Zinc in PDB 5dah: Crystal Structure of Pzp Domain of Human AF10 Protein Fused with Histone H3 Peptide

The structure of Crystal Structure of Pzp Domain of Human AF10 Protein Fused with Histone H3 Peptide, PDB code: 5dah 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)	46.95 / 2.61
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	42.905, 79.995, 59.287, 90.00, 102.01, 90.00
R / Rfree (%)	17.6 / 24

The binding sites of Zinc atom in the Crystal Structure of Pzp Domain of Human AF10 Protein Fused with Histone H3 Peptide (pdb code 5dah). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 10 binding sites of Zinc where determined in the Crystal Structure of Pzp Domain of Human AF10 Protein Fused with Histone H3 Peptide, PDB code: 5dah:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in the Crystal Structure of Pzp Domain of Human AF10 Protein Fused with Histone H3 Peptide


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 Fused with Histone H3 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:20.8 occ:1.00 SG A:CYS28 2.2 30.7 1.0 ND1 A:HIS52 2.2 20.3 1.0 SG A:CYS55 2.3 24.1 1.0 SG A:CYS25 2.4 16.5 1.0 CB A:CYS25 3.1 25.1 1.0 CE1 A:HIS52 3.2 27.2 1.0 CG A:HIS52 3.2 24.9 1.0 CB A:CYS28 3.2 26.6 1.0 CB A:CYS55 3.4 19.9 1.0 CB A:HIS52 3.5 22.9 1.0 N A:CYS28 3.8 20.2 1.0 N A:HIS52 3.9 21.2 1.0 CA A:CYS28 4.1 20.6 1.0 NE2 A:HIS52 4.3 27.4 1.0 CD2 A:HIS52 4.3 25.7 1.0 CA A:HIS52 4.4 20.6 1.0 O A:HOH434 4.4 18.0 1.0 CB A:VAL27 4.6 23.6 1.0 CA A:CYS25 4.6 26.0 1.0 C A:CYS28 4.8 24.8 1.0 CA A:CYS55 4.8 22.5 1.0 C A:VAL27 4.8 23.2 1.0 N A:SER29 4.8 23.7 1.0 CE D:LYS23 4.9 23.9 1.0

Zinc binding site 2 out of 10 in the Crystal Structure of Pzp Domain of Human AF10 Protein Fused with Histone H3 Peptide


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 Fused with Histone H3 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:29.1 occ:1.00 SG A:CYS47 2.3 25.9 1.0 SG A:CYS42 2.4 23.3 1.0 SG A:CYS71 2.4 36.3 1.0 SG A:CYS68 2.4 32.5 1.0 CB A:CYS47 3.1 30.2 1.0 CB A:CYS71 3.2 30.0 1.0 CB A:CYS68 3.5 23.7 1.0 CB A:CYS42 3.5 24.7 1.0 N A:CYS68 3.9 25.7 1.0 N A:CYS71 4.1 28.6 1.0 CA A:CYS68 4.2 24.9 1.0 CA A:CYS71 4.3 28.1 1.0 CA A:GLY44 4.4 34.1 1.0 CA A:CYS47 4.6 33.1 1.0 CB A:VAL49 4.6 20.5 1.0 O A:CYS68 4.7 31.1 1.0 N A:GLY44 4.7 31.8 1.0 C A:CYS68 4.8 26.7 1.0 CG2 A:VAL49 4.9 19.3 1.0 O A:HOH433 4.9 21.6 1.0 CA A:CYS42 4.9 22.8 1.0

Zinc binding site 3 out of 10 in the Crystal Structure of Pzp Domain of Human AF10 Protein Fused with Histone H3 Peptide


