Atomistry » Calcium » PDB 6i1q-6im0 » 6ibv
Atomistry »
  Calcium »
    PDB 6i1q-6im0 »
      6ibv »

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

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

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

Protein crystallography data

The structure of Crystal Structure of Ndm-1 Beta-Lactamase in Complex with Broad Spectrum Boronic Inhibitor Cpd 1, PDB code: 6ibv was solved by L.Maso, A.Quotadamo, P.Bellio, M.Montanari, G.Celenza, A.Venturelli, 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) 42.67 / 1.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 70.407, 73.824, 77.868, 90.00, 90.00, 90.00
R / Rfree (%) 21.8 / 25.2

Other elements in 6ibv:

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

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

Calcium binding site 1 out of 3 in 6ibv

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


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 Cpd 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca304

b:17.9
occ:1.00
 OE2 B:GLU227 2.4 18.2 1.0
OD2 A:ASP223 2.4 16.2 1.0
O A:HOH549 2.4 18.8 1.0
O B:HOH531 2.4 28.5 1.0
O B:HOH563 2.5 17.4 1.0
OE2 A:GLU152 2.6 13.1 1.0
OE1 A:GLU152 2.6 12.8 1.0
OE1 B:GLU227 2.7 19.3 1.0
CD B:GLU227 2.9 18.3 1.0
CD A:GLU152 2.9 14.6 1.0
OD1 A:ASP223 3.0 17.5 1.0
CG A:ASP223 3.0 16.5 1.0
NE2 A:HIS122 4.3 9.4 1.0
CG B:GLU227 4.4 16.1 1.0
CG A:GLU152 4.4 13.6 1.0
O A:HOH459 4.5 11.9 1.0
CB A:ASP223 4.5 16.0 1.0
NE2 B:HIS228 4.5 14.2 1.0
O A:HOH506 4.6 13.5 1.0
CE1 B:HIS228 4.8 13.3 1.0
O B:HOH576 4.9 26.5 1.0
CD2 A:HIS122 4.9 9.6 1.0
O A:HOH604 4.9 19.2 1.0

Calcium binding site 2 out of 3 in 6ibv

Go back to Calcium Binding Sites List in 6ibv
Calcium binding site 2 out of 3 in the Crystal Structure of Ndm-1 Beta-Lactamase in Complex with Broad Spectrum Boronic Inhibitor Cpd 1


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 Cpd 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca305

b:17.2
occ:1.00
 OD2 A:ASP95 2.4 15.5 1.0
OD2 A:ASP130 2.5 14.0 1.0
O A:HOH466 2.5 20.0 1.0
O A:HOH551 2.5 13.2 1.0
O A:HOH541 2.6 32.3 1.0
CG A:ASP95 3.4 13.9 1.0
CG A:ASP130 3.5 12.3 1.0
OD1 A:ASP95 3.7 13.2 1.0
CB A:ASP130 3.8 12.7 1.0
O A:HOH516 4.1 15.7 1.0
O A:GLY127 4.3 12.1 1.0
O A:HOH547 4.3 14.1 1.0
O A:HOH581 4.5 30.4 1.0
OD1 A:ASP130 4.6 13.2 1.0
O A:HOH513 4.6 11.7 1.0
CB A:ASP95 4.7 13.0 1.0
CG2 A:VAL155 4.8 11.7 1.0
N A:ASP130 4.8 10.8 1.0
CA A:ASP130 4.9 12.0 1.0

Calcium binding site 3 out of 3 in 6ibv

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


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 Cpd 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca306

b:16.6
occ:1.00
 O A:HOH512 2.3 20.5 1.0
O A:HOH565 2.4 24.2 1.0
OE2 A:GLU227 2.4 16.8 1.0
OD2 B:ASP223 2.4 17.5 1.0
O B:HOH565 2.4 18.0 1.0
OE1 B:GLU152 2.5 11.4 1.0
OE2 B:GLU152 2.5 12.4 1.0
OE1 A:GLU227 2.7 17.7 1.0
CD B:GLU152 2.8 10.5 1.0
CD A:GLU227 2.9 16.0 1.0
OD1 B:ASP223 2.9 21.3 1.0
CG B:ASP223 3.0 19.8 1.0
O B:HOH405 4.1 38.4 1.0
O B:HOH550 4.2 35.4 1.0
NE2 B:HIS122 4.3 9.8 1.0
O A:HOH405 4.3 31.3 1.0
CG B:GLU152 4.4 11.4 1.0
CG A:GLU227 4.4 15.4 1.0
NE2 A:HIS228 4.5 12.4 1.0
CB B:ASP223 4.5 16.9 1.0
O B:HOH656 4.5 32.7 1.0
O B:HOH517 4.6 11.0 1.0
O B:HOH475 4.6 12.2 1.0
CE1 A:HIS228 4.8 12.5 1.0
CD2 B:HIS122 4.8 8.8 1.0
O B:HOH625 4.9 18.7 1.0
O A:HOH501 4.9 34.0 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 09:21:52 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