Zinc in PDB 7zmx: Crystal Structure of the Plant Homeodomain (Phd) of Human ING3

The structure of Crystal Structure of the Plant Homeodomain (Phd) of Human ING3, PDB code: 7zmx was solved by M.O.Ferreras, F.J.Medrano, F.J.Blanco, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.24 / 1.20
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	40.695, 40.695, 100.595, 90, 90, 120
R / Rfree (%)	17.2 / 20.4

The structure of Crystal Structure of the Plant Homeodomain (Phd) of Human ING3 also contains other interesting chemical elements:

Calcium

(Ca)

3 atoms

The binding sites of Zinc atom in the Crystal Structure of the Plant Homeodomain (Phd) of Human ING3 (pdb code 7zmx). 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 the Plant Homeodomain (Phd) of Human ING3, PDB code: 7zmx:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of the Plant Homeodomain (Phd) of Human ING3


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 the Plant Homeodomain (Phd) of Human ING3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:17.1 occ:1.00 ND1 A:HIS387 2.1 16.1 1.0 SG A:CYS363 2.3 16.5 1.0 SG A:CYS390 2.3 18.4 1.0 SG A:CYS365 2.3 17.3 1.0 HB3 A:CYS363 2.8 18.4 1.0 HB2 A:HIS387 3.0 19.4 1.0 CE1 A:HIS387 3.0 16.9 1.0 CB A:CYS363 3.1 15.2 1.0 HB2 A:CYS390 3.1 20.6 1.0 HB3 A:CYS365 3.1 20.3 1.0 HE1 A:HIS387 3.2 20.4 1.0 CG A:HIS387 3.2 17.5 1.0 H A:HIS387 3.2 20.2 1.0 CB A:CYS390 3.2 17.0 1.0 H A:CYS365 3.2 21.9 1.0 HB2 A:CYS363 3.3 18.4 1.0 CB A:CYS365 3.4 16.8 1.0 HB3 A:CYS390 3.4 20.6 1.0 CB A:HIS387 3.6 16.0 1.0 O A:HOH609 3.8 25.8 1.0 N A:HIS387 4.0 16.7 1.0 N A:CYS365 4.0 18.1 1.0 HB2 A:CYS365 4.1 20.3 1.0 NE2 A:HIS387 4.2 18.1 1.0 CD2 A:HIS387 4.3 17.4 1.0 CA A:CYS365 4.3 17.9 1.0 HB3 A:HIS387 4.3 19.4 1.0 CA A:HIS387 4.4 16.0 1.0 HH A:TYR370 4.4 30.8 1.0 H A:ILE364 4.5 19.9 1.0 H A:CYS390 4.5 22.7 1.0 CA A:CYS363 4.5 15.7 1.0 HA A:PHE386 4.6 21.7 1.0 O A:HOH623 4.6 25.4 1.0 CA A:CYS390 4.6 17.8 1.0 HG22 B:ILE364 4.7 34.9 1.0 HG23 B:ILE364 4.7 34.9 1.0 N A:ILE364 4.7 16.5 1.0 HB2 A:GLN367 4.8 29.2 1.0 H A:GLN367 4.9 24.9 1.0 OH A:TYR370 4.9 25.5 1.0 O A:HIS387 4.9 17.6 1.0 HA A:CYS363 4.9 19.0 1.0 HG21 B:ILE364 4.9 34.9 1.0 C A:CYS363 4.9 15.5 1.0 HE2 A:HIS387 4.9 21.9 1.0 N A:CYS390 5.0 18.8 1.0 H A:ASN366 5.0 20.5 1.0 CG2 B:ILE364 5.0 28.9 1.0 HG3 A:GLN367 5.0 37.0 1.0 HA A:CYS390 5.0 21.5 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of the Plant Homeodomain (Phd) of Human ING3


