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Cadmium in PDB 7up1: NDM1-Inhibitor Co-Structure

Protein crystallography data

The structure of NDM1-Inhibitor Co-Structure, PDB code: 7up1 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) 16.25 / 1.11
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 39.038, 79.062, 134.175, 90, 90, 90
R / Rfree (%) 13.4 / 14.4

Other elements in 7up1:

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

Zinc (Zn) 4 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the NDM1-Inhibitor Co-Structure (pdb code 7up1). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 3 binding sites of Cadmium where determined in the NDM1-Inhibitor Co-Structure, PDB code: 7up1:
Jump to Cadmium binding site number: 1; 2; 3;

Cadmium binding site 1 out of 3 in 7up1

Go back to Cadmium Binding Sites List in 7up1
Cadmium binding site 1 out of 3 in the NDM1-Inhibitor Co-Structure


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of NDM1-Inhibitor Co-Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd303

b:8.3
occ:1.00
OD2 A:ASP223 2.2 8.5 1.0
O B:HOH634 2.3 22.4 1.0
OE2 A:GLU152 2.3 9.2 1.0
OE2 B:GLU227 2.3 13.8 1.0
OE1 A:GLU152 2.4 9.4 1.0
OE1 B:GLU227 2.5 11.5 1.0
CD B:GLU227 2.7 9.9 1.0
CD A:GLU152 2.8 7.6 1.0
CG A:ASP223 2.9 7.7 1.0
OD1 A:ASP223 3.0 9.0 1.0
NE2 A:HIS122 4.2 6.4 1.0
O A:HOH559 4.2 8.8 1.0
CG B:GLU227 4.3 9.4 1.0
CG A:GLU152 4.3 7.8 1.0
NE2 B:HIS228 4.3 8.4 1.0
CB A:ASP223 4.4 6.9 1.0
O A:HOH532 4.4 29.9 1.0
O B:HOH428 4.4 28.9 1.0
O A:HOH463 4.5 12.3 1.0
O A:HOH581 4.6 16.5 1.0
CE1 B:HIS228 4.6 8.5 1.0
CD2 A:HIS122 4.7 6.4 1.0
O B:HOH548 4.8 14.9 1.0

Cadmium binding site 2 out of 3 in 7up1

Go back to Cadmium Binding Sites List in 7up1
Cadmium binding site 2 out of 3 in the NDM1-Inhibitor Co-Structure


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of NDM1-Inhibitor Co-Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd303

b:8.2
occ:1.00
OD2 B:ASP223 2.2 9.1 1.0
OE2 B:GLU152 2.3 8.5 1.0
OE1 A:GLU227 2.4 11.2 1.0
OE2 A:GLU227 2.4 10.9 1.0
OE1 B:GLU152 2.5 8.6 1.0
O A:HOH645 2.5 8.2 1.0
CD B:GLU152 2.8 7.2 1.0
CD A:GLU227 2.8 7.7 1.0
OD1 B:ASP223 2.9 9.4 1.0
CG B:ASP223 2.9 7.7 1.0
O B:HOH653 3.8 78.8 1.0
O B:HOH589 4.1 13.2 0.5
O B:HOH586 4.2 8.7 1.0
NE2 A:HIS228 4.3 8.5 1.0
CG B:GLU152 4.3 7.0 1.0
CG A:GLU227 4.3 8.7 1.0
NE2 B:HIS122 4.3 6.4 1.0
CB B:ASP223 4.4 7.7 1.0
O B:HOH589 4.4 16.9 0.5
CE1 A:HIS228 4.5 8.0 1.0
O A:HOH402 4.5 17.9 1.0
O B:HOH444 4.6 31.1 1.0
O B:HOH641 4.6 33.4 1.0
O A:HOH585 4.7 14.2 1.0
O B:HOH462 4.7 13.8 1.0
CD2 B:HIS122 4.9 7.0 1.0

Cadmium binding site 3 out of 3 in 7up1

Go back to Cadmium Binding Sites List in 7up1
Cadmium binding site 3 out of 3 in the NDM1-Inhibitor Co-Structure


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of NDM1-Inhibitor Co-Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd304

b:8.5
occ:1.00
OD2 B:ASP95 2.2 9.8 1.0
OD2 B:ASP130 2.3 9.0 1.0
O B:HOH483 2.4 9.2 1.0
O B:HOH568 2.4 7.5 1.0
CG B:ASP95 3.1 7.8 1.0
CG B:ASP130 3.2 8.2 1.0
OD1 B:ASP95 3.3 8.6 1.0
CB B:ASP130 3.6 8.4 1.0
O B:GLY127 4.0 6.6 1.0
O B:HOH579 4.1 18.1 1.0
O B:HOH463 4.2 23.4 1.0
O B:HOH574 4.2 11.6 1.0
O B:HOH504 4.3 7.4 1.0
O B:HOH661 4.3 26.0 1.0
OD1 B:ASP130 4.4 10.0 1.0
O B:HOH517 4.4 6.3 1.0
CB B:ASP95 4.5 7.6 1.0
N B:ASP130 4.5 6.6 1.0
CG2 B:VAL155 4.7 8.2 1.0
CA B:ASP130 4.7 7.4 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 20:13:44 2024

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