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Zinc in PDB 6efj: Crystal Structure of Ndm-1 with Compound 9

Enzymatic activity of Crystal Structure of Ndm-1 with Compound 9

All present enzymatic activity of Crystal Structure of Ndm-1 with Compound 9:
3.5.2.6;

Protein crystallography data

The structure of Crystal Structure of Ndm-1 with Compound 9, PDB code: 6efj 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) 33.97 / 1.65
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 41.980, 58.770, 41.980, 90.00, 97.48, 90.00
R / Rfree (%) 17.6 / 22.2

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Ndm-1 with Compound 9 (pdb code 6efj). 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 with Compound 9, PDB code: 6efj:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6efj

Go back to Zinc Binding Sites List in 6efj
Zinc binding site 1 out of 2 in the Crystal Structure of Ndm-1 with Compound 9


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 with Compound 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:15.9
occ:1.00
O A:HOH451 1.9 15.6 1.0
NE2 A:HIS189 2.0 17.7 1.0
NE2 A:HIS120 2.0 9.2 1.0
ND1 A:HIS122 2.0 17.5 1.0
CE1 A:HIS120 3.0 9.1 1.0
CE1 A:HIS189 3.0 15.8 1.0
CG A:HIS122 3.0 11.6 1.0
CD2 A:HIS189 3.0 12.7 1.0
CE1 A:HIS122 3.0 14.9 1.0
CD2 A:HIS120 3.0 11.1 1.0
O A:HOH561 3.1 20.9 1.0
CB A:HIS122 3.3 12.3 1.0
O A:HOH495 3.8 30.8 1.0
ZN A:ZN302 3.9 15.1 0.8
SG A:CYS208 3.9 14.1 1.0
ND1 A:HIS120 4.1 11.6 1.0
OD1 A:ASP124 4.1 16.6 1.0
ND1 A:HIS189 4.1 15.9 1.0
NE2 A:HIS122 4.1 18.0 1.0
CG A:HIS189 4.1 14.1 1.0
CG A:HIS120 4.1 12.7 1.0
CD2 A:HIS122 4.1 17.0 1.0
CB A:CYS208 4.2 18.1 1.0
CG2 A:THR190 4.3 14.3 1.0
N08 A:O5E303 4.3 17.3 0.8
N07 A:O5E303 4.4 18.4 0.8
OD2 A:ASP124 4.7 15.6 1.0
CA A:HIS122 4.8 10.9 1.0
CG A:ASP124 4.8 11.3 1.0
O A:HOH581 4.9 26.8 1.0

Zinc binding site 2 out of 2 in 6efj

Go back to Zinc Binding Sites List in 6efj
Zinc binding site 2 out of 2 in the Crystal Structure of Ndm-1 with Compound 9


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 with Compound 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:15.1
occ:0.78
N08 A:O5E303 2.0 17.3 0.8
NE2 A:HIS250 2.1 11.8 1.0
OD2 A:ASP124 2.1 15.6 1.0
SG A:CYS208 2.3 14.1 1.0
O A:HOH451 2.4 15.6 1.0
N07 A:O5E303 2.7 18.4 0.8
O01 A:O5E303 2.9 22.2 0.8
CD2 A:HIS250 3.0 15.2 1.0
CE1 A:HIS250 3.1 13.2 1.0
C04 A:O5E303 3.2 20.1 0.8
CG A:ASP124 3.3 11.3 1.0
CB A:CYS208 3.6 18.1 1.0
OD1 A:ASP124 3.7 16.6 1.0
C02 A:O5E303 3.8 20.9 0.8
N03 A:O5E303 3.9 22.0 0.8
ZN A:ZN301 3.9 15.9 1.0
N06 A:O5E303 4.0 21.4 0.8
ND1 A:HIS250 4.2 10.4 1.0
N05 A:O5E303 4.2 20.2 0.8
CG A:HIS250 4.2 13.4 1.0
O A:HOH561 4.3 20.9 1.0
CB A:SER249 4.4 12.8 1.0
NE2 A:HIS189 4.4 17.7 1.0
O A:HOH495 4.5 30.8 1.0
CE1 A:HIS189 4.5 15.8 1.0
CB A:ASP124 4.5 10.1 1.0
CA A:CYS208 4.6 16.0 1.0
OG A:SER249 4.7 13.4 1.0
CE1 A:HIS120 4.8 9.1 1.0
NE2 A:HIS120 4.9 9.2 1.0

Reference:

N.J.Torelli, A.Akhtar, K.Defrees, P.Jaishankar, O.A.Pemberton, X.Zhang, C.Johnson, A.R.Renslo, Y.Chen. Active-Site Druggability of Carbapenemases and Broad-Spectrum Inhibitor Discovery. Acs Infect Dis. V. 5 1013 2019.
ISSN: ESSN 2373-8227
PubMed: 30942078
DOI: 10.1021/ACSINFECDIS.9B00052
Page generated: Mon Oct 28 20:08:19 2024

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