Zinc in PDB 6fkp: Crystal Structure of BAZ2A Phd Zinc Finger in Complex with H3 10-Mer Aa Mutant Peptide

The structure of Crystal Structure of BAZ2A Phd Zinc Finger in Complex with H3 10-Mer Aa Mutant Peptide, PDB code: 6fkp was solved by A.Amato, X.Lucas, A.Bortoluzzi, D.Wright, A.Ciulli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.72 / 2.00
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	72.719, 72.719, 99.894, 90.00, 90.00, 90.00
R / Rfree (%)	19.4 / 22.3

The binding sites of Zinc atom in the Crystal Structure of BAZ2A Phd Zinc Finger in Complex with H3 10-Mer Aa Mutant Peptide (pdb code 6fkp). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of BAZ2A Phd Zinc Finger in Complex with H3 10-Mer Aa Mutant Peptide, PDB code: 6fkp:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Crystal Structure of BAZ2A Phd Zinc Finger in Complex with H3 10-Mer Aa Mutant 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 BAZ2A Phd Zinc Finger in Complex with H3 10-Mer Aa Mutant Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1801 b:29.6 occ:1.00 ND1 A:HIS1702 2.1 29.1 1.0 SG A:CYS1679 2.3 30.3 1.0 SG A:CYS1705 2.3 27.5 1.0 SG A:CYS1682 2.3 33.3 1.0 CE1 A:HIS1702 3.0 30.4 1.0 CG A:HIS1702 3.1 28.3 1.0 CB A:CYS1679 3.1 33.0 1.0 CB A:CYS1682 3.3 35.0 1.0 CB A:CYS1705 3.4 26.0 1.0 CB A:HIS1702 3.4 27.0 1.0 N A:CYS1682 3.8 35.0 1.0 N A:HIS1702 4.1 26.9 1.0 CA A:CYS1682 4.1 36.5 1.0 NE2 A:HIS1702 4.2 30.3 1.0 CD2 A:HIS1702 4.2 29.3 1.0 CA A:HIS1702 4.4 26.5 1.0 O A:HOH1909 4.4 53.0 1.0 CE1 A:TYR1704 4.5 26.8 1.0 CA A:CYS1679 4.6 34.7 1.0 CB A:VAL1681 4.6 32.6 1.0 CA A:CYS1705 4.8 25.0 1.0 C A:VAL1681 4.9 35.1 1.0 C A:CYS1682 4.9 39.3 1.0

Zinc binding site 2 out of 8 in the Crystal Structure of BAZ2A Phd Zinc Finger in Complex with H3 10-Mer Aa Mutant 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 BAZ2A Phd Zinc Finger in Complex with H3 10-Mer Aa Mutant Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1802 b:32.2 occ:1.00 SG A:CYS1697 2.3 34.7 1.0 SG A:CYS1694 2.3 33.9 1.0 SG A:CYS1720 2.3 31.4 1.0 SG A:CYS1723 2.3 32.7 1.0 CB A:CYS1694 3.3 34.2 1.0 CB A:CYS1697 3.3 36.6 1.0 CB A:CYS1723 3.3 31.9 1.0 CB A:CYS1720 3.4 30.8 1.0 N A:CYS1697 3.7 38.2 1.0 N A:CYS1720 3.9 31.4 1.0 N A:CYS1723 4.0 31.5 1.0 CA A:CYS1697 4.1 38.1 1.0 C A:GLY1696 4.1 39.1 1.0 CA A:CYS1720 4.2 30.6 1.0 CA A:CYS1723 4.2 31.5 1.0 CA A:GLY1696 4.5 38.7 1.0 O A:CYS1720 4.6 29.5 1.0 N A:GLY1696 4.6 38.5 1.0 C A:CYS1720 4.6 30.3 1.0 C A:CYS1697 4.7 38.7 1.0 CB A:ARG1699 4.7 34.9 1.0 CA A:CYS1694 4.7 35.4 1.0 CD A:ARG1699 4.7 35.6 1.0 O A:GLY1696 4.8 40.1 1.0 NH1 A:ARG1699 4.8 37.1 1.0 C A:PHE1719 5.0 32.3 1.0

