLU552 4.3 36.1 1.0
CE G:MET557 4.3 35.1 1.0
CD I:GLU552 4.4 30.8 1.0
CD G:GLU552 4.5 33.7 1.0
CD H:GLU552 4.6 32.0 1.0
CZ2 I:TRP550 4.9 32.2 1.0
CZ2 H:TRP550 4.9 32.5 1.0
CE I:MET557 5.0 34.6 1.0
CE H:MET557 5.0 30.5 1.0

Magnesium binding site 4 out of 6 in 4osd

Go back to Magnesium Binding Sites List in 4osd
Magnesium binding site 4 out of 6 in the Dimer of A C-Terminal Fragment of Phage T4 GP5 Beta-Helix


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Dimer of A C-Terminal Fragment of Phage T4 GP5 Beta-Helix within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg601

b:35.8
occ:1.00
O K:HOH730 1.9 27.5 1.0
O K:HOH731 1.9 30.8 1.0
O L:HOH737 2.0 33.5 1.0
O L:HOH736 2.0 34.5 1.0
O J:HOH746 2.1 25.0 1.0
O J:HOH745 2.1 29.1 1.0
OE1 K:GLU552 3.8 28.1 1.0
OE2 K:GLU552 3.9 27.4 1.0
OE2 L:GLU552 4.1 28.4 1.0
OE1 L:GLU552 4.1 25.6 1.0
OE2 J:GLU552 4.1 32.6 1.0
OE1 J:GLU552 4.3 32.8 1.0
CD K:GLU552 4.3 28.0 1.0
CD L:GLU552 4.5 25.4 1.0
CE L:MET557 4.6 37.1 1.0
CD J:GLU552 4.7 31.0 1.0
CZ2 K:TRP550 4.7 29.7 1.0
CZ2 J:TRP550 4.8 30.1 1.0
CZ2 L:TRP550 5.0 28.7 1.0

Magnesium binding site 5 out of 6 in 4osd

Go back to Magnesium Binding Sites List in 4osd
Magnesium binding site 5 out of 6 in the Dimer of A C-Terminal Fragment of Phage T4 GP5 Beta-Helix


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Dimer of A C-Terminal Fragment of Phage T4 GP5 Beta-Helix within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Mg601

b:40.1
occ:1.00
O M:HOH721 2.0 29.6 1.0
O M:HOH720 2.0 44.0 1.0
O O:HOH734 2.0 34.7 1.0
O N:HOH722 2.1 40.7 1.0
O N:HOH721 2.2 42.9 1.0
O O:HOH733 2.2 40.7 1.0
OE2 M:GLU552 3.8 36.5 1.0
OE1 M:GLU552 4.0 35.4 1.0
OE2 O:GLU552 4.0 34.6 1.0
O O:HOH727 4.0 54.5 1.0
OE2 N:GLU552 4.1 31.1 1.0
OE1 O:GLU552 4.1 31.1 1.0
O N:HOH709 4.2 36.9 1.0
OE1 N:GLU552 4.3 30.3 1.0
CD M:GLU552 4.3 35.4 1.0
CE M:MET557 4.4 34.2 1.0
CD O:GLU552 4.5 30.4 1.0
CD N:GLU552 4.6 31.9 1.0
CZ2 N:TRP550 4.8 32.2 1.0
CE O:MET557 4.9 31.6 1.0
CZ2 O:TRP550 4.9 37.0 1.0

Magnesium binding site 6 out of 6 in 4osd

Go back to Magnesium Binding Sites List in 4osd
Magnesium binding site 6 out of 6 in the Dimer of A C-Terminal Fragment of Phage T4 GP5 Beta-Helix


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Dimer of A C-Terminal Fragment of Phage T4 GP5 Beta-Helix within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Mg601

b:43.9
occ:1.00
O P:HOH742 1.9 38.9 1.0
O Q:HOH743 2.0 35.1 1.0
O P:HOH743 2.0 27.7 1.0
O Q:HOH744 2.0 41.5 1.0
O R:HOH657 2.0 39.0 1.0
O R:HOH656 2.5 37.6 1.0
OE1 P:GLU552 3.9 30.9 1.0
OE2 Q:GLU552 4.0 29.1 1.0
OE2 P:GLU552 4.0 32.7 1.0
OE1 Q:GLU552 4.1 28.6 1.0
O R:HOH645 4.1 44.3 1.0
O Q:HOH721 4.1 39.9 1.0
OE2 R:GLU552 4.2 29.0 1.0
OE1 R:GLU552 4.3 28.7 1.0
CD P:GLU552 4.4 29.6 1.0
CD Q:GLU552 4.4 27.9 1.0
CE Q:MET557 4.6 30.8 1.0
CD R:GLU552 4.7 27.3 1.0
CZ2 P:TRP550 4.8 33.5 1.0
CE R:MET557 4.9 35.3 1.0
CZ2 Q:TRP550 5.0 29.3 1.0
CZ2 R:TRP550 5.0 32.0 1.0

Reference:

S.A.Buth, S.P.Boudko, L.Menin, J.Engel, M.G.Rossmann, P.G.Leiman. Structure and Biophysical Properties of Phage T4 GP5 Beta-Helix To Be Published.
Page generated: Tue Aug 20 00:57:58 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy