Zinc in PDB 3cjj: Crystal Structure of Human Rage Ligand-Binding Domain

The structure of Crystal Structure of Human Rage Ligand-Binding Domain, PDB code: 3cjj was solved by M.Koch, B.M.Dattilo, A.Schiefner, J.Diez, W.J.Chazin, G.Fritz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.00 / 1.85
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	74.850, 119.960, 28.890, 90.00, 90.00, 90.00
R / Rfree (%)	20.9 / 24

The binding sites of Zinc atom in the Crystal Structure of Human Rage Ligand-Binding Domain (pdb code 3cjj). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Crystal Structure of Human Rage Ligand-Binding Domain, PDB code: 3cjj:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Crystal Structure of Human Rage Ligand-Binding Domain


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 Human Rage Ligand-Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2 b:32.0 occ:1.00 O A:ACT1 1.8 32.7 1.0 NE2 A:HIS158 2.0 17.4 1.0 C A:ACT1 2.9 33.5 1.0 CE1 A:HIS158 3.0 19.4 1.0 CD2 A:HIS158 3.0 18.9 1.0 OXT A:ACT1 3.2 34.0 1.0 ND1 A:HIS158 4.1 17.7 1.0 CG A:HIS158 4.2 16.1 1.0 CH3 A:ACT1 4.3 32.4 1.0 O A:HOH289 4.3 38.4 1.0 CG A:PRO163 4.5 23.5 1.0 CB A:PRO163 4.8 23.9 1.0 CA A:PRO163 4.9 23.8 1.0

Zinc binding site 2 out of 5 in the Crystal Structure of Human Rage Ligand-Binding Domain


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 Human Rage Ligand-Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn3 b:42.1 occ:0.45 O A:HOH397 1.6 35.7 1.0 NE2 A:HIS217 1.9 35.0 1.0 O A:HOH454 2.0 50.3 1.0 O A:HOH394 2.2 62.9 1.0 CD2 A:HIS217 2.8 33.1 1.0 CE1 A:HIS217 2.9 34.4 1.0 CG A:HIS217 4.0 35.7 1.0 ND1 A:HIS217 4.0 34.5 1.0 O A:HOH399 4.2 59.2 1.0 NH2 A:ARG29 4.3 30.1 1.0 CG1 A:ILE120 4.3 16.2 1.0 NH1 A:ARG29 4.4 33.8 1.0 O A:HOH332 4.7 55.3 1.0 CZ A:ARG29 4.9 34.4 1.0 CD1 A:ILE120 4.9 17.2 1.0

Zinc binding site 3 out of 5 in the Crystal Structure of Human Rage Ligand-Binding Domain


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 Human Rage Ligand-Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn4 b:44.3 occ:0.25 ZN A:ZN4 0.0 44.3 0.2 OE1 A:GLU59 2.0 29.3 1.0 ZN A:ZN4 2.9 48.0 0.2 CD A:GLU59 2.9 28.9 1.0 OE2 A:GLU59 3.1 31.1 1.0 O A:HOH313 3.4 44.5 1.0 CG A:GLU59 4.3 23.9 1.0 CB A:GLU59 4.8 22.4 1.0

Zinc binding site 4 out of 5 in the Crystal Structure of Human Rage Ligand-Binding Domain


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 Human Rage Ligand-Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn4 b:48.0 occ:0.20 ZN A:ZN4 0.0 48.0 0.2 ZN A:ZN4 2.9 44.3 0.2 OE1 A:GLU59 4.8 29.3 1.0

Zinc binding site 5 out of 5 in the Crystal Structure of Human Rage Ligand-Binding Domain


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 Human Rage Ligand-Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn5 b:44.7 occ:0.25 O A:HOH444 1.7 60.1 1.0 O A:HOH470 1.8 41.0 1.0 OD1 A:ASP128 2.6 33.8 1.0 OD2 A:ASP128 2.8 32.1 1.0 CG A:ASP128 3.0 28.4 1.0 CG2 A:VAL127 4.1 25.9 1.0 CB A:VAL127 4.1 25.5 1.0 O A:HOH396 4.2 59.4 1.0 CB A:ASP128 4.4 24.6 1.0 N A:ASP128 4.6 24.8 1.0 O A:HOH315 4.7 45.8 1.0 CG1 A:VAL127 4.9 23.9 1.0 CA A:ASP128 4.9 24.9 1.0

M.Koch, S.Chitayat, B.M.Dattilo, A.Schiefner, J.Diez, W.J.Chazin, G.Fritz. Structural Basis For Ligand Recognition and Activation of Rage. Structure V. 18 1342 2010.
ISSN: ISSN 0969-2126
PubMed: 20947022
DOI: 10.1016/J.STR.2010.05.017