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Zinc 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:

Cadmium (Cd) 3 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the NDM1-Inhibitor Co-Structure (pdb code 7up1). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the NDM1-Inhibitor Co-Structure, PDB code: 7up1:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 7up1

Go back to Zinc Binding Sites List in 7up1
Zinc binding site 1 out of 4 in the NDM1-Inhibitor Co-Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of NDM1-Inhibitor Co-Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:5.7
occ:1.00
NE2 A:HIS189 2.0 5.1 1.0
NE2 A:HIS120 2.0 5.8 1.0
ND1 A:HIS122 2.0 5.2 1.0
N4 A:NZR304 2.0 6.0 1.0
S A:NZR304 2.9 6.0 1.0
O1 A:NZR304 3.0 6.3 1.0
CD2 A:HIS189 3.0 4.9 1.0
CE1 A:HIS120 3.0 6.2 1.0
CE1 A:HIS122 3.0 6.1 1.0
CD2 A:HIS120 3.0 5.5 1.0
CE1 A:HIS189 3.0 5.7 1.0
CG A:HIS122 3.1 5.5 1.0
CB A:HIS122 3.4 5.3 1.0
O A:NZR304 3.5 7.4 1.0
ZN A:ZN302 3.8 3.6 1.0
OD1 A:ASP124 4.0 6.9 1.0
SG A:CYS208 4.1 5.8 1.0
CG A:HIS189 4.1 4.9 1.0
ND1 A:HIS120 4.1 6.7 1.0
CG A:HIS120 4.1 5.3 1.0
NE2 A:HIS122 4.2 6.4 1.0
N A:NZR304 4.2 6.1 1.0
ND1 A:HIS189 4.2 5.6 1.0
CD2 A:HIS122 4.2 6.4 1.0
CB A:CYS208 4.3 5.2 1.0
CG2 A:THR190 4.5 6.1 1.0
C11 A:NZR304 4.5 6.8 1.0
N1 A:NZR304 4.7 7.0 1.0
C10 A:NZR304 4.7 6.6 1.0
OD2 A:ASP124 4.8 6.7 1.0
CA A:HIS122 4.8 4.9 1.0
CG A:ASP124 4.8 5.7 1.0

Zinc binding site 2 out of 4 in 7up1

Go back to Zinc Binding Sites List in 7up1
Zinc binding site 2 out of 4 in the NDM1-Inhibitor Co-Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of NDM1-Inhibitor Co-Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:3.6
occ:1.00
OD2 A:ASP124 2.1 6.7 1.0
N A:NZR304 2.2 6.1 1.0
NE2 A:HIS250 2.2 5.4 1.0
SG A:CYS208 2.4 5.8 1.0
N4 A:NZR304 2.5 6.0 1.0
N1 A:NZR304 3.1 7.0 1.0
CG A:ASP124 3.1 5.7 1.0
C10 A:NZR304 3.2 6.6 1.0
CE1 A:HIS250 3.2 5.9 1.0
CD2 A:HIS250 3.2 6.1 1.0
CB A:CYS208 3.4 5.2 1.0
OD1 A:ASP124 3.5 6.9 1.0
C9 A:NZR304 3.5 7.0 1.0
S A:NZR304 3.6 6.0 1.0
C11 A:NZR304 3.6 6.8 1.0
ZN A:ZN301 3.8 5.7 1.0
N2 A:NZR304 4.3 6.6 1.0
O1 A:NZR304 4.3 6.3 1.0
N3 A:NZR304 4.3 7.4 1.0
CB A:SER249 4.3 6.4 1.0
CG A:HIS250 4.4 6.1 1.0
ND1 A:HIS250 4.4 6.4 1.0
NE2 A:HIS189 4.4 5.1 1.0
CB A:ASP124 4.5 5.8 1.0
C1 A:NZR304 4.5 7.9 1.0
CA A:CYS208 4.6 5.6 1.0
C12 A:NZR304 4.6 7.5 1.0
CE1 A:HIS189 4.6 5.7 1.0
OG A:SER249 4.7 6.0 1.0
O A:NZR304 4.7 7.4 1.0
CE1 A:HIS120 4.7 6.2 1.0
NE2 A:HIS120 4.7 5.8 1.0

