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

Enzymatic activity of Crystal Structure of Ndm-1 Beta-Lactamase in Complex with Boronic Inhibitor Cpd 6

All present enzymatic activity of Crystal Structure of Ndm-1 Beta-Lactamase in Complex with Boronic Inhibitor Cpd 6:
3.5.2.6;

Protein crystallography data

The structure of Crystal Structure of Ndm-1 Beta-Lactamase in Complex with Boronic Inhibitor Cpd 6, PDB code: 6ibs 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) 42.59 / 1.37
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 70.285, 73.737, 77.613, 90.00, 90.00, 90.00
R / Rfree (%) 13.2 / 16.3

Other elements in 6ibs:

The structure of Crystal Structure of Ndm-1 Beta-Lactamase in Complex with Boronic Inhibitor Cpd 6 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 Boronic Inhibitor Cpd 6 (pdb code 6ibs). 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 Boronic Inhibitor Cpd 6, PDB code: 6ibs:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 6ibs

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


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 Boronic Inhibitor Cpd 6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca304

b:18.4
occ:1.00
 O B:HOH455 2.3 33.4 1.0
OD2 A:ASP223 2.4 9.2 0.5
O A:HOH421 2.4 27.7 1.0
O B:HOH458 2.4 35.0 1.0
OD2 A:ASP223 2.5 28.9 0.5
OE1 B:GLU227 2.5 32.5 1.0
OE2 A:GLU152 2.5 16.9 1.0
OE2 B:GLU227 2.5 30.4 1.0
OE1 A:GLU152 2.6 14.5 1.0
CD B:GLU227 2.9 26.6 1.0
OD1 A:ASP223 2.9 21.5 0.5
OD1 A:ASP223 2.9 14.3 0.5
CD A:GLU152 2.9 15.4 1.0
CG A:ASP223 3.0 10.4 0.5
CG A:ASP223 3.0 19.3 0.5
NE2 A:HIS122 4.2 12.6 1.0
O B:HOH410 4.3 35.3 1.0
CG B:GLU227 4.4 20.1 1.0
NE2 B:HIS228 4.4 13.8 1.0
CG A:GLU152 4.5 13.6 1.0
CB A:ASP223 4.5 11.9 0.5
O B:HOH407 4.5 33.2 1.0
CB A:ASP223 4.5 19.4 0.5
O A:HOH492 4.5 15.1 1.0
O A:HOH443 4.6 17.1 1.0
CE1 B:HIS228 4.6 14.5 1.0
CD2 A:HIS122 4.9 12.5 1.0

Calcium binding site 2 out of 4 in 6ibs

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


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 Boronic Inhibitor Cpd 6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca305

b:19.4
occ:1.00
 OD2 A:ASP130 2.3 17.9 1.0
OD2 A:ASP95 2.3 17.5 1.0
O A:HOH553 2.3 24.4 1.0
O A:HOH554 2.4 24.9 1.0
O A:HOH465 2.4 28.2 1.0
O A:HOH449 2.5 18.4 1.0
O A:HOH529 2.5 13.9 1.0
CG A:ASP95 3.4 13.5 1.0
CG A:ASP130 3.4 13.7 1.0
CB A:ASP130 3.8 13.1 1.0
OD1 A:ASP95 3.8 12.9 1.0
O A:HOH491 4.3 18.3 1.0
O A:GLY127 4.3 11.6 1.0
O A:HOH459 4.4 16.3 1.0
OD1 A:ASP130 4.5 17.6 1.0
O A:HOH557 4.6 35.4 1.0
O A:HOH448 4.6 12.1 1.0
CB A:ASP95 4.7 11.9 1.0
N A:ASP130 4.8 10.0 1.0
CG2 A:VAL155 4.8 14.3 1.0
CA A:ASP130 4.9 11.8 1.0

Calcium binding site 3 out of 4 in 6ibs

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


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 Boronic Inhibitor Cpd 6 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca304

b:14.7
occ:1.00
 OD2 B:ASP223 2.4 15.0 1.0
O A:HOH510 2.4 25.8 1.0
O B:HOH542 2.4 22.0 1.0
O A:HOH511 2.4 22.9 1.0
OE2 B:GLU152 2.5 13.7 1.0
OE2 A:GLU227 2.5 21.0 1.0
OE1 B:GLU152 2.6 12.4 1.0
OE1 A:GLU227 2.7 24.6 1.0
CD B:GLU152 2.9 10.6 1.0
OD1 B:ASP223 2.9 17.9 1.0
CD A:GLU227 2.9 19.4 1.0
CG B:ASP223 3.0 14.4 1.0
NE2 B:HIS122 4.2 10.8 1.0
O B:HOH408 4.3 33.4 1.0
NE2 A:HIS228 4.4 11.0 1.0
CG B:GLU152 4.4 11.4 1.0
O A:HOH408 4.4 34.4 1.0
CB B:ASP223 4.4 13.2 1.0
CG A:GLU227 4.4 17.7 1.0
O B:HOH428 4.5 14.9 1.0
O B:HOH505 4.6 12.8 1.0
CE1 A:HIS228 4.7 11.8 1.0
CD2 B:HIS122 4.8 10.7 1.0

Calcium binding site 4 out of 4 in 6ibs

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


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 Boronic Inhibitor Cpd 6 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca305

b:22.8
occ:1.00
 OD2 B:ASP95 2.3 16.9 1.0
O B:HOH567 2.4 26.3 1.0
OD2 B:ASP130 2.5 20.1 1.0
O B:HOH429 2.7 29.5 1.0
O B:HOH495 2.7 12.1 1.0
CG B:ASP95 3.3 12.9 1.0
CG B:ASP130 3.5 15.6 1.0
OD1 B:ASP95 3.5 15.1 1.0
CB B:ASP130 3.8 11.1 1.0
O B:HOH434 4.0 15.3 1.0
O B:GLY127 4.3 11.0 1.0
O B:HOH522 4.3 21.8 1.0
O B:HOH467 4.5 13.1 1.0
OD1 B:ASP130 4.6 17.9 1.0
CB B:ASP95 4.6 10.6 1.0
CG2 B:VAL155 4.7 10.2 1.0
O B:HOH444 4.7 11.2 1.0
N B:ASP130 4.8 10.0 1.0
CA B:ASP130 5.0 9.7 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: Sat Dec 12 06:11:09 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy