Iron in PDB 1ff2: Crystal Structure of the C42D Mutant of Azotobacter Vinelandii 7FE Ferredoxin (Fdi)

The structure of Crystal Structure of the C42D Mutant of Azotobacter Vinelandii 7FE Ferredoxin (Fdi), PDB code: 1ff2 was solved by C.D.Stout, B.K.Burgess, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.80 / 2.30
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	55.300, 55.300, 90.590, 90.00, 90.00, 90.00
R / Rfree (%)	21.7 / 26.9

The binding sites of Iron atom in the Crystal Structure of the C42D Mutant of Azotobacter Vinelandii 7FE Ferredoxin (Fdi) (pdb code 1ff2). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 7 binding sites of Iron where determined in the Crystal Structure of the C42D Mutant of Azotobacter Vinelandii 7FE Ferredoxin (Fdi), PDB code: 1ff2:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7;

Iron binding site 1 out of 7 in the Crystal Structure of the C42D Mutant of Azotobacter Vinelandii 7FE Ferredoxin (Fdi)


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 the C42D Mutant of Azotobacter Vinelandii 7FE Ferredoxin (Fdi) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe107 b:23.0 occ:1.00 FE1 A:SF4107 0.0 23.0 1.0 S2 A:SF4107 2.2 23.7 1.0 S4 A:SF4107 2.2 24.0 1.0 SG A:CYS39 2.3 18.6 1.0 S3 A:SF4107 2.3 23.4 1.0 FE3 A:SF4107 2.7 24.7 1.0 FE4 A:SF4107 2.7 24.4 1.0 FE2 A:SF4107 2.7 26.1 1.0 CB A:CYS39 3.4 20.6 1.0 CA A:CYS39 3.8 19.8 1.0 S1 A:SF4107 3.8 23.9 1.0 N A:ILE40 4.0 20.3 1.0 SG A:CYS24 4.0 18.7 1.0 N A:ASP41 4.1 21.9 1.0 C A:CYS39 4.3 20.5 1.0 CG2 A:ILE34 4.5 12.3 1.0 CB A:PHE2 4.5 22.9 1.0 CA A:ASP41 4.6 23.0 1.0 OD2 A:ASP42 4.7 26.8 1.0 SG A:CYS45 4.7 21.8 1.0 N A:ASP42 4.8 24.4 1.0 SG A:CYS20 4.9 22.5 1.0 CD1 A:PHE2 4.9 21.2 1.0 CG A:PHE2 4.9 22.0 1.0

Iron binding site 2 out of 7 in the Crystal Structure of the C42D Mutant of Azotobacter Vinelandii 7FE Ferredoxin (Fdi)


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 the C42D Mutant of Azotobacter Vinelandii 7FE Ferredoxin (Fdi) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe107 b:26.1 occ:1.00 FE2 A:SF4107 0.0 26.1 1.0 OD2 A:ASP42 2.1 26.8 1.0 S3 A:SF4107 2.3 23.4 1.0 S1 A:SF4107 2.3 23.9 1.0 S4 A:SF4107 2.3 24.0 1.0 FE1 A:SF4107 2.7 23.0 1.0 FE4 A:SF4107 2.7 24.4 1.0 FE3 A:SF4107 2.7 24.7 1.0 CG A:ASP42 2.9 27.2 1.0 OD1 A:ASP42 3.1 29.0 1.0 N A:ASP42 3.6 24.4 1.0 S2 A:SF4107 3.9 23.7 1.0 N A:ALA43 4.0 22.1 1.0 CB A:ASP42 4.1 25.4 1.0 CD A:PRO21 4.1 24.3 1.0 CA A:ASP42 4.2 24.0 1.0 N A:LEU44 4.3 23.7 1.0 CG A:PRO21 4.4 24.5 1.0 C A:ASP42 4.4 23.1 1.0 N A:ASP41 4.6 21.9 1.0 C A:ASP41 4.6 23.9 1.0 SG A:CYS39 4.6 18.6 1.0 CG1 A:ILE40 4.6 17.5 1.0 SG A:CYS45 4.7 21.8 1.0 SG A:CYS20 4.7 22.5 1.0 CB A:LEU44 4.7 25.3 1.0 N A:CYS45 4.8 24.9 1.0 CA A:ASP41 4.8 23.0 1.0 CA A:ALA43 4.9 22.0 1.0 N A:ILE40 4.9 20.3 1.0

