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Magnesium in PDB 7mqx: P. Putida Mandelate Racemase Forms An Oxobenzoxaborole Adduct with 2- Formylphenylboronic Acid

Enzymatic activity of P. Putida Mandelate Racemase Forms An Oxobenzoxaborole Adduct with 2- Formylphenylboronic Acid

All present enzymatic activity of P. Putida Mandelate Racemase Forms An Oxobenzoxaborole Adduct with 2- Formylphenylboronic Acid:
5.1.2.2;

Protein crystallography data

The structure of P. Putida Mandelate Racemase Forms An Oxobenzoxaborole Adduct with 2- Formylphenylboronic Acid, PDB code: 7mqx was solved by L.Grandinetti, 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) 40.61 / 1.91
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 225.483, 149.43, 149.523, 90, 129.34, 90
R / Rfree (%) 18.7 / 21.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the P. Putida Mandelate Racemase Forms An Oxobenzoxaborole Adduct with 2- Formylphenylboronic Acid (pdb code 7mqx). 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 Forms An Oxobenzoxaborole Adduct with 2- Formylphenylboronic Acid, PDB code: 7mqx:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 7mqx

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Magnesium binding site 1 out of 8 in the P. Putida Mandelate Racemase Forms An Oxobenzoxaborole Adduct with 2- Formylphenylboronic 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 Forms An Oxobenzoxaborole Adduct with 2- Formylphenylboronic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:14.0
occ:1.00
 O A:HOH525 2.0 14.2 1.0
OE1 A:GLU221 2.0 14.9 1.0
OE1 A:GLU247 2.0 11.4 1.0
OD2 A:ASP195 2.1 14.9 1.0
O A:HOH523 2.1 15.1 1.0
O05 A:ZMD402 2.3 17.7 1.0
CG A:ASP195 3.0 13.9 1.0
CD A:GLU221 3.0 15.9 1.0
CD A:GLU247 3.1 16.8 1.0
OD1 A:ASP195 3.3 13.8 1.0
B04 A:ZMD402 3.3 21.0 1.0
OE2 A:GLU247 3.4 17.4 1.0
O03 A:ZMD402 3.5 22.4 1.0
NZ A:LYS166 3.7 17.6 1.0
OE2 A:GLU221 3.8 15.7 1.0
CG A:GLU221 3.9 12.7 1.0
O A:HOH572 3.9 17.8 1.0
O A:HOH660 4.0 14.1 1.0
ND2 A:ASN197 4.1 15.1 1.0
CB A:ASP195 4.3 14.8 1.0
OE2 A:GLU222 4.3 17.3 1.0
CG A:GLU247 4.4 15.5 1.0
NZ A:LYS164 4.4 21.7 1.0
CE A:MET268 4.5 13.3 1.0
C06 A:ZMD402 4.7 19.8 1.0
CD2 A:HIS297 4.7 14.5 1.0
NE2 A:HIS297 4.7 16.8 1.0
C02 A:ZMD402 4.7 21.5 1.0
CG A:ASN197 4.9 15.4 1.0
CB A:GLU221 4.9 14.0 1.0
O01 A:ZMD402 4.9 19.3 1.0
OD1 A:ASN197 4.9 19.1 1.0

Magnesium binding site 2 out of 8 in 7mqx

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Magnesium binding site 2 out of 8 in the P. Putida Mandelate Racemase Forms An Oxobenzoxaborole Adduct with 2- Formylphenylboronic 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 Forms An Oxobenzoxaborole Adduct with 2- Formylphenylboronic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg401

b:17.2
occ:1.00
 OE1 B:GLU221 2.0 18.1 1.0
O B:HOH518 2.1 18.2 1.0
OE1 B:GLU247 2.1 17.1 1.0
O B:HOH516 2.1 17.9 1.0
OD2 B:ASP195 2.1 15.9 1.0
O05 B:ZMD402 2.2 20.2 1.0
CD B:GLU247 3.0 20.6 1.0
CD B:GLU221 3.1 17.5 1.0
CG B:ASP195 3.1 20.1 1.0
B04 B:ZMD402 3.2 24.1 1.0
OE2 B:GLU247 3.3 19.5 1.0
O03 B:ZMD402 3.4 23.9 1.0
OD1 B:ASP195 3.4 19.3 1.0
NZ B:LYS166 3.8 20.5 1.0
CG B:GLU221 3.9 18.3 1.0
OE2 B:GLU221 3.9 19.2 1.0
ND2 B:ASN197 4.0 18.1 1.0
O B:HOH541 4.1 16.8 1.0
O B:HOH649 4.1 16.6 1.0
OE2 B:GLU222 4.2 19.5 1.0
CB B:ASP195 4.4 21.9 1.0
CG B:GLU247 4.4 17.6 1.0
NZ B:LYS164 4.5 28.4 1.0
CE B:MET268 4.5 14.8 1.0
C06 B:ZMD402 4.6 22.6 1.0
CE B:LYS164 4.6 27.8 1.0
NE2 B:HIS297 4.6 18.4 1.0
CD2 B:HIS297 4.6 15.8 1.0
C02 B:ZMD402 4.6 19.5 1.0
CG B:ASN197 4.8 22.5 1.0
O01 B:ZMD402 4.9 23.2 1.0
OD1 B:ASN197 5.0 22.9 1.0
CB B:GLU221 5.0 17.5 1.0

