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Zinc in PDB 6fi0: Crystal Structure of BAZ2A Phd Zinc Finger in Complex with Fr 19

Protein crystallography data

The structure of Crystal Structure of BAZ2A Phd Zinc Finger in Complex with Fr 19, PDB code: 6fi0 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) 45.34 / 1.90
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 72.095, 72.095, 99.198, 90.00, 90.00, 90.00
R / Rfree (%) 19 / 23.1

Other elements in 6fi0:

The structure of Crystal Structure of BAZ2A Phd Zinc Finger in Complex with Fr 19 also contains other interesting chemical elements:

Potassium (K) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of BAZ2A Phd Zinc Finger in Complex with Fr 19 (pdb code 6fi0). 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 Fr 19, PDB code: 6fi0:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 6fi0

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Zinc binding site 1 out of 8 in the Crystal Structure of BAZ2A Phd Zinc Finger in Complex with Fr 19


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 Fr 19 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1801

b:28.8
occ:1.00
ND1 A:HIS1702 1.9 28.5 1.0
SG A:CYS1705 2.3 28.0 1.0
SG A:CYS1679 2.3 32.8 1.0
SG A:CYS1682 2.4 34.3 1.0
CE1 A:HIS1702 2.9 32.9 1.0
CG A:HIS1702 3.0 27.9 1.0
CB A:CYS1679 3.1 34.5 1.0
CB A:CYS1682 3.2 36.3 1.0
CB A:CYS1705 3.3 26.3 1.0
CB A:HIS1702 3.4 24.9 1.0
N A:CYS1682 3.8 35.8 1.0
NE2 A:HIS1702 4.0 30.8 1.0
CA A:CYS1682 4.1 38.6 1.0
N A:HIS1702 4.1 24.0 1.0
CD2 A:HIS1702 4.1 29.1 1.0
O A:HOH1938 4.1 38.8 1.0
CA A:HIS1702 4.3 24.1 1.0
CE1 A:TYR1704 4.4 28.1 1.0
CA A:CYS1679 4.6 36.3 1.0
CA A:CYS1705 4.7 26.0 1.0
CB A:VAL1681 4.8 33.3 1.0
C A:CYS1682 4.8 42.3 1.0
C A:VAL1681 4.9 36.7 1.0
CD1 A:TYR1704 4.9 26.2 1.0
N A:ARG1683 4.9 44.9 1.0
N A:CYS1705 5.0 24.6 1.0

Zinc binding site 2 out of 8 in 6fi0

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Zinc binding site 2 out of 8 in the Crystal Structure of BAZ2A Phd Zinc Finger in Complex with Fr 19


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 Fr 19 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1802

b:29.6
occ:1.00
SG A:CYS1694 2.2 31.6 1.0
SG A:CYS1697 2.3 35.1 1.0
SG A:CYS1720 2.3 29.2 1.0
SG A:CYS1723 2.3 31.7 1.0
CB A:CYS1694 3.3 32.9 1.0
CB A:CYS1723 3.3 30.8 1.0
CB A:CYS1697 3.4 37.8 1.0
CB A:CYS1720 3.5 28.9 1.0
N A:CYS1697 3.7 37.0 1.0
N A:CYS1723 3.9 29.2 1.0
N A:CYS1720 3.9 29.6 1.0
CA A:CYS1697 4.1 38.8 1.0
C A:GLY1696 4.1 39.6 1.0
CA A:CYS1720 4.2 28.9 1.0
CA A:CYS1723 4.2 29.8 1.0
CA A:GLY1696 4.4 38.0 1.0
N A:GLY1696 4.5 37.0 1.0
NH1 A:ARG1699 4.5 39.7 1.0
CB A:ARG1699 4.6 36.0 1.0
C A:CYS1697 4.7 39.0 1.0
C A:CYS1720 4.7 28.3 1.0
CA A:CYS1694 4.7 32.5 1.0
O A:CYS1720 4.7 27.1 1.0
CD A:ARG1699 4.7 38.2 1.0
O A:GLY1696 4.8 39.2 1.0
O A:CYS1697 4.9 38.8 1.0
CG A:ARG1699 5.0 38.1 1.0

Zinc binding site 3 out of 8 in 6fi0

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Zinc binding site 3 out of 8 in the Crystal Structure of BAZ2A Phd Zinc Finger in Complex with Fr 19


