Zinc in PDB 7d87: Crystal Structure of Zebrafish PHF14-Pzp in Complex with H3(1-25)

The structure of Crystal Structure of Zebrafish PHF14-Pzp in Complex with H3(1-25), PDB code: 7d87 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)	32.21 / 2.11
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	41.921, 151.019, 81.84, 90, 90, 90
R / Rfree (%)	16.5 / 20.4

The structure of Crystal Structure of Zebrafish PHF14-Pzp in Complex with H3(1-25) also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of Zebrafish PHF14-Pzp in Complex with H3(1-25) (pdb code 7d87). 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 Zebrafish PHF14-Pzp in Complex with H3(1-25), PDB code: 7d87:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Crystal Structure of Zebrafish PHF14-Pzp in Complex with H3(1-25)


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 Zebrafish PHF14-Pzp in Complex with H3(1-25) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:30.6 occ:1.00 ND1 A:HIS464 2.1 35.6 1.0 SG A:CYS461 2.3 31.6 1.0 SG A:CYS424 2.3 29.2 1.0 SG A:CYS429 2.3 35.4 1.0 CE1 A:HIS464 3.0 32.4 1.0 CB A:CYS424 3.1 26.6 1.0 CB A:CYS429 3.2 38.0 1.0 CG A:HIS464 3.2 31.2 1.0 CB A:CYS461 3.5 25.8 1.0 CB A:HIS464 3.7 29.4 1.0 N A:CYS461 3.9 28.1 1.0 NE2 A:HIS464 4.1 31.4 1.0 O A:HOH651 4.2 41.7 1.0 CA A:CYS461 4.3 23.8 1.0 CD2 A:HIS464 4.3 26.9 1.0 CB A:ALA426 4.4 28.0 1.0 N A:HIS464 4.6 29.6 1.0 CA A:CYS424 4.6 30.1 1.0 CB A:SER431 4.6 44.6 1.0 CA A:CYS429 4.7 43.3 1.0 CA A:HIS464 4.8 23.2 1.0 C A:CYS461 4.9 27.5 1.0 O A:CYS461 4.9 25.4 1.0

Zinc binding site 2 out of 5 in the Crystal Structure of Zebrafish PHF14-Pzp in Complex with H3(1-25)


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 Zebrafish PHF14-Pzp in Complex with H3(1-25) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:33.5 occ:1.00 ND1 A:HIS371 2.0 31.4 1.0 SG A:CYS354 2.3 35.9 1.0 SG A:CYS374 2.4 33.4 1.0 SG A:CYS351 2.4 34.6 1.0 CE1 A:HIS371 3.0 36.9 1.0 CB A:CYS351 3.1 30.2 1.0 CG A:HIS371 3.1 38.5 1.0 CB A:CYS354 3.3 33.8 1.0 CB A:CYS374 3.5 32.8 1.0 CB A:HIS371 3.5 31.8 1.0 N A:CYS354 3.9 33.6 1.0 N A:HIS371 4.1 28.2 1.0 CA A:CYS354 4.1 36.2 1.0 NE2 A:HIS371 4.1 36.2 1.0 CG2 A:THR436 4.2 38.2 1.0 CD2 A:HIS371 4.2 36.4 1.0 C A:LEU353 4.2 36.6 1.0 CA A:HIS371 4.4 31.9 1.0 OG1 A:THR436 4.5 36.1 1.0 CB A:LEU353 4.5 35.8 1.0 CA A:CYS351 4.6 32.6 1.0 O A:CYS354 4.6 38.0 1.0 C A:CYS354 4.6 41.2 1.0 N A:LEU353 4.7 40.6 1.0 CA A:LEU353 4.7 37.8 1.0 O A:LEU353 4.8 35.6 1.0 CA A:CYS374 4.8 32.6 1.0 O A:HOH641 4.9 32.4 1.0

Zinc binding site 3 out of 5 in the Crystal Structure of Zebrafish PHF14-Pzp in Complex with H3(1-25)


