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Magnesium in PDB 6vim: P. Putida Mandelate Racemase Co-Crystallized with Phenylboronic Acid

Enzymatic activity of P. Putida Mandelate Racemase Co-Crystallized with Phenylboronic Acid

All present enzymatic activity of P. Putida Mandelate Racemase Co-Crystallized with Phenylboronic Acid:
5.1.2.2;

Protein crystallography data

The structure of P. Putida Mandelate Racemase Co-Crystallized with Phenylboronic Acid, PDB code: 6vim was solved by L.Grandinetti, A.N.Sharma, S.L.Bearne, M.St Maurice, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 116.37 / 2.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 228.988, 150.356, 150.275, 90.00, 129.25, 90.00
R / Rfree (%) 15.8 / 19.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the P. Putida Mandelate Racemase Co-Crystallized with Phenylboronic Acid (pdb code 6vim). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the P. Putida Mandelate Racemase Co-Crystallized with Phenylboronic Acid, PDB code: 6vim:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 6vim

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Magnesium binding site 1 out of 8 in the P. Putida Mandelate Racemase Co-Crystallized with Phenylboronic 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 Phenylboronic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:13.0
occ:1.00
 OE1 A:GLU221 1.9 16.2 1.0
O1 A:PBC402 2.0 32.4 1.0
O A:HOH508 2.0 12.5 1.0
OE2 A:GLU247 2.1 16.5 1.0
OD2 A:ASP195 2.1 12.1 1.0
CG A:ASP195 3.0 21.4 1.0
CD A:GLU221 3.0 16.2 1.0
CD A:GLU247 3.0 17.9 1.0
B A:PBC402 3.0 65.7 1.0
OD1 A:ASP195 3.2 15.6 1.0
OE1 A:GLU247 3.3 18.4 1.0
O2 A:PBC402 3.3 23.6 1.0
CG A:GLU221 3.6 14.5 1.0
OE2 A:GLU221 4.0 14.8 1.0
NZ A:LYS164 4.0 12.1 1.0
ND2 A:ASN197 4.0 19.3 1.0
NZ A:LYS166 4.0 18.9 1.0
OE2 A:GLU222 4.1 19.1 1.0
O A:HOH654 4.1 14.2 1.0
NE2 A:HIS297 4.2 23.4 1.0
CB A:ASP195 4.3 11.9 1.0
CD2 A:HIS297 4.4 24.1 1.0
CG A:GLU247 4.4 18.6 1.0
CA A:PBC402 4.5 15.8 1.0
CE A:MET268 4.5 14.0 1.0
CE A:LYS164 4.6 8.1 1.0
CG A:ASN197 4.7 20.3 1.0
CB A:GLU221 4.8 14.0 1.0
CD A:GLU222 4.8 21.9 1.0
CG A:GLU222 4.9 16.7 1.0
OD1 A:ASN197 4.9 17.1 1.0
CB2 A:PBC402 4.9 42.0 1.0

Magnesium binding site 2 out of 8 in 6vim

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Magnesium binding site 2 out of 8 in the P. Putida Mandelate Racemase Co-Crystallized with Phenylboronic 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 Phenylboronic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg401

b:15.8
occ:1.00
 O2 B:PBC402 1.9 26.1 0.5
O2 B:PBC402 2.0 26.9 0.5
OE1 B:GLU221 2.0 18.4 1.0
OE1 B:GLU247 2.0 25.2 1.0
O B:HOH515 2.1 17.9 1.0
OD2 B:ASP195 2.1 19.2 1.0
B B:PBC402 2.9 29.0 0.5
CD B:GLU247 3.0 18.5 1.0
CD B:GLU221 3.0 21.6 1.0
B B:PBC402 3.0 25.8 0.5
CG B:ASP195 3.1 23.0 1.0
O1 B:PBC402 3.1 18.0 0.5
OE2 B:GLU247 3.3 19.6 1.0
O1 B:PBC402 3.3 23.0 0.5
OD1 B:ASP195 3.4 17.0 1.0
CG B:GLU221 3.6 9.9 1.0
NE2 B:HIS297 3.7 17.3 0.5
ND2 B:ASN197 3.9 23.7 1.0
OE2 B:GLU221 4.0 21.9 1.0
NZ B:LYS164 4.0 19.2 1.0
CD2 B:HIS297 4.0 9.8 0.5
O B:HOH654 4.1 14.2 1.0
NZ B:LYS166 4.2 22.2 1.0
OE2 B:GLU222 4.2 20.7 1.0
CD2 B:HIS297 4.3 12.2 0.5
CA B:PBC402 4.3 20.6 0.5
NE2 B:HIS297 4.3 15.8 0.5
CG B:GLU247 4.4 15.9 1.0
CB B:ASP195 4.4 12.5 1.0
CA B:PBC402 4.4 24.6 0.5
CE B:MET268 4.4 15.8 1.0
CB1 B:PBC402 4.6 26.1 0.5
CE B:LYS164 4.7 14.6 1.0
CE1 B:HIS297 4.7 22.4 0.5
CG B:ASN197 4.8 26.0 1.0
CB1 B:PBC402 4.9 30.5 0.5
CB B:GLU221 4.9 15.7 1.0
CD B:GLU222 5.0 25.9 1.0
CB B:GLU247 5.0 20.0 1.0