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 the Plant Homeodomain (Phd) of Human ING3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:25.4 occ:1.00 SG A:CYS403 2.3 24.6 1.0 SG A:CYS381 2.3 25.5 1.0 SG A:CYS406 2.3 26.1 1.0 SG A:CYS376 2.4 24.0 1.0 HB2 A:CYS381 2.6 33.2 1.0 HB2 A:CYS406 2.8 31.1 1.0 CB A:CYS381 3.0 27.6 1.0 HB2 A:CYS376 3.1 30.3 1.0 CB A:CYS376 3.1 25.1 1.0 CB A:CYS406 3.2 25.8 1.0 HB3 A:CYS403 3.2 28.4 1.0 H A:CYS403 3.2 28.8 1.0 HB3 A:CYS376 3.2 30.3 1.0 CB A:CYS403 3.4 23.5 1.0 H A:CYS406 3.6 31.9 1.0 HA A:CYS381 3.7 37.3 1.0 HB3 A:ASN378 3.7 43.6 1.0 HB3 A:CYS381 3.7 33.2 1.0 HB3 A:CYS406 3.8 31.1 1.0 HZ A:PHE386 3.8 25.7 1.0 HE1 A:PHE386 3.9 24.2 1.0 CA A:CYS381 3.9 30.9 1.0 N A:CYS403 4.0 23.9 1.0 HB2 A:CYS403 4.1 28.4 1.0 N A:CYS406 4.2 26.5 1.0 CA A:CYS403 4.2 23.1 1.0 CA A:CYS406 4.3 27.0 1.0 CZ A:PHE386 4.4 21.3 1.0 CE1 A:PHE386 4.4 20.1 1.0 H A:GLU384 4.5 29.7 1.0 CB A:ASN378 4.5 36.2 1.0 HB2 A:ASN378 4.6 43.6 1.0 H A:ASN378 4.6 35.7 1.0 CA A:CYS376 4.6 23.2 1.0 HA A:CYS406 4.7 32.6 1.0 HD2 A:PRO382 4.7 34.4 1.0 HA A:TYR402 4.7 28.0 1.0 HB2 A:GLN405 4.8 34.3 1.0 HA A:CYS376 4.8 28.0 1.0 C A:CYS403 4.9 24.5 1.0 H A:CYS381 4.9 43.9 1.0 N A:CYS381 4.9 36.4 1.0 O A:CYS403 4.9 25.1 1.0 H A:ILE383 4.9 27.2 1.0 C A:CYS381 5.0 28.5 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of the Plant Homeodomain (Phd) of Human ING3


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 the Plant Homeodomain (Phd) of Human ING3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:27.0 occ:1.00 ND1 B:HIS387 2.0 27.3 1.0 SG B:CYS390 2.3 29.9 1.0 SG B:CYS363 2.3 23.2 1.0 SG B:CYS365 2.3 25.9 1.0 HB3 B:CYS363 2.8 27.7 1.0 HB2 B:HIS387 2.9 29.8 1.0 CE1 B:HIS387 3.0 28.6 1.0 HB2 B:CYS390 3.0 33.4 1.0 CB B:CYS363 3.0 22.9 1.0 CG B:HIS387 3.1 27.3 1.0 HE1 B:HIS387 3.1 34.5 1.0 HB3 B:CYS365 3.1 29.5 1.0 CB B:CYS390 3.1 27.7 1.0 H B:CYS365 3.2 27.7 1.0 HB2 B:CYS363 3.3 27.7 1.0 HB3 B:CYS390 3.3 33.4 1.0 CB B:CYS365 3.4 24.4 1.0 H B:HIS387 3.4 28.5 1.0 CB B:HIS387 3.5 24.7 1.0 O B:HOH641 3.9 30.2 1.0 N B:CYS365 4.0 23.0 1.0 HB2 B:CYS365 4.1 29.5 1.0 NE2 B:HIS387 4.1 28.8 1.0 N B:HIS387 4.1 23.6 1.0 CD2 B:HIS387 4.2 27.1 1.0 HB3 B:HIS387 4.2 29.8 1.0 CA B:CYS365 4.3 23.5 1.0 CA B:HIS387 4.4 23.7 1.0 H B:CYS390 4.4 34.1 1.0 CA B:CYS363 4.5 23.5 1.0 H B:ILE364 4.5 29.6 1.0 CA B:CYS390 4.6 26.8 1.0 N B:ILE364 4.7 24.5 1.0 HH B:TYR370 4.8 66.4 1.0 C B:CYS363 4.8 24.2 1.0 H B:ASN366 4.8 31.8 1.0 HE2 B:HIS387 4.9 34.7 1.0 HA B:CYS363 4.9 28.4 1.0 HA B:PHE386 4.9 26.4 1.0 HB2 B:GLN367 4.9 32.9 1.0 HG21 A:ILE364 4.9 29.2 1.0 N B:CYS390 4.9 28.3 1.0 HA B:CYS390 4.9 32.4 1.0 O B:HIS387 5.0 22.4 1.0 HG22 A:ILE364 5.0 29.2 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of the Plant Homeodomain (Phd) of Human ING3


