Atomistry » Cadmium » PDB 7icu-7vip » 7up3
Atomistry »
  Cadmium »
    PDB 7icu-7vip »
      7up3 »

Cadmium in PDB 7up3: NDM1-Inhibitor Co-Structure

Protein crystallography data

The structure of NDM1-Inhibitor Co-Structure, PDB code: 7up3 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) 31.72 / 1.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 69.564, 73.913, 77.325, 90, 90, 90
R / Rfree (%) 18 / 19

Other elements in 7up3:

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

Zinc (Zn) 2 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the NDM1-Inhibitor Co-Structure (pdb code 7up3). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 6 binding sites of Cadmium where determined in the NDM1-Inhibitor Co-Structure, PDB code: 7up3:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6;

Cadmium binding site 1 out of 6 in 7up3

Go back to Cadmium Binding Sites List in 7up3
Cadmium binding site 1 out of 6 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:Cd301

b:19.6
occ:1.00
OE2 A:GLU152 2.3 20.2 1.0
O A:HOH513 2.3 28.6 1.0
OE2 B:GLU227 2.3 25.8 1.0
OD2 A:ASP223 2.3 17.6 1.0
OE1 B:GLU227 2.4 23.5 1.0
OE1 A:GLU152 2.5 20.2 1.0
CD A:GLU152 2.7 21.5 1.0
CD B:GLU227 2.7 23.5 1.0
CG A:ASP223 3.0 21.5 1.0
OD1 A:ASP223 3.0 23.0 1.0
NE2 A:HIS122 4.2 16.4 1.0
CG A:GLU152 4.2 16.8 1.0
CG B:GLU227 4.2 19.9 1.0
O A:HOH477 4.3 17.9 1.0
NE2 B:HIS228 4.3 16.3 1.0
O A:HOH487 4.4 36.5 1.0
CB A:ASP223 4.5 18.6 1.0
CE1 B:HIS228 4.5 16.3 1.0
O A:HOH438 4.6 23.8 1.0
CD2 A:HIS122 4.7 16.0 1.0
O B:HOH513 4.9 22.6 1.0

Cadmium binding site 2 out of 6 in 7up3

Go back to Cadmium Binding Sites List in 7up3
Cadmium binding site 2 out of 6 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
A:Cd302

b:18.0
occ:0.70
OD2 A:ASP130 2.2 22.7 1.0
OD2 A:ASP95 2.3 23.6 1.0
O A:HOH496 2.3 17.1 1.0
CG A:ASP130 3.2 19.6 1.0
CG A:ASP95 3.2 21.6 1.0
OD1 A:ASP95 3.4 20.0 1.0
CB A:ASP130 3.6 16.8 1.0
O A:GLY127 4.1 16.2 1.0
OD1 A:ASP130 4.2 20.8 1.0
O A:HOH486 4.3 21.2 1.0
O A:HOH488 4.3 24.8 1.0
O A:HOH451 4.5 15.6 1.0
N A:ASP130 4.5 15.3 1.0
CB A:ASP95 4.6 17.3 1.0
CA A:ASP130 4.7 16.2 1.0
CG2 A:VAL155 4.7 20.0 1.0

Cadmium binding site 3 out of 6 in 7up3

Go back to Cadmium Binding Sites List in 7up3
Cadmium binding site 3 out of 6 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
A:Cd304

b:17.9
occ:1.00
OD2 A:ASP124 2.2 17.4 1.0
N3 A:NZ0305 2.2 20.9 1.0
NE2 A:HIS250 2.3 16.8 1.0
N4 A:NZ0305 2.5 16.8 1.0
SG A:CYS208 2.5 17.7 1.0
N2 A:NZ0305 3.2 23.9 1.0
CG A:ASP124 3.2 17.3 1.0
C5 A:NZ0305 3.3 21.4 1.0
CE1 A:HIS250 3.3 16.7 1.0
CD2 A:HIS250 3.3 17.5 1.0
C4 A:NZ0305 3.5 24.5 1.0
S A:NZ0305 3.5 19.8 1.0
CB A:CYS208 3.6 15.9 1.0
OD1 A:ASP124 3.6 18.3 1.0
C6 A:NZ0305 3.6 22.6 1.0
ZN A:ZN303 3.7 15.8 1.0
O A:NZ0305 4.1 20.3 1.0
N1 A:NZ0305 4.3 23.5 1.0
NE2 A:HIS189 4.3 13.8 1.0
N A:NZ0305 4.4 22.8 1.0
CG A:HIS250 4.4 18.8 1.0
ND1 A:HIS250 4.4 19.1 1.0
N5 A:NZ0305 4.4 24.6 1.0
CB A:SER249 4.5 16.4 1.0
C3 A:NZ0305 4.5 26.3 1.0
CB A:ASP124 4.6 15.1 1.0
CE1 A:HIS189 4.6 15.5 1.0
O1 A:NZ0305 4.7 19.9 1.0
CA A:CYS208 4.7 16.1 1.0
OG A:SER249 4.7 16.4 1.0
NE2 A:HIS120 4.8 16.1 1.0
CE1 A:HIS120 4.8 17.2 1.0

