Iron in PDB 1jyb: Crystal Structure of Rubrerythrin

The structure of Crystal Structure of Rubrerythrin, PDB code: 1jyb was solved by W.R.Chang, M.Li, M.Y.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 2.20
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	49.670, 81.552, 99.754, 90.00, 90.00, 90.00
R / Rfree (%)	18.2 / 23.1

The structure of Crystal Structure of Rubrerythrin also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Iron atom in the Crystal Structure of Rubrerythrin (pdb code 1jyb). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Crystal Structure of Rubrerythrin, PDB code: 1jyb:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Crystal Structure of Rubrerythrin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of Rubrerythrin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe600 b:36.4 occ:1.00 OE2 A:GLU94 2.1 28.9 1.0 OE1 A:GLU94 2.1 27.9 1.0 OE2 A:GLU128 2.2 19.4 1.0 OE2 A:GLU53 2.2 19.4 1.0 CD A:GLU94 2.4 28.5 1.0 ND1 A:HIS131 2.5 13.2 1.0 CD A:GLU53 3.1 20.6 1.0 CD A:GLU128 3.2 21.7 1.0 OE1 A:GLU53 3.4 26.1 1.0 ZN A:ZN601 3.4 36.1 1.0 CE1 A:HIS131 3.4 14.0 1.0 CG A:HIS131 3.5 12.4 1.0 OE1 A:GLU128 3.6 30.5 1.0 CB A:HIS131 3.8 13.2 1.0 CG A:GLU94 4.0 26.8 1.0 OH A:TYR27 4.2 20.0 1.0 CG A:GLU128 4.2 18.9 1.0 CA A:GLU128 4.2 12.0 1.0 CG A:GLU53 4.4 18.5 1.0 CE2 A:TYR27 4.4 13.4 1.0 CB A:GLU128 4.4 12.8 1.0 CG2 A:THR49 4.5 10.0 1.0 OE2 A:GLU97 4.6 35.3 1.0 NE2 A:HIS131 4.6 17.5 1.0 CD2 A:HIS131 4.7 14.7 1.0 O A:GLU128 4.8 15.5 1.0 CZ A:TYR27 4.8 15.1 1.0 CB A:GLU94 4.9 24.3 1.0

Iron binding site 2 out of 2 in the Crystal Structure of Rubrerythrin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Rubrerythrin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:15.2 occ:1.00 SG A:CYS161 2.3 13.8 1.0 SG A:CYS158 2.3 15.6 1.0 SG A:CYS174 2.3 17.4 1.0 SG A:CYS177 2.3 18.0 1.0 CB A:CYS174 3.2 14.3 1.0 CB A:CYS158 3.2 16.1 1.0 CB A:CYS177 3.4 15.2 1.0 CB A:CYS161 3.4 15.6 1.0 N A:CYS161 3.6 15.3 1.0 N A:CYS177 3.8 19.6 1.0 CA A:CYS161 4.0 13.7 1.0 CA A:CYS177 4.1 17.5 1.0 CB A:TYR163 4.4 13.5 1.0 CA A:CYS174 4.6 18.4 1.0 CB A:ASN160 4.6 9.8 1.0 C A:ASN160 4.6 14.8 1.0 CA A:CYS158 4.6 12.8 1.0 C A:CYS161 4.7 15.4 1.0 CB A:ALA176 4.7 16.5 1.0 N A:GLY162 4.8 17.1 1.0 C A:CYS177 4.8 18.3 1.0 C A:ALA176 4.8 19.3 1.0 N A:TYR163 4.9 15.5 1.0 N A:ALA178 5.0 19.9 1.0 CA A:ASN160 5.0 12.6 1.0

M.Li, M.Y.Liu, J.Legall, L.L.Gui, J.Liao, T.Jiang, J.P.Zhang, D.C.Liang, W.R.Chang. Crystal Structure Studies on Rubrerythrin: Enzymatic Activity in Relation to the Zinc Movement. J.Biol.Inorg.Chem. V. 8 149 2003.
ISSN: ISSN 0949-8257
PubMed: 12459910
DOI: 10.1007/S00775-002-0400-0