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 Fr 19 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1801

b:30.1
occ:1.00
ND1 B:HIS1702 2.1 30.9 1.0
SG B:CYS1679 2.3 34.3 1.0
SG B:CYS1705 2.3 29.4 1.0
SG B:CYS1682 2.4 33.8 1.0
CE1 B:HIS1702 3.1 32.5 1.0
CG B:HIS1702 3.1 29.3 1.0
CB B:CYS1679 3.1 37.9 1.0
CB B:CYS1682 3.3 34.5 1.0
CB B:CYS1705 3.3 27.0 1.0
CB B:HIS1702 3.4 27.1 1.0
N B:CYS1682 3.8 34.9 1.0
CA B:CYS1682 4.1 36.8 1.0
N B:HIS1702 4.2 26.5 1.0
NE2 B:HIS1702 4.2 30.7 1.0
CD2 B:HIS1702 4.2 29.9 1.0
CA B:HIS1702 4.4 25.9 1.0
CE1 B:TYR1704 4.5 27.6 1.0
CA B:CYS1679 4.6 39.7 1.0
CB B:VAL1681 4.7 34.7 1.0
CA B:CYS1705 4.7 25.8 1.0
C B:CYS1682 4.9 38.7 1.0
C B:VAL1681 4.9 36.4 1.0
N B:CYS1705 4.9 24.0 1.0
O B:LYS1684 4.9 43.9 1.0
CD1 B:TYR1704 5.0 26.4 1.0

Zinc binding site 4 out of 8 in 6fi0

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Zinc binding site 4 out of 8 in the Crystal Structure of BAZ2A Phd Zinc Finger in Complex with Fr 19


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 Fr 19 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1802

b:43.8
occ:1.00
SG B:CYS1697 2.3 53.7 1.0
SG B:CYS1720 2.3 45.8 1.0
SG B:CYS1694 2.3 44.4 1.0
SG B:CYS1723 2.4 56.2 1.0
CB B:CYS1694 3.2 44.3 1.0
CB B:CYS1697 3.3 55.8 1.0
CB B:CYS1723 3.4 57.6 1.0
CB B:CYS1720 3.5 45.5 1.0
N B:CYS1697 3.7 54.5 1.0
N B:CYS1720 3.9 44.5 1.0
CA B:CYS1697 4.0 55.2 1.0
N B:CYS1723 4.2 59.1 1.0
CA B:CYS1720 4.2 44.8 1.0
C B:GLY1696 4.2 55.2 1.0
CA B:CYS1723 4.4 58.8 1.0
CD B:ARG1699 4.5 49.8 1.0
CA B:GLY1696 4.6 53.5 1.0
C B:CYS1697 4.6 53.8 1.0
CB B:ARG1699 4.6 46.0 1.0
NH1 B:ARG1699 4.6 53.8 1.0
CA B:CYS1694 4.7 43.7 1.0
N B:GLY1696 4.7 50.6 1.0
O B:CYS1720 4.7 47.1 1.0
C B:CYS1720 4.8 47.1 1.0
O B:GLY1696 4.9 55.9 1.0
O B:CYS1697 4.9 52.5 1.0
CG B:ARG1699 4.9 48.5 1.0
N B:ARG1699 5.0 46.6 1.0

Zinc binding site 5 out of 8 in 6fi0

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Zinc binding site 5 out of 8 in the Crystal Structure of BAZ2A Phd Zinc Finger in Complex with Fr 19


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 Fr 19 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1801

b:25.6
occ:1.00
ND1 C:HIS1702 2.1 25.7 1.0
SG C:CYS1705 2.3 27.3 1.0
SG C:CYS1682 2.3 29.6 1.0
SG C:CYS1679 2.3 27.0 1.0
CE1 C:HIS1702 3.1 26.8 1.0
CB C:CYS1679 3.1 27.7 1.0
CG C:HIS1702 3.1 25.3 1.0
CB C:CYS1682 3.2 29.7 1.0
CB C:CYS1705 3.4 26.3 1.0
CB C:HIS1702 3.5 24.2 1.0
N C:CYS1682 3.7 28.8 1.0
O C:HOH1931 3.9 37.6 1.0
CA C:CYS1682 4.0 30.4 1.0
N C:HIS1702 4.1 23.7 1.0
NE2 C:HIS1702 4.2 25.7 1.0
CD2 C:HIS1702 4.3 25.5 1.0
CA C:HIS1702 4.4 23.8 1.0
CA C:CYS1679 4.6 27.2 1.0
CE1 C:TYR1704 4.6 25.2 1.0
CB C:VAL1681 4.7 28.2 1.0
CA C:CYS1705 4.7 26.3 1.0
C C:VAL1681 4.8 29.3 1.0
C C:CYS1682 4.8 30.6 1.0
N C:ARG1683 5.0 30.2 1.0
N C:CYS1705 5.0 24.7 1.0

Zinc binding site 6 out of 8 in 6fi0

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Zinc binding site 6 out of 8 in the Crystal Structure of BAZ2A Phd Zinc Finger in Complex with Fr 19


