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

The structure of Crystal Structure of Desulfovibrio Vulgaris Rubrerythrin All-Iron(III) Form, PDB code: 1lkm 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)	25.95 / 1.69
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	48.877, 80.609, 100.084, 90.00, 90.00, 90.00
R / Rfree (%)	19 / 21

The binding sites of Iron atom in the Crystal Structure of Desulfovibrio Vulgaris Rubrerythrin All-Iron(III) Form (pdb code 1lkm). 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(III) Form, PDB code: 1lkm:
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(III) 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(III) Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe600 b:18.4 occ:1.00 OE2 A:GLU53 2.0 18.9 1.0 O A:HOH1232 2.1 18.2 1.0 OE1 A:GLU128 2.1 18.3 1.0 OE2 A:GLU94 2.2 17.6 1.0 ND1 A:HIS131 2.2 14.8 1.0 OE1 A:GLU94 2.2 15.9 1.0 CD A:GLU94 2.5 17.7 1.0 CD A:GLU128 3.0 18.1 1.0 CD A:GLU53 3.0 18.5 1.0 CE1 A:HIS131 3.1 13.8 1.0 OE1 A:GLU53 3.3 21.0 1.0 CG A:HIS131 3.3 14.3 1.0 FE A:FE601 3.3 19.9 1.0 OE2 A:GLU128 3.4 19.7 1.0 CB A:HIS131 3.7 13.5 1.0 CG A:GLU94 4.1 16.5 1.0 CA A:GLU128 4.2 14.2 1.0 CG A:GLU128 4.2 14.7 1.0 NE2 A:HIS131 4.3 15.2 1.0 CB A:GLU128 4.3 15.7 1.0 CG A:GLU53 4.3 16.9 1.0 CD2 A:HIS131 4.4 14.9 1.0 OE2 A:GLU97 4.4 30.7 1.0 CG2 A:THR49 4.4 12.1 1.0 CE2 A:TYR27 4.5 16.8 1.0 OE1 A:GLU97 4.6 24.5 1.0 OH A:TYR27 4.6 18.3 1.0 CD A:GLU97 4.8 25.9 1.0 CE1 A:HIS56 4.9 18.6 1.0 CB A:GLU94 4.9 15.5 1.0 ND1 A:HIS56 4.9 21.1 1.0 N A:GLU128 5.0 15.7 1.0 O A:GLU128 5.0 14.5 1.0

Iron binding site 2 out of 3 in the Crystal Structure of Desulfovibrio Vulgaris Rubrerythrin All-Iron(III) 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(III) Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe601 b:19.9 occ:1.00 O A:HOH1232 1.8 18.2 1.0 OE2 A:GLU128 2.0 19.7 1.0 OE1 A:GLU97 2.1 24.5 1.0 OE1 A:GLU20 2.1 19.9 1.0 OE1 A:GLU53 2.2 21.0 1.0 OE2 A:GLU20 2.3 18.4 1.0 CD A:GLU20 2.5 18.3 1.0 CD A:GLU128 3.0 18.1 1.0 CD A:GLU97 3.0 25.9 1.0 CD A:GLU53 3.2 18.5 1.0 OE2 A:GLU97 3.3 30.7 1.0 FE A:FE600 3.3 18.4 1.0 OE1 A:GLU128 3.4 18.3 1.0 OE2 A:GLU53 3.5 18.9 1.0 CG A:GLU20 4.0 17.2 1.0 O A:HOH1106 4.2 37.5 1.0 CG A:GLU128 4.2 14.7 1.0 ND1 A:HIS56 4.2 21.1 1.0 CG A:GLU97 4.4 22.1 1.0 CG A:GLU53 4.4 16.9 1.0 OE1 A:GLU94 4.5 15.9 1.0 OH A:TYR102 4.5 19.0 1.0 CE2 A:TYR102 4.6 18.1 1.0 OE2 A:GLU94 4.7 17.6 1.0 CB A:GLU20 4.8 16.2 1.0 CB A:GLU97 4.8 18.1 1.0 CB A:GLU53 4.9 14.4 1.0 CD A:GLU94 4.9 17.7 1.0 CA A:GLU20 5.0 15.0 1.0 CE1 A:HIS56 5.0 18.6 1.0

Iron binding site 3 out of 3 in the Crystal Structure of Desulfovibrio Vulgaris Rubrerythrin All-Iron(III) 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(III) Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:14.3 occ:1.00 SG A:CYS161 2.3 15.2 1.0 SG A:CYS177 2.3 15.1 1.0 SG A:CYS174 2.3 14.5 1.0 SG A:CYS158 2.4 14.9 1.0 CB A:CYS174 3.2 15.9 1.0 CB A:CYS158 3.2 13.7 1.0 CB A:CYS161 3.4 13.5 1.0 CB A:CYS177 3.4 15.9 1.0 N A:CYS177 3.7 15.7 1.0 N A:CYS161 3.8 13.7 1.0 CA A:CYS161 4.1 14.4 1.0 CA A:CYS177 4.1 15.8 1.0 CB A:TYR163 4.3 14.7 1.0 CB A:ASN160 4.5 14.1 1.0 CB A:ALA176 4.6 14.4 1.0 CA A:CYS174 4.6 15.4 1.0 CA A:CYS158 4.7 13.3 1.0 C A:ASN160 4.7 14.2 1.0 N A:TYR163 4.7 15.0 1.0 C A:CYS161 4.7 12.9 1.0 N A:GLY162 4.8 13.4 1.0 C A:CYS177 4.8 15.6 1.0 C A:ALA176 4.8 17.2 1.0 OD1 A:ASN160 4.9 16.1 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