Zinc binding site 3 out of 8 in the Crystal Structure of BAZ2A Phd Zinc Finger in Complex with H3 10-Mer Aa Mutant 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 BAZ2A Phd Zinc Finger in Complex with H3 10-Mer Aa Mutant Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1801 b:32.5 occ:1.00 ND1 B:HIS1702 2.1 31.9 1.0 SG B:CYS1679 2.3 33.8 1.0 SG B:CYS1705 2.3 30.5 1.0 SG B:CYS1682 2.3 36.9 1.0 CE1 B:HIS1702 3.1 32.8 1.0 CG B:HIS1702 3.1 30.8 1.0 CB B:CYS1679 3.1 36.2 1.0 CB B:CYS1682 3.3 38.9 1.0 CB B:HIS1702 3.4 30.0 1.0 CB B:CYS1705 3.4 28.9 1.0 N B:CYS1682 3.8 39.5 1.0 CA B:CYS1682 4.1 40.8 1.0 N B:HIS1702 4.1 30.5 1.0 NE2 B:HIS1702 4.2 32.3 1.0 CD2 B:HIS1702 4.2 31.3 1.0 O B:HOH1938 4.3 51.0 1.0 CA B:HIS1702 4.4 29.1 1.0 CE1 B:TYR1704 4.6 28.4 1.0 CA B:CYS1679 4.6 38.2 1.0 CB B:VAL1681 4.6 37.4 1.0 CA B:CYS1705 4.7 27.8 1.0 C B:VAL1681 4.9 39.7 1.0 O B:HOH1906 4.9 43.2 1.0 C B:CYS1682 4.9 43.2 1.0 N B:CYS1705 5.0 26.9 1.0

Zinc binding site 4 out of 8 in the Crystal Structure of BAZ2A Phd Zinc Finger in Complex with H3 10-Mer Aa Mutant 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 BAZ2A Phd Zinc Finger in Complex with H3 10-Mer Aa Mutant Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1802 b:40.0 occ:1.00 SG B:CYS1694 2.3 38.2 1.0 SG B:CYS1697 2.3 41.9 1.0 SG B:CYS1720 2.3 38.3 1.0 SG B:CYS1723 2.3 43.3 1.0 CB B:CYS1694 3.3 38.4 1.0 CB B:CYS1697 3.3 44.2 1.0 CB B:CYS1723 3.4 43.1 1.0 CB B:CYS1720 3.4 37.1 1.0 N B:CYS1697 3.7 44.5 1.0 N B:CYS1720 3.9 37.1 1.0 N B:CYS1723 4.0 43.5 1.0 CA B:CYS1697 4.1 44.8 1.0 CA B:CYS1720 4.2 36.6 1.0 CA B:CYS1723 4.3 44.5 1.0 C B:GLY1696 4.3 45.7 1.0 CB B:ARG1699 4.6 42.5 1.0 CA B:GLY1696 4.6 45.0 1.0 CD B:ARG1699 4.7 44.7 1.0 C B:CYS1697 4.7 44.7 1.0 O B:CYS1720 4.7 36.9 1.0 NH1 B:ARG1699 4.7 47.6 1.0 C B:CYS1720 4.7 37.1 1.0 N B:GLY1696 4.7 43.8 1.0 CA B:CYS1694 4.8 38.3 1.0 O B:CYS1697 5.0 44.4 1.0 C B:PHE1719 5.0 37.4 1.0

Zinc binding site 5 out of 8 in the Crystal Structure of BAZ2A Phd Zinc Finger in Complex with H3 10-Mer Aa Mutant 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 BAZ2A Phd Zinc Finger in Complex with H3 10-Mer Aa Mutant Peptide within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1801 b:25.3 occ:1.00 ND1 C:HIS1702 2.1 24.5 1.0 SG C:CYS1682 2.3 27.0 1.0 SG C:CYS1679 2.3 24.3 1.0 SG C:CYS1705 2.3 26.4 1.0 CE1 C:HIS1702 3.0 24.8 1.0 CG C:HIS1702 3.1 24.1 1.0 CB C:CYS1679 3.1 25.2 1.0 CB C:CYS1682 3.3 28.4 1.0 CB C:CYS1705 3.4 25.8 1.0 CB C:HIS1702 3.4 23.9 1.0 N C:CYS1682 3.8 27.9 1.0 CA C:CYS1682 4.1 28.9 1.0 N C:HIS1702 4.1 23.3 1.0 O C:HOH1950 4.1 41.8 1.0 NE2 C:HIS1702 4.1 24.4 1.0 CD2 C:HIS1702 4.2 24.1 1.0 CA C:HIS1702 4.4 23.6 1.0 CE1 C:TYR1704 4.5 25.9 1.0 CA C:CYS1679 4.6 25.6 1.0 CB C:VAL1681 4.7 26.9 1.0 CA C:CYS1705 4.7 26.1 1.0 C C:CYS1682 4.9 29.9 1.0 C C:VAL1681 4.9 27.9 1.0 O C:HOH1905 4.9 39.4 1.0