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 Zebrafish PHF14-Pzp in Complex with H3(1-25) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:36.3 occ:1.00 ND1 A:HIS434 2.1 37.0 1.0 SG A:CYS407 2.3 35.0 1.0 SG A:CYS410 2.3 38.9 1.0 SG A:CYS437 2.3 40.3 1.0 CE1 A:HIS434 3.1 39.4 1.0 CG A:HIS434 3.1 32.9 1.0 CB A:CYS407 3.2 38.5 1.0 CB A:CYS410 3.3 31.5 1.0 CB A:HIS434 3.4 26.2 1.0 CA A:CYS410 3.5 34.9 1.0 CB A:CYS437 3.5 29.4 1.0 N A:CYS410 3.5 40.1 1.0 N A:HIS434 4.2 29.8 1.0 NE2 A:HIS434 4.2 36.3 1.0 CD2 A:HIS434 4.3 34.6 1.0 C A:LEU409 4.3 46.7 1.0 CA A:HIS434 4.5 28.8 1.0 O A:HOH679 4.6 62.3 1.0 CA A:CYS407 4.6 29.3 1.0 CG A:PRO355 4.7 37.6 1.0 CD A:PRO355 4.8 40.4 1.0 CA A:CYS437 4.8 33.8 1.0 O A:LEU409 4.9 36.8 1.0 C A:CYS410 5.0 46.4 1.0 C A:CYS407 5.0 30.1 1.0

Zinc binding site 4 out of 5 in the Crystal Structure of Zebrafish PHF14-Pzp in Complex with H3(1-25)


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 Zebrafish PHF14-Pzp in Complex with H3(1-25) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:41.8 occ:1.00 ND1 A:HIS313 2.1 46.4 1.0 SG A:CYS316 2.2 43.9 1.0 SG A:CYS291 2.3 41.0 1.0 SG A:CYS288 2.3 40.4 1.0 CB A:CYS288 3.0 39.1 1.0 CE1 A:HIS313 3.1 47.6 1.0 CG A:HIS313 3.1 48.8 1.0 CB A:CYS291 3.2 38.1 1.0 CB A:CYS316 3.4 43.3 1.0 CB A:HIS313 3.4 41.3 1.0 N A:CYS291 3.7 43.8 1.0 CA A:CYS291 4.0 42.5 1.0 O A:HOH609 4.2 53.6 1.0 NE2 A:HIS313 4.2 49.1 1.0 N A:HIS313 4.2 42.6 1.0 CD2 A:HIS313 4.2 47.4 1.0 CA A:HIS313 4.5 43.8 1.0 CA A:CYS288 4.5 39.6 1.0 CB A:VAL290 4.7 33.3 1.0 C A:CYS291 4.7 43.8 1.0 CA A:CYS316 4.8 45.8 1.0 C A:VAL290 4.8 44.6 1.0 N A:LEU292 4.9 41.7 1.0 C A:CYS288 4.9 40.1 1.0 N A:GLY293 4.9 39.0 1.0

Zinc binding site 5 out of 5 in the Crystal Structure of Zebrafish PHF14-Pzp in Complex with H3(1-25)


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 Zebrafish PHF14-Pzp in Complex with H3(1-25) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn505 b:49.8 occ:1.00 SG A:CYS308 2.2 47.6 1.0 SG A:CYS305 2.3 51.5 1.0 SG A:CYS340 2.4 47.9 1.0 SG A:CYS343 2.4 52.7 1.0 CB A:CYS308 3.2 49.8 1.0 CB A:CYS305 3.3 47.9 1.0 CB A:CYS343 3.4 51.4 1.0 CB A:CYS340 3.5 38.2 1.0 N A:CYS308 3.7 57.6 1.0 N A:CYS340 4.0 46.7 1.0 CA A:CYS308 4.0 50.3 1.0 N A:CYS343 4.3 51.6 1.0 O A:HOH682 4.3 67.3 1.0 CA A:CYS340 4.3 48.0 1.0 CA A:CYS343 4.4 52.2 1.0 CG2 A:VAL310 4.5 39.6 1.0 CA A:CYS305 4.7 46.9 1.0 N A:GLY309 4.8 56.0 1.0 C A:CYS308 4.8 56.1 1.0 C A:CYS340 4.8 50.7 1.0 C A:ASN307 4.9 62.1 1.0 O A:CYS340 4.9 53.8 1.0 O A:HOH654 4.9 45.3 1.0 CB A:ASN307 4.9 48.5 1.0 ND2 A:ASN307 5.0 56.2 1.0

H.T.Li, S.P.Zheng. Crystal Structure of Zebrafish PHF14-Pzp in Complex with H3(1-25) To Be Published.