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Zinc in PDB 1hwt: Structure of A HAP1/Dna Complex Reveals Dramatically Asymmetric Dna Binding By A Homodimeric Protein

Protein crystallography data

The structure of Structure of A HAP1/Dna Complex Reveals Dramatically Asymmetric Dna Binding By A Homodimeric Protein, PDB code: 1hwt was solved by D.A.King, L.Zhang, L.Guarente, R.Marmorstein, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 85.600, 85.700, 94.000, 90.00, 90.00, 90.00
R / Rfree (%) 24.6 / 29.1

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of A HAP1/Dna Complex Reveals Dramatically Asymmetric Dna Binding By A Homodimeric Protein (pdb code 1hwt). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Structure of A HAP1/Dna Complex Reveals Dramatically Asymmetric Dna Binding By A Homodimeric Protein, PDB code: 1hwt:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 1hwt

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Zinc binding site 1 out of 9 in the Structure of A HAP1/Dna Complex Reveals Dramatically Asymmetric Dna Binding By A Homodimeric Protein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of A HAP1/Dna Complex Reveals Dramatically Asymmetric Dna Binding By A Homodimeric Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn136

b:22.2
occ:1.00
 SG C:CYS81 2.3 18.9 1.0
SG C:CYS67 2.3 20.4 1.0
SG C:CYS64 2.4 18.8 1.0
SG C:CYS74 2.4 19.3 1.0
ZN C:ZN137 2.9 21.1 1.0
CB C:CYS67 3.2 19.5 1.0
CB C:CYS81 3.3 21.0 1.0
CB C:CYS74 3.4 19.3 1.0
CB C:CYS64 3.6 20.0 1.0
CA C:CYS74 3.9 20.8 1.0
N C:CYS64 4.2 20.8 1.0
CA C:CYS67 4.3 19.5 1.0
N C:CYS67 4.3 19.4 1.0
CB C:GLN83 4.4 27.0 1.0
CA C:CYS64 4.4 20.5 1.0
SG C:CYS84 4.5 15.0 1.0
O C:CYS64 4.7 18.4 1.0
CA C:CYS81 4.7 21.9 1.0
SG C:CYS93 4.8 18.5 1.0
C C:CYS74 4.8 20.3 1.0
OH C:TYR95 4.8 21.1 1.0
N C:ASP75 4.8 20.2 1.0
C C:CYS64 4.9 19.7 1.0
N C:CYS74 5.0 20.9 1.0

Zinc binding site 2 out of 9 in 1hwt

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Zinc binding site 2 out of 9 in the Structure of A HAP1/Dna Complex Reveals Dramatically Asymmetric Dna Binding By A Homodimeric Protein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of A HAP1/Dna Complex Reveals Dramatically Asymmetric Dna Binding By A Homodimeric Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn137

b:21.1
occ:1.00
 SG C:CYS64 2.3 18.8 1.0
SG C:CYS93 2.3 18.5 1.0
SG C:CYS84 2.4 15.0 1.0
SG C:CYS81 2.4 18.9 1.0
ZN C:ZN136 2.9 22.2 1.0
CB C:CYS64 3.2 20.0 1.0
CB C:CYS93 3.2 20.4 1.0
CB C:CYS84 3.3 17.4 1.0
CB C:CYS81 3.7 21.0 1.0
N C:CYS81 4.0 22.1 1.0
CA C:CYS93 4.0 21.6 1.0
N C:CYS84 4.3 21.2 1.0
CA C:CYS81 4.4 21.9 1.0
CA C:CYS84 4.4 18.0 1.0
SG C:CYS67 4.4 20.4 1.0
O C:CYS81 4.6 24.1 1.0
CA C:CYS64 4.7 20.5 1.0
SG C:CYS74 4.7 19.3 1.0
CB C:ILE66 4.7 19.0 1.0
C C:CYS93 4.8 23.2 1.0
C C:CYS81 4.8 24.4 1.0
OH C:TYR95 4.9 21.1 1.0

