Zinc in PDB 5dag: Crystal Structure of Pzp Domain of Human AF10 Protein

The structure of Crystal Structure of Pzp Domain of Human AF10 Protein, PDB code: 5dag was solved by S.Chen, D.J.Patel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.87 / 1.60
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	51.907, 51.907, 147.727, 90.00, 90.00, 90.00
R / Rfree (%)	19 / 21.4

The binding sites of Zinc atom in the Crystal Structure of Pzp Domain of Human AF10 Protein (pdb code 5dag). 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 Pzp Domain of Human AF10 Protein, PDB code: 5dag:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Crystal Structure of Pzp Domain of Human AF10 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 Pzp Domain of Human AF10 Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:23.6 occ:0.71 ND1 A:HIS52 2.1 23.4 1.0 SG A:CYS55 2.3 21.9 1.0 SG A:CYS28 2.3 24.3 1.0 SG A:CYS25 2.3 22.3 1.0 CE1 A:HIS52 3.0 28.0 1.0 CB A:CYS25 3.1 24.3 1.0 CG A:HIS52 3.1 20.6 1.0 CB A:CYS28 3.3 25.0 1.0 CB A:CYS55 3.4 21.8 1.0 CB A:HIS52 3.5 19.9 1.0 N A:CYS28 3.7 24.1 1.0 N A:HIS52 3.9 20.4 1.0 CA A:CYS28 4.0 22.3 1.0 O A:HOH504 4.1 34.0 1.0 NE2 A:HIS52 4.1 24.7 1.0 O A:HOH479 4.2 28.3 1.0 CD2 A:HIS52 4.2 23.6 1.0 CA A:HIS52 4.3 19.4 1.0 CA A:CYS25 4.6 26.7 1.0 CB A:VAL27 4.6 20.0 1.0 C A:CYS28 4.6 28.8 1.0 C A:VAL27 4.7 25.3 1.0 O A:CYS28 4.8 28.7 1.0 CA A:CYS55 4.8 20.8 1.0 N A:VAL27 5.0 23.3 1.0 O A:HOH502 5.0 34.9 1.0

Zinc binding site 2 out of 5 in the Crystal Structure of Pzp Domain of Human AF10 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 Pzp Domain of Human AF10 Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:22.6 occ:0.72 ND1 A:HIS197 2.1 19.3 1.0 SG A:CYS162 2.3 21.8 1.0 SG A:CYS194 2.3 20.5 1.0 SG A:CYS157 2.3 20.4 1.0 CE1 A:HIS197 3.0 22.4 1.0 CB A:CYS157 3.1 21.7 1.0 CG A:HIS197 3.2 20.4 1.0 CB A:CYS162 3.2 23.4 1.0 CB A:CYS194 3.4 17.3 1.0 CB A:HIS197 3.6 19.6 1.0 N A:CYS194 3.9 18.4 1.0 NE2 A:HIS197 4.1 20.6 1.0 CA A:CYS194 4.3 18.6 1.0 CD2 A:HIS197 4.3 18.6 1.0 CB A:LYS159 4.4 24.1 1.0 CB A:GLN164 4.4 22.7 1.0 CG A:GLN164 4.5 22.9 1.0 N A:HIS197 4.5 19.3 1.0 CA A:CYS157 4.6 20.4 1.0 CA A:CYS162 4.6 22.5 1.0 CA A:HIS197 4.7 18.7 1.0 C A:CYS194 4.9 18.4 1.0 O A:CYS194 5.0 21.0 1.0

Zinc binding site 3 out of 5 in the Crystal Structure of Pzp Domain of Human AF10 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 Pzp Domain of Human AF10 Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:21.2 occ:0.71 ND1 A:HIS167 2.1 19.9 1.0 SG A:CYS140 2.3 21.1 1.0 SG A:CYS170 2.3 20.4 1.0 SG A:CYS137 2.3 18.9 1.0 CE1 A:HIS167 3.0 20.8 1.0 CB A:CYS137 3.2 19.5 1.0 CG A:HIS167 3.2 18.3 1.0 CB A:CYS140 3.4 21.4 1.0 CB A:CYS170 3.4 17.7 1.0 CB A:HIS167 3.5 17.7 1.0 N A:CYS140 3.7 20.6 1.0 CA A:CYS140 4.0 22.6 1.0 N A:HIS167 4.1 16.3 1.0 NE2 A:HIS167 4.2 19.3 1.0 CD2 A:HIS167 4.3 18.2 1.0 NH2 A:ARG145 4.4 28.5 1.0 CA A:HIS167 4.4 16.5 1.0 CD A:PRO86 4.5 22.8 1.0 CG A:PRO86 4.5 24.4 1.0 CA A:CYS137 4.6 18.6 1.0 NE A:ARG145 4.6 26.0 1.0 C A:ILE139 4.7 22.5 1.0 CB A:ILE139 4.7 20.7 1.0 CA A:CYS170 4.8 18.3 1.0 O A:CYS137 4.9 22.1 1.0 C A:CYS137 5.0 20.6 1.0 CZ A:ARG145 5.0 26.7 1.0

