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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

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