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 Fused with Histone H3 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:20.2 occ:1.00 ND1 A:HIS102 2.1 16.6 1.0 SG A:CYS105 2.3 15.8 1.0 SG A:CYS82 2.4 21.4 1.0 SG A:CYS85 2.4 17.5 1.0 CG A:HIS102 3.0 21.8 1.0 CE1 A:HIS102 3.1 20.0 1.0 CB A:CYS82 3.2 25.8 1.0 CB A:HIS102 3.2 17.0 1.0 CB A:CYS85 3.4 23.9 1.0 CB A:CYS105 3.5 17.2 1.0 CG2 A:THR169 3.9 20.4 1.0 N A:CYS85 4.1 22.5 1.0 N A:HIS102 4.1 24.0 1.0 CD2 A:HIS102 4.1 21.6 1.0 NE2 A:HIS102 4.2 26.9 1.0 CA A:HIS102 4.3 18.6 1.0 CA A:CYS85 4.3 19.9 1.0 C A:LEU84 4.3 28.8 1.0 OG1 A:THR169 4.4 25.7 1.0 CB A:LEU84 4.5 22.4 1.0 CA A:CYS82 4.7 25.3 1.0 CA A:CYS105 4.7 16.4 1.0 CA A:LEU84 4.8 24.3 1.0 O A:LEU84 4.8 30.7 1.0 N A:LEU84 4.8 27.5 1.0 CB A:THR169 4.8 22.4 1.0 C A:CYS85 4.9 23.6 1.0 N A:CYS105 4.9 12.3 1.0

Zinc binding site 4 out of 10 in the Crystal Structure of Pzp Domain of Human AF10 Protein Fused with Histone H3 Peptide


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 Fused with Histone H3 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn304 b:21.6 occ:1.00 ND1 A:HIS167 2.2 18.9 1.0 SG A:CYS170 2.3 21.5 1.0 SG A:CYS140 2.3 26.4 1.0 SG A:CYS137 2.4 12.7 1.0 CE1 A:HIS167 3.1 20.2 1.0 CB A:CYS137 3.1 19.5 1.0 CB A:CYS140 3.2 20.2 1.0 CG A:HIS167 3.2 19.6 1.0 CB A:CYS170 3.5 20.6 1.0 CB A:HIS167 3.6 16.5 1.0 N A:CYS140 3.7 18.8 1.0 CA A:CYS140 3.9 19.9 1.0 NE2 A:HIS167 4.2 20.0 1.0 N A:HIS167 4.3 17.0 1.0 CD2 A:HIS167 4.3 18.6 1.0 CA A:CYS137 4.6 19.4 1.0 CA A:HIS167 4.6 17.7 1.0 C A:ILE139 4.8 20.7 1.0 CB A:ILE139 4.8 17.1 1.0 CD A:PRO86 4.8 23.4 1.0 CG A:PRO86 4.8 22.9 1.0 CA A:CYS170 4.9 18.4 1.0 C A:CYS137 5.0 20.2 1.0

Zinc binding site 5 out of 10 in the Crystal Structure of Pzp Domain of Human AF10 Protein Fused with Histone H3 Peptide


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 Fused with Histone H3 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn305 b:26.1 occ:1.00 ND1 A:HIS197 2.1 28.7 1.0 SG A:CYS194 2.2 25.4 1.0 SG A:CYS157 2.4 19.8 1.0 SG A:CYS162 2.4 20.6 1.0 CE1 A:HIS197 2.9 32.4 1.0 CG A:HIS197 3.1 27.0 1.0 CB A:CYS162 3.3 31.8 1.0 CB A:CYS157 3.3 22.7 1.0 CB A:CYS194 3.4 27.6 1.0 CB A:HIS197 3.6 25.0 1.0 N A:CYS194 3.9 24.8 1.0 NE2 A:HIS197 4.1 33.1 1.0 CA A:CYS194 4.2 24.2 1.0 CD2 A:HIS197 4.2 28.1 1.0 CB A:LYS159 4.3 30.1 1.0 CB A:GLN164 4.3 19.5 1.0 CG A:GLN164 4.3 17.5 1.0 N A:HIS197 4.5 34.7 1.0 CA A:HIS197 4.7 30.0 1.0 C A:CYS194 4.7 26.9 1.0 CA A:CYS162 4.7 28.3 1.0 O A:CYS194 4.8 29.5 1.0 CA A:CYS157 4.8 22.6 1.0 CB A:TYR196 4.8 22.6 1.0 CG A:LYS159 4.9 36.6 1.0

