Iron in PDB 1lkp: Crystal Structure of Desulfovibrio Vulgaris Rubrerythrin All-Iron(II) Form, Azide Adduct

The structure of Crystal Structure of Desulfovibrio Vulgaris Rubrerythrin All-Iron(II) Form, Azide Adduct, PDB code: 1lkp 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)	23.37 / 1.64
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	48.344, 80.092, 100.168, 90.00, 90.00, 90.00
R / Rfree (%)	17.8 / 20.2

The binding sites of Iron atom in the Crystal Structure of Desulfovibrio Vulgaris Rubrerythrin All-Iron(II) Form, Azide Adduct (pdb code 1lkp). 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, Azide Adduct, PDB code: 1lkp:
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, Azide Adduct


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, Azide Adduct within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe600 b:10.8 occ:1.00 OE2 A:GLU53 2.0 8.7 1.0 OE1 A:GLU128 2.1 8.3 1.0 OE1 A:GLU94 2.2 9.2 1.0 N3 A:AZI2000 2.2 11.9 1.0 ND1 A:HIS131 2.2 8.7 1.0 OE2 A:GLU94 2.3 10.0 1.0 CD A:GLU94 2.5 10.7 1.0 N2 A:AZI2000 2.9 21.3 1.0 CD A:GLU53 3.0 9.9 1.0 CE1 A:HIS131 3.1 8.2 1.0 CD A:GLU128 3.2 8.9 1.0 OE1 A:GLU53 3.2 10.0 1.0 CG A:HIS131 3.3 8.5 1.0 CB A:HIS131 3.6 8.2 1.0 OE2 A:GLU128 3.8 9.0 1.0 FE A:FE2601 3.9 11.1 1.0 N1 A:AZI2000 3.9 12.8 1.0 OE2 A:GLU97 4.0 19.2 1.0 CG A:GLU94 4.1 10.3 1.0 CA A:GLU128 4.1 8.4 1.0 CB A:GLU128 4.2 8.9 1.0 CG A:GLU128 4.2 8.7 1.0 NE2 A:HIS131 4.3 9.1 1.0 CE2 A:TYR27 4.3 11.0 1.0 CG A:GLU53 4.4 9.8 1.0 CG2 A:THR49 4.4 8.6 1.0 CD2 A:HIS131 4.4 7.8 1.0 OH A:TYR27 4.4 10.5 1.0 CE1 A:HIS56 4.6 9.2 1.0 N A:GLU128 4.9 9.7 1.0 CB A:GLU94 4.9 9.8 1.0 CZ A:TYR27 4.9 11.6 1.0 O A:GLU128 4.9 9.2 1.0 ND1 A:HIS56 5.0 9.7 1.0

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


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, Azide Adduct within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe601 b:11.1 occ:1.00 OE2 A:GLU128 2.1 9.0 1.0 OE1 A:GLU53 2.1 10.0 1.0 OE1 A:GLU20 2.2 11.3 1.0 N1 A:AZI2000 2.2 12.8 1.0 OE2 A:GLU20 2.2 10.8 1.0 ND1 A:HIS56 2.3 9.7 1.0 CD A:GLU20 2.5 12.0 1.0 N2 A:AZI2000 2.7 21.3 1.0 CD A:GLU128 2.9 8.9 1.0 OE1 A:GLU128 3.1 8.3 1.0 CE1 A:HIS56 3.1 9.2 1.0 CD A:GLU53 3.2 9.9 1.0 CG A:HIS56 3.4 7.8 1.0 N3 A:AZI2000 3.7 11.9 1.0 CB A:HIS56 3.7 7.5 1.0 OE2 A:GLU53 3.8 8.7 1.0 FE A:FE2600 3.9 10.8 1.0 CG A:GLU20 4.0 10.6 1.0 CA A:GLU53 4.2 9.2 1.0 CB A:GLU53 4.3 7.5 1.0 CG A:GLU53 4.3 9.8 1.0 NE2 A:HIS56 4.3 9.3 1.0 CG2 A:ILE124 4.3 11.1 1.0 CG A:GLU128 4.3 8.7 1.0 OE2 A:GLU97 4.4 19.2 1.0 CD2 A:HIS56 4.4 9.3 1.0 OH A:TYR102 4.6 21.7 1.0 OE1 A:GLU97 4.6 20.3 1.0 CD A:GLU97 4.8 16.9 1.0 CB A:GLU20 4.8 9.7 1.0 CE2 A:TYR102 4.9 15.0 1.0 O A:GLU53 4.9 8.3 1.0

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


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, Azide Adduct within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:9.8 occ:1.00 SG A:CYS161 2.3 10.3 1.0 SG A:CYS174 2.3 10.7 1.0 SG A:CYS177 2.3 10.0 1.0 SG A:CYS158 2.3 9.7 1.0 CB A:CYS174 3.2 10.2 1.0 CB A:CYS158 3.2 9.4 1.0 CB A:CYS161 3.4 9.6 1.0 CB A:CYS177 3.4 10.8 1.0 N A:CYS177 3.7 10.9 1.0 N A:CYS161 3.8 9.2 1.0 CA A:CYS161 4.1 9.1 1.0 CA A:CYS177 4.1 11.0 1.0 CB A:TYR163 4.3 10.1 1.0 CB A:ASN160 4.5 8.6 1.0 CB A:ALA176 4.6 11.8 1.0 CA A:CYS174 4.6 10.5 1.0 CA A:CYS158 4.7 8.6 1.0 C A:ASN160 4.7 9.3 1.0 C A:CYS161 4.7 9.8 1.0 N A:TYR163 4.7 9.7 1.0 N A:GLY162 4.8 8.7 1.0 C A:ALA176 4.8 10.9 1.0 C A:CYS177 4.8 10.8 1.0 OD1 A:ASN160 4.8 12.0 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