Magnesium binding site 3 out of 8 in 6vim

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Magnesium binding site 3 out of 8 in the P. Putida Mandelate Racemase Co-Crystallized with Phenylboronic Acid


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 Phenylboronic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg401

b:12.4
occ:1.00
 O2 C:PBC402 1.9 29.8 1.0
O C:HOH517 2.0 11.4 1.0
OE1 C:GLU221 2.0 18.4 1.0
OE1 C:GLU247 2.0 13.2 1.0
OD2 C:ASP195 2.2 11.9 1.0
CD C:GLU247 2.9 13.6 1.0
B C:PBC402 3.0 56.1 1.0
CD C:GLU221 3.0 12.6 1.0
CG C:ASP195 3.1 16.6 1.0
OE2 C:GLU247 3.2 18.5 1.0
O1 C:PBC402 3.2 20.9 1.0
OD1 C:ASP195 3.4 13.4 1.0
CG C:GLU221 3.6 14.1 1.0
O C:HOH600 4.0 14.4 1.0
ND2 C:ASN197 4.0 18.2 1.0
NZ C:LYS164 4.1 11.8 1.0
OE2 C:GLU221 4.1 15.9 1.0
NZ C:LYS166 4.1 24.1 1.0
NE2 C:HIS297 4.2 14.3 1.0
OE2 C:GLU222 4.2 15.6 1.0
CG C:GLU247 4.3 9.8 1.0
CD2 C:HIS297 4.3 9.4 1.0
CB C:ASP195 4.4 8.7 1.0
CA C:PBC402 4.4 26.1 1.0
CE C:MET268 4.5 7.6 1.0
CE C:LYS164 4.7 10.3 1.0
CG C:ASN197 4.8 20.7 1.0
CB C:GLU221 4.8 10.2 1.0
CB1 C:PBC402 4.8 44.7 1.0
CB C:GLU247 4.9 9.3 1.0
OD1 C:ASN197 4.9 19.4 1.0
CD C:GLU222 4.9 13.4 1.0
CG C:GLU222 5.0 14.8 1.0

Magnesium binding site 4 out of 8 in 6vim

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Magnesium binding site 4 out of 8 in the P. Putida Mandelate Racemase Co-Crystallized with Phenylboronic Acid


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 Phenylboronic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg401

b:17.1
occ:1.00
 O1 D:PBC402 1.8 29.7 0.5
OE1 D:GLU221 1.9 23.4 1.0
O1 D:PBC402 1.9 23.7 0.5
OE1 D:GLU247 2.1 16.5 1.0
OD2 D:ASP195 2.1 19.2 1.0
O D:HOH512 2.2 22.6 1.0
B D:PBC402 2.9 19.7 0.5
B D:PBC402 2.9 31.0 0.5
CD D:GLU221 3.0 30.2 1.0
CD D:GLU247 3.0 14.4 1.0
O2 D:PBC402 3.1 10.1 0.5
CG D:ASP195 3.1 24.2 1.0
O2 D:PBC402 3.2 32.4 0.5
OE2 D:GLU247 3.3 21.3 1.0
OD1 D:ASP195 3.5 19.4 1.0
CG D:GLU221 3.7 16.0 1.0
NE2 D:HIS297 3.7 21.2 0.5
ND2 D:ASN197 3.9 24.2 1.0
NZ D:LYS164 3.9 21.2 1.0
OE2 D:GLU221 3.9 21.1 1.0
NZ D:LYS166 4.0 23.6 1.0
CD2 D:HIS297 4.0 5.8 0.5
O D:HOH633 4.1 19.6 1.0
CA D:PBC402 4.2 24.5 0.5
CD2 D:HIS297 4.3 11.9 0.5
OE2 D:GLU222 4.3 20.4 1.0
CA D:PBC402 4.4 26.0 0.5
CB D:ASP195 4.4 20.0 1.0
NE2 D:HIS297 4.4 20.7 0.5
CG D:GLU247 4.4 19.4 1.0
CE D:MET268 4.4 9.2 1.0
CB2 D:PBC402 4.6 32.8 0.5
CE D:LYS164 4.6 14.9 1.0
CE1 D:HIS297 4.7 16.4 0.5
CB2 D:PBC402 4.9 24.6 0.5
CG D:ASN197 4.9 19.4 1.0
CB D:GLU221 4.9 9.7 1.0
CB D:GLU247 5.0 15.7 1.0