Zinc binding site 6 out of 10 in the Crystal Structure of Pzp Domain of Human AF10 Protein Fused with Histone H3 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Pzp Domain of Human AF10 Protein Fused with Histone H3 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:19.5 occ:1.00 ND1 B:HIS52 2.2 20.8 1.0 SG B:CYS55 2.3 21.4 1.0 SG B:CYS25 2.4 23.7 1.0 SG B:CYS28 2.4 21.3 1.0 CB B:CYS25 3.0 21.4 1.0 CG B:HIS52 3.2 22.3 1.0 CE1 B:HIS52 3.2 25.9 1.0 CB B:CYS55 3.4 16.5 1.0 CB B:HIS52 3.4 20.6 1.0 CB B:CYS28 3.5 21.3 1.0 N B:HIS52 3.8 19.1 1.0 N B:CYS28 3.8 21.6 1.0 CA B:CYS28 4.2 19.4 1.0 CA B:HIS52 4.2 19.4 1.0 NE2 B:HIS52 4.3 29.6 1.0 CD2 B:HIS52 4.3 26.3 1.0 CA B:CYS25 4.5 23.5 1.0 C B:CYS28 4.7 23.6 1.0 CB B:VAL27 4.7 18.8 1.0 O B:CYS28 4.7 24.8 1.0 C B:VAL27 4.7 23.7 1.0 CA B:CYS55 4.8 18.1 1.0 N B:VAL27 4.9 18.8 1.0 C B:VAL51 4.9 22.0 1.0 CE C:LYS23 4.9 20.6 1.0 C B:CYS25 5.0 21.6 1.0

Zinc binding site 7 out of 10 in the Crystal Structure of Pzp Domain of Human AF10 Protein Fused with Histone H3 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Pzp Domain of Human AF10 Protein Fused with Histone H3 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:27.9 occ:1.00 SG B:CYS47 2.3 33.5 1.0 SG B:CYS42 2.3 29.6 1.0 SG B:CYS71 2.4 24.1 1.0 SG B:CYS68 2.4 20.8 1.0 CB B:CYS71 3.2 25.0 1.0 CB B:CYS47 3.3 37.0 1.0 CB B:CYS42 3.4 20.5 1.0 CB B:CYS68 3.5 17.7 1.0 N B:CYS68 3.8 24.9 1.0 N B:CYS71 4.0 26.0 1.0 CA B:CYS68 4.2 20.3 1.0 CA B:CYS71 4.2 30.5 1.0 CG2 B:VAL49 4.4 26.0 1.0 CB B:VAL49 4.6 26.1 1.0 CA B:CYS47 4.7 40.7 1.0 O B:CYS68 4.7 24.0 1.0 C B:CYS68 4.8 22.3 1.0 CA B:GLY44 4.8 36.1 1.0 CA B:CYS42 4.8 26.4 1.0 N B:GLY44 4.9 30.9 1.0 C B:PHE67 5.0 22.3 1.0

Zinc binding site 8 out of 10 in the Crystal Structure of Pzp Domain of Human AF10 Protein Fused with Histone H3 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Pzp Domain of Human AF10 Protein Fused with Histone H3 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:18.7 occ:1.00 ND1 B:HIS102 2.1 18.6 1.0 SG B:CYS105 2.4 17.1 1.0 SG B:CYS85 2.4 20.9 1.0 SG B:CYS82 2.4 22.6 1.0 CG B:HIS102 3.1 18.9 1.0 CB B:CYS85 3.2 21.7 1.0 CE1 B:HIS102 3.2 24.4 1.0 CB B:CYS82 3.2 21.6 1.0 CB B:HIS102 3.3 17.3 1.0 CB B:CYS105 3.4 16.1 1.0 N B:CYS85 3.8 20.1 1.0 CA B:CYS85 4.1 29.4 1.0 N B:HIS102 4.1 21.8 1.0 C B:LEU84 4.2 23.8 1.0 CD2 B:HIS102 4.2 19.5 1.0 NE2 B:HIS102 4.3 24.2 1.0 CA B:HIS102 4.4 20.1 1.0 CB B:THR169 4.4 25.4 1.0 CB B:LEU84 4.4 19.6 1.0 OG1 B:THR169 4.5 29.8 1.0 CA B:LEU84 4.6 21.1 1.0 O B:HOH424 4.7 13.4 1.0 CA B:CYS82 4.7 24.4 1.0 N B:LEU84 4.7 22.2 1.0 O B:LEU84 4.7 23.2 1.0 C B:CYS85 4.7 24.9 1.0 CA B:CYS105 4.8 15.1 1.0 O B:CYS85 4.9 27.6 1.0 CG2 B:THR169 4.9 24.0 1.0

