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Magnesium in PDB 3nvs: 1.02 Angstrom Resolution Crystal Structure of 3-Phosphoshikimate 1- Carboxyvinyltransferase From Vibrio Cholerae in Complex with Shikimate-3-Phosphate (Partially Photolyzed) and Glyphosate

Enzymatic activity of 1.02 Angstrom Resolution Crystal Structure of 3-Phosphoshikimate 1- Carboxyvinyltransferase From Vibrio Cholerae in Complex with Shikimate-3-Phosphate (Partially Photolyzed) and Glyphosate

All present enzymatic activity of 1.02 Angstrom Resolution Crystal Structure of 3-Phosphoshikimate 1- Carboxyvinyltransferase From Vibrio Cholerae in Complex with Shikimate-3-Phosphate (Partially Photolyzed) and Glyphosate:
2.5.1.19;

Protein crystallography data

The structure of 1.02 Angstrom Resolution Crystal Structure of 3-Phosphoshikimate 1- Carboxyvinyltransferase From Vibrio Cholerae in Complex with Shikimate-3-Phosphate (Partially Photolyzed) and Glyphosate, PDB code: 3nvs was solved by G.Minasov, S.H.Light, A.Halavaty, G.Shuvalova, L.Papazisi, W.F.Anderson, Center For Structural Genomics Of Infectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 14.89 / 1.02
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 43.866, 87.484, 49.994, 90.00, 105.26, 90.00
R / Rfree (%) 11.4 / 13.8

Other elements in 3nvs:

The structure of 1.02 Angstrom Resolution Crystal Structure of 3-Phosphoshikimate 1- Carboxyvinyltransferase From Vibrio Cholerae in Complex with Shikimate-3-Phosphate (Partially Photolyzed) and Glyphosate also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the 1.02 Angstrom Resolution Crystal Structure of 3-Phosphoshikimate 1- Carboxyvinyltransferase From Vibrio Cholerae in Complex with Shikimate-3-Phosphate (Partially Photolyzed) and Glyphosate (pdb code 3nvs). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the 1.02 Angstrom Resolution Crystal Structure of 3-Phosphoshikimate 1- Carboxyvinyltransferase From Vibrio Cholerae in Complex with Shikimate-3-Phosphate (Partially Photolyzed) and Glyphosate, PDB code: 3nvs:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 3nvs

Go back to Magnesium Binding Sites List in 3nvs
Magnesium binding site 1 out of 3 in the 1.02 Angstrom Resolution Crystal Structure of 3-Phosphoshikimate 1- Carboxyvinyltransferase From Vibrio Cholerae in Complex with Shikimate-3-Phosphate (Partially Photolyzed) and Glyphosate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of 1.02 Angstrom Resolution Crystal Structure of 3-Phosphoshikimate 1- Carboxyvinyltransferase From Vibrio Cholerae in Complex with Shikimate-3-Phosphate (Partially Photolyzed) and Glyphosate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg430

b:10.5
occ:0.50
 OE1 A:GLU123 2.0 11.5 0.5
O A:HOH927 2.0 10.9 0.5
O A:HOH871 2.0 15.0 1.0
O A:HOH901 2.1 20.5 1.0
OE1 A:GLN145 2.1 16.2 0.7
O A:HOH1041 2.1 11.5 0.5
NE2 A:GLN145 2.1 14.5 0.3
O A:HOH753 2.5 13.5 0.5
CD A:GLU123 3.0 11.2 0.5
CD A:GLN145 3.2 12.7 0.7
CD A:GLN145 3.2 13.2 0.3
OE2 A:GLU123 3.3 13.3 0.5
OE1 A:GLN145 3.6 14.8 0.3
NE2 A:GLN145 3.9 16.2 0.7
O A:LYS122 4.0 11.0 1.0
O A:HOH987 4.2 15.8 1.0
O A:HOH933 4.3 10.4 0.5
CG A:GLU123 4.3 9.3 0.5
CB A:GLN145 4.4 10.4 0.7
CG A:GLN145 4.4 11.3 0.7
CA A:GLU123 4.4 7.6 0.5
CG A:GLN145 4.5 12.6 0.3
CA A:GLU123 4.5 8.5 0.5
CD2 A:PHE148 4.5 10.4 1.0
CB A:GLN145 4.6 11.4 0.3
O A:HOH822 4.6 12.2 1.0
CG A:PHE148 4.6 7.5 1.0
CB A:GLU123 4.6 6.8 0.5
CE2 A:PHE148 4.7 14.5 1.0
O A:HOH943 4.7 22.6 1.0
CG A:GLU123 4.8 10.7 0.5
CD1 A:PHE148 4.8 8.1 1.0
CZ A:PHE148 4.9 13.8 1.0
C A:LYS122 4.9 8.4 1.0
O A:HOH815 4.9 12.3 1.0
CE1 A:PHE148 5.0 11.2 1.0

