Zinc in PDB 1hlz: Crystal Structure of the Orphan Nuclear Receptor Rev- Erb(Alpha) Dna-Binding Domain Bound to Its Cognate Response Element

The structure of Crystal Structure of the Orphan Nuclear Receptor Rev- Erb(Alpha) Dna-Binding Domain Bound to Its Cognate Response Element, PDB code: 1hlz was solved by M.L.Sierk, Q.Zhao, F.Rastinejad, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	18.60 / 2.80
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	35.867, 39.603, 58.565, 84.13, 72.09, 70.20
R / Rfree (%)	26 / 31

The binding sites of Zinc atom in the Crystal Structure of the Orphan Nuclear Receptor Rev- Erb(Alpha) Dna-Binding Domain Bound to Its Cognate Response Element (pdb code 1hlz). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of the Orphan Nuclear Receptor Rev- Erb(Alpha) Dna-Binding Domain Bound to Its Cognate Response Element, PDB code: 1hlz:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of the Orphan Nuclear Receptor Rev- Erb(Alpha) Dna-Binding Domain Bound to Its Cognate Response Element


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 the Orphan Nuclear Receptor Rev- Erb(Alpha) Dna-Binding Domain Bound to Its Cognate Response Element within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn450 b:57.8 occ:1.00 SG A:CYS1 2.2 69.1 1.0 SG A:CYS21 2.3 56.5 1.0 SG A:CYS18 2.5 25.4 1.0 SG A:CYS4 2.7 41.3 1.0 CB A:CYS1 3.0 69.1 1.0 CB A:CYS18 3.3 25.4 1.0 CB A:CYS21 3.4 56.5 1.0 N A:CYS4 3.7 41.3 1.0 CB A:CYS4 3.7 41.3 1.0 N A:CYS18 3.7 25.4 1.0 CB A:VAL3 4.0 68.2 1.0 CA A:CYS18 4.1 25.4 1.0 CA A:CYS4 4.2 41.3 1.0 NH1 A:ARG50 4.3 53.1 1.0 N A:CYS21 4.3 56.5 1.0 CA A:CYS1 4.4 69.1 1.0 CB A:ASP6 4.5 64.0 1.0 CA A:CYS21 4.5 56.5 1.0 CG1 A:VAL3 4.5 68.2 1.0 C A:VAL3 4.6 68.2 1.0 CA A:VAL3 4.7 68.2 1.0 C A:CYS4 4.7 41.3 1.0 N A:VAL3 4.7 68.2 1.0 N A:ASP6 4.8 64.0 1.0 N A:GLY5 4.8 51.3 1.0 C A:ALA17 4.8 24.9 1.0 C A:CYS1 4.8 69.1 1.0 C A:CYS18 4.9 25.4 1.0 O A:CYS1 4.9 69.1 1.0 CG2 A:VAL3 5.0 68.2 1.0 CB A:ALA17 5.0 24.9 1.0 CA A:ALA17 5.0 24.9 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of the Orphan Nuclear Receptor Rev- Erb(Alpha) Dna-Binding Domain Bound to Its Cognate Response Element


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 the Orphan Nuclear Receptor Rev- Erb(Alpha) Dna-Binding Domain Bound to Its Cognate Response Element within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn451 b:57.8 occ:1.00 SG A:CYS56 2.3 71.4 1.0 SG A:CYS43 2.5 66.5 1.0 SG A:CYS53 2.8 60.9 1.0 SG A:CYS37 3.0 79.9 1.0 CA A:GLU41 3.0 80.0 1.0 CB A:CYS56 3.0 71.4 1.0 CB A:CYS37 3.3 79.9 1.0 C A:GLU41 3.4 80.0 1.0 CB A:CYS43 3.4 66.5 1.0 N A:CYS43 3.6 66.5 1.0 N A:ASN42 3.6 78.7 1.0 CB A:GLU41 3.7 80.0 1.0 N A:GLU41 4.0 80.0 1.0 O A:GLU41 4.1 80.0 1.0 CA A:CYS43 4.1 66.5 1.0 CB A:CYS53 4.2 60.9 1.0 CA A:CYS56 4.2 71.4 1.0 N A:CYS56 4.5 71.4 1.0 C A:ASN42 4.6 78.7 1.0 CA A:ASN42 4.6 78.7 1.0 O A:LYS39 4.7 80.0 1.0 CA A:CYS37 4.8 79.9 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of the Orphan Nuclear Receptor Rev- Erb(Alpha) Dna-Binding Domain Bound to Its Cognate Response Element


