Magnesium in PDB 6v1o: Structure of Oxa-48 Bound to QPX7728 at 1.80 A

Enzymatic activity of Structure of Oxa-48 Bound to QPX7728 at 1.80 A

All present enzymatic activity of Structure of Oxa-48 Bound to QPX7728 at 1.80 A:
3.5.2.6;

Protein crystallography data

The structure of Structure of Oxa-48 Bound to QPX7728 at 1.80 A, PDB code: 6v1o was solved by O.A.Pemberton, Y.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.85 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 58.440, 105.550, 94.403, 90.00, 107.92, 90.00
R / Rfree (%) 15.8 / 22.4

Other elements in 6v1o:

The structure of Structure of Oxa-48 Bound to QPX7728 at 1.80 A also contains other interesting chemical elements:

Fluorine (F) 4 atoms
Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Oxa-48 Bound to QPX7728 at 1.80 A (pdb code 6v1o). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Structure of Oxa-48 Bound to QPX7728 at 1.80 A, PDB code: 6v1o:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 6v1o

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Magnesium binding site 1 out of 8 in the Structure of Oxa-48 Bound to QPX7728 at 1.80 A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Oxa-48 Bound to QPX7728 at 1.80 A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:34.0
occ:0.96
 OE1 A:GLU37 1.8 47.1 1.0
OE1 A:GLU256 2.0 31.1 1.0
O A:HOH403 2.1 20.3 1.0
O A:HOH456 2.2 34.0 1.0
O A:HOH576 2.2 39.6 1.0
O A:HOH623 2.8 42.3 1.0
CD A:GLU37 2.9 46.4 1.0
CD A:GLU256 3.0 29.2 1.0
OE2 A:GLU37 3.3 49.4 1.0
OE2 A:GLU256 3.4 32.0 1.0
NE2 A:HIS38 3.9 31.2 1.0
CG A:GLU37 4.1 42.1 1.0
O A:HOH609 4.1 42.0 1.0
O A:HOH404 4.3 47.6 1.0
CB A:GLU37 4.3 36.1 1.0
CG A:GLU256 4.3 22.5 1.0
ND1 A:HIS34 4.3 22.5 1.0
O A:HOH639 4.4 39.5 1.0
CE1 A:HIS38 4.6 31.9 1.0
O A:HIS34 4.6 22.5 1.0
CA A:HIS34 4.6 21.2 1.0
CD2 A:HIS38 4.8 30.6 1.0
CB A:HIS34 4.8 21.8 1.0

Magnesium binding site 2 out of 8 in 6v1o

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Magnesium binding site 2 out of 8 in the Structure of Oxa-48 Bound to QPX7728 at 1.80 A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Oxa-48 Bound to QPX7728 at 1.80 A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg303

b:16.0
occ:0.89
 O A:HOH471 2.0 18.3 1.0
OE2 A:GLU147 2.0 14.8 1.0
OD1 A:ASP143 2.0 12.7 1.0
O A:HOH539 2.0 14.6 1.0
O A:HOH492 2.1 19.1 1.0
O A:HOH499 2.1 12.3 1.0
CD A:GLU147 3.0 13.6 1.0
CG A:ASP143 3.2 12.8 1.0
OE1 A:GLU147 3.5 15.9 1.0
CA A:ASP143 3.9 9.0 1.0
CB A:ASP143 3.9 11.3 1.0
O A:HOH671 4.0 28.6 1.0
O A:HOH546 4.1 27.7 1.0
OD2 A:ASP143 4.1 14.1 1.0
ND1 A:HIS140 4.3 17.5 1.0
CG A:GLU147 4.3 11.5 1.0
O A:HIS140 4.4 13.0 1.0
CE1 A:HIS140 4.5 17.9 1.0
C A:ASP143 4.7 7.3 1.0
N A:ASP143 4.9 8.6 1.0
O A:ASP143 5.0 8.9 1.0

