Iron in PDB 6fdr: 7-Fe Ferredoxin From Azotobacter Vinelandii at 100K, Na Dithionite Reduced at pH 8.5, Resolution 1.4 A

The structure of 7-Fe Ferredoxin From Azotobacter Vinelandii at 100K, Na Dithionite Reduced at pH 8.5, Resolution 1.4 A, PDB code: 6fdr was solved by C.G.Schipke, D.B.Goodin, D.E.Mcree, C.D.Stout, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	100.00 / 1.40
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	54.740, 54.740, 93.770, 90.00, 90.00, 90.00
R / Rfree (%)	17.5 / n/a

The binding sites of Iron atom in the 7-Fe Ferredoxin From Azotobacter Vinelandii at 100K, Na Dithionite Reduced at pH 8.5, Resolution 1.4 A (pdb code 6fdr). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 7 binding sites of Iron where determined in the 7-Fe Ferredoxin From Azotobacter Vinelandii at 100K, Na Dithionite Reduced at pH 8.5, Resolution 1.4 A, PDB code: 6fdr:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7;

Iron binding site 1 out of 7 in the 7-Fe Ferredoxin From Azotobacter Vinelandii at 100K, Na Dithionite Reduced at pH 8.5, Resolution 1.4 A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of 7-Fe Ferredoxin From Azotobacter Vinelandii at 100K, Na Dithionite Reduced at pH 8.5, Resolution 1.4 A within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe107 b:11.0 occ:1.00 FE1 A:SF4107 0.0 11.0 1.0 S3 A:SF4107 2.3 9.9 1.0 S2 A:SF4107 2.3 10.9 1.0 SG A:CYS20 2.3 12.1 1.0 S4 A:SF4107 2.3 9.4 1.0 FE3 A:SF4107 2.8 10.9 1.0 FE2 A:SF4107 2.8 10.5 1.0 FE4 A:SF4107 2.8 10.4 1.0 HD2 A:PRO21 3.2 12.8 1.0 HB2 A:CYS20 3.3 15.8 1.0 HA A:CYS20 3.4 13.3 1.0 CB A:CYS20 3.4 13.1 1.0 HE1 A:PHE25 3.4 13.9 1.0 SG A:CYS24 3.5 11.9 1.0 HG23 A:VAL22 3.8 21.6 1.0 CA A:CYS20 3.9 11.1 1.0 S1 A:SF4107 3.9 10.0 1.0 CE1 A:PHE25 4.1 11.6 1.0 CD A:PRO21 4.1 10.6 1.0 HG21 A:VAL22 4.2 21.6 1.0 HB3 A:CYS20 4.2 15.8 1.0 H A:CYS24 4.3 12.1 1.0 H A:VAL22 4.3 14.7 1.0 HD3 A:PRO21 4.4 12.8 1.0 HA A:CYS39 4.4 13.6 1.0 CG2 A:VAL22 4.4 14.4 1.0 HB3 A:CYS45 4.5 13.4 1.0 HD1 A:PHE25 4.6 11.5 1.0 SG A:CYS42 4.6 11.9 1.0 C A:CYS20 4.6 14.6 1.0 CD1 A:PHE25 4.7 9.6 1.0 N A:PRO21 4.7 10.2 1.0 SG A:CYS45 4.8 11.1 1.0 HG22 A:VAL22 4.8 21.6 1.0 H A:ILE40 4.8 10.3 1.0 HZ A:PHE25 4.8 10.7 1.0 CZ A:PHE25 4.9 8.9 1.0 SG A:CYS39 4.9 10.8 1.0 HG12 A:ILE34 5.0 9.7 1.0 HG2 A:PRO21 5.0 20.2 1.0

Iron binding site 2 out of 7 in the 7-Fe Ferredoxin From Azotobacter Vinelandii at 100K, Na Dithionite Reduced at pH 8.5, Resolution 1.4 A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of 7-Fe Ferredoxin From Azotobacter Vinelandii at 100K, Na Dithionite Reduced at pH 8.5, Resolution 1.4 A within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe107 b:10.5 occ:1.00 FE2 A:SF4107 0.0 10.5 1.0 S4 A:SF4107 2.2 9.4 1.0 S3 A:SF4107 2.3 9.9 1.0 SG A:CYS39 2.3 10.8 1.0 S1 A:SF4107 2.3 10.0 1.0 FE1 A:SF4107 2.8 11.0 1.0 FE3 A:SF4107 2.8 10.9 1.0 FE4 A:SF4107 2.8 10.4 1.0 HA A:CYS39 3.2 13.6 1.0 CB A:CYS39 3.4 11.4 1.0 H A:ASP41 3.4 15.2 1.0 H A:ILE40 3.4 10.3 1.0 HB2 A:CYS39 3.5 13.7 1.0 HB2 A:PHE2 3.7 16.5 1.0 CA A:CYS39 3.7 11.3 1.0 S2 A:SF4107 3.9 10.9 1.0 SG A:CYS24 3.9 11.9 1.0 H A:CYS42 4.0 15.0 1.0 HG23 A:ILE34 4.0 19.3 1.0 N A:ILE40 4.0 8.6 1.0 HA A:ASP41 4.1 14.7 1.0 N A:ASP41 4.1 12.7 1.0 H A:PHE2 4.1 16.8 1.0 HG22 A:ILE34 4.2 19.3 1.0 HB3 A:CYS39 4.2 13.7 1.0 C A:CYS39 4.3 10.3 1.0 HD1 A:PHE2 4.4 12.8 1.0 HD11 A:ILE34 4.5 12.0 1.0 CA A:ASP41 4.6 12.2 1.0 CG2 A:ILE34 4.6 12.9 1.0 CB A:PHE2 4.6 13.8 1.0 H A:ALA43 4.6 12.8 1.0 N A:CYS42 4.7 12.5 1.0 SG A:CYS45 4.8 11.1 1.0 CD1 A:PHE2 4.8 10.7 1.0 HG23 A:VAL22 4.8 21.6 1.0 HG12 A:ILE34 4.8 9.7 1.0 SG A:CYS20 4.9 12.1 1.0 N A:PHE2 4.9 14.0 1.0 SG A:CYS42 4.9 11.9 1.0 HG13 A:ILE40 5.0 15.7 1.0 CG A:PHE2 5.0 11.8 1.0 HG12 A:ILE40 5.0 15.7 1.0

