Iron in PDB 1lko: Crystal Structure of Desulfovibrio Vulgaris Rubrerythrin All-Iron(II) Form

The structure of Crystal Structure of Desulfovibrio Vulgaris Rubrerythrin All-Iron(II) Form, PDB code: 1lko was solved by S.Jin, D.M.Kurtz Jr., Z.J.Liu, J.Rose, B.C.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.75 / 1.63
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	48.518, 79.952, 100.066, 90.00, 90.00, 90.00
R / Rfree (%)	18.3 / 20.4

The binding sites of Iron atom in the Crystal Structure of Desulfovibrio Vulgaris Rubrerythrin All-Iron(II) Form (pdb code 1lko). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 3 binding sites of Iron where determined in the Crystal Structure of Desulfovibrio Vulgaris Rubrerythrin All-Iron(II) Form, PDB code: 1lko:
Jump to Iron binding site number: 1; 2; 3;

Iron binding site 1 out of 3 in the Crystal Structure of Desulfovibrio Vulgaris Rubrerythrin All-Iron(II) Form


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 Desulfovibrio Vulgaris Rubrerythrin All-Iron(II) Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe600 b:12.1 occ:1.00 OE2 A:GLU53 2.0 11.4 1.0 OE1 A:GLU128 2.1 10.2 1.0 ND1 A:HIS131 2.2 10.8 1.0 O A:HOH623 2.2 14.0 1.0 OE1 A:GLU94 2.2 10.2 1.0 OE2 A:GLU94 2.3 12.2 1.0 CD A:GLU94 2.6 12.0 1.0 CD A:GLU53 2.9 11.9 1.0 CE1 A:HIS131 3.1 9.7 1.0 OE1 A:GLU53 3.2 11.2 1.0 CD A:GLU128 3.2 10.9 1.0 CG A:HIS131 3.2 9.9 1.0 CB A:HIS131 3.6 10.4 1.0 OE2 A:GLU128 3.8 10.8 1.0 FE A:FE2601 3.9 12.5 1.0 O A:HOH752 4.0 15.6 1.0 OE2 A:GLU97 4.0 17.9 1.0 CG A:GLU94 4.1 11.4 1.0 CA A:GLU128 4.1 10.6 1.0 NE2 A:HIS131 4.2 11.5 1.0 CB A:GLU128 4.3 11.3 1.0 CE2 A:TYR27 4.3 12.5 1.0 CG A:GLU128 4.3 9.2 1.0 CG2 A:THR49 4.3 10.1 1.0 CD2 A:HIS131 4.3 10.5 1.0 CG A:GLU53 4.4 12.5 1.0 OH A:TYR27 4.4 12.7 1.0 CE1 A:HIS56 4.6 10.2 1.0 CZ A:TYR27 4.9 13.3 1.0 CB A:GLU94 4.9 11.1 1.0 N A:GLU128 4.9 11.3 1.0 O A:GLU128 4.9 10.0 1.0 ND1 A:HIS56 4.9 10.7 1.0

Iron binding site 2 out of 3 in the Crystal Structure of Desulfovibrio Vulgaris Rubrerythrin All-Iron(II) Form


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 Desulfovibrio Vulgaris Rubrerythrin All-Iron(II) Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe601 b:12.5 occ:1.00 OE2 A:GLU128 2.1 10.8 1.0 OE1 A:GLU53 2.1 11.2 1.0 OE1 A:GLU20 2.2 12.5 1.0 O A:HOH752 2.2 15.6 1.0 ND1 A:HIS56 2.3 10.7 1.0 OE2 A:GLU20 2.3 11.8 1.0 CD A:GLU20 2.6 14.2 1.0 CD A:GLU128 3.0 10.9 1.0 CE1 A:HIS56 3.1 10.2 1.0 OE1 A:GLU128 3.2 10.2 1.0 CD A:GLU53 3.2 11.9 1.0 CG A:HIS56 3.3 10.4 1.0 CB A:HIS56 3.7 10.1 1.0 O A:HOH623 3.8 14.0 1.0 OE2 A:GLU53 3.9 11.4 1.0 FE A:FE2600 3.9 12.1 1.0 CG A:GLU20 4.1 11.9 1.0 CA A:GLU53 4.2 10.1 1.0 CB A:GLU53 4.2 8.8 1.0 CG A:GLU53 4.3 12.5 1.0 NE2 A:HIS56 4.3 9.6 1.0 CG2 A:ILE124 4.3 12.1 1.0 CG A:GLU128 4.4 9.2 1.0 CD2 A:HIS56 4.4 10.4 1.0 OE2 A:GLU97 4.4 17.9 1.0 OH A:TYR102 4.6 21.2 1.0 OE1 A:GLU97 4.6 19.6 1.0 CD A:GLU97 4.8 18.0 1.0 CB A:GLU20 4.8 11.0 1.0 CE2 A:TYR102 4.9 15.6 1.0 O A:GLU53 4.9 10.0 1.0

Iron binding site 3 out of 3 in the Crystal Structure of Desulfovibrio Vulgaris Rubrerythrin All-Iron(II) Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of Desulfovibrio Vulgaris Rubrerythrin All-Iron(II) Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:12.0 occ:1.00 SG A:CYS161 2.3 11.2 1.0 SG A:CYS174 2.3 11.9 1.0 SG A:CYS158 2.3 10.7 1.0 SG A:CYS177 2.3 11.3 1.0 CB A:CYS174 3.1 12.6 1.0 CB A:CYS158 3.2 11.8 1.0 CB A:CYS177 3.4 13.3 1.0 CB A:CYS161 3.4 10.3 1.0 N A:CYS177 3.8 13.2 1.0 N A:CYS161 3.8 10.5 1.0 CA A:CYS161 4.1 11.2 1.0 CA A:CYS177 4.1 12.9 1.0 CB A:TYR163 4.3 11.9 1.0 CB A:ASN160 4.5 11.0 1.0 CB A:ALA176 4.6 13.8 1.0 CA A:CYS174 4.6 11.7 1.0 CA A:CYS158 4.7 10.2 1.0 C A:ASN160 4.7 11.0 1.0 N A:TYR163 4.7 11.9 1.0 C A:CYS161 4.7 11.0 1.0 N A:GLY162 4.8 10.4 1.0 C A:ALA176 4.8 12.4 1.0 C A:CYS177 4.8 12.2 1.0 OD1 A:ASN160 4.9 13.3 1.0

S.Jin, D.M.Kurtz Jr., Z.J.Liu, J.Rose, B.C.Wang. X-Ray Crystal Structures of Reduced Rubrerythrin and Its Azide Adduct: A Structure-Based Mechanism For A Non-Heme Diiron Peroxidase J.Am.Chem.Soc. V. 124 9845 2002.
ISSN: ISSN 0002-7863
PubMed: 12175244
DOI: 10.1021/JA026587U