Magnesium binding site 3 out of 8 in 6v1o

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Magnesium binding site 3 out of 8 in the Structure of Oxa-48 Bound to QPX7728 at 1.80 A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Oxa-48 Bound to QPX7728 at 1.80 A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:19.1
occ:0.94
 OE2 B:GLU147 2.0 13.3 1.0
OD1 B:ASP143 2.0 15.5 1.0
O B:HOH535 2.1 24.2 1.0
O B:HOH438 2.2 18.6 1.0
O B:HOH404 2.2 22.0 1.0
O B:HOH537 2.2 20.9 1.0
CD B:GLU147 3.0 14.4 1.0
CG B:ASP143 3.2 13.5 1.0
OE1 B:GLU147 3.3 18.0 1.0
CA B:ASP143 3.8 8.3 1.0
CB B:ASP143 3.9 10.1 1.0
OD2 B:ASP143 4.1 13.2 1.0
O B:HOH539 4.2 28.9 1.0
CG B:GLU147 4.3 12.8 1.0
ND1 B:HIS140 4.3 28.9 1.0
O B:HOH708 4.3 52.9 1.0
O B:HIS140 4.4 7.0 1.0
O B:HOH698 4.5 37.2 1.0
O B:HOH729 4.5 44.8 1.0
C B:ASP143 4.6 8.8 1.0
CE1 B:HIS140 4.7 28.9 1.0
N B:ASP143 4.8 9.1 1.0
O B:ASP143 4.9 10.7 1.0

Magnesium binding site 4 out of 8 in 6v1o

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Magnesium binding site 4 out of 8 in the Structure of Oxa-48 Bound to QPX7728 at 1.80 A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Oxa-48 Bound to QPX7728 at 1.80 A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:43.5
occ:1.00
 OE2 B:GLU37 1.9 31.2 1.0
OE1 B:GLU256 1.9 21.5 1.0
O B:HOH485 2.2 25.8 1.0
O B:HOH591 2.3 55.9 1.0
O B:HOH479 2.3 16.1 1.0
O B:HOH410 2.5 18.1 1.0
CD B:GLU256 3.0 19.7 1.0
CD B:GLU37 3.0 31.1 1.0
OE2 B:GLU256 3.4 20.2 1.0
OE1 B:GLU37 3.7 33.6 1.0
O B:HOH696 3.8 32.0 1.0
O B:HOH606 3.8 24.5 1.0
NE2 B:HIS38 4.0 21.0 1.0
CG B:GLU37 4.1 27.9 1.0
CG B:GLU256 4.3 16.1 1.0
CB B:GLU37 4.4 23.2 1.0
O B:HOH447 4.4 43.5 1.0
ND1 B:HIS34 4.4 9.4 1.0
O B:HIS34 4.7 11.6 1.0
CA B:HIS34 4.8 10.2 1.0
CD2 B:HIS38 4.8 18.4 1.0
CE1 B:HIS38 4.8 21.6 1.0
O B:HOH750 4.8 40.8 1.0
CB B:HIS34 5.0 11.0 1.0

Magnesium binding site 5 out of 8 in 6v1o

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Magnesium binding site 5 out of 8 in the Structure of Oxa-48 Bound to QPX7728 at 1.80 A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of Oxa-48 Bound to QPX7728 at 1.80 A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:25.0
occ:0.94
 O C:HOH577 2.0 25.0 1.0
OD1 C:ASP143 2.1 16.4 1.0
OE2 C:GLU147 2.1 19.3 1.0
O C:HOH515 2.1 22.0 1.0
O C:HOH414 2.2 24.5 1.0
O C:HOH467 2.2 16.3 1.0
CG C:ASP143 3.1 18.2 1.0
CD C:GLU147 3.1 21.7 1.0
OE1 C:GLU147 3.6 25.9 1.0
CB C:ASP143 3.9 15.6 1.0
CA C:ASP143 3.9 14.4 1.0
OD2 C:ASP143 4.0 20.5 1.0
O C:HOH630 4.3 34.8 1.0
O C:HOH663 4.3 44.8 1.0
CG C:GLU147 4.3 19.6 1.0
O C:HIS140 4.4 18.3 0.5
O C:HIS140 4.4 18.1 0.5
ND1 C:HIS140 4.5 19.3 0.5
CE1 C:HIS140 4.7 19.6 0.5
C C:ASP143 4.7 15.3 1.0
N C:ASP143 4.9 14.1 1.0
O C:HOH417 4.9 41.9 1.0
O C:ASP143 5.0 15.4 1.0

