Zinc in PDB 7d86: Crystal Structure of ZEBRAFISHPHF14-Pzp

The structure of Crystal Structure of ZEBRAFISHPHF14-Pzp, PDB code: 7d86 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)	41.68 / 1.84
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	42.193, 41.907, 52.878, 90, 98.95, 90
R / Rfree (%)	17.4 / 22.5

The structure of Crystal Structure of ZEBRAFISHPHF14-Pzp also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Zinc atom in the Crystal Structure of ZEBRAFISHPHF14-Pzp (pdb code 7d86). 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 ZEBRAFISHPHF14-Pzp, PDB code: 7d86:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Crystal Structure of ZEBRAFISHPHF14-Pzp


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 ZEBRAFISHPHF14-Pzp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:32.9 occ:1.00 ND1 A:HIS464 2.1 34.1 1.0 SG A:CYS429 2.3 33.4 1.0 SG A:CYS424 2.3 28.6 1.0 SG A:CYS461 2.3 30.6 1.0 CE1 A:HIS464 2.9 33.2 1.0 CB A:CYS424 3.1 28.3 1.0 CB A:CYS429 3.1 32.9 1.0 CG A:HIS464 3.2 32.3 1.0 CB A:CYS461 3.4 26.6 1.0 CB A:HIS464 3.7 26.1 1.0 N A:CYS461 3.8 25.2 1.0 NE2 A:HIS464 4.0 34.8 1.0 CA A:CYS461 4.2 25.7 1.0 CD2 A:HIS464 4.2 36.3 1.0 O A:HOH631 4.3 51.2 1.0 OG A:SER431 4.5 53.2 1.0 CB A:ALA426 4.5 27.8 1.0 O A:HOH690 4.6 58.0 1.0 CA A:CYS424 4.6 31.5 1.0 CA A:CYS429 4.6 37.8 1.0 N A:HIS464 4.7 26.9 1.0 CB A:SER431 4.8 36.7 1.0 CA A:HIS464 4.8 25.7 1.0 C A:CYS461 4.9 26.6 1.0 O A:ALA426 5.0 35.7 1.0

Zinc binding site 2 out of 5 in the Crystal Structure of ZEBRAFISHPHF14-Pzp


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 ZEBRAFISHPHF14-Pzp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:32.6 occ:1.00 ND1 A:HIS371 2.0 30.5 1.0 SG A:CYS354 2.3 33.7 1.0 SG A:CYS374 2.3 29.7 1.0 SG A:CYS351 2.4 29.4 1.0 CE1 A:HIS371 2.9 31.1 1.0 CB A:CYS351 3.0 28.9 1.0 CG A:HIS371 3.1 26.6 1.0 CB A:CYS354 3.2 32.5 1.0 CB A:HIS371 3.5 28.0 1.0 CB A:CYS374 3.5 30.3 1.0 N A:CYS354 3.9 28.0 1.0 N A:HIS371 4.0 28.2 1.0 CG2 A:THR436 4.1 31.5 1.0 NE2 A:HIS371 4.1 31.4 1.0 CA A:CYS354 4.1 32.3 1.0 CD2 A:HIS371 4.2 32.0 1.0 CA A:HIS371 4.3 31.0 1.0 C A:LEU353 4.4 32.3 1.0 CA A:CYS351 4.5 33.5 1.0 OG1 A:THR436 4.6 29.3 1.0 O A:CYS354 4.6 35.8 1.0 CB A:LEU353 4.6 27.5 1.0 C A:CYS354 4.6 35.9 1.0 CA A:CYS374 4.8 27.2 1.0 N A:LEU353 4.8 28.9 1.0 CA A:LEU353 4.8 32.9 1.0 O A:HOH644 4.8 31.5 1.0 O A:LEU353 4.9 34.0 1.0 N A:CYS374 5.0 28.7 1.0 CB A:THR436 5.0 29.1 1.0