Magnesium binding site 3 out of 8 in 7mqx

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Magnesium binding site 3 out of 8 in the P. Putida Mandelate Racemase Forms An Oxobenzoxaborole Adduct with 2- Formylphenylboronic 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 Forms An Oxobenzoxaborole Adduct with 2- Formylphenylboronic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg401

b:12.9
occ:1.00
 OE1 C:GLU247 2.0 14.8 1.0
O C:HOH508 2.1 15.0 1.0
OE1 C:GLU221 2.1 13.4 1.0
O C:HOH519 2.1 13.5 1.0
OD2 C:ASP195 2.1 14.2 1.0
O05 C:ZMD402 2.3 15.8 1.0
CD C:GLU247 3.0 19.2 1.0
CD C:GLU221 3.1 15.9 1.0
CG C:ASP195 3.1 13.6 1.0
OE2 C:GLU247 3.3 17.1 1.0
B04 C:ZMD402 3.3 20.7 1.0
OD1 C:ASP195 3.4 16.3 1.0
O03 C:ZMD402 3.5 18.9 1.0
NZ C:LYS166 3.8 17.6 1.0
OE2 C:GLU221 3.9 16.0 1.0
NZ C:LYS164 3.9 22.7 1.0
CG C:GLU221 3.9 15.9 1.0
O C:HOH522 4.0 14.1 1.0
ND2 C:ASN197 4.1 17.1 1.0
O C:HOH675 4.2 14.4 1.0
OE2 C:GLU222 4.3 18.6 1.0
CG C:GLU247 4.4 14.8 1.0
CB C:ASP195 4.4 15.1 1.0
CE C:MET268 4.6 11.9 1.0
NE2 C:HIS297 4.6 17.4 1.0
CD2 C:HIS297 4.6 14.6 1.0
C06 C:ZMD402 4.7 19.2 1.0
CE C:LYS164 4.7 26.3 1.0
C02 C:ZMD402 4.8 19.2 1.0
CG C:ASN197 4.8 17.9 1.0
CB C:GLU221 5.0 14.2 1.0
OD1 C:ASN197 5.0 15.6 1.0
O01 C:ZMD402 5.0 22.3 1.0

Magnesium binding site 4 out of 8 in 7mqx

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Magnesium binding site 4 out of 8 in the P. Putida Mandelate Racemase Forms An Oxobenzoxaborole Adduct with 2- Formylphenylboronic 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 Forms An Oxobenzoxaborole Adduct with 2- Formylphenylboronic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg401

b:14.5
occ:1.00
 OE1 D:GLU221 2.0 19.3 1.0
OD2 D:ASP195 2.0 17.4 1.0
O D:HOH510 2.0 18.7 1.0
O D:HOH503 2.1 20.6 1.0
OE1 D:GLU247 2.2 19.1 1.0
O05 D:ZMD402 2.3 20.2 1.0
CG D:ASP195 3.0 18.4 1.0
CD D:GLU221 3.0 20.4 1.0
CD D:GLU247 3.1 21.5 1.0
B04 D:ZMD402 3.3 24.3 1.0
OD1 D:ASP195 3.3 17.3 1.0
O03 D:ZMD402 3.4 19.8 1.0
OE2 D:GLU247 3.4 21.0 1.0
NZ D:LYS166 3.6 18.7 1.0
CG D:GLU221 3.8 20.1 1.0
OE2 D:GLU221 3.9 19.9 1.0
O D:HOH562 4.0 19.1 1.0
ND2 D:ASN197 4.1 17.8 1.0
O D:HOH641 4.2 20.3 1.0
CB D:ASP195 4.3 20.9 1.0
OE2 D:GLU222 4.4 21.0 1.0
CE D:LYS164 4.4 26.0 1.0
NZ D:LYS164 4.4 23.5 1.0
CG D:GLU247 4.5 16.3 1.0
CE D:MET268 4.5 16.4 1.0
NE2 D:HIS297 4.6 20.4 1.0
CD2 D:HIS297 4.6 19.8 1.0
C06 D:ZMD402 4.6 22.4 1.0
C02 D:ZMD402 4.7 19.6 1.0
CG D:ASN197 4.9 19.1 1.0
O01 D:ZMD402 4.9 24.1 1.0
CB D:GLU221 5.0 19.1 1.0