Zinc binding site 3 out of 9 in 1hwt

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Zinc binding site 3 out of 9 in the Structure of A HAP1/Dna Complex Reveals Dramatically Asymmetric Dna Binding By A Homodimeric Protein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of A HAP1/Dna Complex Reveals Dramatically Asymmetric Dna Binding By A Homodimeric Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn136

b:18.7
occ:1.00
 SG D:CYS74 2.2 14.3 1.0
SG D:CYS67 2.4 17.6 1.0
SG D:CYS81 2.4 16.1 1.0
SG D:CYS64 2.4 10.9 1.0
ZN D:ZN137 3.0 16.7 1.0
CB D:CYS67 3.2 17.4 1.0
CB D:CYS74 3.2 18.1 1.0
CB D:CYS81 3.5 18.3 1.0
CB D:CYS64 3.5 15.5 1.0
CA D:CYS74 3.8 18.5 1.0
N D:CYS64 4.0 15.7 1.0
N D:CYS67 4.3 19.0 1.0
CB D:GLN83 4.3 19.4 1.0
CA D:CYS67 4.3 18.9 1.0
CA D:CYS64 4.3 16.0 1.0
SG D:CYS84 4.5 14.8 1.0
O D:HOH150 4.6 4.6 1.0
O D:CYS64 4.7 18.6 1.0
C D:CYS74 4.7 18.5 1.0
N D:ASP75 4.7 18.5 1.0
SG D:CYS93 4.8 13.6 1.0
N D:CYS74 4.9 18.4 1.0
C D:CYS64 4.9 16.9 1.0
OH D:TYR95 4.9 13.7 1.0
CG D:GLN83 4.9 20.5 1.0
CA D:CYS81 5.0 19.4 1.0
N D:LYS76 5.0 15.7 1.0

Zinc binding site 4 out of 9 in 1hwt

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Zinc binding site 4 out of 9 in the Structure of A HAP1/Dna Complex Reveals Dramatically Asymmetric Dna Binding By A Homodimeric Protein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of A HAP1/Dna Complex Reveals Dramatically Asymmetric Dna Binding By A Homodimeric Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn137

b:16.7
occ:1.00
 SG D:CYS84 2.3 14.8 1.0
SG D:CYS64 2.3 10.9 1.0
SG D:CYS81 2.3 16.1 1.0
SG D:CYS93 2.3 13.6 1.0
ZN D:ZN136 3.0 18.7 1.0
CB D:CYS93 3.3 15.9 1.0
CB D:CYS84 3.3 18.3 1.0
CB D:CYS64 3.3 15.5 1.0
CB D:CYS81 3.6 18.3 1.0
N D:CYS81 4.0 20.5 1.0
CA D:CYS93 4.1 17.3 1.0
O D:HOH150 4.2 4.6 1.0
N D:CYS84 4.2 19.1 1.0
CA D:CYS81 4.3 19.4 1.0
CA D:CYS84 4.3 19.1 1.0
SG D:CYS67 4.4 17.6 1.0
CB D:ILE66 4.6 16.2 1.0
O D:CYS81 4.7 21.2 1.0
CA D:CYS64 4.8 16.0 1.0
C D:CYS81 4.8 20.6 1.0
N D:CYS67 4.8 19.0 1.0
SG D:CYS74 4.9 14.3 1.0
CG1 D:ILE66 4.9 17.1 1.0
C D:CYS93 5.0 18.7 1.0

Zinc binding site 5 out of 9 in 1hwt

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Zinc binding site 5 out of 9 in the Structure of A HAP1/Dna Complex Reveals Dramatically Asymmetric Dna Binding By A Homodimeric Protein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of A HAP1/Dna Complex Reveals Dramatically Asymmetric Dna Binding By A Homodimeric Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn138

