Zinc in PDB 7vqj: Crystal Structure of Ndm-1 in Complex with Hydrolyzed 1U.

The structure of Crystal Structure of Ndm-1 in Complex with Hydrolyzed 1U., PDB code: 7vqj was solved by H.X.Xie, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.06 / 2.45
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	39.385, 74.188, 147.982, 90, 90, 90
R / Rfree (%)	19.5 / 25.2

The binding sites of Zinc atom in the Crystal Structure of Ndm-1 in Complex with Hydrolyzed 1U. (pdb code 7vqj). 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 in Complex with Hydrolyzed 1U., PDB code: 7vqj:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Ndm-1 in Complex with Hydrolyzed 1U.


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 in Complex with Hydrolyzed 1U. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:26.1 occ:1.00 NE2 A:HIS189 1.9 27.4 1.0 ND1 A:HIS122 2.2 19.1 1.0 NE2 A:HIS120 2.2 19.8 1.0 O4 A:7T6303 2.3 32.9 1.0 CE1 A:HIS189 2.9 26.6 1.0 CD2 A:HIS189 2.9 25.6 1.0 CG A:HIS122 3.1 20.5 1.0 C8 A:7T6303 3.2 37.4 1.0 CE1 A:HIS120 3.2 22.8 1.0 CD2 A:HIS120 3.2 22.8 1.0 O5 A:7T6303 3.2 38.1 1.0 CE1 A:HIS122 3.2 24.6 1.0 CB A:HIS122 3.3 20.9 1.0 SG A:CYS208 3.9 30.1 1.0 ZN A:ZN302 4.0 33.5 1.0 ND1 A:HIS189 4.0 21.4 1.0 OD1 A:ASP124 4.1 28.7 1.0 CG A:HIS189 4.1 24.5 1.0 CB A:CYS208 4.2 23.5 1.0 CG2 A:THR190 4.3 21.7 1.0 ND1 A:HIS120 4.3 22.2 1.0 CD2 A:HIS122 4.3 23.4 1.0 NE2 A:HIS122 4.3 27.5 1.0 CG A:HIS120 4.3 21.1 1.0 OD2 A:ASP124 4.5 26.5 1.0 C7 A:7T6303 4.6 37.4 1.0 N1 A:7T6303 4.7 39.0 1.0 CG A:ASP124 4.7 26.5 1.0 CA A:HIS122 4.8 20.4 1.0 O2 A:7T6303 4.8 33.5 1.0 O9 A:7T6303 4.9 39.4 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Ndm-1 in Complex with Hydrolyzed 1U.


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 in Complex with Hydrolyzed 1U. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:33.5 occ:1.00 NE2 A:HIS250 2.2 31.3 1.0 SG A:CYS208 2.3 30.1 1.0 OD2 A:ASP124 2.3 26.5 1.0 O2 A:7T6303 2.3 33.5 1.0 N1 A:7T6303 2.4 39.0 1.0 O4 A:7T6303 2.9 32.9 1.0 C3 A:7T6303 3.1 41.4 1.0 C4 A:7T6303 3.1 39.8 1.0 C6 A:7T6303 3.1 36.5 1.0 CE1 A:HIS250 3.2 28.7 1.0 CD2 A:HIS250 3.2 32.4 1.0 C8 A:7T6303 3.4 37.4 1.0 CB A:CYS208 3.4 23.5 1.0 CG A:ASP124 3.5 26.5 1.0 C7 A:7T6303 3.8 37.4 1.0 ZN A:ZN301 4.0 26.1 1.0 OD1 A:ASP124 4.0 28.7 1.0 O5 A:7T6303 4.1 38.1 1.0 CE1 A:HIS189 4.3 26.6 1.0 CB A:SER249 4.3 29.4 1.0 ND1 A:HIS250 4.3 35.0 1.0 NE2 A:HIS189 4.3 27.4 1.0 CG A:HIS250 4.3 34.9 1.0 O9 A:7T6303 4.3 39.4 1.0 O1 A:7T6303 4.3 37.5 1.0 C2 A:7T6303 4.4 37.2 1.0 CA A:CYS208 4.4 26.1 1.0 OG A:SER249 4.5 29.8 1.0 CB A:ASP124 4.7 27.0 1.0 S A:7T6303 4.7 41.1 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Ndm-1 in Complex with Hydrolyzed 1U.


