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Zinc in PDB 6fhu: Crystal Structure of BAZ2A Phd Zinc Finger in Complex with H3 3-Mer Peptide

Protein crystallography data

The structure of Crystal Structure of BAZ2A Phd Zinc Finger in Complex with H3 3-Mer Peptide, PDB code: 6fhu 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) 46.03 / 2.00
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 73.385, 73.385, 99.671, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 23.5

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of BAZ2A Phd Zinc Finger in Complex with H3 3-Mer Peptide (pdb code 6fhu). 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 3-Mer Peptide, PDB code: 6fhu:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 6fhu

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Zinc binding site 1 out of 8 in the Crystal Structure of BAZ2A Phd Zinc Finger in Complex with H3 3-Mer 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 3-Mer Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1801

b:25.9
occ:1.00
 ND1 A:HIS1702 2.0 31.1 1.0
SG A:CYS1705 2.3 26.9 1.0
SG A:CYS1679 2.3 28.8 1.0
SG A:CYS1682 2.4 35.0 1.0
CE1 A:HIS1702 3.0 33.0 1.0
CG A:HIS1702 3.0 29.7 1.0
CB A:CYS1679 3.2 32.2 1.0
CB A:CYS1682 3.3 36.2 1.0
CB A:HIS1702 3.4 26.9 1.0
CB A:CYS1705 3.4 25.4 1.0
N A:CYS1682 3.8 34.2 1.0
NE2 A:HIS1702 4.1 32.4 1.0
CA A:CYS1682 4.2 36.8 1.0
N A:HIS1702 4.2 25.4 1.0
CD2 A:HIS1702 4.2 31.3 1.0
CA A:HIS1702 4.4 25.7 1.0
CE1 A:TYR1704 4.5 26.1 1.0
O A:HOH1944 4.5 46.5 1.0
CA A:CYS1679 4.7 33.3 1.0
CB A:VAL1681 4.7 30.4 1.0
O A:HOH1904 4.7 43.2 1.0
CA A:CYS1705 4.7 23.8 1.0
C A:CYS1682 4.9 40.1 1.0
C A:VAL1681 5.0 33.1 1.0
N A:CYS1705 5.0 22.9 1.0
CD1 A:TYR1704 5.0 24.8 1.0

Zinc binding site 2 out of 8 in 6fhu

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Zinc binding site 2 out of 8 in the Crystal Structure of BAZ2A Phd Zinc Finger in Complex with H3 3-Mer 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 3-Mer Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1802

b:30.7
occ:1.00
 SG A:CYS1694 2.3 35.2 1.0
SG A:CYS1697 2.3 37.1 1.0
SG A:CYS1723 2.3 34.8 1.0
SG A:CYS1720 2.4 32.4 1.0
CB A:CYS1694 3.3 36.1 1.0
CB A:CYS1697 3.3 39.6 1.0
CB A:CYS1723 3.4 33.9 1.0
CB A:CYS1720 3.5 31.8 1.0
N A:CYS1697 3.8 40.7 1.0
N A:CYS1720 3.9 32.4 1.0
N A:CYS1723 4.0 32.2 1.0
CA A:CYS1697 4.1 41.0 1.0
CA A:CYS1720 4.2 31.1 1.0
C A:GLY1696 4.2 41.8 1.0
CA A:CYS1723 4.2 32.4 1.0
CA A:GLY1696 4.5 41.2 1.0
O A:CYS1720 4.6 29.8 1.0
C A:CYS1720 4.6 31.0 1.0
CD A:ARG1699 4.6 37.0 1.0
N A:GLY1696 4.6 41.2 1.0
CB A:ARG1699 4.7 37.0 1.0
C A:CYS1697 4.7 42.5 1.0
NH1 A:ARG1699 4.7 37.9 1.0
CA A:CYS1694 4.8 37.8 1.0
O A:GLY1696 4.9 42.0 1.0
C A:PHE1719 5.0 33.3 1.0