Iron binding site 3 out of 7 in the Crystal Structure of the C42D Mutant of Azotobacter Vinelandii 7FE Ferredoxin (Fdi)


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 the C42D Mutant of Azotobacter Vinelandii 7FE Ferredoxin (Fdi) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe107 b:24.7 occ:1.00 FE3 A:SF4107 0.0 24.7 1.0 S1 A:SF4107 2.3 23.9 1.0 S2 A:SF4107 2.3 23.7 1.0 S4 A:SF4107 2.3 24.0 1.0 SG A:CYS45 2.3 21.8 1.0 FE1 A:SF4107 2.7 23.0 1.0 FE4 A:SF4107 2.7 24.4 1.0 FE2 A:SF4107 2.7 26.1 1.0 CB A:CYS45 3.2 23.5 1.0 S3 A:SF4107 3.9 23.4 1.0 N A:CYS45 3.9 24.9 1.0 CA A:CYS45 4.2 24.8 1.0 CE2 A:PHE25 4.3 14.9 1.0 CZ A:PHE25 4.3 17.1 1.0 OD2 A:ASP42 4.4 26.8 1.0 CB A:PHE2 4.6 22.9 1.0 CD1 A:ILE34 4.7 12.4 1.0 SG A:CYS39 4.7 18.6 1.0 SG A:CYS20 4.8 22.5 1.0 N A:LEU44 4.8 23.7 1.0 CG A:PHE2 4.9 22.0 1.0

Iron binding site 4 out of 7 in the Crystal Structure of the C42D Mutant of Azotobacter Vinelandii 7FE Ferredoxin (Fdi)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of the C42D Mutant of Azotobacter Vinelandii 7FE Ferredoxin (Fdi) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe107 b:24.4 occ:1.00 FE4 A:SF4107 0.0 24.4 1.0 S3 A:SF4107 2.3 23.4 1.0 S2 A:SF4107 2.3 23.7 1.0 S1 A:SF4107 2.3 23.9 1.0 SG A:CYS20 2.3 22.5 1.0 FE3 A:SF4107 2.7 24.7 1.0 FE1 A:SF4107 2.7 23.0 1.0 FE2 A:SF4107 2.7 26.1 1.0 CB A:CYS20 3.5 23.1 1.0 SG A:CYS24 3.5 18.7 1.0 S4 A:SF4107 3.9 24.0 1.0 CA A:CYS20 3.9 23.6 1.0 CE2 A:PHE25 4.1 14.9 1.0 CD A:PRO21 4.2 24.3 1.0 CG2 A:VAL22 4.4 23.3 1.0 OD2 A:ASP42 4.6 26.8 1.0 C A:CYS20 4.6 23.5 1.0 CD2 A:PHE25 4.7 16.1 1.0 N A:PRO21 4.7 24.3 1.0 CG A:PRO21 4.8 24.5 1.0 SG A:CYS45 4.8 21.8 1.0 SG A:CYS39 4.8 18.6 1.0 CZ A:PHE25 4.9 17.1 1.0

Iron binding site 5 out of 7 in the Crystal Structure of the C42D Mutant of Azotobacter Vinelandii 7FE Ferredoxin (Fdi)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of the C42D Mutant of Azotobacter Vinelandii 7FE Ferredoxin (Fdi) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe108 b:25.0 occ:1.00 FE1 A:F3S108 0.0 25.0 1.0 S2 A:F3S108 2.2 23.7 1.0 S1 A:F3S108 2.3 22.5 1.0 S3 A:F3S108 2.4 23.1 1.0 SG A:CYS16 2.4 22.6 1.0 FE4 A:F3S108 2.6 23.8 1.0 FE3 A:F3S108 2.7 23.9 1.0 CB A:CYS16 3.1 23.4 1.0 S4 A:F3S108 3.8 23.4 1.0 N A:THR14 3.9 22.8 1.0 N A:CYS16 4.0 23.6 1.0 CA A:THR14 4.0 22.7 1.0 CA A:CYS16 4.2 22.7 1.0 N A:ASP15 4.4 24.4 1.0 C A:THR14 4.5 23.6 1.0 CD1 A:ILE54 4.6 13.5 1.0 CD1 A:LEU32 4.6 16.5 1.0 CG A:LEU32 4.7 18.4 1.0 SG A:CYS49 4.7 23.8 1.0 SG A:CYS8 4.9 19.3 1.0 CB A:LEU32 4.9 16.8 1.0 CB A:CYS49 4.9 22.4 1.0