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 the Orphan Nuclear Receptor Rev- Erb(Alpha) Dna-Binding Domain Bound to Its Cognate Response Element within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn550 b:57.8 occ:1.00 SG B:CYS21 1.8 28.4 1.0 SG B:CYS1 2.2 37.6 1.0 SG B:CYS4 2.2 35.0 1.0 SG B:CYS18 2.4 27.8 1.0 CB B:CYS21 3.2 28.4 1.0 CB B:CYS1 3.3 37.6 1.0 CB B:CYS18 3.5 27.8 1.0 CB B:CYS4 3.5 35.0 1.0 N B:CYS4 3.7 35.0 1.0 NH1 B:ARG50 4.1 22.1 1.0 N B:CYS21 4.1 28.4 1.0 CA B:CYS4 4.2 35.0 1.0 N B:CYS18 4.2 27.8 1.0 CA B:CYS21 4.3 28.4 1.0 CB B:VAL3 4.3 27.5 1.0 CB B:ASP6 4.4 52.0 1.0 CA B:CYS18 4.5 27.8 1.0 C B:VAL3 4.7 27.5 1.0 CA B:CYS1 4.7 37.6 1.0 NH2 B:ARG57 4.7 50.9 1.0 C B:CYS4 4.7 35.0 1.0 N B:ASP6 4.8 52.0 1.0 CA B:VAL3 4.9 27.5 1.0 O B:CYS18 4.9 27.8 1.0 CG1 B:VAL3 4.9 27.5 1.0 N B:VAL3 4.9 27.5 1.0 N B:GLY5 4.9 63.5 1.0 CD B:ARG50 5.0 22.1 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of the Orphan Nuclear Receptor Rev- Erb(Alpha) Dna-Binding Domain Bound to Its Cognate Response Element


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 the Orphan Nuclear Receptor Rev- Erb(Alpha) Dna-Binding Domain Bound to Its Cognate Response Element within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn551 b:57.8 occ:1.00 SG B:CYS53 2.2 58.7 1.0 SG B:CYS43 2.3 40.8 1.0 SG B:CYS37 2.3 65.2 1.0 SG B:CYS56 2.5 54.7 1.0 CB B:CYS53 3.2 58.7 1.0 CB B:CYS43 3.2 40.8 1.0 CB B:CYS37 3.4 65.2 1.0 CB B:CYS56 3.6 54.7 1.0 N B:CYS56 4.2 54.7 1.0 CA B:CYS37 4.3 65.2 1.0 N B:CYS43 4.3 40.8 1.0 CA B:CYS43 4.3 40.8 1.0 N B:LEU38 4.5 80.0 1.0 CA B:CYS56 4.5 54.7 1.0 CA B:CYS53 4.6 58.7 1.0 CA B:GLU41 4.8 75.7 1.0 C B:CYS37 4.9 65.2 1.0 N B:LYS39 4.9 65.9 1.0 O B:LYS39 4.9 65.9 1.0 CB B:GLN55 4.9 48.2 1.0 O B:ASN42 4.9 78.8 1.0

M.L.Sierk, Q.Zhao, F.Rastinejad. Dna Deformability As A Recognition Feature in the Reverb Response Element Biochemistry V. 40 12833 2001.
ISSN: ISSN 0006-2960
PubMed: 11669620
DOI: 10.1021/BI011086R