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Zinc in PDB 6ny7: Crystal Structure of Ndm-1 D199N with Compound 16

Enzymatic activity of Crystal Structure of Ndm-1 D199N with Compound 16

All present enzymatic activity of Crystal Structure of Ndm-1 D199N with Compound 16:
3.5.2.6;

Protein crystallography data

The structure of Crystal Structure of Ndm-1 D199N with Compound 16, PDB code: 6ny7 was solved by A.Akhtar, Y.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.07 / 1.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 41.571, 59.774, 42.531, 90.00, 97.88, 90.00
R / Rfree (%) 14.4 / 17.5

Other elements in 6ny7:

The structure of Crystal Structure of Ndm-1 D199N with Compound 16 also contains other interesting chemical elements:

Bromine (Br) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Ndm-1 D199N with Compound 16 (pdb code 6ny7). 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 D199N with Compound 16, PDB code: 6ny7:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6ny7

Go back to Zinc Binding Sites List in 6ny7
Zinc binding site 1 out of 2 in the Crystal Structure of Ndm-1 D199N with Compound 16


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 D199N with Compound 16 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:15.6
occ:1.00
O A:HOH443 1.9 13.3 1.0
ND1 A:HIS122 2.0 14.6 1.0
NE2 A:HIS189 2.0 13.8 1.0
NE2 A:HIS120 2.1 13.2 1.0
O A:HOH416 2.5 19.2 1.0
CG A:HIS122 3.0 13.2 1.0
CE1 A:HIS189 3.0 15.1 1.0
CE1 A:HIS120 3.0 13.7 1.0
CE1 A:HIS122 3.0 15.3 1.0
CD2 A:HIS189 3.1 14.8 1.0
CD2 A:HIS120 3.1 12.0 1.0
CB A:HIS122 3.3 11.9 1.0
O12 A:L8J303 3.8 15.4 0.8
NE2 A:HIS122 4.1 15.3 1.0
CD2 A:HIS122 4.1 13.7 1.0
ND1 A:HIS189 4.1 14.6 1.0
ND1 A:HIS120 4.1 12.5 1.0
CG2 A:THR190 4.1 13.7 1.0
CG A:HIS189 4.2 14.8 1.0
CG A:HIS120 4.2 11.6 1.0
OD1 A:ASP124 4.3 13.8 1.0
O A:HOH605 4.3 25.2 1.0
O A:HOH568 4.3 23.6 1.0
O14 A:L8J303 4.4 17.3 0.8
ZN A:ZN302 4.6 14.6 1.0
SG A:CYS208 4.6 13.1 1.0
P11 A:L8J303 4.8 16.4 0.8
CB A:CYS208 4.8 14.0 1.0
CA A:HIS122 4.8 11.0 1.0
O A:HOH608 4.8 6.9 0.5
O A:HOH608 4.8 11.1 0.5

Zinc binding site 2 out of 2 in 6ny7

Go back to Zinc Binding Sites List in 6ny7
Zinc binding site 2 out of 2 in the Crystal Structure of Ndm-1 D199N with Compound 16


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 D199N with Compound 16 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:14.6
occ:1.00
O12 A:L8J303 1.9 15.4 0.8
OD2 A:ASP124 2.0 12.6 1.0
NE2 A:HIS250 2.1 12.7 1.0
SG A:CYS208 2.3 13.1 1.0
CE1 A:HIS250 3.0 11.6 1.0
CD2 A:HIS250 3.1 13.0 1.0
CG A:ASP124 3.1 12.5 1.0
P11 A:L8J303 3.2 16.4 0.8
O A:HOH443 3.2 13.3 1.0
CB A:CYS208 3.4 14.0 1.0
OD1 A:ASP124 3.5 13.8 1.0
C10 A:L8J303 3.6 24.4 0.8
O13 A:L8J303 3.9 18.9 0.8
CB A:SER249 4.1 12.2 1.0
ND1 A:HIS250 4.1 12.0 1.0
CG A:HIS250 4.2 12.4 1.0
CB A:ASP124 4.3 10.0 1.0
O14 A:L8J303 4.4 17.3 0.8
OG A:SER249 4.4 11.7 1.0
O A:HOH608 4.4 6.9 0.5
CA A:CYS208 4.5 13.2 1.0
ZN A:ZN301 4.6 15.6 1.0
NE2 A:HIS189 4.7 13.8 1.0
CE1 A:HIS189 4.7 15.1 1.0
CE1 A:HIS120 4.8 13.7 1.0
O A:HOH453 4.9 21.6 1.0
CE A:LYS125 5.0 11.5 1.0

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 12:24:40 2020

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