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Zinc in PDB 6d1k: Crystal Structure of Ndm-1 Complexed with Compound 14

Enzymatic activity of Crystal Structure of Ndm-1 Complexed with Compound 14

All present enzymatic activity of Crystal Structure of Ndm-1 Complexed with Compound 14:
3.5.2.6;

Protein crystallography data

The structure of Crystal Structure of Ndm-1 Complexed with Compound 14, PDB code: 6d1k 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) 27.43 / 1.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 41.550, 60.110, 41.930, 90.00, 97.82, 90.00
R / Rfree (%) 15.6 / 18.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Ndm-1 Complexed with Compound 14 (pdb code 6d1k). 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 14, PDB code: 6d1k:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6d1k

Go back to Zinc Binding Sites List in 6d1k
Zinc binding site 1 out of 2 in the Crystal Structure of Ndm-1 Complexed with Compound 14


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 14 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:10.4
occ:1.00
O01 A:M3Q303 1.9 10.6 1.0
NE2 A:HIS189 2.0 9.7 1.0
ND1 A:HIS122 2.0 10.3 1.0
NE2 A:HIS120 2.1 9.8 1.0
P02 A:M3Q303 2.9 11.9 1.0
O03 A:M3Q303 3.0 13.2 1.0
CD2 A:HIS189 3.0 10.1 1.0
CE1 A:HIS120 3.0 9.8 1.0
CE1 A:HIS122 3.0 11.6 1.0
CE1 A:HIS189 3.0 9.9 1.0
CG A:HIS122 3.0 9.9 1.0
CD2 A:HIS120 3.0 8.7 1.0
CB A:HIS122 3.3 8.7 1.0
O04 A:M3Q303 3.9 13.6 1.0
SG A:CYS208 3.9 9.7 1.0
OD1 A:ASP124 4.1 10.2 1.0
ND1 A:HIS120 4.1 9.4 1.0
NE2 A:HIS122 4.1 11.7 1.0
ND1 A:HIS189 4.1 10.3 1.0
CD2 A:HIS122 4.1 10.4 1.0
CG A:HIS189 4.1 10.2 1.0
CG A:HIS120 4.2 8.5 1.0
ZN A:ZN302 4.2 11.5 0.7
CB A:CYS208 4.3 10.4 1.0
CG2 A:THR190 4.4 10.6 1.0
C05 A:M3Q303 4.4 13.7 1.0
O A:HOH481 4.7 18.7 1.0
OD2 A:ASP124 4.7 12.4 1.0
CA A:HIS122 4.8 8.3 1.0
CG A:ASP124 4.8 10.0 1.0
OXT A:ACT304 4.9 12.8 0.8
ND2 A:ASN220 5.0 15.4 1.0

Zinc binding site 2 out of 2 in 6d1k

Go back to Zinc Binding Sites List in 6d1k
Zinc binding site 2 out of 2 in the Crystal Structure of Ndm-1 Complexed with Compound 14


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 14 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:11.5
occ:0.70
O04 A:M3Q303 1.8 13.6 1.0
NE2 A:HIS250 1.9 11.8 1.0
OXT A:ACT304 2.0 12.8 0.8
SG A:CYS208 2.3 9.7 1.0
CD2 A:HIS250 2.8 13.2 1.0
C A:ACT304 3.0 13.2 0.8
OD2 A:ASP124 3.0 12.4 1.0
CE1 A:HIS250 3.0 11.4 1.0
P02 A:M3Q303 3.1 11.9 1.0
CB A:CYS208 3.2 10.4 1.0
CH3 A:ACT304 3.3 14.9 0.8
O01 A:M3Q303 3.3 10.6 1.0
O03 A:M3Q303 3.9 13.2 1.0
CG A:HIS250 4.0 13.0 1.0
ND1 A:HIS250 4.0 12.6 1.0
CG A:ASP124 4.1 10.0 1.0
O A:ACT304 4.1 14.9 0.8
CB A:SER249 4.2 10.0 1.0
CE1 A:HIS189 4.2 9.9 1.0
ZN A:ZN301 4.2 10.4 1.0
NE2 A:HIS189 4.3 9.7 1.0
CA A:CYS208 4.3 10.6 1.0
C05 A:M3Q303 4.4 13.7 1.0
OD1 A:ASP124 4.4 10.2 1.0
O A:HOH559 4.6 27.3 1.0
OG A:SER249 4.6 9.7 1.0
C07 A:M3Q303 4.6 15.7 1.0
NZ A:LYS211 4.8 18.1 1.0
C06 A:M3Q303 4.9 15.3 1.0
ND1 A:HIS189 5.0 10.3 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 11:38:53 2020

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