Iron in PDB 2rdv: Rubredoxin From Desulfovibrio Vulgaris Miyazaki F, Monoclinic Crystal Form

The structure of Rubredoxin From Desulfovibrio Vulgaris Miyazaki F, Monoclinic Crystal Form, PDB code: 2rdv was solved by Y.Higuchi, N.Yasuoka, 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	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	27.300, 44.900, 51.200, 90.00, 90.60, 90.00
R / Rfree (%)	17.5 / 21.6

The binding sites of Iron atom in the Rubredoxin From Desulfovibrio Vulgaris Miyazaki F, Monoclinic Crystal Form (pdb code 2rdv). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 3 binding sites of Iron where determined in the Rubredoxin From Desulfovibrio Vulgaris Miyazaki F, Monoclinic Crystal Form, PDB code: 2rdv:
Jump to Iron binding site number: 1; 2; 3;

Iron binding site 1 out of 3 in the Rubredoxin From Desulfovibrio Vulgaris Miyazaki F, Monoclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Rubredoxin From Desulfovibrio Vulgaris Miyazaki F, Monoclinic Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe53 b:6.8 occ:1.00 SG A:CYS39 2.3 6.4 1.0 SG A:CYS6 2.3 6.2 1.0 SG A:CYS9 2.3 7.0 1.0 SG A:CYS42 2.3 9.7 1.0 CB A:CYS6 3.3 4.4 1.0 CB A:CYS39 3.3 2.0 1.0 CB A:CYS42 3.4 5.8 1.0 CB A:CYS9 3.4 4.6 1.0 N A:CYS9 3.8 6.6 1.0 N A:CYS42 3.9 9.3 1.0 CA A:CYS42 4.2 6.0 1.0 CA A:CYS9 4.2 7.6 1.0 CB A:TYR11 4.4 10.4 1.0 CB A:ALA44 4.4 4.6 1.0 CB A:VAL8 4.5 8.4 1.0 CA A:CYS6 4.6 4.9 1.0 CA A:CYS39 4.7 5.9 1.0 C A:VAL8 4.8 9.4 1.0 C A:ILE41 4.8 12.7 1.0 N A:TYR11 4.8 9.5 1.0 C A:CYS42 4.9 5.2 1.0 C A:CYS9 4.9 9.8 1.0 CB A:ILE41 4.9 15.8 1.0 N A:GLY43 4.9 5.7 1.0 N A:GLY10 4.9 8.9 1.0 N A:ALA44 4.9 8.3 1.0 CA A:VAL8 5.0 8.2 1.0 C A:CYS6 5.0 7.4 1.0 CG2 A:ILE41 5.0 15.6 1.0

Iron binding site 2 out of 3 in the Rubredoxin From Desulfovibrio Vulgaris Miyazaki F, Monoclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Rubredoxin From Desulfovibrio Vulgaris Miyazaki F, Monoclinic Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe53 b:8.5 occ:1.00 SG B:CYS39 2.3 7.5 1.0 SG B:CYS42 2.3 13.1 1.0 SG B:CYS6 2.3 9.2 1.0 SG B:CYS9 2.3 10.7 1.0 CB B:CYS39 3.3 4.1 1.0 CB B:CYS6 3.3 9.3 1.0 CB B:CYS42 3.4 10.1 1.0 CB B:CYS9 3.4 10.6 1.0 N B:CYS9 3.7 12.5 1.0 N B:CYS42 3.8 11.8 1.0 CA B:CYS9 4.1 12.6 1.0 CA B:CYS42 4.2 10.0 1.0 CB B:TYR11 4.3 3.5 1.0 CB B:ALA44 4.4 10.4 1.0 CB B:VAL8 4.4 15.4 1.0 CB B:ILE41 4.5 16.7 1.0 C B:ILE41 4.6 13.3 1.0 C B:VAL8 4.7 14.4 1.0 CA B:CYS39 4.7 5.9 1.0 CA B:CYS6 4.7 11.5 1.0 N B:TYR11 4.8 10.0 1.0 C B:CYS9 4.8 13.2 1.0 N B:GLY10 4.8 11.8 1.0 C B:CYS42 4.8 9.8 1.0 CA B:VAL8 4.9 14.5 1.0 N B:ILE41 4.9 10.3 1.0 CA B:ILE41 5.0 12.2 1.0 N B:ALA44 5.0 7.3 1.0 N B:GLY43 5.0 7.2 1.0

Iron binding site 3 out of 3 in the Rubredoxin From Desulfovibrio Vulgaris Miyazaki F, Monoclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Rubredoxin From Desulfovibrio Vulgaris Miyazaki F, Monoclinic Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe53 b:7.1 occ:1.00 SG C:CYS42 2.3 6.9 1.0 SG C:CYS9 2.3 8.3 1.0 SG C:CYS39 2.3 6.8 1.0 SG C:CYS6 2.3 5.2 1.0 CB C:CYS39 3.3 7.3 1.0 CB C:CYS6 3.3 3.6 1.0 CB C:CYS42 3.4 7.0 1.0 CB C:CYS9 3.4 8.6 1.0 N C:CYS9 3.8 5.7 1.0 N C:CYS42 4.0 6.8 1.0 CA C:CYS9 4.1 7.7 1.0 CA C:CYS42 4.2 7.3 1.0 CB C:TYR11 4.4 4.1 1.0 CB C:VAL8 4.6 4.9 1.0 CA C:CYS39 4.7 9.1 1.0 CA C:CYS6 4.7 5.0 1.0 C C:VAL8 4.7 7.7 1.0 CB C:ALA44 4.8 8.4 1.0 C C:ILE41 4.8 7.9 1.0 C C:CYS9 4.8 8.6 1.0 C C:CYS42 4.8 7.2 1.0 N C:TYR11 4.8 4.5 1.0 CB C:ILE41 4.8 7.9 1.0 N C:GLY43 4.9 7.0 1.0 N C:GLY10 5.0 7.3 1.0

S.Misaki, Y.Morimoto, M.Ogata, T.Yagi, Y.Higuchi, N.Yasuoka. Structure Determination of Rubredoxin From Desulfovibrio Vulgaris Miyazaki F in Two Crystal Forms. Acta Crystallogr.,Sect.D V. 55 408 1999.
ISSN: ISSN 0907-4449
PubMed: 10089348
DOI: 10.1107/S0907444998011810