Atomistry » Magnesium » PDB 6uy0-6vck » 6v1o
Atomistry »
  Magnesium »
    PDB 6uy0-6vck »
      6v1o »

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

Go back to Magnesium Binding Sites List in 6v1o
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

Go back to Magnesium Binding Sites List in 6v1o
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

Go back to Magnesium Binding Sites List in 6v1o
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

Go back to Magnesium Binding Sites List in 6v1o
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

Go back to Magnesium Binding Sites List in 6v1o
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

Go back to Magnesium Binding Sites List in 6v1o
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

Go back to Magnesium Binding Sites List in 6v1o
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

Go back to Magnesium Binding Sites List in 6v1o
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 Oct 1 21:22:03 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy