Atomistry » Calcium » PDB 6pu4-6q6x » 6q2y
Atomistry »
  Calcium »
    PDB 6pu4-6q6x »
      6q2y »

Calcium in PDB 6q2y: Crystal Structure of Ndm-1 Beta-Lactamase in Complex with Broad Spectrum Boronic Inhibitor CPD3

Enzymatic activity of Crystal Structure of Ndm-1 Beta-Lactamase in Complex with Broad Spectrum Boronic Inhibitor CPD3

All present enzymatic activity of Crystal Structure of Ndm-1 Beta-Lactamase in Complex with Broad Spectrum Boronic Inhibitor CPD3:
3.5.2.6;

Protein crystallography data

The structure of Crystal Structure of Ndm-1 Beta-Lactamase in Complex with Broad Spectrum Boronic Inhibitor CPD3, PDB code: 6q2y was solved by L.Maso, A.Quotadamo, P.Bellio, M.Montanari, A.Venturelli, G.Celenza, M.P.Costi, D.Tondi, L.Cendron, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 53.62 / 1.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 70.425, 73.950, 77.687, 90.00, 90.00, 90.00
R / Rfree (%) 16.6 / 17.6

Other elements in 6q2y:

The structure of Crystal Structure of Ndm-1 Beta-Lactamase in Complex with Broad Spectrum Boronic Inhibitor CPD3 also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Ndm-1 Beta-Lactamase in Complex with Broad Spectrum Boronic Inhibitor CPD3 (pdb code 6q2y). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Ndm-1 Beta-Lactamase in Complex with Broad Spectrum Boronic Inhibitor CPD3, PDB code: 6q2y:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 6q2y

Go back to Calcium Binding Sites List in 6q2y
Calcium binding site 1 out of 4 in the Crystal Structure of Ndm-1 Beta-Lactamase in Complex with Broad Spectrum Boronic Inhibitor CPD3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Ndm-1 Beta-Lactamase in Complex with Broad Spectrum Boronic Inhibitor CPD3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:10.1
occ:0.80
 OD2 A:ASP223 2.4 11.6 1.0
O A:HOH516 2.5 16.5 1.0
OE1 B:GLU227 2.5 17.8 1.0
OE2 B:GLU227 2.5 17.5 1.0
OE2 A:GLU152 2.5 11.1 1.0
OE1 A:GLU152 2.6 10.7 1.0
CD B:GLU227 2.9 14.8 1.0
OD1 A:ASP223 2.9 14.5 1.0
CD A:GLU152 2.9 9.8 1.0
CG A:ASP223 3.1 10.2 1.0
NE2 A:HIS122 4.3 7.9 1.0
CG B:GLU227 4.4 13.5 1.0
NE2 B:HIS228 4.4 10.6 1.0
CG A:GLU152 4.5 9.1 1.0
CB A:ASP223 4.5 10.3 1.0
O A:HOH439 4.6 11.4 1.0
O A:HOH472 4.6 10.7 1.0
CE1 B:HIS228 4.7 10.0 1.0
CD2 A:HIS122 4.8 7.8 1.0

Calcium binding site 2 out of 4 in 6q2y

Go back to Calcium Binding Sites List in 6q2y
Calcium binding site 2 out of 4 in the Crystal Structure of Ndm-1 Beta-Lactamase in Complex with Broad Spectrum Boronic Inhibitor CPD3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Ndm-1 Beta-Lactamase in Complex with Broad Spectrum Boronic Inhibitor CPD3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca304

b:9.3
occ:0.80
 OD2 A:ASP95 2.3 11.7 1.0
OD2 A:ASP130 2.4 12.1 1.0
O A:HOH518 2.4 16.8 1.0
O A:HOH434 2.4 12.6 1.0
O A:HOH468 2.5 20.4 1.0
O A:HOH496 2.5 8.6 1.0
CG A:ASP130 3.4 10.1 1.0
CG A:ASP95 3.4 8.7 1.0
OD1 A:ASP95 3.8 9.0 1.0
CB A:ASP130 3.8 8.8 1.0
O A:GLY127 4.3 7.7 1.0
O A:HOH473 4.3 14.3 1.0
O A:HOH453 4.4 10.1 1.0
OD1 A:ASP130 4.5 12.3 1.0
O A:HOH449 4.6 8.0 1.0
CB A:ASP95 4.7 8.2 1.0
O A:HOH524 4.8 24.2 1.0
N A:ASP130 4.8 6.8 1.0
CG2 A:VAL155 4.8 9.2 1.0
CA A:ASP130 4.9 7.5 1.0

