Zinc in PDB 7d8a: Crystal Structure of H3(1-13)/PHF14-Pzp Fusion Protein

The structure of Crystal Structure of H3(1-13)/PHF14-Pzp Fusion Protein, PDB code: 7d8a was solved by H.T.Li, S.P.Zheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.71 / 2.00
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	41.781, 150.423, 81.42, 90, 90, 90
R / Rfree (%)	17.7 / 21.2

The structure of Crystal Structure of H3(1-13)/PHF14-Pzp Fusion Protein also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of H3(1-13)/PHF14-Pzp Fusion Protein (pdb code 7d8a). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Crystal Structure of H3(1-13)/PHF14-Pzp Fusion Protein, PDB code: 7d8a:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Crystal Structure of H3(1-13)/PHF14-Pzp Fusion Protein


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 H3(1-13)/PHF14-Pzp Fusion Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:25.8 occ:1.00 ND1 A:HIS464 2.2 29.5 1.0 SG A:CYS461 2.3 24.3 1.0 SG A:CYS424 2.3 25.0 1.0 SG A:CYS429 2.4 28.9 1.0 CE1 A:HIS464 3.1 21.1 1.0 CB A:CYS424 3.1 22.7 1.0 CB A:CYS429 3.2 27.6 1.0 CG A:HIS464 3.3 25.0 1.0 CB A:CYS461 3.5 20.8 1.0 CB A:HIS464 3.7 26.3 1.0 N A:CYS461 3.8 23.5 1.0 CA A:CYS461 4.2 26.0 1.0 NE2 A:HIS464 4.2 23.5 1.0 CD2 A:HIS464 4.4 25.6 1.0 O A:HOH686 4.4 48.9 1.0 CB A:ALA426 4.5 19.4 1.0 N A:HIS464 4.5 25.3 1.0 CA A:CYS424 4.6 30.7 1.0 CB A:SER431 4.6 32.6 1.0 CA A:CYS429 4.6 36.9 1.0 CA A:HIS464 4.8 24.9 1.0 C A:CYS461 4.8 25.7 1.0 O A:CYS461 4.9 21.0 1.0 C A:TYR460 5.0 23.8 1.0

Zinc binding site 2 out of 5 in the Crystal Structure of H3(1-13)/PHF14-Pzp Fusion Protein


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 H3(1-13)/PHF14-Pzp Fusion Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:28.3 occ:1.00 ND1 A:HIS371 2.1 27.7 1.0 SG A:CYS354 2.3 28.6 1.0 SG A:CYS374 2.3 28.6 1.0 SG A:CYS351 2.4 29.4 1.0 CE1 A:HIS371 3.0 33.2 1.0 CB A:CYS351 3.1 28.7 1.0 CG A:HIS371 3.1 35.2 1.0 CB A:CYS354 3.3 28.9 1.0 CB A:CYS374 3.4 24.6 1.0 CB A:HIS371 3.5 24.7 1.0 N A:CYS354 3.9 31.0 1.0 CG2 A:THR436 4.0 21.6 1.0 N A:HIS371 4.0 27.0 1.0 CA A:CYS354 4.1 26.8 1.0 NE2 A:HIS371 4.2 30.0 1.0 CD2 A:HIS371 4.2 32.0 1.0 C A:LEU353 4.3 29.9 1.0 CA A:HIS371 4.4 25.8 1.0 OG1 A:THR436 4.5 28.6 1.0 CB A:LEU353 4.5 25.3 1.0 CA A:CYS351 4.6 27.2 1.0 C A:CYS354 4.7 34.0 1.0 O A:CYS354 4.7 33.0 1.0 CA A:CYS374 4.7 22.8 1.0 CA A:LEU353 4.7 31.2 1.0 O A:LEU353 4.8 29.6 1.0 N A:LEU353 4.8 31.5 1.0 CB A:THR436 4.9 30.4 1.0 N A:CYS374 5.0 26.9 1.0

Zinc binding site 3 out of 5 in the Crystal Structure of H3(1-13)/PHF14-Pzp Fusion Protein


