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Magnesium in PDB 3uxk: P. Putida Mandelate Racemase Co-Crystallized with the Intermediate Analogue Benzohydroxamate

Enzymatic activity of P. Putida Mandelate Racemase Co-Crystallized with the Intermediate Analogue Benzohydroxamate

All present enzymatic activity of P. Putida Mandelate Racemase Co-Crystallized with the Intermediate Analogue Benzohydroxamate:
5.1.2.2;

Protein crystallography data

The structure of P. Putida Mandelate Racemase Co-Crystallized with the Intermediate Analogue Benzohydroxamate, PDB code: 3uxk was solved by A.D.Lietzan, E.Pellmann, M.St Maurice, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.20
Space group I 4
Cell size a, b, c (Å), α, β, γ (°) 148.309, 148.309, 169.552, 90.00, 90.00, 90.00
R / Rfree (%) 16.2 / 19.3

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 4 in 3uxk

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Magnesium binding site 1 out of 4 in the P. Putida Mandelate Racemase Co-Crystallized with the Intermediate Analogue Benzohydroxamate


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 the Intermediate Analogue Benzohydroxamate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg360

b:11.4
occ:1.00
OE1 A:GLU221 2.0 13.2 1.0
O A:HOH722 2.1 9.5 1.0
O1 A:BHO361 2.1 35.6 1.0
OD1 A:ASP195 2.2 9.9 1.0
OE1 A:GLU247 2.2 12.2 1.0
O2 A:BHO361 2.4 31.5 1.0
C A:BHO361 2.7 36.5 1.0
N A:BHO361 2.7 35.1 1.0
CD A:GLU247 3.0 12.3 1.0
OE2 A:GLU247 3.2 13.6 1.0
CG A:ASP195 3.2 10.4 1.0
CD A:GLU221 3.2 11.9 1.0
OD2 A:ASP195 3.6 10.5 1.0
NZ A:LYS166 3.8 18.6 1.0
ND2 A:ASN197 4.0 12.9 1.0
NZ A:LYS164 4.0 9.9 1.0
OE2 A:GLU221 4.1 11.8 1.0
CG A:GLU221 4.1 11.2 1.0
NE2 A:HIS297 4.2 12.4 1.0
C1 A:BHO361 4.2 38.7 1.0
CD2 A:HIS297 4.2 11.6 1.0
O A:HOH373 4.3 7.9 1.0
OE2 A:GLU222 4.4 11.1 1.0
CG A:GLU247 4.4 11.7 1.0
CB A:ASP195 4.5 9.9 1.0
CE A:LYS164 4.6 10.0 1.0
CE A:MET268 4.6 9.1 1.0
CG A:ASN197 4.9 12.8 1.0

Magnesium binding site 2 out of 4 in 3uxk

Go back to Magnesium Binding Sites List in 3uxk
Magnesium binding site 2 out of 4 in the P. Putida Mandelate Racemase Co-Crystallized with the Intermediate Analogue Benzohydroxamate


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 the Intermediate Analogue Benzohydroxamate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg360

b:14.5
occ:1.00
OE1 B:GLU221 2.0 18.7 1.0
OE1 B:GLU247 2.1 15.7 1.0
O B:HOH723 2.2 13.8 1.0
OD1 B:ASP195 2.2 14.4 1.0
O2 B:BHO361 2.3 39.9 1.0
O1 B:BHO361 2.3 40.4 1.0
N B:BHO361 2.7 44.1 1.0
C B:BHO361 2.8 43.6 1.0
CD B:GLU247 3.0 16.2 1.0
CD B:GLU221 3.2 17.2 1.0
CG B:ASP195 3.2 14.9 1.0
OE2 B:GLU247 3.2 17.8 1.0
OD2 B:ASP195 3.5 14.6 1.0
NZ B:LYS166 3.9 25.4 1.0
NZ B:LYS164 4.0 18.8 1.0
CG B:GLU221 4.0 14.8 1.0
OE2 B:GLU221 4.1 17.2 1.0
ND2 B:ASN197 4.1 18.4 1.0
C1 B:BHO361 4.3 46.7 1.0
NE2 B:HIS297 4.3 15.0 1.0
O B:HOH362 4.3 13.1 1.0
OE2 B:GLU222 4.4 17.9 1.0
CD2 B:HIS297 4.4 14.3 1.0
CG B:GLU247 4.4 14.4 1.0
CE B:MET268 4.5 13.7 1.0
CB B:ASP195 4.5 15.4 1.0
CE B:LYS164 4.5 17.7 1.0
CG B:ASN197 4.8 18.6 1.0

