Zinc in PDB 1ga5: 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: 1ga5 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)	19.60 / 2.40
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	44.920, 52.020, 78.880, 85.84, 76.61, 74.48
R / Rfree (%)	25.3 / 29.9

The structure of Crystal Structure of the Orphan Nuclear Receptor Rev-Erb(Alpha) Dna- Binding Domain Bound to Its Cognate Response Element also contains other interesting chemical elements:

Iodine

(I)

2 atoms

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 1ga5). 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 the Orphan Nuclear Receptor Rev-Erb(Alpha) Dna- Binding Domain Bound to Its Cognate Response Element, PDB code: 1ga5:
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 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:42.4 occ:1.00 SG A:CYS1 2.1 30.9 1.0 SG A:CYS18 2.1 25.9 1.0 SG A:CYS21 2.4 47.9 1.0 SG A:CYS4 2.5 33.3 1.0 CB A:CYS1 3.1 29.9 1.0 CB A:CYS4 3.3 29.7 1.0 N A:CYS4 3.4 33.2 1.0 CB A:CYS21 3.5 44.6 1.0 CB A:CYS18 3.6 26.7 1.0 CA A:CYS4 3.9 32.3 1.0 N A:CYS18 4.1 26.5 1.0 CB A:VAL3 4.4 34.1 1.0 CA A:CYS18 4.4 29.2 1.0 C A:VAL3 4.4 32.5 1.0 N A:CYS21 4.5 41.5 1.0 CA A:CYS1 4.5 34.9 1.0 CB A:ASP6 4.5 36.4 1.0 NH1 A:ARG50 4.5 34.5 1.0 C A:CYS4 4.6 35.2 1.0 N A:GLY5 4.6 35.5 1.0 CA A:CYS21 4.6 45.6 1.0 N A:ASP6 4.7 32.4 1.0 CA A:VAL3 4.7 31.1 1.0 N A:VAL3 4.8 32.5 1.0 CD A:ARG50 4.8 35.4 1.0 C A:CYS1 4.9 37.5 1.0 NH2 A:ARG57 4.9 32.5 1.0 O A:CYS1 5.0 43.5 1.0

Zinc binding site 2 out of 8 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:49.9 occ:1.00 SG A:CYS56 2.1 51.5 1.0 SG A:CYS43 2.4 56.4 1.0 SG A:CYS53 2.4 44.9 1.0 SG A:CYS37 2.8 72.4 1.0 CB A:CYS56 3.0 55.1 1.0 CB A:CYS43 3.5 54.5 1.0 CB A:CYS53 3.6 53.5 1.0 CB A:CYS37 3.9 76.2 1.0 N A:CYS56 4.0 50.5 1.0 CA A:CYS56 4.0 50.6 1.0 CA A:CYS37 4.3 76.0 1.0 N A:CYS43 4.5 64.6 1.0 CA A:CYS43 4.6 60.6 1.0 O A:ASN40 4.6 80.0 1.0 O A:CYS53 4.7 56.6 1.0 N A:LEU38 4.8 73.1 1.0 CA A:CYS53 5.0 54.5 1.0

Zinc binding site 3 out of 8 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:34.0 occ:1.00 SG B:CYS18 1.9 29.7 1.0 SG B:CYS4 2.3 33.8 1.0 SG B:CYS21 2.4 27.6 1.0 SG B:CYS1 2.5 35.6 1.0 CB B:CYS21 3.2 25.6 1.0 CB B:CYS18 3.2 30.1 1.0 CB B:CYS1 3.3 37.3 1.0 CB B:CYS4 3.5 36.7 1.0 N B:CYS18 3.8 31.0 1.0 N B:CYS4 3.8 39.0 1.0 N B:CYS21 4.0 24.4 1.0 CA B:CYS18 4.1 32.7 1.0 CA B:CYS4 4.2 37.6 1.0 CA B:CYS21 4.2 27.6 1.0 CB B:ASP6 4.3 51.1 1.0 O B:HOH997 4.4 80.0 1.0 CB B:VAL3 4.4 37.0 1.0 NH1 B:ARG50 4.5 34.8 1.0 C B:VAL3 4.6 40.5 1.0 CA B:CYS1 4.8 35.6 1.0 N B:ASP6 4.8 53.0 1.0 C B:CYS18 4.8 32.4 1.0 C B:CYS4 4.8 38.8 1.0 O B:CYS18 4.8 33.0 1.0 C B:ALA17 4.9 31.8 1.0 CA B:VAL3 4.9 38.6 1.0 N B:GLY5 4.9 41.0 1.0 CD B:ARG50 4.9 32.1 1.0 NH2 B:ARG57 4.9 42.9 1.0 N B:VAL3 5.0 36.3 1.0

Zinc binding site 4 out of 8 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:41.0 occ:1.00 SG B:CYS43 1.8 44.1 1.0 SG B:CYS53 2.3 38.6 1.0 SG B:CYS37 2.3 49.6 1.0 SG B:CYS56 2.6 51.6 1.0 CB B:CYS43 3.0 40.7 1.0 CB B:CYS37 3.2 46.7 1.0 CB B:CYS53 3.3 38.4 1.0 CB B:CYS56 3.4 37.0 1.0 N B:CYS43 3.8 47.6 1.0 CA B:CYS43 4.0 42.2 1.0 CA B:CYS37 4.2 52.3 1.0 CA B:GLU41 4.3 62.1 1.0 N B:CYS56 4.4 38.3 1.0 CA B:CYS56 4.4 35.9 1.0 N B:ASN42 4.5 56.6 1.0 O B:HOH875 4.5 35.7 1.0 C B:GLU41 4.6 60.7 1.0 CA B:CYS53 4.7 36.7 1.0 N B:GLU41 4.8 63.1 1.0 C B:CYS37 4.9 52.9 1.0

