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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: Tue Jul 16 09:21:51 2024

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