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 Fr 19 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1802

b:24.5
occ:1.00
SG C:CYS1694 2.3 26.6 1.0
SG C:CYS1720 2.3 24.9 1.0
SG C:CYS1697 2.3 25.7 1.0
SG C:CYS1723 2.3 29.6 1.0
CB C:CYS1694 3.3 27.2 1.0
CB C:CYS1697 3.3 28.3 1.0
CB C:CYS1723 3.4 29.8 1.0
CB C:CYS1720 3.5 25.3 1.0
N C:CYS1697 3.7 30.7 1.0
N C:CYS1720 3.9 28.0 1.0
N C:CYS1723 4.0 27.5 1.0
CA C:CYS1697 4.1 29.8 1.0
CA C:CYS1720 4.2 26.5 1.0
C C:GLY1696 4.2 32.1 1.0
CA C:CYS1723 4.2 29.6 1.0
CA C:GLY1696 4.5 32.6 1.0
O C:HOH1934 4.6 37.8 1.0
NH1 C:ARG1699 4.6 25.0 1.0
C C:CYS1697 4.6 30.0 1.0
N C:GLY1696 4.6 33.5 1.0
O C:CYS1720 4.7 26.4 1.0
C C:CYS1720 4.7 25.9 1.0
CA C:CYS1694 4.7 28.0 1.0
CB C:ARG1699 4.7 23.6 1.0
CD C:ARG1699 4.8 23.9 1.0
O C:GLY1696 4.8 32.1 1.0
O C:CYS1697 4.9 30.6 1.0

Zinc binding site 7 out of 8 in 6fi0

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Zinc binding site 7 out of 8 in the Crystal Structure of BAZ2A Phd Zinc Finger in Complex with Fr 19


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 Fr 19 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1801

b:26.3
occ:1.00
ND1 D:HIS1702 2.0 28.9 1.0
SG D:CYS1705 2.3 29.6 1.0
SG D:CYS1682 2.3 30.1 1.0
SG D:CYS1679 2.3 26.4 1.0
CE1 D:HIS1702 3.0 32.0 1.0
CB D:CYS1679 3.0 27.1 1.0
CG D:HIS1702 3.1 28.1 1.0
CB D:CYS1682 3.3 30.7 1.0
CB D:CYS1705 3.3 27.9 1.0
CB D:HIS1702 3.4 26.5 1.0
N D:CYS1682 3.7 28.1 1.0
O D:HOH1938 3.8 40.8 1.0
CA D:CYS1682 4.1 31.1 1.0
N D:HIS1702 4.1 24.4 1.0
NE2 D:HIS1702 4.1 30.9 1.0
CD2 D:HIS1702 4.2 30.0 1.0
CA D:HIS1702 4.4 25.6 1.0
CA D:CYS1679 4.5 27.5 1.0
CE1 D:TYR1704 4.6 27.6 1.0
CA D:CYS1705 4.7 28.2 1.0
CB D:VAL1681 4.8 27.6 1.0
C D:VAL1681 4.8 29.6 1.0
C D:CYS1682 4.9 32.6 1.0

Zinc binding site 8 out of 8 in 6fi0

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Zinc binding site 8 out of 8 in the Crystal Structure of BAZ2A Phd Zinc Finger in Complex with Fr 19


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 Fr 19 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1802

b:24.7
occ:1.00
SG D:CYS1694 2.2 27.4 1.0
SG D:CYS1697 2.3 29.8 1.0
SG D:CYS1723 2.3 25.4 1.0
SG D:CYS1720 2.4 23.6 1.0
CB D:CYS1694 3.2 29.2 1.0
CB D:CYS1723 3.3 24.6 1.0
CB D:CYS1697 3.4 29.9 1.0
CB D:CYS1720 3.5 23.3 1.0
N D:CYS1697 3.7 29.3 1.0
N D:CYS1720 4.0 24.4 1.0
N D:CYS1723 4.0 22.9 1.0
CA D:CYS1697 4.1 30.5 1.0
C D:GLY1696 4.2 30.0 1.0
CA D:CYS1723 4.2 23.1 1.0
CA D:CYS1720 4.3 23.3 1.0
CA D:GLY1696 4.5 30.4 1.0
O D:CYS1720 4.6 23.8 1.0
N D:GLY1696 4.7 31.8 1.0
CA D:CYS1694 4.7 29.8 1.0
C D:CYS1720 4.7 23.2 1.0
C D:CYS1697 4.7 31.6 1.0
NH1 D:ARG1699 4.7 27.1 1.0
CB D:ARG1699 4.7 26.4 1.0
O D:GLY1696 4.8 29.2 1.0
CD D:ARG1699 4.8 26.6 1.0
O D:CYS1697 5.0 30.5 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: Wed Dec 16 11:48:17 2020

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