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Magnesium in PDB 4h4i: OYE1-W116V Complexed with the Dismutation Product of (S)-Carvone

Enzymatic activity of OYE1-W116V Complexed with the Dismutation Product of (S)-Carvone

All present enzymatic activity of OYE1-W116V Complexed with the Dismutation Product of (S)-Carvone:
1.6.99.1;

Protein crystallography data

The structure of OYE1-W116V Complexed with the Dismutation Product of (S)-Carvone, PDB code: 4h4i was solved by Y.A.Pompeu, J.D.Stewart, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 23.55 / 1.25
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 141.004, 141.004, 42.818, 90.00, 90.00, 90.00
R / Rfree (%) 12.3 / 14.6

Other elements in 4h4i:

The structure of OYE1-W116V Complexed with the Dismutation Product of (S)-Carvone also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Sodium (Na) 5 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the OYE1-W116V Complexed with the Dismutation Product of (S)-Carvone (pdb code 4h4i). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the OYE1-W116V Complexed with the Dismutation Product of (S)-Carvone, PDB code: 4h4i:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 4h4i

Go back to Magnesium Binding Sites List in 4h4i
Magnesium binding site 1 out of 3 in the OYE1-W116V Complexed with the Dismutation Product of (S)-Carvone


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of OYE1-W116V Complexed with the Dismutation Product of (S)-Carvone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:22.9
occ:1.00
O A:HOH1123 1.9 29.6 1.0
O A:HOH1052 2.0 28.2 1.0
O A:HOH1089 2.0 20.7 1.0
O A:HOH1124 2.1 24.3 1.0
O A:HOH1088 2.4 23.6 1.0
OD1 A:ASP370 4.2 16.5 1.0
OD2 A:ASP370 4.3 13.1 1.0
OD2 A:ASP372 4.5 17.6 1.0
CG A:ASP370 4.6 13.9 1.0
CB A:ASP372 4.8 13.4 1.0
C24 A:1PE415 4.9 34.4 1.0

Magnesium binding site 2 out of 3 in 4h4i

Go back to Magnesium Binding Sites List in 4h4i
Magnesium binding site 2 out of 3 in the OYE1-W116V Complexed with the Dismutation Product of (S)-Carvone


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of OYE1-W116V Complexed with the Dismutation Product of (S)-Carvone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg406

b:7.0
occ:0.37
O A:HOH1017 2.0 17.8 1.0
O A:HOH1051 2.1 21.1 0.5
O A:HOH1129 2.1 24.9 1.0
O A:HOH1043 2.1 22.4 0.7
O A:HOH790 4.0 22.3 1.0
O A:HOH628 4.0 15.4 1.0
O A:HOH731 4.1 20.9 1.0
O A:HOH663 4.3 16.1 1.0
O A:GLN158 4.5 10.6 1.0
OD2 A:ASP139 4.5 19.3 1.0
CB A:ASP139 4.8 15.4 1.0
CG A:ASP139 4.9 17.2 1.0
O A:HOH1077 5.0 43.0 1.0

Magnesium binding site 3 out of 3 in 4h4i

Go back to Magnesium Binding Sites List in 4h4i
Magnesium binding site 3 out of 3 in the OYE1-W116V Complexed with the Dismutation Product of (S)-Carvone


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of OYE1-W116V Complexed with the Dismutation Product of (S)-Carvone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg411

b:38.1
occ:0.64
O A:HOH1015 1.9 24.4 1.0
O A:HOH1036 2.0 34.2 1.0
O A:HOH1092 2.0 33.1 1.0
OE1 A:GLU336 2.0 15.3 0.3
OE1 A:GLU336 2.4 16.1 0.7
O A:HOH1060 2.7 38.1 1.0
OE2 A:GLU336 2.8 15.8 0.7
CD A:GLU336 2.8 14.1 0.7
CD A:GLU336 2.9 14.7 0.3
OE2 A:GLU336 3.0 15.6 0.3
OD2 A:ASP310 4.1 14.9 1.0
OD1 A:ASP310 4.1 12.7 1.0
CG A:GLU336 4.2 11.8 0.7
CG A:GLU336 4.3 12.6 0.3
C12 A:1PE405 4.5 39.9 0.7
CG A:ASP310 4.5 10.7 1.0
O A:HOH732 4.6 20.9 1.0
NH2 A:ARG322 4.7 10.7 0.6
NH1 A:ARG322 4.8 9.2 0.4
O A:HOH1058 4.9 43.1 1.0
CA A:GLU336 5.0 8.3 0.7
CB A:GLU336 5.0 9.3 0.7

Reference:

Y.A.Pompeu, B.Sullivan, J.D.Stewart. X-Ray Crystallography Reveals How Subtle Changes Control the Orientation of Substrate Binding in An Alkene Reductase Acs Catalysis V. 3 2376 2013.
ISSN: ESSN 2155-5435
DOI: 10.1021/CS400622E
Page generated: Mon Dec 14 17:12:00 2020

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