Zinc binding site 3 out of 8 in 6fhu

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Zinc binding site 3 out of 8 in the Crystal Structure of BAZ2A Phd Zinc Finger in Complex with H3 3-Mer 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 3-Mer Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1801

b:26.2
occ:1.00
 ND1 B:HIS1702 2.1 32.9 1.0
SG B:CYS1705 2.3 30.0 1.0
SG B:CYS1679 2.3 32.9 1.0
SG B:CYS1682 2.4 36.8 1.0
CE1 B:HIS1702 3.0 34.3 1.0
CG B:HIS1702 3.1 31.4 1.0
CB B:CYS1679 3.1 35.6 1.0
CB B:CYS1682 3.3 38.1 1.0
CB B:CYS1705 3.4 28.6 1.0
CB B:HIS1702 3.4 29.6 1.0
N B:CYS1682 3.7 37.7 1.0
CA B:CYS1682 4.1 39.1 1.0
NE2 B:HIS1702 4.2 33.4 1.0
CD2 B:HIS1702 4.2 32.0 1.0
N B:HIS1702 4.2 29.3 1.0
O B:HOH1937 4.4 41.1 1.0
CA B:HIS1702 4.5 28.3 1.0
CE1 B:TYR1704 4.5 26.6 1.0
CA B:CYS1679 4.6 37.2 1.0
CB B:VAL1681 4.7 34.6 1.0
CA B:CYS1705 4.8 27.0 1.0
O B:HOH1904 4.8 42.7 1.0
C B:VAL1681 4.9 37.5 1.0
C B:CYS1682 4.9 41.7 1.0

Zinc binding site 4 out of 8 in 6fhu

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Zinc binding site 4 out of 8 in the Crystal Structure of BAZ2A Phd Zinc Finger in Complex with H3 3-Mer 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 3-Mer Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1802

b:34.5
occ:1.00
 SG B:CYS1697 2.3 46.9 1.0
SG B:CYS1723 2.3 48.3 1.0
SG B:CYS1720 2.3 40.2 1.0
SG B:CYS1694 2.4 43.2 1.0
CB B:CYS1697 3.3 50.1 1.0
CB B:CYS1723 3.4 47.2 1.0
CB B:CYS1694 3.4 41.8 1.0
CB B:CYS1720 3.4 37.9 1.0
N B:CYS1697 3.8 49.6 1.0
N B:CYS1720 3.9 37.1 1.0
N B:CYS1723 4.0 44.5 1.0
CA B:CYS1697 4.1 50.8 1.0
CA B:CYS1720 4.2 36.7 1.0
CA B:CYS1723 4.2 46.5 1.0
C B:GLY1696 4.3 50.7 1.0
CA B:GLY1696 4.6 49.9 1.0
CD B:ARG1699 4.6 48.1 1.0
CB B:ARG1699 4.7 45.0 1.0
O B:CYS1720 4.7 36.2 1.0
C B:CYS1720 4.7 36.6 1.0
N B:GLY1696 4.8 48.1 1.0
C B:CYS1697 4.8 50.9 1.0
CA B:CYS1694 4.8 40.5 1.0
NH1 B:ARG1699 4.8 51.9 1.0
C B:PHE1719 5.0 37.0 1.0

Zinc binding site 5 out of 8 in 6fhu

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Zinc binding site 5 out of 8 in the Crystal Structure of BAZ2A Phd Zinc Finger in Complex with H3 3-Mer 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 3-Mer Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1801

b:21.0
occ:1.00
 ND1 C:HIS1702 2.1 24.4 1.0
SG C:CYS1705 2.3 24.5 1.0
SG C:CYS1682 2.3 24.5 1.0
SG C:CYS1679 2.3 23.8 1.0
CE1 C:HIS1702 3.1 25.4 1.0
CB C:CYS1679 3.1 25.2 1.0
CG C:HIS1702 3.1 23.9 1.0
CB C:CYS1682 3.3 25.8 1.0
CB C:CYS1705 3.4 23.8 1.0
CB C:HIS1702 3.4 23.0 1.0
N C:CYS1682 3.8 24.6 1.0
CA C:CYS1682 4.1 25.8 1.0
N C:HIS1702 4.2 22.4 1.0
NE2 C:HIS1702 4.2 24.8 1.0
CD2 C:HIS1702 4.2 24.0 1.0
CA C:HIS1702 4.4 22.6 1.0
CA C:CYS1679 4.6 25.1 1.0
CE1 C:TYR1704 4.6 24.1 1.0
CB C:VAL1681 4.7 23.7 1.0
CA C:CYS1705 4.8 23.8 1.0
C C:VAL1681 4.9 24.1 1.0
C C:CYS1682 4.9 27.2 1.0
O C:HOH1912 5.0 31.9 1.0

