Zinc in PDB 6d1j: Crystal Structure of Ndm-1 Complexed with Compound 13

Enzymatic activity of Crystal Structure of Ndm-1 Complexed with Compound 13

All present enzymatic activity of Crystal Structure of Ndm-1 Complexed with Compound 13:
3.5.2.6;

Protein crystallography data

The structure of Crystal Structure of Ndm-1 Complexed with Compound 13, PDB code: 6d1j 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) 27.83 / 1.15
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 41.530, 60.150, 41.890, 90.00, 97.64, 90.00
R / Rfree (%) 13.1 / 15.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Ndm-1 Complexed with Compound 13 (pdb code 6d1j). 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 13, PDB code: 6d1j:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6d1j

Go back to Zinc Binding Sites List in 6d1j
Zinc binding site 1 out of 2 in the Crystal Structure of Ndm-1 Complexed with Compound 13


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

b:7.3
occ:0.89
O10 A:7SX303 1.9 8.5 0.8
ND1 A:HIS122 2.0 8.2 1.0
NE2 A:HIS189 2.0 7.4 1.0
NE2 A:HIS120 2.0 7.3 1.0
O12 A:7SX303 2.9 8.7 0.8
P09 A:7SX303 3.0 9.3 0.8
CE1 A:HIS122 3.0 9.1 1.0
CE1 A:HIS120 3.0 7.6 1.0
CD2 A:HIS189 3.0 7.7 1.0
CD2 A:HIS120 3.0 7.1 1.0
CE1 A:HIS189 3.0 7.8 1.0
CG A:HIS122 3.0 7.8 1.0
CB A:HIS122 3.4 6.3 1.0
SG A:CYS208 3.9 9.4 1.0
O11 A:7SX303 3.9 13.0 0.8
OD1 A:ASP124 4.0 10.0 1.0
ND1 A:HIS120 4.1 7.7 1.0
NE2 A:HIS122 4.1 9.6 1.0
CG A:HIS120 4.1 6.7 1.0
ND1 A:HIS189 4.1 8.0 1.0
CD2 A:HIS122 4.1 8.7 1.0
CG A:HIS189 4.2 7.8 1.0
ZN A:ZN302 4.2 10.6 0.5
CB A:CYS208 4.2 9.8 1.0
C08 A:7SX303 4.4 10.9 0.8
CG2 A:THR190 4.5 8.7 1.0
OD2 A:ASP124 4.6 12.3 1.0
C05 A:7SX303 4.6 15.8 0.8
CG A:ASP124 4.7 10.3 1.0
CA A:HIS122 4.8 5.7 1.0
OXT A:ACT304 4.9 12.2 0.7
ND2 A:ASN220 5.0 12.1 1.0

Zinc binding site 2 out of 2 in 6d1j

Go back to Zinc Binding Sites List in 6d1j
Zinc binding site 2 out of 2 in the Crystal Structure of Ndm-1 Complexed with Compound 13


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

b:10.6
occ:0.51
O11 A:7SX303 1.8 13.0 0.8
NE2 A:HIS250 1.9 12.0 1.0
OXT A:ACT304 2.0 12.2 0.7
SG A:CYS208 2.2 9.4 1.0
CD2 A:HIS250 2.7 12.6 1.0
P09 A:7SX303 3.0 9.3 0.8
CE1 A:HIS250 3.0 11.1 1.0
OD2 A:ASP124 3.0 12.3 1.0
C A:ACT304 3.1 12.1 0.7
O10 A:7SX303 3.1 8.5 0.8
CB A:CYS208 3.2 9.8 1.0
CH3 A:ACT304 3.6 12.2 0.7
CG A:HIS250 3.9 12.2 1.0
O12 A:7SX303 4.0 8.7 0.8
ND1 A:HIS250 4.0 11.3 1.0
CB A:SER249 4.1 9.0 1.0
CG A:ASP124 4.2 10.3 1.0
O A:ACT304 4.2 14.2 0.7
C08 A:7SX303 4.2 10.9 0.8
CA A:CYS208 4.2 9.3 1.0
ZN A:ZN301 4.2 7.3 0.9
CE1 A:HIS189 4.2 7.8 1.0
NE2 A:HIS189 4.3 7.4 1.0
O A:HOH557 4.4 35.7 1.0
OG A:SER249 4.6 9.2 1.0
OD1 A:ASP124 4.6 10.0 1.0
O A:HOH544 4.7 48.5 1.0
NZ A:LYS211 4.8 17.5 1.0
C13 A:7SX303 4.9 15.0 0.8
C07 A:7SX303 5.0 13.2 0.8

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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