Iron binding site 6 out of 7 in the Crystal Structure of the C42D Mutant of Azotobacter Vinelandii 7FE Ferredoxin (Fdi)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of the C42D Mutant of Azotobacter Vinelandii 7FE Ferredoxin (Fdi) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe108 b:23.9 occ:1.00 FE3 A:F3S108 0.0 23.9 1.0 S4 A:F3S108 2.2 23.4 1.0 S1 A:F3S108 2.3 22.5 1.0 SG A:CYS8 2.3 19.3 1.0 S3 A:F3S108 2.4 23.1 1.0 FE4 A:F3S108 2.6 23.8 1.0 FE1 A:F3S108 2.7 25.0 1.0 CB A:CYS8 3.3 20.3 1.0 S2 A:F3S108 3.8 23.7 1.0 CA A:LYS12 4.0 19.6 1.0 CA A:CYS8 4.0 17.8 1.0 N A:TYR13 4.4 20.9 1.0 N A:LYS12 4.4 19.4 1.0 CB A:LEU32 4.5 16.8 1.0 C A:LYS12 4.5 20.9 1.0 CG1 A:VAL4 4.6 21.6 1.0 O A:CYS8 4.6 16.1 1.0 CG A:LEU32 4.6 18.4 1.0 C A:CYS8 4.7 18.4 1.0 SG A:CYS49 4.7 23.8 1.0 N A:THR14 4.8 22.8 1.0 SG A:CYS16 4.8 22.6 1.0 N A:LEU32 4.9 16.7 1.0

Iron binding site 7 out of 7 in the Crystal Structure of the C42D Mutant of Azotobacter Vinelandii 7FE Ferredoxin (Fdi)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of the C42D Mutant of Azotobacter Vinelandii 7FE Ferredoxin (Fdi) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe108 b:23.8 occ:1.00 FE4 A:F3S108 0.0 23.8 1.0 S2 A:F3S108 2.3 23.7 1.0 S4 A:F3S108 2.3 23.4 1.0 S3 A:F3S108 2.3 23.1 1.0 SG A:CYS49 2.3 23.8 1.0 FE1 A:F3S108 2.6 25.0 1.0 FE3 A:F3S108 2.6 23.9 1.0 CB A:CYS49 3.3 22.4 1.0 S1 A:F3S108 3.8 22.5 1.0 CA A:CYS49 3.9 22.5 1.0 CD A:PRO50 4.4 21.4 1.0 CB A:ALA51 4.5 18.3 1.0 C A:CYS49 4.6 22.3 1.0 SG A:CYS8 4.6 19.3 1.0 CD2 A:TYR13 4.7 18.6 1.0 N A:PRO50 4.7 21.4 1.0 N A:ALA51 4.8 21.4 1.0 SG A:CYS16 4.8 22.6 1.0 CB A:CYS8 4.8 20.3 1.0 CD1 A:ILE54 4.8 13.5 1.0 CB A:ALA53 4.8 17.0 1.0 CB A:CYS16 4.8 23.4 1.0 CG1 A:ILE54 4.8 16.9 1.0 CB A:TYR13 4.9 19.0 1.0 N A:TYR13 4.9 20.9 1.0

Y.S.Jung, C.A.Bonagura, G.J.Tilley, H.S.Gao-Sheridan, F.A.Armstrong, C.D.Stout, B.K.Burgess. Structure of C42D Azotobacter Vinelandii Fdi. A Cys-X-X-Asp-X-X-Cys Motif Ligates An Air-Stable [4FE-4S]2+/+ Cluster J.Biol.Chem. V. 275 36974 2000.
ISSN: ISSN 0021-9258
PubMed: 10961993
DOI: 10.1074/JBC.M004947200