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Magnesium in PDB 4fp1: P. Putida Mandelate Racemase Co-Crystallized with 3,3,3-Trifluoro-2- Hydroxy-2-(Trifluoromethyl) Propionic Acid

Enzymatic activity of P. Putida Mandelate Racemase Co-Crystallized with 3,3,3-Trifluoro-2- Hydroxy-2-(Trifluoromethyl) Propionic Acid

All present enzymatic activity of P. Putida Mandelate Racemase Co-Crystallized with 3,3,3-Trifluoro-2- Hydroxy-2-(Trifluoromethyl) Propionic Acid:
5.1.2.2;

Protein crystallography data

The structure of P. Putida Mandelate Racemase Co-Crystallized with 3,3,3-Trifluoro-2- Hydroxy-2-(Trifluoromethyl) Propionic Acid, PDB code: 4fp1 was solved by A.D.Lietzan, M.St.Maurice, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.68
Space group I 4 2 2
Cell size a, b, c (Å), α, β, γ (°) 148.870, 148.870, 169.640, 90.00, 90.00, 90.00
R / Rfree (%) 16.9 / 19.3

Other elements in 4fp1:

The structure of P. Putida Mandelate Racemase Co-Crystallized with 3,3,3-Trifluoro-2- Hydroxy-2-(Trifluoromethyl) Propionic Acid also contains other interesting chemical elements:

Fluorine (F) 12 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the P. Putida Mandelate Racemase Co-Crystallized with 3,3,3-Trifluoro-2- Hydroxy-2-(Trifluoromethyl) Propionic Acid (pdb code 4fp1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the P. Putida Mandelate Racemase Co-Crystallized with 3,3,3-Trifluoro-2- Hydroxy-2-(Trifluoromethyl) Propionic Acid, PDB code: 4fp1:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 4fp1

Go back to Magnesium Binding Sites List in 4fp1
Magnesium binding site 1 out of 2 in the P. Putida Mandelate Racemase Co-Crystallized with 3,3,3-Trifluoro-2- Hydroxy-2-(Trifluoromethyl) Propionic Acid


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of P. Putida Mandelate Racemase Co-Crystallized with 3,3,3-Trifluoro-2- Hydroxy-2-(Trifluoromethyl) Propionic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:13.0
occ:1.00
 O A:HOH732 1.8 24.9 1.0
O A:HOH733 2.1 20.1 1.0
OE2 A:GLU247 2.1 9.1 0.5
OE2 A:GLU221 2.2 9.6 1.0
OD2 A:ASP195 2.2 11.1 1.0
O A:HOH730 2.3 15.0 1.0
OE1 A:GLU247 2.3 13.8 0.5
OE2 A:GLU247 2.8 13.9 0.5
CD A:GLU247 2.9 12.9 0.5
CD A:GLU247 3.0 10.1 0.5
CG A:ASP195 3.1 10.5 1.0
CD A:GLU221 3.2 9.6 1.0
O05 A:BFM402 3.3 25.5 0.5
OE1 A:GLU247 3.3 10.9 0.5
OD1 A:ASP195 3.4 9.9 1.0
O A:HOH750 3.6 21.0 1.0
O04 A:BFM402 3.8 26.4 0.5
C03 A:BFM402 3.8 26.0 0.5
NZ A:LYS166 3.9 14.9 1.0
NZ A:LYS164 4.0 8.5 1.0
CG A:GLU221 4.0 8.7 1.0
ND2 A:ASN197 4.1 15.2 1.0
OE1 A:GLU221 4.1 9.6 1.0
OE1 A:GLU222 4.3 13.1 1.0
CG A:GLU247 4.3 11.4 0.5
NE2 A:HIS297 4.4 11.0 1.0
CD2 A:HIS297 4.4 9.8 1.0
CG A:GLU247 4.4 9.5 0.5
CB A:ASP195 4.4 9.1 1.0
O A:HOH731 4.4 14.8 1.0
CE A:MET268 4.6 7.7 1.0
CE A:LYS164 4.7 8.2 1.0
CG A:ASN197 4.9 14.8 1.0
O A:HOH729 5.0 19.0 1.0

Magnesium binding site 2 out of 2 in 4fp1

Go back to Magnesium Binding Sites List in 4fp1
Magnesium binding site 2 out of 2 in the P. Putida Mandelate Racemase Co-Crystallized with 3,3,3-Trifluoro-2- Hydroxy-2-(Trifluoromethyl) Propionic Acid


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of P. Putida Mandelate Racemase Co-Crystallized with 3,3,3-Trifluoro-2- Hydroxy-2-(Trifluoromethyl) Propionic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg401

b:17.7
occ:1.00
 O B:HOH682 1.7 29.8 1.0
O B:HOH687 2.0 29.3 1.0
OE2 B:GLU221 2.2 14.4 1.0
OE1 B:GLU247 2.2 12.3 0.5
O B:HOH681 2.3 19.5 1.0
OD2 B:ASP195 2.3 16.1 1.0
OE1 B:GLU247 2.4 16.8 0.5
OE2 B:GLU247 2.8 18.1 0.5
CD B:GLU247 2.9 16.6 0.5
CD B:GLU247 3.1 13.5 0.5
CG B:ASP195 3.2 16.0 1.0
O04 B:BFM402 3.3 39.0 1.0
CD B:GLU221 3.3 14.2 1.0
OE2 B:GLU247 3.3 13.9 0.5
OD1 B:ASP195 3.5 14.8 1.0
O B:HOH689 3.7 31.5 1.0
C03 B:BFM402 3.8 38.2 1.0
O05 B:BFM402 3.8 43.0 1.0
NZ B:LYS166 4.0 21.1 1.0
NZ B:LYS164 4.0 14.2 1.0
CG B:GLU221 4.0 13.8 1.0
ND2 B:ASN197 4.1 20.7 1.0
OE1 B:GLU221 4.1 14.5 1.0
OE1 B:GLU222 4.3 17.8 1.0
CG B:GLU247 4.4 14.6 0.5
CB B:ASP195 4.5 14.7 1.0
O B:HOH526 4.5 21.4 1.0
CG B:GLU247 4.5 12.7 0.5
NE2 B:HIS297 4.5 15.6 1.0
CD2 B:HIS297 4.5 15.6 1.0
CE B:MET268 4.6 11.5 1.0
CE B:LYS164 4.7 14.6 1.0
CG B:ASN197 4.9 19.8 1.0
O B:HOH548 5.0 22.7 1.0

Reference:

M.Nagar, A.D.Lietzan, M.St Maurice, S.L.Bearne. Potent Inhibition of Mandelate Racemase By A Fluorinated Substrate-Product Analogue with A Novel Binding Mode. Biochemistry V. 53 1169 2014.
ISSN: ISSN 0006-2960
PubMed: 24472022
DOI: 10.1021/BI401703H
Page generated: Fri Aug 16 15:13:50 2024

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