Zinc in PDB 8i8f: Crystal Structure of Ndm-1 at PH5.5 (Succinate) in Complex with Hydrolyzed Compound 1

The structure of Crystal Structure of Ndm-1 at PH5.5 (Succinate) in Complex with Hydrolyzed Compound 1, PDB code: 8i8f was solved by X.Shi, W.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.77 / 1.89
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	39.114, 78.847, 133.534, 90, 90, 90
R / Rfree (%)	15.1 / 19

The binding sites of Zinc atom in the Crystal Structure of Ndm-1 at PH5.5 (Succinate) in Complex with Hydrolyzed Compound 1 (pdb code 8i8f). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Ndm-1 at PH5.5 (Succinate) in Complex with Hydrolyzed Compound 1, PDB code: 8i8f:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Ndm-1 at PH5.5 (Succinate) in Complex with Hydrolyzed Compound 1


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 at PH5.5 (Succinate) in Complex with Hydrolyzed Compound 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:16.6 occ:1.00 O A:HOH410 2.0 15.2 1.0 ND1 A:HIS122 2.1 13.9 1.0 NE2 A:HIS189 2.2 15.4 1.0 NE2 A:HIS120 2.2 14.3 1.0 O4 A:OL6303 2.6 15.9 0.8 CG A:HIS122 3.0 13.7 1.0 CD2 A:HIS189 3.1 11.0 1.0 CD2 A:HIS120 3.2 17.4 1.0 H1 A:OL6303 3.2 29.2 0.8 H9 A:OL6303 3.2 25.4 0.8 CE1 A:HIS122 3.2 17.7 1.0 CE1 A:HIS120 3.2 18.5 1.0 CE1 A:HIS189 3.2 15.4 1.0 CB A:HIS122 3.3 10.9 1.0 C19 A:OL6303 3.4 24.5 0.8 C6 A:OL6303 3.8 24.3 0.8 N A:OL6303 4.0 21.2 0.8 OD1 A:ASP124 4.1 15.0 1.0 CD2 A:HIS122 4.2 11.8 1.0 NE2 A:HIS122 4.2 17.5 1.0 CG A:HIS189 4.3 13.9 1.0 CG2 A:THR190 4.3 12.8 1.0 ND1 A:HIS120 4.3 14.8 1.0 ND1 A:HIS189 4.3 13.2 1.0 CG A:HIS120 4.3 14.2 1.0 SG A:CYS208 4.4 15.8 1.0 O5 A:OL6303 4.4 28.9 0.8 ZN A:ZN302 4.4 19.0 1.0 CB A:CYS208 4.5 13.8 1.0 C5 A:OL6303 4.6 25.8 0.8 CA A:HIS122 4.7 13.7 1.0 O A:HOH569 4.8 28.7 1.0 H8 A:OL6303 4.8 23.4 0.8 O A:HOH407 4.8 31.2 1.0 OD2 A:ASP124 4.9 18.1 1.0 C3 A:OL6303 4.9 19.5 0.8 CG A:ASP124 5.0 16.7 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Ndm-1 at PH5.5 (Succinate) in Complex with Hydrolyzed Compound 1


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 at PH5.5 (Succinate) in Complex with Hydrolyzed Compound 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:19.0 occ:1.00 OD2 A:ASP124 2.1 18.1 1.0 NE2 A:HIS250 2.2 19.9 1.0 O A:OL6303 2.3 17.4 0.8 H9 A:OL6303 2.3 25.4 0.8 SG A:CYS208 2.3 15.8 1.0 N A:OL6303 2.3 21.2 0.8 O A:HOH410 2.8 15.2 1.0 CD2 A:HIS250 3.1 15.3 1.0 C4 A:OL6303 3.2 18.0 0.8 H6 A:OL6303 3.2 27.7 0.8 CE1 A:HIS250 3.2 17.8 1.0 H A:OL6303 3.3 30.9 0.8 CG A:ASP124 3.3 16.7 1.0 C5 A:OL6303 3.3 25.8 0.8 C3 A:OL6303 3.3 19.5 0.8 CB A:CYS208 3.4 13.8 1.0 OD1 A:ASP124 3.7 15.0 1.0 C2 A:OL6303 3.8 23.1 0.8 H1 A:OL6303 3.9 29.2 0.8 H7 A:OL6303 3.9 27.7 0.8 C1 A:OL6303 4.0 21.8 0.8 H8 A:OL6303 4.1 23.4 0.8 C6 A:OL6303 4.2 24.3 0.8 CB A:SER249 4.2 16.3 1.0 CG A:HIS250 4.3 18.5 1.0 ND1 A:HIS250 4.3 17.7 1.0 O1 A:OL6303 4.4 18.9 0.8 ZN A:ZN301 4.4 16.6 1.0 CA A:CYS208 4.5 15.2 1.0 CB A:ASP124 4.5 14.3 1.0 S A:OL6303 4.5 30.5 0.8 O4 A:OL6303 4.5 15.9 0.8 OG A:SER249 4.6 15.1 1.0 NE2 A:HIS189 4.6 15.4 1.0 H5 A:OL6303 4.7 27.7 0.8 CE1 A:HIS189 4.8 15.4 1.0 C19 A:OL6303 4.9 24.5 0.8