Calcium binding site 3 out of 4 in 6q2y

Go back to Calcium Binding Sites List in 6q2y
Calcium binding site 3 out of 4 in the Crystal Structure of Ndm-1 Beta-Lactamase in Complex with Broad Spectrum Boronic Inhibitor CPD3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Ndm-1 Beta-Lactamase in Complex with Broad Spectrum Boronic Inhibitor CPD3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca303

b:9.9
occ:0.90
 O A:HOH463 2.3 20.8 1.0
OD2 B:ASP223 2.4 10.4 1.0
O B:HOH522 2.4 15.7 1.0
O B:HOH517 2.4 17.7 1.0
OE2 B:GLU152 2.5 9.6 1.0
OE2 A:GLU227 2.5 16.5 1.0
OE1 A:GLU227 2.5 15.8 1.0
OE1 B:GLU152 2.6 10.0 1.0
CD A:GLU227 2.9 13.7 1.0
OD1 B:ASP223 2.9 13.4 1.0
CD B:GLU152 2.9 7.9 1.0
CG B:ASP223 3.0 10.2 1.0
NE2 B:HIS122 4.3 7.8 1.0
CG A:GLU227 4.4 12.2 1.0
CG B:GLU152 4.4 8.3 1.0
NE2 A:HIS228 4.5 8.5 1.0
CB B:ASP223 4.5 9.8 1.0
O B:HOH436 4.5 11.2 1.0
O B:HOH481 4.6 10.3 1.0
CD2 B:HIS122 4.8 7.1 1.0
CE1 A:HIS228 4.8 8.6 1.0
O B:HOH534 5.0 15.5 1.0

Calcium binding site 4 out of 4 in 6q2y

Go back to Calcium Binding Sites List in 6q2y
Calcium binding site 4 out of 4 in the Crystal Structure of Ndm-1 Beta-Lactamase in Complex with Broad Spectrum Boronic Inhibitor CPD3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Ndm-1 Beta-Lactamase in Complex with Broad Spectrum Boronic Inhibitor CPD3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca304

b:10.8
occ:0.70
 OD2 B:ASP95 2.4 12.5 1.0
O B:HOH529 2.4 17.1 1.0
O B:HOH457 2.5 15.6 1.0
OD2 B:ASP130 2.5 13.0 1.0
O B:HOH493 2.6 9.3 1.0
CG B:ASP95 3.3 9.2 1.0
CG B:ASP130 3.5 9.0 1.0
OD1 B:ASP95 3.6 11.1 1.0
CB B:ASP130 3.8 7.3 1.0
O B:HOH431 4.1 9.7 1.0
O B:GLY127 4.3 7.5 1.0
O B:HOH512 4.3 16.5 1.0
O B:HOH464 4.5 8.5 1.0
OD1 B:ASP130 4.5 13.2 1.0
CB B:ASP95 4.7 8.2 1.0
O B:HOH455 4.7 7.1 1.0
CG2 B:VAL155 4.7 7.5 1.0
N B:ASP130 4.8 6.2 1.0
CA B:ASP130 4.9 6.4 1.0

Reference:

L.Cendron, A.Quotadamo, L.Maso, P.Bellio, M.Montanari, G.Celenza, A.Venturelli, M.P.Costi, D.Tondi. X-Ray Crystallography Deciphers the Activity of Broad-Spectrum Boronic Acid Beta-Lactamase Inhibitors. Acs Med.Chem.Lett. V. 10 650 2019.
ISSN: ISSN 1948-5875
PubMed: 30996812
DOI: 10.1021/ACSMEDCHEMLETT.8B00607
Page generated: Tue Jul 16 13:15:26 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy