Zinc in PDB 5t8r: Crystal Structure of Human BAZ2A Phd Zinc Finger in Complex with Unmodified H3 10-Mer

The structure of Crystal Structure of Human BAZ2A Phd Zinc Finger in Complex with Unmodified H3 10-Mer, PDB code: 5t8r was solved by A.Amato, M.S.Gadd, A.Bortoluzzi, A.Ciulli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.62 / 2.40
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	72.607, 72.607, 99.431, 90.00, 90.00, 90.00
R / Rfree (%)	18.5 / 23.5

The binding sites of Zinc atom in the Crystal Structure of Human BAZ2A Phd Zinc Finger in Complex with Unmodified H3 10-Mer (pdb code 5t8r). 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 Unmodified H3 10-Mer, PDB code: 5t8r:
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 Unmodified H3 10-Mer


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 Unmodified H3 10-Mer within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1801 b:35.3 occ:1.00 ND1 A:HIS1702 2.1 41.0 1.0 SG A:CYS1705 2.3 37.1 1.0 SG A:CYS1682 2.3 42.6 1.0 SG A:CYS1679 2.3 40.0 1.0 CE1 A:HIS1702 3.1 43.4 1.0 CG A:HIS1702 3.1 39.5 1.0 CB A:CYS1679 3.1 43.8 1.0 CB A:CYS1705 3.3 34.5 1.0 CB A:CYS1682 3.4 44.7 1.0 CB A:HIS1702 3.4 37.1 1.0 N A:CYS1682 3.9 43.3 1.0 N A:HIS1702 4.1 36.9 1.0 NE2 A:HIS1702 4.2 42.5 1.0 CA A:CYS1682 4.2 46.3 1.0 CD2 A:HIS1702 4.2 40.6 1.0 O A:HOH1918 4.2 42.3 1.0 CA A:HIS1702 4.4 35.8 1.0 CE1 A:TYR1704 4.4 35.9 1.0 CB A:VAL1681 4.6 40.1 1.0 CA A:CYS1679 4.6 45.6 1.0 CA A:CYS1705 4.7 32.9 1.0 C A:CYS1682 4.9 50.5 1.0 C A:VAL1681 4.9 43.1 1.0 CZ A:TYR1704 5.0 37.6 1.0 N A:CYS1705 5.0 31.7 1.0 N A:ARG1683 5.0 52.5 1.0

Zinc binding site 2 out of 8 in the Crystal Structure of Human BAZ2A Phd Zinc Finger in Complex with Unmodified H3 10-Mer


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 Unmodified H3 10-Mer within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1802 b:43.5 occ:1.00 SG A:CYS1697 2.3 48.7 1.0 SG A:CYS1694 2.3 46.5 1.0 SG A:CYS1723 2.3 48.5 1.0 SG A:CYS1720 2.3 45.8 1.0 CB A:CYS1694 3.2 46.8 1.0 CB A:CYS1720 3.4 41.9 1.0 CB A:CYS1697 3.4 52.5 1.0 CB A:CYS1723 3.4 47.3 1.0 N A:CYS1697 3.7 52.7 1.0 N A:CYS1720 3.7 42.1 1.0 N A:CYS1723 4.0 44.8 1.0 CA A:CYS1720 4.0 41.4 1.0 CA A:CYS1697 4.1 53.9 1.0 C A:GLY1696 4.2 54.9 1.0 CA A:CYS1723 4.3 46.6 1.0 C A:CYS1720 4.5 42.0 1.0 O A:CYS1720 4.5 41.9 1.0 CB A:ARG1699 4.6 48.4 1.0 CA A:GLY1696 4.7 54.5 1.0 CD A:ARG1699 4.7 49.4 1.0 CA A:CYS1694 4.7 46.9 1.0 NH1 A:ARG1699 4.7 54.4 1.0 N A:GLY1696 4.7 53.5 1.0 C A:CYS1697 4.7 54.6 1.0 C A:PHE1719 4.9 43.0 1.0 O A:GLY1696 4.9 57.0 1.0 CB A:VAL1722 5.0 45.6 1.0 C A:VAL1722 5.0 46.0 1.0

Zinc binding site 3 out of 8 in the Crystal Structure of Human BAZ2A Phd Zinc Finger in Complex with Unmodified H3 10-Mer


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 Unmodified H3 10-Mer within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1801 b:46.4 occ:1.00 ND1 B:HIS1702 2.1 48.9 1.0 SG B:CYS1679 2.3 48.1 1.0 SG B:CYS1705 2.3 45.9 1.0 SG B:CYS1682 2.4 59.4 1.0 CG B:HIS1702 3.1 46.9 1.0 CE1 B:HIS1702 3.1 51.0 1.0 CB B:CYS1679 3.1 52.9 1.0 CB B:HIS1702 3.3 44.1 1.0 CB B:CYS1705 3.4 45.1 1.0 CB B:CYS1682 3.4 60.1 1.0 N B:CYS1682 3.8 57.8 1.0 CA B:CYS1682 4.2 61.4 1.0 NE2 B:HIS1702 4.2 49.5 1.0 CD2 B:HIS1702 4.2 46.6 1.0 N B:HIS1702 4.2 43.3 1.0 CA B:HIS1702 4.4 42.3 1.0 CE1 B:TYR1704 4.5 45.2 1.0 CA B:CYS1679 4.6 54.7 1.0 CB B:VAL1681 4.7 51.7 1.0 CA B:CYS1705 4.8 42.0 1.0 O B:LYS1684 4.9 62.4 1.0 C B:VAL1681 4.9 57.5 1.0 C B:CYS1682 4.9 64.1 1.0

Zinc binding site 4 out of 8 in the Crystal Structure of Human BAZ2A Phd Zinc Finger in Complex with Unmodified H3 10-Mer


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 Unmodified H3 10-Mer within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1802 b:46.9 occ:1.00 SG B:CYS1697 2.3 57.2 1.0 SG B:CYS1694 2.3 54.0 1.0 SG B:CYS1723 2.3 60.3 1.0 SG B:CYS1720 2.4 53.3 1.0 CB B:CYS1697 3.3 62.6 1.0 CB B:CYS1694 3.3 52.9 1.0 CB B:CYS1723 3.4 60.6 1.0 CB B:CYS1720 3.4 50.3 1.0 N B:CYS1697 3.9 60.7 1.0 N B:CYS1720 3.9 50.6 1.0 N B:CYS1723 4.0 60.0 1.0 CA B:CYS1697 4.2 63.6 1.0 CA B:CYS1720 4.2 49.8 1.0 CA B:CYS1723 4.2 62.6 1.0 C B:GLY1696 4.4 61.6 1.0 O B:CYS1720 4.7 51.7 1.0 CA B:GLY1696 4.7 59.6 1.0 C B:CYS1720 4.7 51.0 1.0 CA B:CYS1694 4.8 52.5 1.0 CD B:ARG1699 4.8 67.5 1.0 C B:CYS1697 4.8 65.0 1.0 N B:GLY1696 4.8 56.6 1.0 CB B:ARG1699 4.8 61.9 1.0 CB B:VAL1722 5.0 59.5 1.0

Zinc binding site 5 out of 8 in the Crystal Structure of Human BAZ2A Phd Zinc Finger in Complex with Unmodified H3 10-Mer


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 Unmodified H3 10-Mer within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1801 b:32.7 occ:1.00 ND1 C:HIS1702 2.1 34.7 1.0 SG C:CYS1705 2.3 33.8 1.0 SG C:CYS1682 2.3 39.0 1.0 SG C:CYS1679 2.3 32.4 1.0 CG C:HIS1702 3.0 34.8 1.0 CE1 C:HIS1702 3.0 36.3 1.0 CB C:CYS1679 3.1 34.5 1.0 CB C:CYS1705 3.3 33.5 1.0 CB C:HIS1702 3.3 33.5 1.0 CB C:CYS1682 3.4 41.6 1.0 N C:CYS1682 3.9 38.6 1.0 N C:HIS1702 4.1 32.5 1.0 NE2 C:HIS1702 4.2 35.8 1.0 CD2 C:HIS1702 4.2 34.8 1.0 CA C:CYS1682 4.2 40.9 1.0 CA C:HIS1702 4.3 32.5 1.0 CA C:CYS1679 4.6 35.1 1.0 CE1 C:TYR1704 4.6 36.7 1.0 CA C:CYS1705 4.7 33.5 1.0 CB C:VAL1681 4.7 35.9 1.0 C C:CYS1682 4.9 41.6 1.0 C C:VAL1681 4.9 37.1 1.0 N C:CYS1705 5.0 33.1 1.0

Zinc binding site 6 out of 8 in the Crystal Structure of Human BAZ2A Phd Zinc Finger in Complex with Unmodified H3 10-Mer