Zinc binding site 5 out of 8 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 5 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 E:Zn450 b:32.3 occ:1.00 SG E:CYS18 2.0 31.8 1.0 SG E:CYS4 2.4 29.4 1.0 SG E:CYS1 2.4 36.9 1.0 SG E:CYS21 2.4 40.0 1.0 CB E:CYS1 3.1 31.6 1.0 CB E:CYS4 3.4 24.4 1.0 CB E:CYS18 3.5 29.8 1.0 N E:CYS4 3.5 38.0 1.0 CB E:CYS21 3.6 36.4 1.0 CA E:CYS4 4.0 33.2 1.0 N E:CYS18 4.0 27.7 1.0 CA E:CYS18 4.3 28.8 1.0 N E:CYS21 4.3 39.9 1.0 CB E:VAL3 4.4 45.3 1.0 NH1 E:ARG50 4.5 39.7 1.0 CB E:ASP6 4.5 38.9 1.0 C E:VAL3 4.6 39.8 1.0 CA E:CYS1 4.6 37.6 1.0 C E:CYS4 4.6 35.5 1.0 N E:GLY5 4.6 36.0 1.0 CA E:CYS21 4.6 37.8 1.0 CD E:ARG50 4.7 39.6 1.0 N E:ASP6 4.7 33.5 1.0 CG1 E:VAL3 4.8 41.5 1.0 CA E:VAL3 4.9 42.1 1.0 C E:CYS18 5.0 30.6 1.0 N E:VAL3 5.0 43.1 1.0 O E:CYS18 5.0 30.1 1.0

Zinc binding site 6 out of 8 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 6 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 E:Zn451 b:50.8 occ:1.00 SG E:CYS56 2.0 53.8 1.0 SG E:CYS53 2.1 49.8 1.0 SG E:CYS37 2.5 65.6 1.0 SG E:CYS43 3.0 62.8 1.0 CB E:CYS56 3.0 55.4 1.0 CB E:CYS53 3.4 48.8 1.0 CB E:CYS37 3.5 69.5 1.0 CB E:CYS43 3.7 63.7 1.0 N E:CYS56 4.1 56.0 1.0 CA E:CYS56 4.1 56.8 1.0 O E:ASN40 4.1 73.4 1.0 N E:CYS43 4.4 64.9 1.0 CA E:CYS37 4.5 71.3 1.0 CA E:CYS43 4.7 65.5 1.0 CA E:CYS53 4.7 55.6 1.0 CA E:GLU41 4.8 59.3 1.0 N E:ASN42 4.8 56.3 1.0 O E:CYS53 4.9 53.9 1.0

Zinc binding site 7 out of 8 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 7 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 F:Zn550 b:31.2 occ:1.00 SG F:CYS21 2.1 32.8 1.0 SG F:CYS4 2.1 37.6 1.0 SG F:CYS1 2.3 36.5 1.0 SG F:CYS18 2.4 30.8 1.0 CB F:CYS21 3.1 24.6 1.0 CB F:CYS1 3.2 37.1 1.0 CB F:CYS4 3.4 36.1 1.0 CB F:CYS18 3.6 31.1 1.0 N F:CYS4 3.7 40.8 1.0 N F:CYS18 3.9 33.4 1.0 N F:CYS21 4.0 28.9 1.0 CA F:CYS4 4.1 39.1 1.0 CA F:CYS21 4.1 26.8 1.0 CB F:ASP6 4.3 42.4 1.0 CA F:CYS18 4.3 32.7 1.0 NH1 F:ARG50 4.6 36.2 1.0 C F:VAL3 4.6 42.3 1.0 CB F:VAL3 4.6 39.6 1.0 CA F:CYS1 4.6 36.4 1.0 N F:ASP6 4.7 45.5 1.0 C F:CYS4 4.7 37.5 1.0 N F:GLY5 4.7 37.5 1.0 O F:CYS18 4.8 35.5 1.0 C F:CYS18 4.9 32.8 1.0 CA F:VAL3 5.0 40.5 1.0 N F:VAL3 5.0 40.8 1.0

Zinc binding site 8 out of 8 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 8 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 F:Zn551 b:51.3 occ:1.00 SG F:CYS43 2.1 35.7 1.0 SG F:CYS37 2.3 52.1 1.0 SG F:CYS56 2.4 44.0 1.0 SG F:CYS53 2.5 43.0 1.0 CB F:CYS43 2.9 23.3 1.0 CB F:CYS53 3.3 42.8 1.0 CB F:CYS56 3.3 30.5 1.0 CB F:CYS37 3.6 50.9 1.0 N F:CYS43 3.9 37.2 1.0 CA F:CYS43 4.0 33.5 1.0 CA F:GLU41 4.5 67.1 1.0 CA F:CYS37 4.5 53.6 1.0 CA F:CYS56 4.5 28.4 1.0 O F:HOH924 4.6 43.3 1.0 N F:ASN42 4.6 53.6 1.0 N F:CYS56 4.6 33.5 1.0 O F:LYS39 4.6 68.5 1.0 C F:GLU41 4.7 62.1 1.0 CA F:CYS53 4.8 40.4 1.0 N F:GLU41 4.9 72.5 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