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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: Wed Jul 9 17:02:09 2025

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