Iron in PDB 1dvb: Rubrerythrin

The structure of Rubrerythrin, PDB code: 1dvb was solved by L.C.Sieker, M.Holmes, I.Le Trong, S.Turley, M.Y.Liu, J.Legall, R.E.Stenkamp, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.90
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	50.630, 81.550, 100.260, 90.00, 90.00, 90.00
R / Rfree (%)	19.9 / 27

The structure of Rubrerythrin also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

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

Iron binding site 1 out of 2 in the Rubrerythrin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Rubrerythrin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe192 b:18.0 occ:1.00 SG A:CYS161 2.2 19.9 1.0 SG A:CYS158 2.3 20.6 1.0 SG A:CYS174 2.3 20.8 1.0 SG A:CYS177 2.3 27.0 1.0 CB A:CYS174 3.1 15.1 1.0 CB A:CYS177 3.2 17.8 1.0 CB A:CYS158 3.2 22.7 1.0 CB A:CYS161 3.4 18.8 1.0 N A:CYS177 3.6 28.4 1.0 N A:CYS161 3.8 22.6 1.0 CA A:CYS177 4.0 22.0 1.0 CA A:CYS161 4.1 20.2 1.0 CB A:TYR163 4.2 24.9 1.0 CB A:ALA176 4.5 29.0 1.0 CB A:ASN160 4.5 19.4 1.0 CA A:CYS174 4.6 21.8 1.0 C A:ALA176 4.6 34.4 1.0 C A:CYS161 4.6 21.2 1.0 CA A:CYS158 4.7 19.9 1.0 N A:TYR163 4.7 24.2 1.0 C A:CYS177 4.7 23.4 1.0 C A:ASN160 4.7 22.7 1.0 ND2 A:ASN160 4.8 17.0 1.0 N A:GLY162 4.9 20.2 1.0 N A:ALA178 4.9 21.9 1.0 CA A:ALA176 4.9 35.0 1.0 N A:ALA176 5.0 33.4 1.0

Iron binding site 2 out of 2 in the Rubrerythrin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Rubrerythrin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe193 b:35.3 occ:1.00 OE1 A:GLU128 2.0 26.2 1.0 OE2 A:GLU94 2.0 32.8 1.0 OE2 A:GLU53 2.1 30.2 1.0 OE1 A:GLU94 2.1 39.9 1.0 ND1 A:HIS131 2.2 18.4 1.0 O A:HOH196 2.2 30.6 1.0 CD A:GLU94 2.5 32.8 1.0 CD A:GLU128 2.9 31.0 1.0 CE1 A:HIS131 3.0 18.8 1.0 CD A:GLU53 3.2 25.2 1.0 CG A:HIS131 3.3 19.4 1.0 OE1 A:GLU53 3.5 28.6 1.0 OE2 A:GLU128 3.5 38.3 1.0 ZN A:ZN194 3.7 20.6 1.0 CB A:HIS131 3.8 21.7 1.0 CG A:GLU128 3.9 22.2 1.0 CB A:GLU128 3.9 18.1 1.0 CG A:GLU94 4.0 26.6 1.0 CA A:GLU128 4.0 16.4 1.0 NE2 A:HIS131 4.2 17.8 1.0 OH A:TYR27 4.3 18.3 1.0 CD2 A:HIS131 4.3 19.1 1.0 O A:HOH347 4.5 47.5 0.7 CG A:GLU53 4.5 15.4 1.0 CE2 A:TYR27 4.5 12.1 1.0 CG2 A:THR49 4.5 6.7 1.0 OE1 A:GLU97 4.6 37.7 1.0 CE1 A:HIS56 4.8 15.5 1.0 CB A:GLU94 4.9 21.9 1.0 N A:GLU128 4.9 13.1 1.0 CZ A:TYR27 4.9 11.3 1.0

L.C.Sieker, M.Holmes, I.Le Trong, S.Turley, M.Y.Liu, J.Legall, R.E.Stenkamp. The 1.9 A Crystal Structure of the "As Isolated" Rubrerythrin From Desulfovibrio Vulgaris: Some Surprising Results. J.Biol.Inorg.Chem. V. 5 505 2000.
ISSN: ISSN 0949-8257
PubMed: 10968622
DOI: 10.1007/S007750050011