Zinc binding site 6 out of 8 in 6fhu

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Zinc binding site 6 out of 8 in the Crystal Structure of BAZ2A Phd Zinc Finger in Complex with H3 3-Mer 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 3-Mer Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1802

b:22.7
occ:1.00
 SG C:CYS1697 2.3 26.4 1.0
SG C:CYS1723 2.3 31.8 1.0
SG C:CYS1694 2.3 28.6 1.0
SG C:CYS1720 2.3 26.1 1.0
CB C:CYS1723 3.3 32.4 1.0
CB C:CYS1694 3.4 29.5 1.0
CB C:CYS1697 3.4 28.7 1.0
CB C:CYS1720 3.5 26.9 1.0
N C:CYS1697 3.7 29.9 1.0
N C:CYS1720 3.9 30.4 1.0
N C:CYS1723 4.0 29.7 1.0
CA C:CYS1697 4.1 29.5 1.0
CA C:CYS1720 4.2 27.8 1.0
C C:GLY1696 4.2 31.3 1.0
CA C:CYS1723 4.3 32.3 1.0
CA C:GLY1696 4.6 32.3 1.0
N C:GLY1696 4.6 32.4 1.0
O C:CYS1720 4.7 27.8 1.0
C C:CYS1697 4.7 29.3 1.0
C C:CYS1720 4.7 27.1 1.0
CB C:ARG1699 4.7 24.1 1.0
O C:HOH1935 4.7 40.0 1.0
NH1 C:ARG1699 4.8 24.1 1.0
CA C:CYS1694 4.8 30.3 1.0
CD C:ARG1699 4.8 23.8 1.0
O C:GLY1696 4.8 31.5 1.0
O C:CYS1697 4.9 29.4 1.0
C C:PHE1719 5.0 33.7 1.0

Zinc binding site 7 out of 8 in 6fhu

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Zinc binding site 7 out of 8 in the Crystal Structure of BAZ2A Phd Zinc Finger in Complex with H3 3-Mer 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 3-Mer Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1801

b:24.8
occ:1.00
 ND1 D:HIS1702 2.0 27.0 1.0
SG D:CYS1705 2.3 26.9 1.0
SG D:CYS1679 2.3 25.5 1.0
SG D:CYS1682 2.3 29.9 1.0
CE1 D:HIS1702 3.0 28.8 1.0
CG D:HIS1702 3.0 26.9 1.0
CB D:CYS1679 3.1 27.3 1.0
CB D:CYS1705 3.4 25.2 1.0
CB D:CYS1682 3.4 30.0 1.0
CB D:HIS1702 3.4 25.4 1.0
N D:CYS1682 3.8 27.7 1.0
NE2 D:HIS1702 4.1 28.0 1.0
N D:HIS1702 4.1 24.7 1.0
CA D:CYS1682 4.2 30.2 1.0
CD2 D:HIS1702 4.2 27.4 1.0
CA D:HIS1702 4.4 25.0 1.0
CA D:CYS1679 4.6 27.3 1.0
CE1 D:TYR1704 4.6 24.7 1.0
CB D:VAL1681 4.7 25.9 1.0
CA D:CYS1705 4.7 24.6 1.0
O D:HOH1956 4.8 45.4 1.0
C D:VAL1681 4.9 27.2 1.0
C D:CYS1682 4.9 31.9 1.0

Zinc binding site 8 out of 8 in 6fhu

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Zinc binding site 8 out of 8 in the Crystal Structure of BAZ2A Phd Zinc Finger in Complex with H3 3-Mer 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 3-Mer Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1802

b:23.7
occ:1.00
 SG D:CYS1697 2.3 29.0 1.0
SG D:CYS1694 2.3 29.1 1.0
SG D:CYS1723 2.3 25.7 1.0
SG D:CYS1720 2.3 24.1 1.0
CB D:CYS1694 3.3 29.7 1.0
CB D:CYS1723 3.3 25.2 1.0
CB D:CYS1697 3.4 31.1 1.0
CB D:CYS1720 3.4 23.8 1.0
N D:CYS1697 3.8 32.4 1.0
N D:CYS1720 3.9 24.6 1.0
N D:CYS1723 4.0 23.7 1.0
CA D:CYS1697 4.1 32.8 1.0
CA D:CYS1720 4.2 23.7 1.0
C D:GLY1696 4.2 32.9 1.0
CA D:CYS1723 4.3 23.9 1.0
CA D:GLY1696 4.6 32.9 1.0
O D:CYS1720 4.6 22.8 1.0
N D:GLY1696 4.6 33.0 1.0
C D:CYS1720 4.7 23.1 1.0
C D:CYS1697 4.7 34.0 1.0
CA D:CYS1694 4.8 31.1 1.0
CB D:ARG1699 4.8 26.4 1.0
NH1 D:ARG1699 4.8 25.7 1.0
CD D:ARG1699 4.9 25.3 1.0
O D:GLY1696 4.9 33.2 1.0
O D:CYS1697 5.0 33.0 1.0
O D:HOH1955 5.0 41.9 1.0

Reference:

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
Page generated: Mon Oct 28 21:04:29 2024

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