b:21.4
occ:1.00
 NE2 D:HIS80 1.8 14.1 1.0
NE2 H:HIS80 2.0 13.7 1.0
ND1 D:HIS91 2.0 12.3 1.0
ND1 H:HIS91 2.1 17.4 1.0
CD2 D:HIS80 2.7 12.6 1.0
CE1 D:HIS80 2.8 13.9 1.0
CE1 H:HIS80 3.0 15.1 1.0
CD2 H:HIS80 3.0 14.3 1.0
CE1 D:HIS91 3.0 14.2 1.0
CG D:HIS91 3.0 12.5 1.0
CG H:HIS91 3.0 15.0 1.0
CE1 H:HIS91 3.1 14.5 1.0
CB H:HIS91 3.3 16.3 1.0
CB D:HIS91 3.3 14.1 1.0
CA D:HIS91 3.6 15.5 1.0
CA H:HIS91 3.7 15.8 1.0
CG D:HIS80 3.9 13.6 1.0
ND1 D:HIS80 3.9 13.4 1.0
ND1 H:HIS80 4.1 14.6 1.0
CG H:HIS80 4.1 15.4 1.0
NE2 D:HIS91 4.2 13.1 1.0
CD2 D:HIS91 4.2 11.7 1.0
CD2 H:HIS91 4.2 13.5 1.0
NE2 H:HIS91 4.2 14.7 1.0
N D:HIS91 4.4 17.1 1.0
N H:HIS91 4.5 17.9 1.0
C D:HIS91 4.6 15.5 1.0
O H:HIS91 4.6 12.9 1.0
C H:HIS91 4.7 14.5 1.0
O D:HIS91 4.7 15.6 1.0
O D:ALA90 5.0 18.7 1.0
C D:ALA90 5.0 17.8 1.0

Zinc binding site 6 out of 9 in 1hwt

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Zinc binding site 6 out of 9 in the Structure of A HAP1/Dna Complex Reveals Dramatically Asymmetric Dna Binding By A Homodimeric Protein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of A HAP1/Dna Complex Reveals Dramatically Asymmetric Dna Binding By A Homodimeric Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn136

b:20.0
occ:1.00
 SG G:CYS67 2.3 19.7 1.0
SG G:CYS64 2.3 19.4 1.0
SG G:CYS74 2.3 19.5 1.0
SG G:CYS81 2.4 20.2 1.0
ZN G:ZN137 3.0 23.0 1.0
CB G:CYS67 3.1 20.1 1.0
CB G:CYS74 3.3 19.3 1.0
CB G:CYS81 3.4 20.6 1.0
CB G:CYS64 3.5 20.0 1.0
CA G:CYS74 3.9 19.7 1.0
N G:CYS64 4.1 19.2 1.0
CA G:CYS67 4.3 19.4 1.0
N G:CYS67 4.3 18.8 1.0
CA G:CYS64 4.4 19.1 1.0
CB G:GLN83 4.4 25.0 1.0
SG G:CYS84 4.5 18.9 1.0
O G:CYS64 4.6 18.0 1.0
O G:HOH141 4.6 11.9 1.0
SG G:CYS93 4.8 19.2 1.0
CA G:CYS81 4.8 22.1 1.0
C G:CYS74 4.8 19.5 1.0
OH G:TYR95 4.8 24.0 1.0
C G:CYS64 4.9 19.7 1.0
N G:ASP75 4.9 20.5 1.0
N G:CYS74 4.9 20.4 1.0

Zinc binding site 7 out of 9 in 1hwt

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Zinc binding site 7 out of 9 in the Structure of A HAP1/Dna Complex Reveals Dramatically Asymmetric Dna Binding By A Homodimeric Protein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of A HAP1/Dna Complex Reveals Dramatically Asymmetric Dna Binding By A Homodimeric Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn137

b:23.0
occ:1.00
 SG G:CYS93 2.3 19.2 1.0
SG G:CYS84 2.3 18.9 1.0
SG G:CYS64 2.3 19.4 1.0
SG G:CYS81 2.4 20.2 1.0
ZN G:ZN136 3.0 20.0 1.0
CB G:CYS93 3.2 19.5 1.0
CB G:CYS84 3.2 18.3 1.0
CB G:CYS64 3.3 20.0 1.0
CB G:CYS81 3.7 20.6 1.0
CA G:CYS93 4.0 21.1 1.0
N G:CYS81 4.1 23.1 1.0
N G:CYS84 4.2 21.1 1.0
CA G:CYS84 4.3 19.1 1.0
CA G:CYS81 4.4 22.1 1.0
SG G:CYS67 4.5 19.7 1.0
O G:CYS81 4.6 22.7 1.0
CB G:ILE66 4.7 20.3 1.0
O G:HOH141 4.7 11.9 1.0
CA G:CYS64 4.7 19.1 1.0
SG G:CYS74 4.8 19.5 1.0
C G:CYS81 4.8 22.2 1.0
C G:CYS93 4.8 23.8 1.0
OH G:TYR95 5.0 24.0 1.0
N G:CYS67 5.0 18.8 1.0