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 Unmodified H3 10-Mer within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1802 b:33.4 occ:1.00 SG C:CYS1697 2.3 36.5 1.0 SG C:CYS1694 2.3 38.8 1.0 SG C:CYS1720 2.3 35.8 1.0 SG C:CYS1723 2.3 40.4 1.0 CB C:CYS1723 3.3 40.7 1.0 CB C:CYS1694 3.3 37.7 1.0 CB C:CYS1697 3.4 40.2 1.0 CB C:CYS1720 3.5 34.2 1.0 N C:CYS1720 3.9 37.9 1.0 N C:CYS1697 3.9 42.3 1.0 N C:CYS1723 4.0 37.5 1.0 CA C:CYS1697 4.2 42.0 1.0 CA C:CYS1723 4.2 40.4 1.0 CA C:CYS1720 4.2 35.0 1.0 C C:GLY1696 4.4 44.4 1.0 O C:HOH1910 4.6 36.7 1.0 NH1 C:ARG1699 4.6 34.4 1.0 CD C:ARG1699 4.6 31.1 1.0 O C:CYS1720 4.7 34.3 1.0 N C:GLY1696 4.7 45.0 1.0 C C:CYS1720 4.7 34.5 1.0 CB C:ARG1699 4.7 31.3 1.0 CA C:GLY1696 4.7 45.3 1.0 C C:CYS1697 4.7 40.9 1.0 CA C:CYS1694 4.8 38.5 1.0 O C:CYS1697 5.0 39.9 1.0

Zinc binding site 7 out of 8 in the Crystal Structure of Human BAZ2A Phd Zinc Finger in Complex with Unmodified H3 10-Mer


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 Unmodified H3 10-Mer within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1801 b:38.6 occ:1.00 ND1 D:HIS1702 2.1 44.6 1.0 SG D:CYS1682 2.3 49.2 1.0 SG D:CYS1705 2.3 41.5 1.0 SG D:CYS1679 2.3 44.3 1.0 CG D:HIS1702 3.1 43.3 1.0 CB D:CYS1679 3.1 44.3 1.0 CE1 D:HIS1702 3.1 46.0 1.0 CB D:CYS1682 3.3 50.0 1.0 CB D:HIS1702 3.4 42.2 1.0 CB D:CYS1705 3.4 40.7 1.0 N D:CYS1682 3.9 47.8 1.0 N D:HIS1702 4.0 38.9 1.0 CA D:CYS1682 4.2 50.6 1.0 NE2 D:HIS1702 4.2 44.7 1.0 CD2 D:HIS1702 4.3 43.8 1.0 CA D:HIS1702 4.3 40.7 1.0 CE1 D:TYR1704 4.4 40.6 1.0 CA D:CYS1679 4.6 43.7 1.0 CB D:VAL1681 4.7 45.9 1.0 O D:HOH1902 4.7 41.6 1.0 CA D:CYS1705 4.8 40.7 1.0 C D:CYS1682 4.8 52.5 1.0 O D:LYS1684 4.9 48.9 1.0 CZ D:TYR1704 4.9 40.4 1.0 C D:VAL1681 5.0 48.0 1.0 N D:ARG1683 5.0 52.3 1.0 OH D:TYR1704 5.0 40.5 1.0

Zinc binding site 8 out of 8 in the Crystal Structure of Human BAZ2A Phd Zinc Finger in Complex with Unmodified H3 10-Mer


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 Unmodified H3 10-Mer within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1802 b:37.7 occ:1.00 SG D:CYS1697 2.3 41.7 1.0 SG D:CYS1694 2.3 42.6 1.0 SG D:CYS1720 2.3 37.5 1.0 SG D:CYS1723 2.3 37.6 1.0 CB D:CYS1694 3.2 42.9 1.0 CB D:CYS1697 3.3 46.4 1.0 CB D:CYS1723 3.3 36.4 1.0 CB D:CYS1720 3.5 36.2 1.0 N D:CYS1697 3.7 47.2 1.0 N D:CYS1720 4.0 36.1 1.0 N D:CYS1723 4.0 35.2 1.0 CA D:CYS1697 4.1 48.6 1.0 CA D:CYS1720 4.2 35.2 1.0 C D:GLY1696 4.2 49.1 1.0 CA D:CYS1723 4.2 35.4 1.0 O D:CYS1720 4.5 35.7 1.0 C D:CYS1720 4.6 34.4 1.0 CA D:GLY1696 4.6 49.3 1.0 CA D:CYS1694 4.7 45.6 1.0 C D:CYS1697 4.7 51.4 1.0 NH1 D:ARG1699 4.7 42.4 1.0 N D:GLY1696 4.7 48.6 1.0 CB D:ARG1699 4.7 39.5 1.0 CD D:ARG1699 4.8 38.8 1.0 O D:GLY1696 4.9 50.6 1.0 CB D:VAL1722 4.9 35.7 1.0 O D:CYS1697 4.9 52.0 1.0 C D:VAL1722 5.0 35.6 1.0

A.Bortoluzzi, A.Amato, X.Lucas, M.Blank, A.Ciulli. Structural Basis of Molecular Recognition of Helical Histone H3 Tail By Phd Finger Domains. Biochem. J. V. 474 1633 2017.
ISSN: ESSN 1470-8728
PubMed: 28341809
DOI: 10.1042/BCJ20161053