Cadmium binding site 4 out of 6 in 7up3

Go back to Cadmium Binding Sites List in 7up3
Cadmium binding site 4 out of 6 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 4 of NDM1-Inhibitor Co-Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd301

b:19.8
occ:1.00
OD2 B:ASP223 2.2 18.8 1.0
OE2 B:GLU152 2.3 19.6 1.0
OE2 A:GLU227 2.3 26.5 1.0
O B:HOH539 2.3 30.8 1.0
OE1 A:GLU227 2.4 27.0 1.0
OE1 B:GLU152 2.5 19.5 1.0
CD A:GLU227 2.7 24.8 1.0
CD B:GLU152 2.7 18.4 1.0
CG B:ASP223 3.0 18.8 1.0
OD1 B:ASP223 3.1 22.3 1.0
NE2 B:HIS122 4.2 16.7 1.0
CG A:GLU227 4.2 22.6 1.0
CG B:GLU152 4.2 16.2 1.0
NE2 A:HIS228 4.2 18.8 1.0
O B:HOH512 4.3 19.3 1.0
O A:HOH432 4.4 45.3 1.0
CB B:ASP223 4.4 16.2 1.0
O B:HOH489 4.4 29.8 1.0
CE1 A:HIS228 4.5 18.4 1.0
O B:HOH438 4.6 22.0 1.0
CD2 B:HIS122 4.7 15.8 1.0
O A:HOH473 4.8 23.3 1.0

Cadmium binding site 5 out of 6 in 7up3

Go back to Cadmium Binding Sites List in 7up3
Cadmium binding site 5 out of 6 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 5 of NDM1-Inhibitor Co-Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd302

b:20.2
occ:0.70
O B:HOH473 2.3 26.8 1.0
OD2 B:ASP95 2.3 21.3 1.0
OD2 B:ASP130 2.3 27.3 1.0
O B:HOH484 2.4 17.0 1.0
O B:HOH550 2.4 24.8 1.0
CG B:ASP95 3.2 19.5 1.0
CG B:ASP130 3.2 25.1 1.0
OD1 B:ASP95 3.3 20.0 1.0
CB B:ASP130 3.6 16.6 1.0
O B:HOH423 4.1 20.9 1.0
O B:GLY127 4.2 16.5 1.0
O B:HOH492 4.3 24.1 1.0
OD1 B:ASP130 4.3 25.9 1.0
O B:HOH563 4.4 28.6 1.0
O B:HOH461 4.4 21.1 1.0
N B:ASP130 4.5 14.8 1.0
O B:HOH465 4.5 15.3 1.0
CB B:ASP95 4.6 17.8 1.0
CG2 B:VAL155 4.6 20.6 1.0
CA B:ASP130 4.7 14.9 1.0

Cadmium binding site 6 out of 6 in 7up3

Go back to Cadmium Binding Sites List in 7up3
Cadmium binding site 6 out of 6 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 6 of NDM1-Inhibitor Co-Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd304

b:16.6
occ:1.00
OD2 B:ASP124 2.2 18.6 1.0
N3 B:NZ0305 2.2 19.6 1.0
NE2 B:HIS250 2.3 16.3 1.0
N4 B:NZ0305 2.4 17.1 1.0
SG B:CYS208 2.5 16.2 1.0
N2 B:NZ0305 3.2 17.5 1.0
CG B:ASP124 3.2 18.2 1.0
CD2 B:HIS250 3.2 16.4 1.0
C5 B:NZ0305 3.3 22.1 1.0
CE1 B:HIS250 3.3 16.7 1.0
S B:NZ0305 3.5 18.3 1.0
C4 B:NZ0305 3.5 21.6 1.0
CB B:CYS208 3.5 12.6 1.0
C6 B:NZ0305 3.6 19.5 1.0
OD1 B:ASP124 3.6 17.4 1.0
ZN B:ZN303 3.7 15.5 1.0
O B:NZ0305 4.1 17.8 1.0
N1 B:NZ0305 4.3 20.1 1.0
NE2 B:HIS189 4.4 13.3 1.0
N B:NZ0305 4.4 20.4 1.0
CB B:SER249 4.4 12.5 1.0
CG B:HIS250 4.4 16.5 1.0
ND1 B:HIS250 4.4 16.2 1.0
N5 B:NZ0305 4.4 21.8 1.0
C3 B:NZ0305 4.5 25.1 1.0
CB B:ASP124 4.5 14.2 1.0
CE1 B:HIS189 4.6 13.8 1.0
O1 B:NZ0305 4.7 21.1 1.0
CA B:CYS208 4.7 13.3 1.0
OG B:SER249 4.7 13.2 1.0
NE2 B:HIS120 4.7 13.6 1.0
CE1 B:HIS120 4.7 14.9 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: Thu Jul 10 15:36:35 2025

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy