Zinc in PDB 7uyd: Inhibitor Bound VIM1

The structure of Inhibitor Bound VIM1, PDB code: 7uyd was solved by T.O.Fischmann, G.Scapin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	14.64 / 1.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	102.652, 78.957, 67.764, 90, 130.52, 90
R / Rfree (%)	14.7 / 16.1

The binding sites of Zinc atom in the Inhibitor Bound VIM1 (pdb code 7uyd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Inhibitor Bound VIM1, PDB code: 7uyd:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Inhibitor Bound VIM1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Inhibitor Bound VIM1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn308 b:6.8 occ:1.00 ND1 A:HIS116 2.0 7.4 1.0 NE2 A:HIS179 2.0 6.6 1.0 NE2 A:HIS114 2.0 6.6 1.0 O A:HOH629 2.3 3.0 0.7 CE1 A:HIS116 2.9 7.7 1.0 CE1 A:HIS114 3.0 7.0 1.0 CE1 A:HIS179 3.0 6.7 1.0 CG A:HIS116 3.0 7.1 1.0 CD2 A:HIS114 3.0 6.4 1.0 CD2 A:HIS179 3.0 6.6 1.0 O A:HOH629 3.3 7.0 0.3 CB A:HIS116 3.4 6.7 1.0 O A:HOH651 3.7 10.1 0.3 ZN A:ZN309 3.7 7.7 1.0 OD1 A:ASP118 3.9 8.1 1.0 O A:HOH651 4.1 18.0 0.7 NE2 A:HIS116 4.1 8.2 1.0 CB A:CYS198 4.1 6.2 1.0 ND1 A:HIS114 4.1 6.4 1.0 CD2 A:HIS116 4.1 8.1 1.0 ND1 A:HIS179 4.2 6.5 1.0 CG A:HIS114 4.2 5.8 1.0 CG A:HIS179 4.2 6.1 1.0 SG A:CYS198 4.4 6.8 1.0 OD2 A:ASP118 4.6 7.8 1.0 CG A:ASP118 4.7 6.6 1.0 CA A:HIS116 4.8 7.0 1.0

Zinc binding site 2 out of 6 in the Inhibitor Bound VIM1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Inhibitor Bound VIM1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn309 b:7.7 occ:1.00 OD2 A:ASP118 2.0 7.8 1.0 NE2 A:HIS240 2.0 7.2 1.0 SG A:CYS198 2.3 6.8 1.0 O A:HOH629 2.3 3.0 0.7 CG A:ASP118 3.0 6.6 1.0 CE1 A:HIS240 3.0 6.7 1.0 CD2 A:HIS240 3.1 7.1 1.0 O A:HOH629 3.3 7.0 0.3 CB A:CYS198 3.4 6.2 1.0 OD1 A:ASP118 3.4 8.1 1.0 ZN A:ZN308 3.7 6.8 1.0 NH2 A:ARG119 3.8 10.5 1.0 NE A:ARG119 4.0 8.2 1.0 ND1 A:HIS240 4.2 6.8 1.0 CE1 A:HIS114 4.2 7.0 1.0 CG A:HIS240 4.2 6.7 1.0 CZ A:ARG119 4.3 8.1 1.0 CB A:ASP118 4.3 8.5 1.0 NE2 A:HIS114 4.4 6.6 1.0 O A:HOH499 4.6 7.7 1.0 CA A:CYS198 4.6 6.1 1.0 NE2 A:HIS179 4.6 6.6 1.0 O A:HOH651 4.6 10.1 0.3 CE1 A:HIS179 4.9 6.7 1.0 CH3 A:ACT307 5.0 17.4 1.0

Zinc binding site 3 out of 6 in the Inhibitor Bound VIM1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Inhibitor Bound VIM1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn310 b:6.6 occ:1.00 O A:ACT306 2.0 7.3 1.0 OXT A:ACT305 2.0 6.9 1.0 NE2 A:HIS153 2.0 7.1 1.0 C A:ACT305 2.6 7.5 1.0 O A:ACT305 2.6 8.1 1.0 CE1 A:HIS153 2.9 7.8 1.0 C A:ACT306 3.0 6.8 1.0 CD2 A:HIS153 3.1 6.7 1.0 CH3 A:ACT306 3.2 4.8 1.0 CB A:ALA132 4.1 7.6 1.0 ND1 A:HIS153 4.1 8.0 1.0 CH3 A:ACT305 4.1 9.4 1.0 OXT A:ACT306 4.2 10.9 1.0 CG A:HIS153 4.2 7.0 1.0 CA A:ALA132 4.7 6.5 1.0 O A:HOH416 4.8 10.5 1.0