Magnesium binding site 2 out of 3 in 3nvs

Go back to Magnesium Binding Sites List in 3nvs
Magnesium binding site 2 out of 3 in the 1.02 Angstrom Resolution Crystal Structure of 3-Phosphoshikimate 1- Carboxyvinyltransferase From Vibrio Cholerae in Complex with Shikimate-3-Phosphate (Partially Photolyzed) and Glyphosate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of 1.02 Angstrom Resolution Crystal Structure of 3-Phosphoshikimate 1- Carboxyvinyltransferase From Vibrio Cholerae in Complex with Shikimate-3-Phosphate (Partially Photolyzed) and Glyphosate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg431

b:17.5
occ:0.50
 O A:HOH732 2.0 30.0 1.0
O A:HOH734 2.0 22.2 0.5
O A:HOH733 2.0 34.9 1.0
O A:HOH608 2.1 18.1 0.4
O A:HOH1102 2.1 27.3 1.0
O A:HOH608 2.1 21.6 0.6
O A:HOH735 2.2 28.8 1.0
OE2 A:GLU223 4.3 21.9 1.0
O A:HOH439 4.3 23.9 1.0
O A:HOH667 4.3 29.3 1.0
OE1 A:GLU223 4.4 27.7 1.0
CD A:GLU223 4.8 19.5 1.0

Magnesium binding site 3 out of 3 in 3nvs

Go back to Magnesium Binding Sites List in 3nvs
Magnesium binding site 3 out of 3 in the 1.02 Angstrom Resolution Crystal Structure of 3-Phosphoshikimate 1- Carboxyvinyltransferase From Vibrio Cholerae in Complex with Shikimate-3-Phosphate (Partially Photolyzed) and Glyphosate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of 1.02 Angstrom Resolution Crystal Structure of 3-Phosphoshikimate 1- Carboxyvinyltransferase From Vibrio Cholerae in Complex with Shikimate-3-Phosphate (Partially Photolyzed) and Glyphosate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg432

b:16.1
occ:0.50
 O A:HOH742 1.9 22.0 0.6
O A:HOH741 2.0 25.4 0.6
O A:HOH744 2.1 18.0 0.5
O A:HOH533 2.1 21.0 0.6
O A:HOH740 2.2 37.2 1.0
O A:HOH743 2.2 20.4 1.0
O A:HOH524 2.8 16.4 0.4
O A:HOH742 3.2 14.8 0.4
O A:HOH744 3.8 21.4 0.5
O A:HOH524 4.0 28.5 0.6
O A:HOH1002 4.2 17.3 1.0
O A:HOH1146 4.8 30.4 1.0

Reference:

G.Minasov, S.H.Light, A.Halavaty, G.Shuvalova, L.Papazisi, W.F.Anderson, Center For Structural Genomics Of Infectious Diseases(Csgid). 1.02 Angstrom Resolution Crystal Structure of 3-Phosphoshikimate 1-Carboxyvinyltransferase From Vibrio Cholerae in Complex with Shikimate-3-Phosphate (Partially Photolyzed) and Glyphosate To Be Published.
Page generated: Thu Aug 15 08:07:33 2024

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