Magnesium binding site 3 out of 4 in 3uxk

Go back to Magnesium Binding Sites List in 3uxk
Magnesium binding site 3 out of 4 in the P. Putida Mandelate Racemase Co-Crystallized with the Intermediate Analogue Benzohydroxamate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of P. Putida Mandelate Racemase Co-Crystallized with the Intermediate Analogue Benzohydroxamate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg360

b:13.7
occ:1.00
OE1 C:GLU221 2.0 17.8 1.0
OE1 C:GLU247 2.1 14.6 1.0
O C:HOH721 2.2 13.1 1.0
OD1 C:ASP195 2.2 14.4 1.0
O1 C:BHO361 2.2 39.9 1.0
O2 C:BHO361 2.4 40.3 1.0
N C:BHO361 2.7 44.5 1.0
C C:BHO361 2.7 43.5 1.0
CD C:GLU247 3.0 15.0 1.0
CG C:ASP195 3.2 14.9 1.0
OE2 C:GLU247 3.2 16.2 1.0
CD C:GLU221 3.2 16.7 1.0
OD2 C:ASP195 3.5 14.5 1.0
NZ C:LYS166 3.9 25.8 1.0
NZ C:LYS164 4.0 18.6 1.0
ND2 C:ASN197 4.0 17.3 1.0
CG C:GLU221 4.0 14.6 1.0
OE2 C:GLU221 4.1 16.3 1.0
C1 C:BHO361 4.2 45.6 1.0
OE2 C:GLU222 4.3 17.5 1.0
O C:HOH363 4.4 12.2 1.0
CG C:GLU247 4.4 13.6 1.0
NE2 C:HIS297 4.4 15.2 1.0
CB C:ASP195 4.4 15.4 1.0
CD2 C:HIS297 4.4 14.5 1.0
CE C:MET268 4.6 13.7 1.0
CE C:LYS164 4.6 17.2 1.0
CG C:ASN197 4.8 17.4 1.0
OD1 C:ASN197 4.9 17.7 1.0

Magnesium binding site 4 out of 4 in 3uxk

Go back to Magnesium Binding Sites List in 3uxk
Magnesium binding site 4 out of 4 in the P. Putida Mandelate Racemase Co-Crystallized with the Intermediate Analogue Benzohydroxamate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of P. Putida Mandelate Racemase Co-Crystallized with the Intermediate Analogue Benzohydroxamate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg360

b:11.3
occ:1.00
O1 D:BHO361 2.1 31.1 1.0
OE1 D:GLU221 2.1 13.2 1.0
O D:HOH724 2.2 9.0 1.0
OD1 D:ASP195 2.2 10.4 1.0
OE1 D:GLU247 2.2 11.9 1.0
O2 D:BHO361 2.4 30.2 1.0
C D:BHO361 2.6 33.4 1.0
N D:BHO361 2.7 33.8 1.0
CD D:GLU247 3.0 11.9 1.0
OE2 D:GLU247 3.1 13.1 1.0
CG D:ASP195 3.2 10.9 1.0
CD D:GLU221 3.2 11.7 1.0
OD2 D:ASP195 3.6 11.1 1.0
NZ D:LYS166 3.8 18.4 1.0
ND2 D:ASN197 3.9 12.2 1.0
NZ D:LYS164 4.0 10.0 1.0
CG D:GLU221 4.1 10.9 1.0
CE1 D:HIS297 4.1 12.2 1.0
OE2 D:GLU221 4.1 11.6 1.0
C1 D:BHO361 4.1 36.8 1.0
ND1 D:HIS297 4.3 12.1 1.0
O D:HOH384 4.4 7.6 1.0
OE2 D:GLU222 4.4 11.8 1.0
CG D:GLU247 4.4 11.3 1.0
CB D:ASP195 4.5 10.4 1.0
CE D:MET268 4.5 9.3 1.0
CE D:LYS164 4.6 10.0 1.0
CG D:ASN197 4.8 12.4 1.0
C6 D:BHO361 4.9 37.7 1.0
CE D:LYS166 5.0 18.6 1.0

Reference:

A.D.Lietzan, M.Nagar, E.A.Pellmann, J.R.Bourque, S.L.Bearne, M.St Maurice. Structure of Mandelate Racemase with Bound Intermediate Analogues Benzohydroxamate and Cupferron. Biochemistry V. 51 1160 2012.
ISSN: ISSN 0006-2960
PubMed: 22264153
DOI: 10.1021/BI2018514
Page generated: Mon Dec 14 08:57:27 2020

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