Zinc binding site 6 out of 8 in the Crystal Structure of BAZ2A Phd Zinc Finger in Complex with H3 10-Mer Aa Mutant 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 BAZ2A Phd Zinc Finger in Complex with H3 10-Mer Aa Mutant Peptide within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1802 b:25.8 occ:1.00 SG C:CYS1694 2.3 28.1 1.0 SG C:CYS1723 2.3 28.8 1.0 SG C:CYS1697 2.3 25.4 1.0 SG C:CYS1720 2.3 25.2 1.0 CB C:CYS1694 3.3 28.2 1.0 CB C:CYS1723 3.3 29.3 1.0 CB C:CYS1697 3.4 27.4 1.0 CB C:CYS1720 3.5 26.1 1.0 N C:CYS1697 3.7 29.4 1.0 N C:CYS1720 3.9 29.3 1.0 N C:CYS1723 4.0 28.5 1.0 CA C:CYS1697 4.1 28.5 1.0 CA C:CYS1720 4.2 27.1 1.0 C C:GLY1696 4.3 31.1 1.0 CA C:CYS1723 4.3 29.9 1.0 O C:HOH1948 4.5 45.1 1.0 CA C:GLY1696 4.6 32.2 1.0 N C:GLY1696 4.7 32.3 1.0 NH1 C:ARG1699 4.7 23.7 1.0 O C:CYS1720 4.7 26.2 1.0 C C:CYS1720 4.7 26.7 1.0 C C:CYS1697 4.7 28.1 1.0 CD C:ARG1699 4.7 23.2 1.0 CB C:ARG1699 4.7 23.5 1.0 CA C:CYS1694 4.7 29.1 1.0 O C:GLY1696 4.9 32.0 1.0 O C:CYS1697 5.0 28.1 1.0

Zinc binding site 7 out of 8 in the Crystal Structure of BAZ2A Phd Zinc Finger in Complex with H3 10-Mer Aa Mutant 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 BAZ2A Phd Zinc Finger in Complex with H3 10-Mer Aa Mutant Peptide within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1801 b:27.6 occ:1.00 ND1 D:HIS1702 2.1 27.4 1.0 SG D:CYS1705 2.3 27.4 1.0 SG D:CYS1679 2.3 26.6 1.0 SG D:CYS1682 2.3 30.0 1.0 CE1 D:HIS1702 3.0 28.2 1.0 CG D:HIS1702 3.1 27.1 1.0 CB D:CYS1679 3.1 27.6 1.0 CB D:CYS1682 3.3 30.8 1.0 CB D:CYS1705 3.4 26.4 1.0 CB D:HIS1702 3.4 26.6 1.0 N D:CYS1682 3.8 29.9 1.0 O D:HOH1936 3.9 54.8 1.0 N D:HIS1702 4.1 26.2 1.0 NE2 D:HIS1702 4.1 28.1 1.0 CA D:CYS1682 4.2 31.4 1.0 CD2 D:HIS1702 4.2 27.5 1.0 CA D:HIS1702 4.4 26.4 1.0 CE1 D:TYR1704 4.5 26.4 1.0 CA D:CYS1679 4.6 27.9 1.0 CB D:VAL1681 4.7 28.2 1.0 CA D:CYS1705 4.7 26.5 1.0 O D:HOH1911 4.8 42.3 1.0 C D:CYS1682 4.9 32.9 1.0 C D:VAL1681 4.9 29.7 1.0

Zinc binding site 8 out of 8 in the Crystal Structure of BAZ2A Phd Zinc Finger in Complex with H3 10-Mer Aa Mutant 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 BAZ2A Phd Zinc Finger in Complex with H3 10-Mer Aa Mutant Peptide within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1802 b:26.8 occ:1.00 SG D:CYS1694 2.3 29.2 1.0 SG D:CYS1697 2.3 28.2 1.0 SG D:CYS1723 2.3 26.3 1.0 SG D:CYS1720 2.3 25.1 1.0 CB D:CYS1694 3.3 29.8 1.0 CB D:CYS1723 3.3 25.3 1.0 CB D:CYS1697 3.3 29.7 1.0 CB D:CYS1720 3.5 25.0 1.0 N D:CYS1697 3.7 31.2 1.0 N D:CYS1720 3.9 26.1 1.0 N D:CYS1723 4.0 23.9 1.0 CA D:CYS1697 4.1 31.1 1.0 C D:GLY1696 4.2 31.9 1.0 CA D:CYS1720 4.2 25.0 1.0 CA D:CYS1723 4.3 24.3 1.0 CA D:GLY1696 4.5 32.1 1.0 O D:CYS1720 4.6 24.1 1.0 N D:GLY1696 4.6 32.1 1.0 C D:CYS1720 4.7 24.5 1.0 C D:CYS1697 4.7 31.9 1.0 CA D:CYS1694 4.7 31.3 1.0 CB D:ARG1699 4.7 28.5 1.0 NH1 D:ARG1699 4.7 28.6 1.0 CD D:ARG1699 4.8 28.2 1.0 O D:GLY1696 4.8 32.0 1.0 O D:HOH1938 4.9 39.1 1.0 O D:CYS1697 5.0 32.2 1.0

A.Amato, X.Lucas, A.Bortoluzzi, D.Wright, A.Ciulli. Targeting Ligandable Pockets on Plant Homeodomain (Phd) Zinc Finger Domains By A Fragment-Based Approach. Acs Chem. Biol. V. 13 915 2018.
ISSN: ESSN 1554-8937
PubMed: 29529862
DOI: 10.1021/ACSCHEMBIO.7B01093