Magnesium binding site 5 out of 8 in 6vim

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Magnesium binding site 5 out of 8 in the P. Putida Mandelate Racemase Co-Crystallized with Phenylboronic Acid


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of P. Putida Mandelate Racemase Co-Crystallized with Phenylboronic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg401

b:12.7
occ:1.00
 O1 E:PBC402 1.9 28.2 1.0
OE1 E:GLU221 2.0 15.0 1.0
O E:HOH509 2.0 10.6 1.0
OE1 E:GLU247 2.1 15.1 1.0
OD2 E:ASP195 2.1 14.3 1.0
B E:PBC402 2.9 54.7 1.0
CD E:GLU247 3.0 17.3 1.0
CG E:ASP195 3.0 18.6 1.0
CD E:GLU221 3.1 15.8 1.0
O2 E:PBC402 3.2 28.3 1.0
OE2 E:GLU247 3.2 21.2 1.0
OD1 E:ASP195 3.4 17.5 1.0
CG E:GLU221 3.7 14.3 1.0
NZ E:LYS166 4.0 19.8 1.0
ND2 E:ASN197 4.0 14.5 1.0
NZ E:LYS164 4.1 8.5 1.0
OE2 E:GLU221 4.1 13.4 1.0
O E:HOH604 4.1 14.3 1.0
OE2 E:GLU222 4.2 16.4 1.0
NE2 E:HIS297 4.2 16.7 1.0
CB E:ASP195 4.3 12.6 1.0
CD2 E:HIS297 4.3 13.6 1.0
CA E:PBC402 4.4 19.3 1.0
CG E:GLU247 4.4 18.7 1.0
CE E:MET268 4.6 12.0 1.0
CE E:LYS164 4.6 13.3 1.0
CG E:ASN197 4.8 13.5 1.0
CB2 E:PBC402 4.8 31.1 1.0
CB E:GLU221 4.9 12.4 1.0
CE E:LYS166 4.9 26.5 1.0
O E:HOH521 4.9 14.5 1.0
CD E:GLU222 4.9 18.9 1.0

Magnesium binding site 6 out of 8 in 6vim

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Magnesium binding site 6 out of 8 in the P. Putida Mandelate Racemase Co-Crystallized with Phenylboronic Acid


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of P. Putida Mandelate Racemase Co-Crystallized with Phenylboronic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg401

b:14.2
occ:1.00
 O1 F:PBC402 1.8 27.1 0.5
O1 F:PBC402 1.9 29.8 0.5
OE1 F:GLU221 2.0 16.1 1.0
OE1 F:GLU247 2.1 16.1 1.0
O F:HOH522 2.1 15.4 1.0
OD2 F:ASP195 2.1 11.8 1.0
B F:PBC402 2.9 24.0 0.5
CD F:GLU247 3.0 18.7 1.0
CD F:GLU221 3.0 23.7 1.0
B F:PBC402 3.0 11.2 0.5
CG F:ASP195 3.1 21.8 1.0
O2 F:PBC402 3.2 11.8 0.5
OE2 F:GLU247 3.2 19.6 1.0
O2 F:PBC402 3.4 44.8 0.5
OD1 F:ASP195 3.4 18.5 1.0
CG F:GLU221 3.7 10.7 1.0
NE2 F:HIS297 3.8 10.3 0.5
ND2 F:ASN197 4.0 20.9 1.0
OE2 F:GLU221 4.0 20.5 1.0
NZ F:LYS164 4.0 12.5 1.0
CD2 F:HIS297 4.1 9.1 0.5
NZ F:LYS166 4.1 21.2 1.0
O F:HOH668 4.2 10.7 1.0
OE2 F:GLU222 4.2 20.5 1.0
CA F:PBC402 4.3 15.9 0.5
CA F:PBC402 4.3 23.4 0.5
CG F:GLU247 4.4 15.5 1.0
CB F:ASP195 4.4 14.7 1.0
CD2 F:HIS297 4.4 15.6 0.5
NE2 F:HIS297 4.5 16.2 0.5
CE F:MET268 4.5 15.2 1.0
CB2 F:PBC402 4.6 22.5 0.5
CB2 F:PBC402 4.7 27.2 0.5
CE F:LYS164 4.7 10.9 1.0
CE1 F:HIS297 4.7 15.1 0.5
CG F:ASN197 4.8 28.3 1.0
CB F:GLU221 4.9 15.8 1.0
CD F:GLU222 5.0 27.9 1.0
CB F:GLU247 5.0 15.6 1.0

