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Calcium in PDB 6q30: Crystal Structure of Ndm-1 Beta-Lactamase in Complex with Boronic Inhibitor Cpd 5

Enzymatic activity of Crystal Structure of Ndm-1 Beta-Lactamase in Complex with Boronic Inhibitor Cpd 5

All present enzymatic activity of Crystal Structure of Ndm-1 Beta-Lactamase in Complex with Boronic Inhibitor Cpd 5:
3.5.2.6;

Protein crystallography data

The structure of Crystal Structure of Ndm-1 Beta-Lactamase in Complex with Boronic Inhibitor Cpd 5, PDB code: 6q30 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) 42.52 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 70.250, 73.748, 77.276, 90.00, 90.00, 90.00
R / Rfree (%) 13.9 / 19.1

Other elements in 6q30:

The structure of Crystal Structure of Ndm-1 Beta-Lactamase in Complex with Boronic Inhibitor Cpd 5 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 5 (pdb code 6q30). 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 5, PDB code: 6q30:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 6q30

Go back to Calcium Binding Sites List in 6q30
Calcium binding site 1 out of 4 in the Crystal Structure of Ndm-1 Beta-Lactamase in Complex with Boronic Inhibitor Cpd 5


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 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:20.6
occ:1.00
 OD2 A:ASP223 2.4 16.5 1.0
O B:HOH533 2.4 36.7 1.0
O A:HOH540 2.5 34.0 1.0
OE2 B:GLU227 2.5 36.4 1.0
O B:HOH428 2.5 32.0 1.0
OE2 A:GLU152 2.5 18.5 1.0
OE1 A:GLU152 2.6 18.9 1.0
OE1 B:GLU227 2.6 42.2 1.0
CD B:GLU227 2.9 25.5 1.0
CD A:GLU152 2.9 17.7 1.0
OD1 A:ASP223 3.0 18.2 1.0
CG A:ASP223 3.0 17.5 1.0
NE2 A:HIS122 4.2 14.2 1.0
O B:HOH405 4.2 49.7 1.0
CG B:GLU227 4.4 18.7 1.0
CG A:GLU152 4.4 19.2 1.0
NE2 B:HIS228 4.4 15.5 1.0
O A:HOH431 4.5 24.4 1.0
CB A:ASP223 4.5 16.8 1.0
O A:HOH506 4.6 18.4 1.0
O B:HOH407 4.6 34.8 1.0
CE1 B:HIS228 4.6 16.4 1.0
CD2 A:HIS122 4.8 14.3 1.0

Calcium binding site 2 out of 4 in 6q30

Go back to Calcium Binding Sites List in 6q30
Calcium binding site 2 out of 4 in the Crystal Structure of Ndm-1 Beta-Lactamase in Complex with Boronic Inhibitor Cpd 5


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

b:29.1
occ:1.00
 O A:HOH547 2.3 37.1 1.0
OD2 A:ASP130 2.3 28.3 1.0
OD2 A:ASP95 2.4 24.4 1.0
O A:HOH557 2.5 41.5 1.0
O A:HOH512 2.5 17.9 1.0
O A:HOH432 2.6 37.0 1.0
O A:HOH417 2.7 30.8 1.0
CG A:ASP130 3.3 25.4 1.0
CG A:ASP95 3.4 18.0 1.0
OD1 A:ASP95 3.7 16.5 1.0
CB A:ASP130 3.8 18.1 1.0
O A:GLY127 4.3 15.9 1.0
O A:HOH465 4.3 25.1 1.0
OD1 A:ASP130 4.4 23.8 1.0
O A:HOH464 4.4 21.7 1.0
O A:HOH453 4.6 15.6 1.0
O A:HOH555 4.6 52.3 1.0
CG2 A:VAL155 4.7 18.7 1.0
N A:ASP130 4.7 13.7 1.0
CB A:ASP95 4.8 16.2 1.0
CA A:ASP130 4.8 16.1 1.0

Calcium binding site 3 out of 4 in 6q30

Go back to Calcium Binding Sites List in 6q30
Calcium binding site 3 out of 4 in the Crystal Structure of Ndm-1 Beta-Lactamase in Complex with Boronic Inhibitor Cpd 5


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 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca303

b:16.7
occ:1.00
 OD2 B:ASP223 2.4 16.6 1.0
O A:HOH430 2.4 32.8 1.0
O A:HOH505 2.4 23.3 1.0
OE2 A:GLU227 2.5 25.9 1.0
OE2 B:GLU152 2.5 15.9 1.0
O B:HOH539 2.5 25.3 1.0
OE1 A:GLU227 2.6 27.9 1.0
OE1 B:GLU152 2.6 15.9 1.0
CD B:GLU152 2.9 13.2 1.0
CD A:GLU227 2.9 16.2 1.0
OD1 B:ASP223 2.9 20.2 1.0
CG B:ASP223 3.0 13.6 1.0
NE2 B:HIS122 4.3 13.7 1.0
CG B:GLU152 4.4 13.5 1.0
CG A:GLU227 4.4 18.6 1.0
CB B:ASP223 4.4 15.2 1.0
NE2 A:HIS228 4.4 13.5 1.0
O B:HOH418 4.5 17.2 1.0
O B:HOH496 4.5 14.1 1.0
O B:HOH416 4.6 36.2 1.0
CE1 A:HIS228 4.8 15.4 1.0
CD2 B:HIS122 4.9 13.1 1.0

Calcium binding site 4 out of 4 in 6q30

Go back to Calcium Binding Sites List in 6q30
Calcium binding site 4 out of 4 in the Crystal Structure of Ndm-1 Beta-Lactamase in Complex with Boronic Inhibitor Cpd 5


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 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca304

b:27.0
occ:1.00
 OD2 B:ASP95 2.3 22.4 1.0
O B:HOH564 2.4 26.4 1.0
OD2 B:ASP130 2.5 20.8 1.0
O B:HOH476 2.6 14.4 1.0
O B:HOH404 2.9 41.8 1.0
CG B:ASP95 3.3 14.8 1.0
CG B:ASP130 3.4 20.4 1.0
OD1 B:ASP95 3.5 19.4 1.0
CB B:ASP130 3.9 16.6 1.0
O B:HOH438 4.0 17.1 1.0
O B:HOH509 4.3 22.8 1.0
O B:GLY127 4.3 14.2 1.0
O B:HOH472 4.4 16.5 1.0
OD1 B:ASP130 4.5 21.8 1.0
CB B:ASP95 4.6 14.0 1.0
CG2 B:VAL155 4.7 13.9 1.0
O B:HOH465 4.7 12.7 1.0
N B:ASP130 4.8 12.1 1.0
CA B:ASP130 5.0 15.0 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: Wed Jul 9 17:02:23 2025

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