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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

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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

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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

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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

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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

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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

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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

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