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Calcium in PDB 7uox: NDM1-Inhibitor Co-Structure

Protein crystallography data

The structure of NDM1-Inhibitor Co-Structure, PDB code: 7uox was solved by G.Scapin, T.O.Fischmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 14.49 / 0.99
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 39.03, 78.81, 134.81, 90, 90, 90
R / Rfree (%) 13.7 / 14.8

Other elements in 7uox:

The structure of NDM1-Inhibitor Co-Structure also contains other interesting chemical elements:

Zinc (Zn) 4 atoms
Cadmium (Cd) 3 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the NDM1-Inhibitor Co-Structure (pdb code 7uox). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the NDM1-Inhibitor Co-Structure, PDB code: 7uox:

Calcium binding site 1 out of 1 in 7uox

Go back to Calcium Binding Sites List in 7uox
Calcium binding site 1 out of 1 in the NDM1-Inhibitor Co-Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of NDM1-Inhibitor Co-Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca302

b:8.2
occ:1.00
OD2 A:ASP95 2.3 13.7 1.0
O A:HOH655 2.3 24.6 1.0
OD2 A:ASP130 2.4 13.6 1.0
O A:HOH640 2.4 21.7 1.0
O A:HOH466 2.4 18.3 1.0
O A:HOH602 2.5 9.4 1.0
CG A:ASP95 3.2 10.3 1.0
CG A:ASP130 3.3 8.1 1.0
OD1 A:ASP95 3.4 11.3 1.0
CB A:ASP130 3.8 7.5 1.0
O A:HOH554 3.9 16.9 0.5
O A:GLY127 4.1 8.0 1.0
OD1 A:ASP130 4.2 9.4 1.0
O A:HOH554 4.3 12.2 0.5
O A:HOH499 4.4 11.0 1.0
CB A:ASP95 4.6 8.4 1.0
O A:HOH485 4.6 8.8 1.0
N A:ASP130 4.7 6.5 1.0
CG2 A:VAL155 4.7 9.2 1.0
CA A:ASP130 4.9 6.9 1.0

Reference:

M.Mandal, L.Xiao, W.Pan, G.Scapin, G.Li, H.Tang, S.W.Yang, J.Pan, Y.Root, R.K.De Jesus, C.Yang, W.Prosise, P.Dayananth, A.Mirza, A.G.Therien, K.Young, A.Flattery, C.Garlisi, R.Zhang, D.Chu, P.Sheth, I.Chu, J.Wu, C.Markgraf, H.Y.Kim, R.Painter, T.W.Mayhood, E.Dinunzio, D.F.Wyss, A.V.Buevich, T.Fischmann, A.Pasternak, S.Dong, J.D.Hicks, A.Villafania, L.Liang, N.Murgolo, T.Black, W.K.Hagmann, J.Tata, E.R.Parmee, A.E.Weber, J.Su, H.Tang. Rapid Evolution of A Fragment-Like Molecule to Pan-Metallo-Beta-Lactamase Inhibitors: Initial Leads Toward Clinical Candidates. J.Med.Chem. V. 65 16234 2022.
ISSN: ISSN 0022-2623
PubMed: 36475645
DOI: 10.1021/ACS.JMEDCHEM.2C00766
Page generated: Fri Jul 19 05:04:17 2024

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