Calcium in PDB 6tgd: Crystal Structure of Ndm-1 in Complex with Triazole-Based Inhibitor OP31

Protein crystallography data

The structure of Crystal Structure of Ndm-1 in Complex with Triazole-Based Inhibitor OP31, PDB code: 6tgd was solved by L.Maso, F.Spirakis, M.Santucci, C.Simon, J.D.Docquier, G.Cruciani, 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) 42.42 / 1.33
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 69.678, 73.665, 77.501, 90.00, 90.00, 90.00
R / Rfree (%) 18.5 / 20.7

Other elements in 6tgd:

The structure of Crystal Structure of Ndm-1 in Complex with Triazole-Based Inhibitor OP31 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 in Complex with Triazole-Based Inhibitor OP31 (pdb code 6tgd). 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 in Complex with Triazole-Based Inhibitor OP31, PDB code: 6tgd:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 6tgd

Go back to Calcium Binding Sites List in 6tgd
Calcium binding site 1 out of 4 in the Crystal Structure of Ndm-1 in Complex with Triazole-Based Inhibitor OP31


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 in Complex with Triazole-Based Inhibitor OP31 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:24.7
occ:1.00
O B:HOH477 2.2 32.5 1.0
O A:HOH544 2.4 27.6 1.0
O B:HOH527 2.5 32.7 1.0
OE2 B:GLU227 2.5 29.0 1.0
OD2 A:ASP223 2.5 23.7 1.0
OE1 B:GLU227 2.5 27.4 1.0
OE1 A:GLU152 2.7 21.5 1.0
OE2 A:GLU152 2.7 21.3 1.0
CD B:GLU227 2.9 26.0 1.0
OD1 A:ASP223 3.0 23.3 1.0
CD A:GLU152 3.1 21.6 1.0
CG A:ASP223 3.1 23.4 1.0
NE2 A:HIS122 4.1 18.7 1.0
CG B:GLU227 4.4 19.9 1.0
O A:HOH413 4.4 26.3 1.0
O B:HOH453 4.5 30.5 1.0
CB A:ASP223 4.6 21.8 1.0
CG A:GLU152 4.6 19.2 1.0
NE2 B:HIS228 4.7 17.6 1.0
CD2 A:HIS122 4.7 16.5 1.0
O A:HOH527 4.7 31.0 1.0
O A:HOH486 4.7 17.7 1.0
O A:HOH438 4.8 37.0 1.0
O A:HOH409 4.8 31.2 1.0
CE1 B:HIS228 4.9 17.0 1.0
O B:HOH513 5.0 26.9 1.0

Calcium binding site 2 out of 4 in 6tgd

Go back to Calcium Binding Sites List in 6tgd
Calcium binding site 2 out of 4 in the Crystal Structure of Ndm-1 in Complex with Triazole-Based Inhibitor OP31


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 in Complex with Triazole-Based Inhibitor OP31 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca304

b:22.4
occ:1.00
OD2 A:ASP130 2.3 22.6 1.0
OD2 A:ASP95 2.4 21.3 1.0
O A:HOH427 2.4 21.9 1.0
O A:HOH519 2.4 17.2 1.0
CG A:ASP130 3.3 18.6 1.0
CG A:ASP95 3.4 18.0 1.0
CB A:ASP130 3.7 16.4 1.0
OD1 A:ASP95 3.7 17.5 1.0
O A:GLY127 4.3 16.1 1.0
O A:HOH480 4.4 23.6 1.0
OD1 A:ASP130 4.4 22.8 1.0
O A:HOH448 4.4 19.1 1.0
O A:HOH440 4.6 17.3 1.0
N A:ASP130 4.7 14.9 1.0
CG2 A:VAL155 4.8 18.6 1.0
CB A:ASP95 4.8 17.7 1.0
CA A:ASP130 4.9 16.4 1.0

Calcium binding site 3 out of 4 in 6tgd

Go back to Calcium Binding Sites List in 6tgd
Calcium binding site 3 out of 4 in the Crystal Structure of Ndm-1 in Complex with Triazole-Based Inhibitor OP31


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 in Complex with Triazole-Based Inhibitor OP31 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca303

b:26.0
occ:1.00
OD2 B:ASP95 2.3 18.0 1.0
O B:HOH561 2.5 25.5 1.0
OD2 B:ASP130 2.5 20.4 1.0
O B:HOH424 2.6 26.7 1.0
O B:HOH464 2.7 16.0 1.0
CG B:ASP95 3.3 16.3 1.0
CG B:ASP130 3.5 17.7 1.0
OD1 B:ASP95 3.6 17.5 1.0
CB B:ASP130 3.8 13.8 1.0
O B:HOH512 4.4 22.3 1.0
O B:HOH444 4.5 16.8 1.0
O B:GLY127 4.5 15.0 1.0
OD1 B:ASP130 4.5 19.7 1.0
CG2 B:VAL155 4.6 14.2 1.0
CB B:ASP95 4.7 15.5 1.0
O B:HOH454 4.8 15.1 1.0
N B:ASP130 4.8 12.8 1.0
CA B:ASP130 4.9 13.5 1.0

Calcium binding site 4 out of 4 in 6tgd

Go back to Calcium Binding Sites List in 6tgd
Calcium binding site 4 out of 4 in the Crystal Structure of Ndm-1 in Complex with Triazole-Based Inhibitor OP31


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 in Complex with Triazole-Based Inhibitor OP31 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca304

b:28.9
occ:1.00
O A:HOH403 2.0 33.7 1.0
O B:HOH541 2.4 29.0 1.0
O B:HOH498 2.4 36.7 1.0
OE2 A:GLU227 2.5 30.7 1.0
OE1 A:GLU227 2.5 28.4 1.0
OE1 B:GLU152 2.6 20.5 1.0
OE2 B:GLU152 2.6 18.8 1.0
OD2 B:ASP223 2.7 30.6 1.0
CD A:GLU227 2.9 23.8 1.0
CD B:GLU152 2.9 20.9 1.0
OD1 B:ASP223 3.3 34.0 1.0
CG B:ASP223 3.4 33.3 1.0
NE2 B:HIS122 4.1 17.2 1.0
CG A:GLU227 4.4 22.9 1.0
CG B:GLU152 4.4 16.5 1.0
O B:HOH415 4.5 18.1 1.0
NE2 A:HIS228 4.5 15.6 1.0
O B:HOH447 4.6 19.9 1.0
CD2 B:HIS122 4.7 18.1 1.0
CE1 A:HIS228 4.9 14.7 1.0
CB B:ASP223 4.9 31.0 1.0

Reference:

F.Spyrakis, M.Santucci, L.Maso, S.Cross, E.Gianquinto, F.Sannio, F.Verdirosa, F.De Luca, J.D.Docquier, L.Cendron, D.Tondi, A.Venturelli, G.Cruciani, M.P.Costi. Virtual Screening Identifies Broad-Spectrum Beta-Lactamase Inhibitors with Activity on Clinically Relevant Serine- and Metallo-Carbapenemases. Sci Rep V. 10 12763 2020.
ISSN: ESSN 2045-2322
PubMed: 32728062
DOI: 10.1038/S41598-020-69431-Y
Page generated: Sat Dec 12 07:42:11 2020

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