Zinc binding site 8 out of 9 in 1hwt

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Zinc binding site 8 out of 9 in the Structure of A HAP1/Dna Complex Reveals Dramatically Asymmetric Dna Binding By A Homodimeric Protein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of A HAP1/Dna Complex Reveals Dramatically Asymmetric Dna Binding By A Homodimeric Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn136

b:21.2
occ:1.00
 SG H:CYS81 2.3 18.0 1.0
SG H:CYS67 2.3 17.2 1.0
SG H:CYS74 2.3 18.1 1.0
SG H:CYS64 2.4 18.1 1.0
ZN H:ZN137 2.9 20.6 1.0
CB H:CYS67 3.2 15.4 1.0
CB H:CYS74 3.3 18.4 1.0
CB H:CYS81 3.5 20.9 1.0
CB H:CYS64 3.6 18.3 1.0
CA H:CYS74 3.8 18.6 1.0
N H:CYS64 4.2 17.8 1.0
CB H:GLN83 4.3 19.4 1.0
N H:CYS67 4.4 19.5 1.0
CA H:CYS67 4.4 18.4 1.0
CA H:CYS64 4.4 17.6 1.0
SG H:CYS84 4.5 18.0 1.0
N H:ASP75 4.7 17.7 1.0
C H:CYS74 4.7 18.5 1.0
O H:CYS64 4.8 18.6 1.0
SG H:CYS93 4.8 16.0 1.0
CG H:GLN83 4.8 19.7 1.0
CA H:CYS81 4.9 21.4 1.0
N H:CYS74 4.9 19.0 1.0
OH H:TYR95 4.9 12.7 1.0
C H:CYS64 5.0 16.9 1.0

Zinc binding site 9 out of 9 in 1hwt

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Zinc binding site 9 out of 9 in the Structure of A HAP1/Dna Complex Reveals Dramatically Asymmetric Dna Binding By A Homodimeric Protein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Structure of A HAP1/Dna Complex Reveals Dramatically Asymmetric Dna Binding By A Homodimeric Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn137

b:20.6
occ:1.00
 SG H:CYS93 2.3 16.0 1.0
SG H:CYS64 2.3 18.1 1.0
SG H:CYS84 2.3 18.0 1.0
SG H:CYS81 2.4 18.0 1.0
ZN H:ZN136 2.9 21.2 1.0
CB H:CYS93 3.2 17.4 1.0
CB H:CYS84 3.3 18.3 1.0
CB H:CYS64 3.3 18.3 1.0
CB H:CYS81 3.5 20.9 1.0
N H:CYS81 3.9 21.0 1.0
CA H:CYS93 4.1 18.6 1.0
CA H:CYS81 4.2 21.4 1.0
N H:CYS84 4.3 19.5 1.0
CA H:CYS84 4.4 19.9 1.0
SG H:CYS67 4.4 17.2 1.0
O H:CYS81 4.6 21.7 1.0
CB H:ILE66 4.7 16.8 1.0
C H:CYS81 4.7 21.4 1.0
CA H:CYS64 4.8 17.6 1.0
SG H:CYS74 4.9 18.1 1.0
C H:CYS93 4.9 19.0 1.0
OH H:TYR95 4.9 12.7 1.0
N H:CYS67 5.0 19.5 1.0
CG1 H:ILE66 5.0 15.2 1.0

Reference:

D.A.King, L.Zhang, L.Guarente, R.Marmorstein. Structure of A HAP1-Dna Complex Reveals Dramatically Asymmetric Dna Binding By A Homodimeric Protein. Nat.Struct.Biol. V. 6 64 1999.
ISSN: ISSN 1072-8368
PubMed: 9886294
DOI: 10.1038/4940
Page generated: Tue Aug 19 20:43:16 2025

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