Zinc binding site 4 out of 6 in the Inhibitor Bound VIM1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Inhibitor Bound VIM1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn308 b:7.5 occ:1.00 NE2 B:HIS179 2.0 7.9 1.0 ND1 B:HIS116 2.0 8.2 1.0 NE2 B:HIS114 2.0 7.1 1.0 O B:HOH622 2.3 3.0 0.7 CE1 B:HIS116 3.0 8.7 1.0 CE1 B:HIS179 3.0 7.4 1.0 CE1 B:HIS114 3.0 7.2 1.0 CD2 B:HIS179 3.0 7.1 1.0 CD2 B:HIS114 3.0 7.1 1.0 CG B:HIS116 3.0 7.7 1.0 O B:HOH622 3.3 7.0 0.3 CB B:HIS116 3.4 7.2 1.0 ZN B:ZN309 3.7 8.7 1.0 OD1 B:ASP118 3.9 9.0 1.0 NE2 B:HIS116 4.1 9.1 1.0 CB B:CYS198 4.1 7.1 1.0 ND1 B:HIS114 4.1 7.2 1.0 ND1 B:HIS179 4.1 7.6 1.0 CG B:HIS179 4.1 6.9 1.0 CG B:HIS114 4.2 6.7 1.0 CD2 B:HIS116 4.2 9.0 1.0 SG B:CYS198 4.4 7.5 1.0 OD2 B:ASP118 4.7 8.7 1.0 CG B:ASP118 4.7 7.2 1.0 CA B:HIS116 4.8 6.9 1.0

Zinc binding site 5 out of 6 in the Inhibitor Bound VIM1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Inhibitor Bound VIM1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn309 b:8.7 occ:1.00 OD2 B:ASP118 2.0 8.7 1.0 NE2 B:HIS240 2.0 7.6 1.0 O B:HOH622 2.3 3.0 0.7 SG B:CYS198 2.3 7.5 1.0 CG B:ASP118 3.0 7.2 1.0 CE1 B:HIS240 3.0 7.5 1.0 CD2 B:HIS240 3.0 7.2 1.0 O B:HOH622 3.3 7.0 0.3 CB B:CYS198 3.4 7.1 1.0 OD1 B:ASP118 3.4 9.0 1.0 ZN B:ZN308 3.7 7.5 1.0 NH2 B:ARG119 3.7 11.3 1.0 NE B:ARG119 4.0 9.3 1.0 ND1 B:HIS240 4.1 7.2 1.0 CG B:HIS240 4.2 7.1 1.0 CE1 B:HIS114 4.3 7.2 1.0 CZ B:ARG119 4.3 8.2 1.0 CB B:ASP118 4.3 8.8 1.0 NE2 B:HIS114 4.4 7.1 1.0 O B:HOH479 4.6 9.1 1.0 NE2 B:HIS179 4.6 7.9 1.0 CA B:CYS198 4.6 6.6 1.0 CE1 B:HIS179 4.9 7.4 1.0 OXT B:ACT307 5.0 15.0 1.0

Zinc binding site 6 out of 6 in the Inhibitor Bound VIM1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Inhibitor Bound VIM1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn310 b:7.8 occ:1.00 OXT B:ACT305 2.0 8.5 1.0 O B:ACT306 2.0 8.6 1.0 ND1 B:HIS251 2.0 8.4 1.0 C B:ACT305 2.6 8.9 1.0 O B:ACT305 2.6 11.0 1.0 C B:ACT306 3.0 7.3 1.0 CE1 B:HIS251 3.0 7.9 1.0 CG B:HIS251 3.1 7.5 1.0 OXT B:ACT306 3.3 8.3 1.0 CB B:HIS251 3.5 7.4 1.0 CA B:HIS251 3.8 7.4 1.0 CH3 B:ACT305 4.1 13.1 1.0 NE2 B:HIS251 4.2 8.2 1.0 CD2 B:HIS251 4.2 8.5 1.0 ND2 B:ASN254 4.3 8.4 1.0 CH3 B:ACT306 4.3 8.5 1.0 O B:HIS251 4.5 7.2 1.0 C B:HIS251 4.6 7.3 1.0 CD2 B:LEU203 4.6 9.9 1.0 N B:HIS251 4.9 7.4 1.0

T.O.Fischmann, G.Scapin. Inhibitor Bound VIM1 To Be Published.