Zinc binding site 4 out of 5 in the Crystal Structure of Pzp Domain of Human AF10 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 Pzp Domain of Human AF10 Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn304 b:20.4 occ:0.72 ND1 A:HIS102 2.1 19.3 1.0 SG A:CYS82 2.3 18.0 1.0 SG A:CYS105 2.3 17.3 1.0 SG A:CYS85 2.3 19.6 1.0 CE1 A:HIS102 3.1 18.5 1.0 CB A:CYS82 3.1 20.1 1.0 CG A:HIS102 3.1 18.0 1.0 CB A:CYS85 3.2 20.7 1.0 CB A:HIS102 3.4 17.3 1.0 CB A:CYS105 3.5 17.4 1.0 N A:CYS85 3.8 20.1 1.0 CG2 A:THR169 4.1 19.2 1.0 CA A:CYS85 4.1 21.5 1.0 N A:HIS102 4.1 18.3 1.0 NE2 A:HIS102 4.2 22.0 1.0 CD2 A:HIS102 4.2 21.2 1.0 C A:LEU84 4.3 22.2 1.0 OG1 A:THR169 4.3 18.6 1.0 CA A:HIS102 4.4 18.9 1.0 CB A:LEU84 4.4 20.4 1.0 CA A:CYS82 4.6 22.8 1.0 CA A:LEU84 4.7 18.0 1.0 N A:LEU84 4.7 20.6 1.0 C A:CYS85 4.8 23.0 1.0 CA A:CYS105 4.8 17.1 1.0 O A:HOH467 4.8 18.9 1.0 O A:LEU84 4.9 20.6 1.0 CB A:THR169 4.9 18.6 1.0 O A:CYS85 4.9 23.1 1.0 N A:CYS105 4.9 17.2 1.0

Zinc binding site 5 out of 5 in the Crystal Structure of Pzp Domain of Human AF10 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 Pzp Domain of Human AF10 Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn305 b:30.0 occ:0.72 SG A:CYS47 2.3 31.4 1.0 SG A:CYS42 2.3 27.3 1.0 SG A:CYS71 2.3 30.6 1.0 SG A:CYS68 2.4 24.9 1.0 CB A:CYS47 3.2 32.0 1.0 CB A:CYS71 3.2 23.7 1.0 CB A:CYS42 3.3 25.9 1.0 CB A:CYS68 3.5 23.6 1.0 N A:CYS68 3.9 26.2 1.0 N A:CYS71 4.1 30.5 1.0 CA A:CYS68 4.2 25.5 1.0 CA A:CYS71 4.3 29.9 1.0 O A:HOH500 4.3 36.3 1.0 CB A:VAL49 4.4 26.6 1.0 CG2 A:VAL49 4.5 26.5 1.0 CA A:CYS47 4.6 34.0 1.0 CA A:CYS42 4.7 29.5 1.0 O A:CYS68 4.8 29.7 1.0 N A:GLY44 4.8 34.5 1.0 CA A:GLY44 4.8 37.0 1.0 C A:CYS68 4.8 30.3 1.0

S.Chen, Z.Yang, A.W.Wilkinson, A.J.Deshpande, S.Sidoli, K.Krajewski, B.D.Strahl, B.A.Garcia, S.A.Armstrong, D.J.Patel, O.Gozani. The Pzp Domain of AF10 Senses Unmodified H3K27 to Regulate DOT1L-Mediated Methylation of H3K79. Mol.Cell V. 60 319 2015.
ISSN: ISSN 1097-2765
PubMed: 26439302
DOI: 10.1016/J.MOLCEL.2015.08.019