Zinc binding site 3 out of 4 in 7up1

Go back to Zinc Binding Sites List in 7up1
Zinc binding site 3 out of 4 in the NDM1-Inhibitor Co-Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of NDM1-Inhibitor Co-Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:5.8
occ:1.00
NE2 B:HIS189 2.0 5.5 1.0
N4 B:NZR305 2.0 5.9 1.0
NE2 B:HIS120 2.0 6.0 1.0
ND1 B:HIS122 2.0 5.3 1.0
S B:NZR305 2.9 6.0 1.0
O1 B:NZR305 3.0 6.5 1.0
CD2 B:HIS189 3.0 5.2 1.0
CE1 B:HIS120 3.0 6.2 1.0
CE1 B:HIS189 3.0 5.3 1.0
CD2 B:HIS120 3.0 5.5 1.0
CE1 B:HIS122 3.0 6.2 1.0
CG B:HIS122 3.0 5.4 1.0
CB B:HIS122 3.3 5.0 1.0
O B:NZR305 3.5 7.4 1.0
ZN B:ZN302 3.8 3.5 1.0
OD1 B:ASP124 4.0 7.0 1.0
CG B:HIS189 4.1 5.0 1.0
ND1 B:HIS120 4.1 6.5 1.0
CG B:HIS120 4.1 5.5 1.0
ND1 B:HIS189 4.2 5.4 1.0
N B:NZR305 4.2 6.2 1.0
NE2 B:HIS122 4.2 6.4 1.0
SG B:CYS208 4.2 6.1 1.0
CD2 B:HIS122 4.2 7.0 1.0
CB B:CYS208 4.3 5.7 1.0
CG2 B:THR190 4.5 5.9 1.0
C11 B:NZR305 4.5 7.5 1.0
N1 B:NZR305 4.6 6.7 1.0
C10 B:NZR305 4.7 6.3 1.0
OD2 B:ASP124 4.8 7.0 1.0
CA B:HIS122 4.8 5.0 1.0
CG B:ASP124 4.8 5.8 1.0

Zinc binding site 4 out of 4 in 7up1

Go back to Zinc Binding Sites List in 7up1
Zinc binding site 4 out of 4 in the NDM1-Inhibitor Co-Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of NDM1-Inhibitor Co-Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:3.5
occ:1.00
OD2 B:ASP124 2.1 7.0 1.0
N B:NZR305 2.2 6.2 1.0
NE2 B:HIS250 2.2 5.7 1.0
SG B:CYS208 2.4 6.1 1.0
N4 B:NZR305 2.4 5.9 1.0
N1 B:NZR305 3.1 6.7 1.0
CG B:ASP124 3.1 5.8 1.0
C10 B:NZR305 3.2 6.3 1.0
CD2 B:HIS250 3.2 6.1 1.0
CE1 B:HIS250 3.2 6.2 1.0
CB B:CYS208 3.4 5.7 1.0
OD1 B:ASP124 3.5 7.0 1.0
S B:NZR305 3.5 6.0 1.0
C9 B:NZR305 3.5 7.1 1.0
C11 B:NZR305 3.6 7.5 1.0
ZN B:ZN301 3.8 5.8 1.0
O1 B:NZR305 4.2 6.5 1.0
N2 B:NZR305 4.3 6.9 1.0
N3 B:NZR305 4.3 7.0 1.0
ND1 B:HIS250 4.4 6.6 1.0
CG B:HIS250 4.4 6.5 1.0
CB B:SER249 4.4 6.2 1.0
NE2 B:HIS189 4.4 5.5 1.0
CB B:ASP124 4.5 5.8 1.0
C1 B:NZR305 4.6 8.2 1.0
C12 B:NZR305 4.6 8.3 1.0
CA B:CYS208 4.6 5.4 1.0
CE1 B:HIS120 4.6 6.2 1.0
CE1 B:HIS189 4.6 5.3 1.0
O B:NZR305 4.6 7.4 1.0
OG B:SER249 4.7 6.3 1.0
NE2 B:HIS120 4.7 6.0 1.0
C8 B:NZR305 5.0 12.4 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: Sat Apr 8 04:24:27 2023

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