Magnesium binding site 7 out of 8 in 6vim

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Magnesium binding site 7 out of 8 in the P. Putida Mandelate Racemase Co-Crystallized with Phenylboronic Acid


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of P. Putida Mandelate Racemase Co-Crystallized with Phenylboronic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg401

b:11.7
occ:1.00
 O G:HOH524 2.0 12.5 1.0
OE2 G:GLU221 2.0 14.5 1.0
O2 G:PBC402 2.0 32.0 1.0
OE1 G:GLU247 2.0 13.4 1.0
OD2 G:ASP195 2.2 13.1 1.0
CD G:GLU247 3.0 22.2 1.0
CD G:GLU221 3.0 11.8 1.0
CG G:ASP195 3.0 23.4 1.0
B G:PBC402 3.1 55.2 1.0
OE2 G:GLU247 3.3 18.7 1.0
OD1 G:ASP195 3.3 17.8 1.0
O1 G:PBC402 3.4 25.0 1.0
CG G:GLU221 3.7 17.7 1.0
NZ G:LYS164 3.9 13.8 1.0
OE1 G:GLU221 4.0 14.2 1.0
ND2 G:ASN197 4.0 19.0 1.0
O G:HOH638 4.1 12.1 1.0
OE2 G:GLU222 4.1 15.8 1.0
NZ G:LYS166 4.1 22.6 1.0
NE2 G:HIS297 4.2 17.5 1.0
CG G:GLU247 4.3 14.6 1.0
CB G:ASP195 4.3 13.5 1.0
CD2 G:HIS297 4.3 15.0 1.0
CE G:MET268 4.4 13.8 1.0
CA G:PBC402 4.5 19.4 1.0
CE G:LYS164 4.6 11.2 1.0
CG G:ASN197 4.8 19.5 1.0
CB G:GLU221 4.8 11.9 1.0
CB1 G:PBC402 4.9 25.1 1.0
CD G:GLU222 4.9 19.8 1.0
O G:HOH521 4.9 17.0 1.0
CG G:GLU222 4.9 17.1 1.0
CB G:GLU247 5.0 14.8 1.0

Magnesium binding site 8 out of 8 in 6vim

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Magnesium binding site 8 out of 8 in the P. Putida Mandelate Racemase Co-Crystallized with Phenylboronic Acid


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of P. Putida Mandelate Racemase Co-Crystallized with Phenylboronic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg401

b:16.0
occ:1.00
 O2 H:PBC402 1.8 33.5 1.0
OE1 H:GLU221 2.0 24.8 1.0
O H:HOH526 2.0 18.8 1.0
OE1 H:GLU247 2.0 19.3 1.0
OD2 H:ASP195 2.1 19.5 1.0
B H:PBC402 2.9 37.5 1.0
CD H:GLU247 3.0 19.3 1.0
CD H:GLU221 3.0 25.0 1.0
CG H:ASP195 3.0 19.8 1.0
O1 H:PBC402 3.2 23.9 1.0
OE2 H:GLU247 3.2 15.6 1.0
OD1 H:ASP195 3.4 18.4 1.0
CG H:GLU221 3.6 15.2 1.0
ND2 H:ASN197 3.9 22.4 1.0
OE2 H:GLU221 3.9 23.8 1.0
O H:HOH651 4.1 14.9 1.0
NZ H:LYS164 4.1 19.5 1.0
OE2 H:GLU222 4.1 19.3 1.0
NE2 H:HIS297 4.1 22.4 1.0
NZ H:LYS166 4.2 22.6 1.0
CD2 H:HIS297 4.3 15.8 1.0
CA H:PBC402 4.3 27.2 1.0
CB H:ASP195 4.3 16.0 1.0
CG H:GLU247 4.3 20.6 1.0
CE H:MET268 4.5 17.8 1.0
CE H:LYS164 4.7 13.3 1.0
CB1 H:PBC402 4.7 24.2 1.0
CG H:ASN197 4.8 22.3 1.0
CD H:GLU222 4.9 21.7 1.0
CB H:GLU221 4.9 12.8 1.0
O H:HOH544 4.9 18.2 1.0
CB H:GLU247 5.0 17.6 1.0

Reference:

A.N.Sharma, L.Grandinetti, E.R.Johnson, M.St Maurice, S.L.Bearne. Potent Inhibition of Mandelate Racemase By Boronic Acids: Boron As A Mimic of A Carbon Acid Center. Biochemistry V. 59 3026 2020.
ISSN: ISSN 0006-2960
PubMed: 32786399
DOI: 10.1021/ACS.BIOCHEM.0C00478
Page generated: Tue Oct 1 22:05:50 2024

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