Magnesium binding site 5 out of 8 in 7mqx

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Magnesium binding site 5 out of 8 in the P. Putida Mandelate Racemase Forms An Oxobenzoxaborole Adduct with 2- Formylphenylboronic 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 Forms An Oxobenzoxaborole Adduct with 2- Formylphenylboronic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg401

b:13.4
occ:1.00
 O E:HOH512 2.1 16.5 1.0
OE1 E:GLU247 2.1 14.7 1.0
O E:HOH527 2.1 15.7 1.0
OE1 E:GLU221 2.1 15.4 1.0
OD2 E:ASP195 2.1 14.9 1.0
O05 E:ZMD402 2.3 17.7 1.0
CD E:GLU247 3.0 19.2 1.0
CG E:ASP195 3.1 14.6 1.0
CD E:GLU221 3.1 16.6 1.0
OE2 E:GLU247 3.2 17.1 1.0
B04 E:ZMD402 3.3 17.6 1.0
OD1 E:ASP195 3.4 16.1 1.0
O03 E:ZMD402 3.4 18.6 1.0
NZ E:LYS166 3.7 17.3 1.0
CG E:GLU221 3.9 16.5 1.0
OE2 E:GLU221 4.0 14.9 1.0
O E:HOH517 4.0 15.9 1.0
O E:HOH611 4.1 15.4 1.0
ND2 E:ASN197 4.1 15.6 1.0
NZ E:LYS164 4.2 21.5 1.0
OE2 E:GLU222 4.4 17.4 1.0
CB E:ASP195 4.4 13.6 1.0
CG E:GLU247 4.4 16.1 1.0
CE E:MET268 4.5 15.2 1.0
NE2 E:HIS297 4.5 16.7 1.0
CD2 E:HIS297 4.6 14.6 1.0
C06 E:ZMD402 4.6 15.9 1.0
C02 E:ZMD402 4.7 19.5 1.0
O01 E:ZMD402 4.8 19.1 1.0
CG E:ASN197 4.9 18.6 1.0
CB E:GLU221 5.0 14.0 1.0

Magnesium binding site 6 out of 8 in 7mqx

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Magnesium binding site 6 out of 8 in the P. Putida Mandelate Racemase Forms An Oxobenzoxaborole Adduct with 2- Formylphenylboronic 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 Forms An Oxobenzoxaborole Adduct with 2- Formylphenylboronic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg401

b:18.4
occ:1.00
 O F:HOH515 2.1 19.7 1.0
OE1 F:GLU247 2.1 16.2 1.0
O F:HOH509 2.1 18.1 1.0
OD2 F:ASP195 2.1 16.9 1.0
OE1 F:GLU221 2.1 19.0 1.0
O05 F:ZMD402 2.4 20.6 1.0
CD F:GLU247 3.0 21.2 1.0
CG F:ASP195 3.1 18.1 1.0
CD F:GLU221 3.1 21.1 1.0
OE2 F:GLU247 3.3 24.4 1.0
B04 F:ZMD402 3.3 24.6 1.0
OD1 F:ASP195 3.4 18.0 1.0
O03 F:ZMD402 3.5 22.9 1.0
NZ F:LYS166 3.7 20.6 1.0
NZ F:LYS164 3.8 29.2 1.0
OE2 F:GLU221 3.9 21.5 1.0
CG F:GLU221 4.0 17.9 1.0
O F:HOH514 4.0 19.4 1.0
O F:HOH628 4.1 16.9 1.0
ND2 F:ASN197 4.1 18.9 1.0
CB F:ASP195 4.3 18.1 1.0
OE2 F:GLU222 4.4 20.1 1.0
CG F:GLU247 4.4 18.9 1.0
CE F:MET268 4.5 16.0 1.0
CE F:LYS164 4.6 29.1 1.0
C06 F:ZMD402 4.7 22.6 1.0
CD2 F:HIS297 4.7 18.6 1.0
C02 F:ZMD402 4.8 21.4 1.0
NE2 F:HIS297 4.8 18.5 1.0
CG F:ASN197 4.9 21.5 1.0
OD1 F:ASN197 4.9 19.1 1.0
O01 F:ZMD402 5.0 25.4 1.0
CB F:GLU221 5.0 17.6 1.0