Zinc binding site 3 out of 5 in the Crystal Structure of ZEBRAFISHPHF14-Pzp


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 ZEBRAFISHPHF14-Pzp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:34.4 occ:1.00 ND1 A:HIS434 2.1 30.2 1.0 SG A:CYS437 2.3 32.1 1.0 SG A:CYS410 2.4 31.7 1.0 SG A:CYS407 2.4 27.3 1.0 CE1 A:HIS434 3.0 26.7 1.0 CB A:CYS407 3.1 27.0 1.0 CG A:HIS434 3.2 27.5 1.0 CB A:CYS410 3.4 32.8 1.0 CB A:CYS437 3.4 31.2 1.0 CA A:CYS410 3.5 33.3 1.0 CB A:HIS434 3.6 25.2 1.0 N A:CYS410 3.8 33.0 1.0 N A:HIS434 4.1 25.6 1.0 NE2 A:HIS434 4.1 31.3 1.0 CD2 A:HIS434 4.2 27.1 1.0 C A:LEU409 4.4 32.0 1.0 CA A:HIS434 4.5 22.5 1.0 CG A:PRO355 4.5 37.4 1.0 O A:HOH608 4.6 36.5 1.0 CA A:CYS407 4.6 30.6 1.0 CD A:PRO355 4.6 33.4 1.0 O1 A:EDO507 4.7 50.7 1.0 O2 A:EDO507 4.7 43.2 1.0 CA A:CYS437 4.8 29.7 1.0 O A:LEU409 4.9 38.0 1.0 C A:CYS410 5.0 36.3 1.0 C A:CYS407 5.0 29.7 1.0

Zinc binding site 4 out of 5 in the Crystal Structure of ZEBRAFISHPHF14-Pzp


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 ZEBRAFISHPHF14-Pzp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:41.2 occ:1.00 ND1 A:HIS313 2.1 49.1 1.0 SG A:CYS291 2.3 37.1 1.0 SG A:CYS316 2.3 38.7 1.0 SG A:CYS288 2.3 35.6 1.0 CE1 A:HIS313 3.0 44.9 1.0 CG A:HIS313 3.0 42.6 1.0 CB A:CYS288 3.0 37.4 1.0 CB A:CYS291 3.3 38.3 1.0 CB A:HIS313 3.4 42.1 1.0 CB A:CYS316 3.4 35.2 1.0 N A:CYS291 3.7 39.5 1.0 O A:HOH634 4.0 62.4 1.0 CA A:CYS291 4.1 36.7 1.0 NE2 A:HIS313 4.1 47.0 1.0 N A:HIS313 4.2 38.3 1.0 CD2 A:HIS313 4.2 46.2 1.0 CA A:HIS313 4.4 35.7 1.0 CB A:VAL290 4.5 29.5 1.0 CA A:CYS288 4.5 41.1 1.0 O A:HOH689 4.7 40.5 1.0 CA A:CYS316 4.7 38.5 1.0 C A:VAL290 4.8 39.3 1.0 C A:CYS291 4.9 33.9 1.0 C A:CYS288 5.0 36.8 1.0 N A:VAL290 5.0 31.4 1.0 CA A:VAL290 5.0 33.8 1.0

Zinc binding site 5 out of 5 in the Crystal Structure of ZEBRAFISHPHF14-Pzp


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 ZEBRAFISHPHF14-Pzp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn505 b:47.2 occ:1.00 SG A:CYS308 2.3 43.2 1.0 SG A:CYS343 2.4 46.4 1.0 SG A:CYS305 2.4 45.9 1.0 SG A:CYS340 2.5 38.2 1.0 CB A:CYS305 3.3 40.8 1.0 CB A:CYS308 3.3 46.2 1.0 CB A:CYS343 3.4 45.3 1.0 CB A:CYS340 3.5 33.1 1.0 N A:CYS308 3.7 45.7 1.0 N A:CYS340 3.9 38.8 1.0 CA A:CYS308 4.1 48.3 1.0 O A:HOH653 4.3 44.7 1.0 CA A:CYS340 4.3 35.0 1.0 CG1 A:VAL310 4.3 36.4 1.0 N A:CYS343 4.3 45.0 1.0 CA A:CYS343 4.5 48.0 1.0 CB A:ASN307 4.5 57.6 1.0 CA A:CYS305 4.7 39.0 1.0 C A:ASN307 4.8 46.9 1.0 C A:CYS340 4.9 38.1 1.0 C A:CYS308 4.9 46.9 1.0 O A:CYS340 4.9 40.0 1.0 O A:HOH667 5.0 35.3 1.0 N A:GLY309 5.0 41.9 1.0

H.T.Li, S.P.Zheng. Crystal Structure of ZEBRAFISHPHF14-Pzp To Be Published.