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 the Plant Homeodomain (Phd) of Human ING3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:19.8 occ:1.00 SG B:CYS406 2.3 21.0 1.0 SG B:CYS403 2.3 19.9 1.0 SG B:CYS381 2.3 20.6 1.0 SG B:CYS376 2.4 18.6 1.0 HB2 B:CYS381 2.9 24.4 1.0 HB2 B:CYS406 3.0 25.8 1.0 HB2 B:CYS376 3.2 22.1 1.0 CB B:CYS381 3.2 20.2 1.0 H B:CYS403 3.2 22.4 1.0 HB3 B:CYS403 3.2 23.1 1.0 CB B:CYS376 3.2 18.2 1.0 CB B:CYS406 3.3 21.3 1.0 HB3 B:CYS376 3.3 22.1 1.0 CB B:CYS403 3.4 19.1 1.0 HB3 B:ASN378 3.6 23.9 1.0 HA B:CYS381 3.7 24.8 1.0 H B:CYS406 3.7 25.3 1.0 HZ B:PHE386 3.8 24.3 1.0 HB3 B:CYS406 3.9 25.8 1.0 HD2 B:PRO382 3.9 30.7 1.0 N B:CYS403 4.0 18.5 1.0 HB3 B:CYS381 4.0 24.4 1.0 CA B:CYS381 4.0 20.5 1.0 HE1 B:PHE386 4.0 25.1 1.0 HB2 B:CYS403 4.1 23.1 1.0 HD22 B:ASN378 4.2 26.7 1.0 CA B:CYS403 4.2 19.5 1.0 N B:CYS406 4.3 20.9 1.0 CZ B:PHE386 4.4 20.1 1.0 CA B:CYS406 4.4 22.9 1.0 CB B:ASN378 4.5 19.8 1.0 CE1 B:PHE386 4.5 20.8 1.0 H B:GLU384 4.5 24.7 1.0 HB2 B:ASN378 4.5 23.9 1.0 H B:ASN378 4.6 22.1 1.0 CA B:CYS376 4.7 19.3 1.0 HA B:TYR402 4.7 22.6 1.0 H B:ILE383 4.7 27.1 1.0 CD B:PRO382 4.8 25.5 1.0 HA B:CYS406 4.8 27.6 1.0 O B:HOH643 4.8 34.6 1.0 C B:CYS403 4.9 19.9 1.0 ND2 B:ASN378 4.9 22.1 1.0 HD1 B:TYR402 4.9 23.9 1.0 C B:CYS381 4.9 22.3 1.0 HA B:CYS376 4.9 23.3 1.0 O B:CYS403 5.0 18.0 1.0 HB2 B:GLN405 5.0 34.3 1.0

M.O.Ferreras, F.J.Medrano, F.J.Blanco. Crystal Structure of the Plant Homeodomain (Phd) of Human ING3 To Be Published.