Magnesium binding site 7 out of 8 in 7mqx

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Magnesium binding site 7 out of 8 in the P. Putida Mandelate Racemase Forms An Oxobenzoxaborole Adduct with 2- Formylphenylboronic 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 Forms An Oxobenzoxaborole Adduct with 2- Formylphenylboronic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg401

b:15.4
occ:1.00
 O G:HOH509 2.0 14.3 1.0
OE1 G:GLU247 2.1 16.1 1.0
OE1 G:GLU221 2.1 13.6 1.0
OD2 G:ASP195 2.1 14.0 1.0
O G:HOH523 2.1 15.0 1.0
O05 G:ZMD402 2.3 17.7 1.0
CD G:GLU247 3.0 19.0 1.0
CG G:ASP195 3.1 18.1 1.0
CD G:GLU221 3.1 14.2 1.0
B04 G:ZMD402 3.3 17.0 1.0
OE2 G:GLU247 3.3 15.2 1.0
OD1 G:ASP195 3.4 16.1 1.0
O03 G:ZMD402 3.4 16.5 1.0
NZ G:LYS166 3.7 16.6 1.0
OE2 G:GLU221 4.0 14.9 1.0
NZ G:LYS164 4.0 22.6 0.5
O G:HOH599 4.0 14.9 1.0
CG G:GLU221 4.0 17.3 1.0
ND2 G:ASN197 4.1 16.3 1.0
OE2 G:GLU222 4.3 17.0 1.0
CG G:GLU247 4.4 17.8 1.0
CB G:ASP195 4.4 16.3 1.0
CE G:MET268 4.5 12.4 1.0
NE2 G:HIS297 4.5 14.9 1.0
NZ G:LYS164 4.6 22.6 0.5
CD2 G:HIS297 4.6 15.8 1.0
C06 G:ZMD402 4.6 17.0 1.0
C02 G:ZMD402 4.7 19.0 1.0
CE G:LYS164 4.7 20.6 0.5
CE G:LYS164 4.8 17.9 0.5
CG G:ASN197 4.9 17.9 1.0
O01 G:ZMD402 4.9 19.9 1.0
OD1 G:ASN197 4.9 20.9 1.0
CB G:GLU221 5.0 14.0 1.0

Magnesium binding site 8 out of 8 in 7mqx

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Magnesium binding site 8 out of 8 in the P. Putida Mandelate Racemase Forms An Oxobenzoxaborole Adduct with 2- Formylphenylboronic 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 Forms An Oxobenzoxaborole Adduct with 2- Formylphenylboronic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg401

b:17.3
occ:1.00
 OE1 H:GLU221 2.0 19.6 1.0
OD2 H:ASP195 2.1 17.1 1.0
O H:HOH509 2.1 19.2 1.0
OE1 H:GLU247 2.1 18.3 1.0
O H:HOH508 2.2 21.6 1.0
O05 H:ZMD402 2.2 20.0 1.0
CG H:ASP195 3.0 19.6 1.0
CD H:GLU247 3.1 19.4 1.0
CD H:GLU221 3.1 20.8 1.0
B04 H:ZMD402 3.2 24.5 1.0
O03 H:ZMD402 3.3 23.5 1.0
OD1 H:ASP195 3.4 17.2 1.0
OE2 H:GLU247 3.4 23.2 1.0
NZ H:LYS166 3.7 22.8 1.0
O H:HOH518 3.9 18.2 1.0
OE2 H:GLU221 3.9 18.2 1.0
O H:HOH625 4.0 19.2 1.0
CG H:GLU221 4.0 18.6 1.0
ND2 H:ASN197 4.0 21.6 1.0
CB H:ASP195 4.3 20.8 1.0
OE2 H:GLU222 4.3 18.4 1.0
CG H:GLU247 4.4 18.0 1.0
CE H:LYS164 4.4 22.4 1.0
NZ H:LYS164 4.4 28.1 1.0
CE H:MET268 4.5 16.9 1.0
C06 H:ZMD402 4.5 21.4 1.0
C02 H:ZMD402 4.6 20.4 1.0
CD2 H:HIS297 4.7 14.5 1.0
NE2 H:HIS297 4.7 18.4 1.0
CG H:ASN197 4.8 21.7 1.0
O01 H:ZMD402 4.9 22.0 1.0
CB H:GLU221 4.9 17.6 1.0
OD1 H:ASN197 5.0 22.0 1.0

Reference:

C.D.Douglas, L.Grandinetti, N.M.Easton, O.P.Kuehm, J.A.Hayden, M.C.Hamilton, S.L.Bearne. Slow-Onset, Potent Inhibition of Mandelate Racemase By 2-Formylphenylboronic Acid. An Unexpected Adduct Clasps the Catalytic Machinery Biochemistry 2021.
ISSN: ISSN 0006-2960
DOI: 10.1021/ACS.BIOCHEM.1C00374
Page generated: Thu Oct 3 01:07:56 2024

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