Zinc binding site 3 out of 4 in the Crystal Structure of Ndm-1 at PH5.5 (Succinate) in Complex with Hydrolyzed Compound 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Ndm-1 at PH5.5 (Succinate) in Complex with Hydrolyzed Compound 1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:17.6 occ:1.00 O B:HOH416 2.0 18.9 1.0 ND1 B:HIS122 2.1 17.2 1.0 NE2 B:HIS189 2.2 14.0 1.0 NE2 B:HIS120 2.2 13.9 1.0 O5 B:OL6303 2.7 22.7 0.7 CD2 B:HIS189 3.1 13.6 1.0 CG B:HIS122 3.1 20.4 1.0 CE1 B:HIS120 3.1 13.1 1.0 H1 B:OL6303 3.1 37.3 0.7 CE1 B:HIS122 3.1 18.5 1.0 CE1 B:HIS189 3.3 14.7 1.0 CD2 B:HIS120 3.3 16.7 1.0 H9 B:OL6303 3.3 20.3 0.7 C19 B:OL6303 3.3 26.3 0.7 CB B:HIS122 3.3 14.1 1.0 C6 B:OL6303 3.7 31.1 0.7 N B:OL6303 4.1 16.9 0.7 O4 B:OL6303 4.1 29.5 0.7 OD1 B:ASP124 4.2 18.2 1.0 ND1 B:HIS120 4.2 13.8 1.0 NE2 B:HIS122 4.2 17.8 1.0 CD2 B:HIS122 4.2 17.2 1.0 CG B:HIS189 4.2 12.6 1.0 ND1 B:HIS189 4.3 15.5 1.0 CG B:HIS120 4.3 13.7 1.0 SG B:CYS208 4.3 14.4 1.0 CG2 B:THR190 4.4 13.3 1.0 ZN B:ZN302 4.5 19.9 1.0 C5 B:OL6303 4.5 23.9 0.7 CB B:CYS208 4.5 14.7 1.0 O B:HOH425 4.8 40.3 1.0 CA B:HIS122 4.8 13.7 1.0 OD2 B:ASP124 4.9 18.7 1.0 H8 B:OL6303 4.9 24.8 0.7 H B:OL6303 4.9 28.7 0.7 CG B:ASP124 5.0 19.8 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Ndm-1 at PH5.5 (Succinate) in Complex with Hydrolyzed Compound 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Ndm-1 at PH5.5 (Succinate) in Complex with Hydrolyzed Compound 1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:19.9 occ:1.00 OD2 B:ASP124 2.1 18.7 1.0 NE2 B:HIS250 2.2 17.4 1.0 H9 B:OL6303 2.2 20.3 0.7 N B:OL6303 2.2 16.9 0.7 SG B:CYS208 2.3 14.4 1.0 O B:OL6303 2.4 20.1 0.7 O B:HOH416 2.8 18.9 1.0 H B:OL6303 3.0 28.7 0.7 C5 B:OL6303 3.1 23.9 0.7 CE1 B:HIS250 3.1 13.7 1.0 CD2 B:HIS250 3.1 15.0 1.0 C4 B:OL6303 3.3 24.8 0.7 C3 B:OL6303 3.3 20.6 0.7 H7 B:OL6303 3.3 32.9 0.7 CG B:ASP124 3.3 19.8 1.0 CB B:CYS208 3.4 14.7 1.0 H1 B:OL6303 3.8 37.3 0.7 OD1 B:ASP124 3.8 18.2 1.0 C2 B:OL6303 4.0 27.4 0.7 H8 B:OL6303 4.1 24.8 0.7 H5 B:OL6303 4.1 32.9 0.7 C1 B:OL6303 4.1 24.2 0.7 C6 B:OL6303 4.1 31.1 0.7 CB B:SER249 4.2 14.4 1.0 ND1 B:HIS250 4.2 18.6 1.0 CG B:HIS250 4.3 18.8 1.0 CA B:CYS208 4.5 10.5 1.0 S B:OL6303 4.5 31.9 0.7 ZN B:ZN301 4.5 17.6 1.0 CB B:ASP124 4.5 16.9 1.0 O1 B:OL6303 4.5 23.4 0.7 O5 B:OL6303 4.5 22.7 0.7 OG B:SER249 4.6 13.0 1.0 NE2 B:HIS189 4.7 14.0 1.0 H6 B:OL6303 4.8 32.9 0.7 CE1 B:HIS189 4.9 14.7 1.0 C19 B:OL6303 4.9 26.3 0.7

X.Shi, W.Liu. Crystal Structure of Ndm-1 at PH5.5 (Succinate) in Complex with Hydrolyzed Compound 1 To Be Published.