Iron in PDB 1ryt: Rubrerythrin

The structure of Rubrerythrin, PDB code: 1ryt was solved by F.Demare, D.M.Kurtz, P.Nordlund, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 2.10
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	50.400, 82.000, 100.700, 90.00, 90.00, 90.00
R / Rfree (%)	18.2 / 25.6

The binding sites of Iron atom in the Rubrerythrin (pdb code 1ryt). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 3 binding sites of Iron where determined in the Rubrerythrin, PDB code: 1ryt:
Jump to Iron binding site number: 1; 2; 3;

Iron binding site 1 out of 3 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:Fe600 b:24.6 occ:0.90 OE1 A:GLU128 2.1 22.7 1.0 OE2 A:GLU53 2.1 28.3 1.0 OE1 A:GLU94 2.1 22.1 1.0 O A:HOH680 2.2 20.6 1.0 OE2 A:GLU94 2.3 24.3 1.0 ND1 A:HIS131 2.5 17.5 1.0 CD A:GLU94 2.5 24.6 1.0 CD A:GLU53 2.9 19.9 1.0 CD A:GLU128 3.0 24.2 1.0 FE A:FE601 3.2 22.7 0.9 OE1 A:GLU53 3.2 21.2 1.0 CE1 A:HIS131 3.3 16.1 1.0 OE2 A:GLU128 3.5 25.3 1.0 CG A:HIS131 3.6 14.6 1.0 CB A:HIS131 3.9 15.1 1.0 CG A:GLU94 4.0 20.1 1.0 CG A:GLU53 4.2 21.5 1.0 CG A:GLU128 4.3 18.4 1.0 CA A:GLU128 4.3 11.4 1.0 CB A:GLU128 4.4 13.1 1.0 OH A:TYR27 4.5 20.6 1.0 CE2 A:TYR27 4.5 15.0 1.0 NE2 A:HIS131 4.5 18.4 1.0 CG2 A:THR49 4.5 10.1 1.0 O A:HOH679 4.5 20.6 1.0 CD2 A:HIS131 4.7 16.2 1.0 OE1 A:GLU97 4.7 23.1 1.0 CB A:GLU94 4.8 18.7 1.0 CE1 A:HIS56 4.9 19.2 1.0 OE2 A:GLU97 4.9 28.0 1.0 ND1 A:HIS56 5.0 20.9 1.0 CZ A:TYR27 5.0 18.3 1.0

Iron binding site 2 out of 3 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:Fe601 b:22.7 occ:0.90 O A:HOH680 1.9 20.6 1.0 OE2 A:GLU128 2.0 25.3 1.0 OE1 A:GLU20 2.1 30.8 1.0 OE1 A:GLU53 2.2 21.2 1.0 OE1 A:GLU97 2.2 23.1 1.0 OE2 A:GLU20 2.5 28.2 1.0 CD A:GLU20 2.6 28.4 1.0 CD A:GLU128 2.8 24.2 1.0 CD A:GLU97 3.0 25.4 1.0 CD A:GLU53 3.1 19.9 1.0 OE1 A:GLU128 3.1 22.7 1.0 OE2 A:GLU97 3.1 28.0 1.0 FE A:FE600 3.2 24.6 0.9 OE2 A:GLU53 3.5 28.3 1.0 CG A:GLU128 4.2 18.4 1.0 CG A:GLU20 4.2 23.2 1.0 ND1 A:HIS56 4.2 20.9 1.0 OE1 A:GLU94 4.2 22.1 1.0 CG A:GLU53 4.3 21.5 1.0 O A:HOH679 4.3 20.6 1.0 CG A:GLU97 4.4 26.8 1.0 OH A:TYR102 4.6 30.5 1.0 CE2 A:TYR102 4.6 32.2 1.0 CB A:GLU97 4.9 24.4 1.0 CE1 A:HIS56 4.9 19.2 1.0 CB A:GLU53 4.9 16.0 1.0 CD A:GLU94 4.9 24.6 1.0 OE2 A:GLU94 4.9 24.3 1.0 CB A:GLU20 5.0 16.7 1.0

Iron binding site 3 out of 3 in the Rubrerythrin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Rubrerythrin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:17.8 occ:1.00 SG A:CYS161 2.1 14.7 1.0 SG A:CYS158 2.2 13.1 1.0 SG A:CYS174 2.3 19.9 1.0 SG A:CYS177 2.4 18.4 1.0 CB A:CYS174 3.2 16.7 1.0 CB A:CYS158 3.2 12.4 1.0 CB A:CYS161 3.3 17.5 1.0 CB A:CYS177 3.4 16.2 1.0 N A:CYS161 3.7 16.6 1.0 N A:CYS177 3.8 20.1 1.0 CA A:CYS161 4.0 14.1 1.0 CA A:CYS177 4.1 19.2 1.0 CB A:TYR163 4.4 16.5 1.0 CB A:ASN160 4.6 15.5 1.0 CA A:CYS174 4.6 17.1 1.0 CA A:CYS158 4.6 16.0 1.0 C A:CYS161 4.7 14.2 1.0 C A:ASN160 4.7 17.4 1.0 CB A:ALA176 4.7 16.2 1.0 N A:GLY162 4.7 14.3 1.0 N A:TYR163 4.8 17.7 1.0 C A:CYS177 4.8 19.6 1.0 C A:ALA176 4.9 21.4 1.0 N A:ALA178 5.0 19.9 1.0

F.Demare, D.M.Kurtz Jr., P.Nordlund. The Structure of Desulfovibrio Vulgaris Rubrerythrin Reveals A Unique Combination of Rubredoxin-Like FES4 and Ferritin-Like Diiron Domains. Nat.Struct.Biol. V. 3 539 1996.
ISSN: ISSN 1072-8368
PubMed: 8646540
DOI: 10.1038/NSB0696-539