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 in Complex with Hydrolyzed 1U. within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1001 b:21.3 occ:1.00 O4 B:7T61003 2.2 26.8 1.0 NE2 B:HIS189 2.2 21.5 1.0 NE2 B:HIS120 2.2 18.9 1.0 ND1 B:HIS122 2.2 17.3 1.0 C8 B:7T61003 2.9 37.6 1.0 O5 B:7T61003 2.9 43.6 1.0 CG B:HIS122 3.1 20.3 1.0 CE1 B:HIS120 3.1 19.7 1.0 CD2 B:HIS189 3.1 21.9 1.0 CE1 B:HIS189 3.2 23.9 1.0 CD2 B:HIS120 3.2 18.4 1.0 CE1 B:HIS122 3.3 19.4 1.0 CB B:HIS122 3.3 23.9 1.0 SG B:CYS208 3.8 25.5 1.0 OD1 B:ASP124 4.0 24.3 1.0 ZN B:ZN1002 4.0 31.6 1.0 CB B:CYS208 4.1 20.0 1.0 ND1 B:HIS120 4.3 15.6 1.0 ND1 B:HIS189 4.3 21.8 1.0 CG B:HIS189 4.3 21.0 1.0 CD2 B:HIS122 4.3 27.5 1.0 CG B:HIS120 4.3 19.7 1.0 C7 B:7T61003 4.3 36.0 1.0 NE2 B:HIS122 4.4 23.7 1.0 CG2 B:THR190 4.5 17.3 1.0 N1 B:7T61003 4.5 34.0 1.0 O9 B:7T61003 4.7 31.1 1.0 OD2 B:ASP124 4.7 20.7 1.0 CA B:HIS122 4.8 18.3 1.0 CG B:ASP124 4.8 22.1 1.0 O2 B:7T61003 4.9 33.7 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Ndm-1 in Complex with Hydrolyzed 1U.


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 in Complex with Hydrolyzed 1U. within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1002 b:31.6 occ:1.00 O2 B:7T61003 2.2 33.7 1.0 NE2 B:HIS250 2.2 26.1 1.0 SG B:CYS208 2.3 25.5 1.0 N1 B:7T61003 2.3 34.0 1.0 OD2 B:ASP124 2.4 20.7 1.0 O4 B:7T61003 2.7 26.8 1.0 C4 B:7T61003 2.9 38.0 1.0 C3 B:7T61003 3.0 39.2 1.0 C6 B:7T61003 3.2 35.2 1.0 CE1 B:HIS250 3.2 24.9 1.0 CD2 B:HIS250 3.2 20.4 1.0 C8 B:7T61003 3.3 37.6 1.0 CB B:CYS208 3.4 20.0 1.0 CG B:ASP124 3.5 22.1 1.0 OD1 B:ASP124 3.8 24.3 1.0 C7 B:7T61003 3.8 36.0 1.0 ZN B:ZN1001 4.0 21.3 1.0 O5 B:7T61003 4.1 43.6 1.0 O1 B:7T61003 4.2 40.9 1.0 CB B:SER249 4.2 21.9 1.0 C2 B:7T61003 4.3 41.7 1.0 ND1 B:HIS250 4.3 22.0 1.0 CA B:CYS208 4.3 19.6 1.0 CG B:HIS250 4.3 23.1 1.0 NE2 B:HIS189 4.5 21.5 1.0 CE1 B:HIS189 4.5 23.9 1.0 OG B:SER249 4.5 22.1 1.0 O9 B:7T61003 4.6 31.1 1.0 S B:7T61003 4.7 38.8 1.0 CB B:ASP124 4.7 19.7 1.0

H.X.Xie, H.X.Xie. N/A N/A.