Zinc in PDB 6fap: Crystal Structure of Human BAZ2A Phd Zinc Finger in Complex with FR23

The structure of Crystal Structure of Human BAZ2A Phd Zinc Finger in Complex with FR23, PDB code: 6fap 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)	45.73 / 2.70
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	72.796, 72.796, 99.630, 90.00, 90.00, 90.00
R / Rfree (%)	20.9 / 24.8

The binding sites of Zinc atom in the Crystal Structure of Human BAZ2A Phd Zinc Finger in Complex with FR23 (pdb code 6fap). 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 Human BAZ2A Phd Zinc Finger in Complex with FR23, PDB code: 6fap:
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 Human BAZ2A Phd Zinc Finger in Complex with FR23


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 Human BAZ2A Phd Zinc Finger in Complex with FR23 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1801 b:52.9 occ:1.00 ND1 A:HIS1702 2.0 56.7 1.0 SG A:CYS1679 2.3 58.6 1.0 SG A:CYS1705 2.3 56.9 1.0 SG A:CYS1682 2.3 62.5 1.0 CE1 A:HIS1702 3.0 60.8 1.0 CG A:HIS1702 3.0 54.6 1.0 CB A:CYS1679 3.3 62.9 1.0 CB A:HIS1702 3.3 51.4 1.0 CB A:CYS1682 3.4 64.0 1.0 CB A:CYS1705 3.4 55.2 1.0 N A:CYS1682 4.0 62.0 1.0 NE2 A:HIS1702 4.1 60.0 1.0 CD2 A:HIS1702 4.1 57.2 1.0 N A:HIS1702 4.2 50.9 1.0 CA A:CYS1682 4.3 65.5 1.0 CA A:HIS1702 4.4 50.0 1.0 CE1 A:TYR1704 4.4 51.0 1.0 CB A:VAL1681 4.7 55.0 1.0 CA A:CYS1679 4.7 64.5 1.0 CA A:CYS1705 4.8 52.3 1.0

Zinc binding site 2 out of 8 in the Crystal Structure of Human BAZ2A Phd Zinc Finger in Complex with FR23


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 Human BAZ2A Phd Zinc Finger in Complex with FR23 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1802 b:56.0 occ:1.00 SG A:CYS1694 2.3 63.4 1.0 SG A:CYS1697 2.3 67.0 1.0 SG A:CYS1723 2.3 66.9 1.0 SG A:CYS1720 2.3 60.5 1.0 CB A:CYS1694 3.3 64.2 1.0 CB A:CYS1723 3.4 62.4 1.0 CB A:CYS1697 3.4 71.9 1.0 CB A:CYS1720 3.4 57.4 1.0 N A:CYS1697 3.8 73.3 1.0 N A:CYS1723 3.9 57.7 1.0 N A:CYS1720 3.9 57.7 1.0 CA A:CYS1697 4.1 74.1 1.0 CA A:CYS1720 4.2 56.6 1.0 CA A:CYS1723 4.2 60.0 1.0 C A:GLY1696 4.4 76.1 1.0 O A:CYS1720 4.5 58.5 1.0 NH1 A:ARG1699 4.6 75.7 1.0 C A:CYS1720 4.6 56.5 1.0 CD A:ARG1699 4.6 70.8 1.0 CA A:GLY1696 4.7 74.2 1.0 CA A:CYS1694 4.8 65.0 1.0 C A:CYS1697 4.8 74.8 1.0 CB A:ARG1699 4.8 69.1 1.0 N A:GLY1696 4.8 72.9 1.0 CB A:VAL1722 4.9 59.4 1.0 C A:VAL1722 4.9 57.9 1.0

Zinc binding site 3 out of 8 in the Crystal Structure of Human BAZ2A Phd Zinc Finger in Complex with FR23


