Zinc in PDB 3cbb: Crystal Structure of Hepatocyte Nuclear Factor 4ALPHA in Complex with Dna: Diabetes Gene Product

The structure of Crystal Structure of Hepatocyte Nuclear Factor 4ALPHA in Complex with Dna: Diabetes Gene Product, PDB code: 3cbb was solved by P.Lu, G.B.Rha, M.Melikishvili, B.C.Adkins, M.G.Fried, Y.I.Chi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	121.628, 35.425, 70.985, 90.00, 119.36, 90.00
R / Rfree (%)	21.3 / 25.2

The binding sites of Zinc atom in the Crystal Structure of Hepatocyte Nuclear Factor 4ALPHA in Complex with Dna: Diabetes Gene Product (pdb code 3cbb). 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 Hepatocyte Nuclear Factor 4ALPHA in Complex with Dna: Diabetes Gene Product, PDB code: 3cbb:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Hepatocyte Nuclear Factor 4ALPHA in Complex with Dna: Diabetes Gene Product


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 Hepatocyte Nuclear Factor 4ALPHA in Complex with Dna: Diabetes Gene Product within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:19.2 occ:1.00 SG A:CYS54 2.3 22.4 1.0 SG A:CYS71 2.3 15.6 1.0 SG A:CYS68 2.4 19.6 1.0 SG A:CYS51 2.5 20.3 1.0 CB A:CYS71 3.3 14.4 1.0 CB A:CYS51 3.3 22.5 1.0 CB A:CYS54 3.5 21.9 1.0 N A:CYS54 3.6 20.2 1.0 CB A:CYS68 3.7 19.2 1.0 N A:CYS68 3.9 18.5 1.0 N A:CYS71 4.1 14.6 1.0 CA A:CYS54 4.1 20.7 1.0 NH1 A:ARG100 4.2 18.5 1.0 CA A:CYS71 4.3 14.7 1.0 CB A:ILE53 4.3 17.5 1.0 CA A:CYS68 4.4 19.7 1.0 CB A:ASP56 4.6 26.8 1.0 C A:ILE53 4.7 20.1 1.0 NH2 A:ARG107 4.7 15.3 1.0 CA A:CYS51 4.7 22.6 1.0 CG2 A:ILE53 4.8 18.7 1.0 C A:CYS54 4.8 20.3 1.0 N A:GLY55 4.9 20.3 1.0 CA A:ILE53 4.9 19.9 1.0 N A:ASP56 4.9 26.6 1.0 CB A:SER67 4.9 25.1 1.0 N A:ILE53 5.0 21.5 1.0 C A:SER67 5.0 21.1 1.0 C A:CYS68 5.0 20.4 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Hepatocyte Nuclear Factor 4ALPHA in Complex with Dna: Diabetes Gene Product


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 Hepatocyte Nuclear Factor 4ALPHA in Complex with Dna: Diabetes Gene Product within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:30.9 occ:1.00 SG A:CYS103 2.4 23.4 1.0 SG A:CYS93 2.5 31.9 1.0 SG A:CYS87 2.5 31.6 1.0 SG A:CYS106 2.5 25.3 1.0 CB A:CYS87 3.2 30.1 1.0 CB A:CYS93 3.3 32.8 1.0 CB A:CYS106 3.4 22.9 1.0 CB A:CYS103 3.4 20.8 1.0 O A:HOH1022 3.8 29.2 1.0 N A:CYS106 4.1 20.1 1.0 N A:CYS93 4.1 36.0 1.0 CA A:CYS87 4.1 31.1 1.0 CA A:ARG91 4.2 43.2 1.0 CA A:CYS106 4.3 20.8 1.0 CA A:CYS93 4.4 32.5 1.0 N A:ARG91 4.5 44.1 1.0 N A:GLN92 4.5 41.9 1.0 C A:ARG91 4.6 42.9 1.0 CD2 A:TYR105 4.7 24.2 1.0 CB A:TYR105 4.8 20.7 1.0 CA A:CYS103 4.8 22.5 1.0 CD1 A:PHE89 4.9 46.0 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Hepatocyte Nuclear Factor 4ALPHA in Complex with Dna: Diabetes Gene Product


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 Hepatocyte Nuclear Factor 4ALPHA in Complex with Dna: Diabetes Gene Product within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn2001 b:23.7 occ:1.00 SG B:CYS54 2.4 23.7 1.0 SG B:CYS71 2.4 21.8 1.0 SG B:CYS68 2.4 21.5 1.0 SG B:CYS51 2.4 21.1 1.0 CB B:CYS71 3.2 21.4 1.0 CB B:CYS51 3.3 25.6 1.0 CB B:CYS54 3.5 26.5 1.0 CB B:CYS68 3.7 23.0 1.0 N B:CYS54 3.7 25.4 1.0 N B:CYS68 4.0 23.5 1.0 N B:CYS71 4.2 19.8 1.0 CA B:CYS54 4.2 26.6 1.0 NH1 B:ARG100 4.2 30.1 1.0 CA B:CYS71 4.3 20.4 1.0 CB B:ILE53 4.4 24.5 1.0 CA B:CYS68 4.4 22.8 1.0 CB B:ASP56 4.6 35.6 1.0 CA B:CYS51 4.7 27.2 1.0 C B:ILE53 4.8 26.2 1.0 CG2 B:ILE53 4.8 22.9 1.0 C B:CYS54 4.9 27.6 1.0 CD B:ARG100 4.9 31.4 1.0 N B:GLY55 4.9 29.8 1.0 N B:ASP56 5.0 34.5 1.0 CA B:ILE53 5.0 25.4 1.0 CB B:SER67 5.0 26.4 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Hepatocyte Nuclear Factor 4ALPHA in Complex with Dna: Diabetes Gene Product


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 Hepatocyte Nuclear Factor 4ALPHA in Complex with Dna: Diabetes Gene Product within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn2002 b:36.0 occ:1.00 SG B:CYS103 2.4 27.9 1.0 SG B:CYS106 2.4 26.5 1.0 SG B:CYS93 2.4 33.6 1.0 SG B:CYS87 2.5 37.8 1.0 CB B:CYS93 3.2 35.5 1.0 CB B:CYS103 3.3 25.8 1.0 CB B:CYS106 3.4 23.6 1.0 CB B:CYS87 3.4 39.8 1.0 N B:CYS93 4.1 39.1 1.0 N B:CYS106 4.1 21.5 1.0 CA B:ARG91 4.1 44.2 1.0 CA B:CYS93 4.3 37.3 1.0 CA B:CYS87 4.3 41.3 1.0 CA B:CYS106 4.3 22.0 1.0 N B:ARG91 4.4 44.3 1.0 CD2 B:TYR105 4.6 28.2 1.0 C B:ARG91 4.6 43.0 1.0 N B:GLN92 4.6 41.9 1.0 CA B:CYS103 4.7 26.9 1.0 CB B:TYR105 4.9 22.6 1.0

P.Lu, G.B.Rha, M.Melikishvili, G.Wu, B.C.Adkins, M.G.Fried, Y.I.Chi. Structural Basis of Natural Promoter Recognition By A Unique Nuclear Receptor, HNF4ALPHA. Diabetes Gene Product. J.Biol.Chem. V. 283 33685 2008.
ISSN: ISSN 0021-9258
PubMed: 18829458
DOI: 10.1074/JBC.M806213200