Magnesium binding site 6 out of 8 in 6v1o

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Magnesium binding site 6 out of 8 in the Structure of Oxa-48 Bound to QPX7728 at 1.80 A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of Oxa-48 Bound to QPX7728 at 1.80 A within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:11.0
occ:1.00
 O D:HOH520 2.0 11.8 1.0
OE2 D:GLU147 2.0 10.2 1.0
OD1 D:ASP143 2.0 9.4 1.0
O D:HOH436 2.1 15.5 1.0
O D:HOH551 2.1 12.6 1.0
O D:HOH492 2.1 8.7 1.0
CD D:GLU147 3.0 10.9 1.0
CG D:ASP143 3.2 9.3 1.0
OE1 D:GLU147 3.4 12.9 1.0
CA D:ASP143 3.8 8.2 1.0
CB D:ASP143 3.9 8.2 1.0
OD2 D:ASP143 4.2 9.7 1.0
O D:HOH706 4.3 33.3 1.0
CG D:GLU147 4.4 9.8 1.0
O D:HIS140 4.5 7.9 0.6
O D:HIS140 4.5 9.6 0.4
CD2 D:HIS140 4.6 13.6 0.4
O D:HOH709 4.6 35.2 1.0
C D:ASP143 4.6 7.7 1.0
O D:HOH435 4.8 16.3 1.0
N D:ASP143 4.9 8.4 1.0
O D:ASP143 4.9 7.9 1.0
NE2 D:HIS140 5.0 12.8 0.4

Magnesium binding site 7 out of 8 in 6v1o

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Magnesium binding site 7 out of 8 in the Structure of Oxa-48 Bound to QPX7728 at 1.80 A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of Oxa-48 Bound to QPX7728 at 1.80 A within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg303

b:41.8
occ:0.83
 O D:HOH704 2.2 42.0 1.0
O D:HOH658 2.2 26.0 1.0
O C:HOH437 2.3 27.3 1.0
O D:HOH422 2.5 32.1 1.0
O C:HOH708 2.6 36.8 1.0
O C:HOH445 3.8 24.6 1.0
O D:HOH478 4.0 32.5 1.0
O C:HOH569 4.2 42.6 1.0
O D:HOH705 4.4 39.1 1.0
O D:HOH727 4.5 45.4 1.0
O D:HOH504 4.5 22.6 1.0
ND1 C:HIS90 4.6 23.4 1.0
OH D:TYR177 4.6 16.5 1.0
O D:ASP230 4.8 21.7 1.0
C D:ASP230 4.8 21.2 1.0
ND2 C:ASN110 4.8 19.2 1.0
O C:HOH428 5.0 19.8 1.0

Magnesium binding site 8 out of 8 in 6v1o

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Magnesium binding site 8 out of 8 in the Structure of Oxa-48 Bound to QPX7728 at 1.80 A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of Oxa-48 Bound to QPX7728 at 1.80 A within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg304

b:41.9
occ:0.83
 O D:HOH530 2.0 21.5 1.0
O D:HOH564 2.1 35.9 1.0
NE2 D:HIS140 2.1 8.8 0.6
O D:HOH501 2.4 56.7 1.0
O D:HOH665 2.4 40.5 1.0
CD2 D:HIS140 3.0 8.7 0.6
CE1 D:HIS140 3.2 8.3 0.6
OE1 D:GLU147 4.1 12.9 1.0
CG D:HIS140 4.2 8.2 0.6
ND1 D:HIS140 4.3 8.8 0.6
O D:GLU147 4.6 13.4 1.0
CB D:GLU147 4.7 10.0 1.0
O D:HOH649 4.7 37.4 1.0
CD2 D:HIS140 5.0 13.6 0.4

Reference:

S.J.Hecker, K.R.Reddy, O.Lomovskaya, D.C.Griffith, D.Rubio-Aparicio, K.Nelson, R.Tsivkovski, D.Sun, M.Sabet, Z.Tarazi, J.Parkinson, M.Totrov, S.H.Boyer, T.W.Glinka, O.A.Pemberton, Y.Chen, M.N.Dudley. Discovery of Cyclic Boronic Acid QPX7728, An Ultra-Broad-Spectrum Inhibitor of Serine and Metallo Beta-Lactamases. J.Med.Chem. 2020.
ISSN: ISSN 0022-2623
PubMed: 32150407
DOI: 10.1021/ACS.JMEDCHEM.9B01976
Page generated: Tue Dec 15 01:06:32 2020

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