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 Human BAZ2A Phd Zinc Finger in Complex with FR23 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1801 b:52.7 occ:1.00 ND1 B:HIS1702 2.1 59.0 1.0 SG B:CYS1682 2.3 64.3 1.0 SG B:CYS1705 2.3 55.9 1.0 SG B:CYS1679 2.3 57.2 1.0 CE1 B:HIS1702 3.0 61.5 1.0 CG B:HIS1702 3.0 56.3 1.0 CB B:CYS1679 3.3 60.5 1.0 CB B:CYS1682 3.4 64.4 1.0 CB B:HIS1702 3.4 53.7 1.0 CB B:CYS1705 3.4 54.0 1.0 N B:CYS1682 3.9 62.3 1.0 NE2 B:HIS1702 4.1 60.0 1.0 N B:HIS1702 4.2 53.6 1.0 CD2 B:HIS1702 4.2 57.3 1.0 CA B:CYS1682 4.2 65.4 1.0 CA B:HIS1702 4.4 52.1 1.0 O B:HOH1904 4.5 60.2 1.0 CE1 B:TYR1704 4.5 54.3 1.0 CB B:VAL1681 4.7 55.0 1.0 CA B:CYS1679 4.7 61.5 1.0 CA B:CYS1705 4.8 51.8 1.0 C B:CYS1682 4.9 68.3 1.0 O B:LYS1684 5.0 70.4 1.0 C B:VAL1681 5.0 61.5 1.0 O B:HOH1903 5.0 50.3 1.0

Zinc binding site 4 out of 8 in the Crystal Structure of Human BAZ2A Phd Zinc Finger in Complex with FR23


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 Human BAZ2A Phd Zinc Finger in Complex with FR23 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1802 b:68.3 occ:1.00 SG B:CYS1697 2.3 83.2 1.0 SG B:CYS1694 2.3 74.9 1.0 SG B:CYS1720 2.3 80.3 1.0 SG B:CYS1723 2.3 91.7 1.0 CB B:CYS1697 3.3 88.4 1.0 CB B:CYS1723 3.4 89.4 1.0 CB B:CYS1694 3.4 71.1 1.0 CB B:CYS1720 3.4 73.6 1.0 N B:CYS1697 3.8 84.7 1.0 N B:CYS1720 3.9 71.5 1.0 N B:CYS1723 4.1 87.2 1.0 CA B:CYS1697 4.1 87.3 1.0 CA B:CYS1720 4.2 71.8 1.0 CA B:CYS1723 4.3 90.4 1.0 C B:GLY1696 4.4 87.6 1.0 C B:CYS1697 4.7 84.9 1.0 CA B:GLY1696 4.7 85.9 1.0 C B:CYS1720 4.7 72.8 1.0 O B:CYS1720 4.8 72.1 1.0 CA B:CYS1694 4.8 68.5 1.0 N B:GLY1696 4.8 81.3 1.0 C B:PHE1719 5.0 70.1 1.0

Zinc binding site 5 out of 8 in the Crystal Structure of Human BAZ2A Phd Zinc Finger in Complex with FR23


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 Human BAZ2A Phd Zinc Finger in Complex with FR23 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1801 b:45.7 occ:1.00 ND1 C:HIS1702 2.0 46.2 1.0 SG C:CYS1682 2.3 53.8 1.0 SG C:CYS1705 2.3 48.3 1.0 SG C:CYS1679 2.3 45.5 1.0 CE1 C:HIS1702 3.0 46.8 1.0 CG C:HIS1702 3.0 44.8 1.0 CB C:CYS1679 3.3 47.4 1.0 CB C:HIS1702 3.3 44.3 1.0 CB C:CYS1705 3.3 48.1 1.0 CB C:CYS1682 3.4 55.0 1.0 N C:CYS1682 4.0 53.2 1.0 NE2 C:HIS1702 4.1 45.6 1.0 CD2 C:HIS1702 4.1 44.7 1.0 N C:HIS1702 4.2 45.5 1.0 CA C:CYS1682 4.3 55.6 1.0 CA C:HIS1702 4.4 44.5 1.0 CE1 C:TYR1704 4.6 45.7 1.0 CA C:CYS1705 4.7 47.2 1.0 CA C:CYS1679 4.8 47.9 1.0 CB C:VAL1681 4.8 49.0 1.0 N C:CYS1705 5.0 45.4 1.0 C C:VAL1681 5.0 52.1 1.0

Zinc binding site 6 out of 8 in the Crystal Structure of Human BAZ2A Phd Zinc Finger in Complex with FR23


