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Zinc in PDB 6d1f: Crystal Structure of Ndm-1 Complexed with Compound 8

Enzymatic activity of Crystal Structure of Ndm-1 Complexed with Compound 8

All present enzymatic activity of Crystal Structure of Ndm-1 Complexed with Compound 8:
3.5.2.6;

Protein crystallography data

The structure of Crystal Structure of Ndm-1 Complexed with Compound 8, PDB code: 6d1f was solved by O.A.Pemberton, Y.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.32 / 1.15
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 41.510, 60.100, 41.750, 90.00, 97.97, 90.00
R / Rfree (%) 14.5 / 17.9

Other elements in 6d1f:

The structure of Crystal Structure of Ndm-1 Complexed with Compound 8 also contains other interesting chemical elements:

Fluorine (F) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Ndm-1 Complexed with Compound 8 (pdb code 6d1f). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Ndm-1 Complexed with Compound 8, PDB code: 6d1f:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6d1f

Go back to Zinc Binding Sites List in 6d1f
Zinc binding site 1 out of 2 in the Crystal Structure of Ndm-1 Complexed with Compound 8


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Ndm-1 Complexed with Compound 8 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:8.8
occ:0.94
O09 A:P9T303 1.9 9.7 0.9
NE2 A:HIS189 2.0 8.9 1.0
ND1 A:HIS122 2.0 10.2 1.0
NE2 A:HIS120 2.1 8.4 1.0
O07 A:P9T303 2.9 9.9 0.9
P06 A:P9T303 2.9 10.4 0.9
CD2 A:HIS189 3.0 9.4 1.0
CE1 A:HIS120 3.0 8.4 1.0
CG A:HIS122 3.0 9.6 1.0
CE1 A:HIS189 3.0 9.2 1.0
CE1 A:HIS122 3.0 11.3 1.0
CD2 A:HIS120 3.0 7.2 1.0
CB A:HIS122 3.3 8.2 1.0
O08 A:P9T303 3.9 12.6 0.9
SG A:CYS208 3.9 8.8 1.0
OD1 A:ASP124 4.1 9.6 1.0
ND1 A:HIS120 4.1 8.2 1.0
ND1 A:HIS189 4.1 9.5 1.0
NE2 A:HIS122 4.1 11.8 1.0
CG A:HIS189 4.1 9.5 1.0
CD2 A:HIS122 4.1 10.9 1.0
CG A:HIS120 4.2 6.6 1.0
ZN A:ZN302 4.2 11.5 0.8
CB A:CYS208 4.3 9.9 1.0
C05 A:P9T303 4.3 12.2 0.9
CG2 A:THR190 4.4 9.9 1.0
OD2 A:ASP124 4.7 11.2 1.0
CA A:HIS122 4.8 7.2 1.0
OXT A:ACT304 4.8 13.7 1.0
CG A:ASP124 4.8 9.2 1.0
F12 A:P9T303 4.9 20.1 0.9
ND2 A:ASN220 4.9 13.1 1.0

Zinc binding site 2 out of 2 in 6d1f

Go back to Zinc Binding Sites List in 6d1f
Zinc binding site 2 out of 2 in the Crystal Structure of Ndm-1 Complexed with Compound 8


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Ndm-1 Complexed with Compound 8 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:11.5
occ:0.77
O08 A:P9T303 1.8 12.6 0.9
NE2 A:HIS250 2.0 11.1 1.0
OXT A:ACT304 2.0 13.7 1.0
SG A:CYS208 2.3 8.8 1.0
CD2 A:HIS250 2.9 10.8 1.0
OD2 A:ASP124 2.9 11.2 1.0
P06 A:P9T303 3.0 10.4 0.9
CE1 A:HIS250 3.0 9.7 1.0
C A:ACT304 3.0 14.5 1.0
O09 A:P9T303 3.2 9.7 0.9
CB A:CYS208 3.3 9.9 1.0
CH3 A:ACT304 3.5 15.0 1.0
O07 A:P9T303 3.8 9.9 0.9
CG A:ASP124 4.0 9.2 1.0
CG A:HIS250 4.0 10.6 1.0
ND1 A:HIS250 4.1 10.1 1.0
O A:ACT304 4.2 16.5 1.0
ZN A:ZN301 4.2 8.8 0.9
CB A:SER249 4.2 8.7 1.0
CE1 A:HIS189 4.2 9.2 1.0
NE2 A:HIS189 4.3 8.9 1.0
OD1 A:ASP124 4.3 9.6 1.0
CA A:CYS208 4.3 9.8 1.0
C05 A:P9T303 4.3 12.2 0.9
O A:HOH582 4.5 34.4 1.0
OG A:SER249 4.6 8.6 1.0
NZ A:LYS211 4.9 16.1 1.0
C03 A:P9T303 4.9 15.2 0.9

Reference:

O.A.Pemberton, P.Jaishankar, A.Akhtar, J.L.Adams, L.N.Shaw, A.R.Renslo, Y.Chen. Heteroaryl Phosphonates As Noncovalent Inhibitors of Both Serine- and Metallocarbapenemases. J.Med.Chem. V. 62 8480 2019.
ISSN: ISSN 0022-2623
PubMed: 31483651
DOI: 10.1021/ACS.JMEDCHEM.9B00728
Page generated: Wed Dec 16 11:38:48 2020

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