Zinc binding site 9 out of 10 in the Crystal Structure of Pzp Domain of Human AF10 Protein Fused with Histone H3 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of Pzp Domain of Human AF10 Protein Fused with Histone H3 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn304 b:22.9 occ:1.00 ND1 B:HIS167 2.2 25.4 1.0 SG B:CYS170 2.3 24.8 1.0 SG B:CYS137 2.3 17.7 1.0 SG B:CYS140 2.4 22.6 1.0 CB B:CYS137 3.0 24.3 1.0 CE1 B:HIS167 3.1 26.1 1.0 CG B:HIS167 3.2 23.6 1.0 CB B:CYS140 3.3 25.5 1.0 CB B:CYS170 3.5 20.9 1.0 CB B:HIS167 3.6 16.3 1.0 N B:CYS140 3.7 22.1 1.0 CA B:CYS140 4.0 22.7 1.0 NE2 B:HIS167 4.2 21.4 1.0 N B:HIS167 4.2 19.5 1.0 CD2 B:HIS167 4.2 20.9 1.0 CA B:HIS167 4.5 18.2 1.0 CA B:CYS137 4.5 24.7 1.0 CB B:ILE139 4.7 19.5 1.0 C B:ILE139 4.7 24.8 1.0 O B:HOH436 4.8 31.0 1.0 CA B:CYS170 4.9 21.4 1.0 CG B:PRO86 4.9 21.7 1.0 O B:CYS137 4.9 19.9 1.0 O B:LYS148 4.9 29.5 1.0 C B:CYS137 4.9 21.1 1.0 CD B:PRO86 5.0 20.6 1.0

Zinc binding site 10 out of 10 in the Crystal Structure of Pzp Domain of Human AF10 Protein Fused with Histone H3 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of Pzp Domain of Human AF10 Protein Fused with Histone H3 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn305 b:25.1 occ:1.00 SG B:CYS194 2.2 28.2 1.0 ND1 B:HIS197 2.3 33.0 1.0 SG B:CYS157 2.3 27.1 1.0 SG B:CYS162 2.4 31.4 1.0 CE1 B:HIS197 3.0 32.7 1.0 CB B:CYS157 3.2 30.3 1.0 CB B:CYS162 3.3 33.0 1.0 CG B:HIS197 3.4 31.5 1.0 CB B:CYS194 3.4 21.1 1.0 CB B:HIS197 3.8 27.6 1.0 N B:CYS194 3.9 25.4 1.0 NE2 B:HIS197 4.1 35.1 1.0 CA B:CYS194 4.2 26.3 1.0 CG B:GLN164 4.2 30.6 1.0 CB B:GLN164 4.3 28.1 1.0 CD2 B:HIS197 4.3 30.2 1.0 CB B:LYS159 4.4 29.7 1.0 CA B:CYS157 4.7 26.7 1.0 N B:HIS197 4.7 29.0 1.0 CA B:CYS162 4.8 36.8 1.0 O B:CYS194 4.8 28.8 1.0 C B:CYS194 4.8 25.5 1.0 CG B:LYS159 4.9 33.2 1.0 CA B:HIS197 4.9 27.9 1.0 CB B:TYR196 4.9 24.1 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