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 H3(1-13)/PHF14-Pzp Fusion Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:30.6 occ:1.00 ND1 A:HIS434 2.2 28.7 1.0 SG A:CYS407 2.2 28.9 1.0 SG A:CYS437 2.3 33.4 1.0 SG A:CYS410 2.4 34.6 1.0 CE1 A:HIS434 3.1 27.0 1.0 CG A:HIS434 3.1 21.8 1.0 CB A:CYS407 3.2 31.5 1.0 CB A:CYS410 3.3 30.5 1.0 CB A:CYS437 3.3 33.5 1.0 CB A:HIS434 3.4 20.6 1.0 CA A:CYS410 3.5 24.9 1.0 N A:CYS410 3.6 32.0 1.0 N A:HIS434 4.2 24.6 1.0 NE2 A:HIS434 4.2 28.4 1.0 CD2 A:HIS434 4.3 25.3 1.0 C A:LEU409 4.4 32.8 1.0 CA A:HIS434 4.4 23.7 1.0 CA A:CYS407 4.6 26.2 1.0 CG A:PRO355 4.7 31.6 1.0 CA A:CYS437 4.7 31.8 1.0 O A:HOH697 4.7 54.5 1.0 CD A:PRO355 4.8 26.5 1.0 O A:LEU409 4.9 36.0 1.0 C A:CYS410 5.0 40.4 1.0

Zinc binding site 4 out of 5 in the Crystal Structure of H3(1-13)/PHF14-Pzp Fusion Protein


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 H3(1-13)/PHF14-Pzp Fusion Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:33.8 occ:1.00 SG A:CYS316 2.2 34.9 1.0 ND1 A:HIS313 2.3 35.0 1.0 SG A:CYS288 2.3 37.1 1.0 SG A:CYS291 2.4 32.0 1.0 CB A:CYS288 3.1 31.4 1.0 CG A:HIS313 3.1 38.5 1.0 CB A:HIS313 3.3 32.0 1.0 CE1 A:HIS313 3.3 33.9 1.0 CB A:CYS316 3.3 39.5 1.0 CB A:CYS291 3.4 30.1 1.0 N A:CYS291 3.8 29.9 1.0 CA A:CYS291 4.1 32.8 1.0 N A:HIS313 4.2 31.8 1.0 O A:HOH609 4.2 42.3 1.0 CD2 A:HIS313 4.3 34.4 1.0 CA A:HIS313 4.4 34.9 1.0 NE2 A:HIS313 4.4 38.8 1.0 CA A:CYS288 4.6 30.8 1.0 CB A:VAL290 4.6 31.3 1.0 CA A:CYS316 4.7 40.0 1.0 C A:CYS291 4.8 34.0 1.0 C A:VAL290 4.8 33.8 1.0 O A:HOH710 4.9 34.2 1.0 N A:LEU292 4.9 34.7 1.0 C A:CYS288 5.0 36.9 1.0

Zinc binding site 5 out of 5 in the Crystal Structure of H3(1-13)/PHF14-Pzp Fusion Protein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of H3(1-13)/PHF14-Pzp Fusion Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn505 b:39.9 occ:1.00 SG A:CYS308 2.2 37.0 1.0 SG A:CYS340 2.3 40.9 1.0 SG A:CYS305 2.4 44.9 1.0 SG A:CYS343 2.5 48.2 1.0 CB A:CYS305 3.3 43.8 1.0 CB A:CYS308 3.3 41.0 1.0 CB A:CYS343 3.4 39.1 1.0 CB A:CYS340 3.4 38.6 1.0 N A:CYS308 3.8 47.1 1.0 N A:CYS340 3.9 43.6 1.0 CA A:CYS308 4.1 42.8 1.0 CA A:CYS340 4.2 41.4 1.0 N A:CYS343 4.3 42.0 1.0 O A:HOH705 4.3 52.8 1.0 CG2 A:VAL310 4.4 40.2 1.0 CA A:CYS343 4.5 42.0 1.0 CA A:CYS305 4.7 42.4 1.0 CB A:ASN307 4.8 45.2 1.0 C A:CYS340 4.8 39.0 1.0 O A:CYS340 4.8 35.1 1.0 C A:CYS308 4.8 45.3 1.0 C A:ASN307 4.9 52.0 1.0 N A:GLY309 4.9 39.7 1.0 O A:HOH669 4.9 36.5 1.0

H.T.Li, S.P.Zheng. Crystal Structure of H3(1-13)/PHF14-Pzp Fusion Protein To Be Published.