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 Human BAZ2A Phd Zinc Finger in Complex with FR23 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1802 b:48.1 occ:1.00 SG C:CYS1694 2.3 54.0 1.0 SG C:CYS1720 2.3 52.4 1.0 SG C:CYS1697 2.3 53.1 1.0 SG C:CYS1723 2.3 60.5 1.0 CB C:CYS1694 3.4 52.5 1.0 CB C:CYS1723 3.4 58.6 1.0 CB C:CYS1697 3.4 56.9 1.0 CB C:CYS1720 3.4 50.4 1.0 N C:CYS1697 3.8 57.7 1.0 N C:CYS1720 3.9 53.7 1.0 N C:CYS1723 4.1 54.5 1.0 CA C:CYS1697 4.1 57.9 1.0 CA C:CYS1720 4.2 50.7 1.0 C C:GLY1696 4.3 60.9 1.0 CA C:CYS1723 4.3 58.2 1.0 CA C:GLY1696 4.5 61.2 1.0 NH1 C:ARG1699 4.5 49.8 1.0 N C:GLY1696 4.6 60.1 1.0 O C:CYS1720 4.6 51.5 1.0 C C:CYS1720 4.7 50.4 1.0 C C:CYS1697 4.8 56.9 1.0 CA C:CYS1694 4.8 52.4 1.0 CD C:ARG1699 4.8 47.6 1.0 CB C:ARG1699 4.9 47.2 1.0

Zinc binding site 7 out of 8 in the Crystal Structure of Human BAZ2A Phd Zinc Finger in Complex with FR23


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 Human BAZ2A Phd Zinc Finger in Complex with FR23 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1801 b:49.5 occ:1.00 ND1 D:HIS1702 2.0 53.8 1.0 SG D:CYS1682 2.3 57.9 1.0 SG D:CYS1705 2.3 51.8 1.0 SG D:CYS1679 2.3 51.7 1.0 CE1 D:HIS1702 3.0 56.1 1.0 CG D:HIS1702 3.0 53.5 1.0 CB D:CYS1679 3.3 52.3 1.0 CB D:CYS1682 3.4 59.0 1.0 CB D:CYS1705 3.4 52.6 1.0 CB D:HIS1702 3.4 51.8 1.0 N D:CYS1682 4.0 55.0 1.0 NE2 D:HIS1702 4.1 56.6 1.0 N D:HIS1702 4.1 49.5 1.0 CD2 D:HIS1702 4.2 55.5 1.0 CA D:CYS1682 4.2 59.0 1.0 CA D:HIS1702 4.4 51.1 1.0 CE1 D:TYR1704 4.5 48.9 1.0 CA D:CYS1679 4.7 51.8 1.0 CA D:CYS1705 4.7 52.4 1.0 CB D:VAL1681 4.8 49.9 1.0 CZ D:TYR1704 5.0 50.4 1.0 C D:CYS1682 5.0 61.7 1.0

Zinc binding site 8 out of 8 in the Crystal Structure of Human BAZ2A Phd Zinc Finger in Complex with FR23


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 Human BAZ2A Phd Zinc Finger in Complex with FR23 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1802 b:50.2 occ:1.00 SG D:CYS1694 2.3 54.9 1.0 SG D:CYS1697 2.3 55.3 1.0 SG D:CYS1723 2.3 56.5 1.0 SG D:CYS1720 2.3 52.9 1.0 CB D:CYS1694 3.3 56.3 1.0 CB D:CYS1723 3.4 52.6 1.0 CB D:CYS1720 3.4 51.2 1.0 CB D:CYS1697 3.4 59.3 1.0 N D:CYS1697 3.9 61.0 1.0 N D:CYS1720 4.0 52.2 1.0 N D:CYS1723 4.0 49.0 1.0 CA D:CYS1720 4.2 50.7 1.0 CA D:CYS1697 4.2 61.6 1.0 CA D:CYS1723 4.3 50.2 1.0 C D:GLY1696 4.3 62.9 1.0 O D:CYS1720 4.6 52.1 1.0 CA D:GLY1696 4.6 63.3 1.0 C D:CYS1720 4.6 50.5 1.0 CD D:ARG1699 4.7 52.0 1.0 N D:GLY1696 4.7 63.0 1.0 CB D:ARG1699 4.7 53.0 1.0 CA D:CYS1694 4.8 58.1 1.0 C D:CYS1697 4.8 62.5 1.0 NH1 D:ARG1699 4.8 53.8 1.0 CB D:VAL1722 5.0 48.7 1.0 O D:GLY1696 5.0 65.1 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