Iron binding site 3 out of 7 in the 7-Fe Ferredoxin From Azotobacter Vinelandii at 100K, Na Dithionite Reduced at pH 8.5, Resolution 1.4 A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of 7-Fe Ferredoxin From Azotobacter Vinelandii at 100K, Na Dithionite Reduced at pH 8.5, Resolution 1.4 A within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe107 b:10.9 occ:1.00 FE3 A:SF4107 0.0 10.9 1.0 SG A:CYS42 2.2 11.9 1.0 S2 A:SF4107 2.2 10.9 1.0 S4 A:SF4107 2.3 9.4 1.0 S1 A:SF4107 2.3 10.0 1.0 FE4 A:SF4107 2.7 10.4 1.0 FE1 A:SF4107 2.8 11.0 1.0 FE2 A:SF4107 2.8 10.5 1.0 H A:CYS42 3.0 15.0 1.0 H A:ALA43 3.3 12.8 1.0 HD2 A:PRO21 3.3 12.8 1.0 CB A:CYS42 3.5 13.8 1.0 H A:LEU44 3.5 12.1 1.0 N A:CYS42 3.6 12.5 1.0 HB3 A:CYS42 3.8 16.6 1.0 S3 A:SF4107 3.8 9.9 1.0 N A:ALA43 3.8 10.7 1.0 CA A:CYS42 3.9 14.6 1.0 HD3 A:PRO21 4.0 12.8 1.0 CD A:PRO21 4.1 10.6 1.0 H A:CYS45 4.1 12.2 1.0 HB2 A:LEU44 4.1 13.1 1.0 HG13 A:ILE40 4.2 15.7 1.0 C A:CYS42 4.2 13.6 1.0 N A:LEU44 4.2 10.1 1.0 HA A:CYS20 4.3 13.3 1.0 HB2 A:CYS42 4.3 16.6 1.0 H A:ILE40 4.4 10.3 1.0 H A:ASP41 4.4 15.2 1.0 HG2 A:PRO21 4.5 20.2 1.0 HG12 A:ILE40 4.6 15.7 1.0 C A:ASP41 4.6 17.9 1.0 HA A:ALA43 4.6 14.9 1.0 SG A:CYS45 4.7 11.1 1.0 HA A:ASP41 4.7 14.7 1.0 CG A:PRO21 4.7 16.8 1.0 SG A:CYS20 4.7 12.1 1.0 N A:ASP41 4.7 12.7 1.0 HG3 A:PRO21 4.7 20.2 1.0 CA A:ALA43 4.7 12.4 1.0 SG A:CYS39 4.8 10.8 1.0 HG23 A:VAL22 4.8 21.6 1.0 HB3 A:CYS45 4.8 13.4 1.0 HG A:LEU44 4.8 19.2 1.0 CG1 A:ILE40 4.9 13.1 1.0 HA A:CYS42 4.9 17.5 1.0 N A:CYS45 4.9 10.2 1.0 C A:ALA43 4.9 10.1 1.0 CA A:ASP41 4.9 12.2 1.0 CB A:LEU44 4.9 10.9 1.0

Iron binding site 4 out of 7 in the 7-Fe Ferredoxin From Azotobacter Vinelandii at 100K, Na Dithionite Reduced at pH 8.5, Resolution 1.4 A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of 7-Fe Ferredoxin From Azotobacter Vinelandii at 100K, Na Dithionite Reduced at pH 8.5, Resolution 1.4 A within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe107 b:10.4 occ:1.00 FE4 A:SF4107 0.0 10.4 1.0 SG A:CYS45 2.2 11.1 1.0 S2 A:SF4107 2.2 10.9 1.0 S3 A:SF4107 2.3 9.9 1.0 S1 A:SF4107 2.3 10.0 1.0 FE3 A:SF4107 2.7 10.9 1.0 FE2 A:SF4107 2.8 10.5 1.0 FE1 A:SF4107 2.8 11.0 1.0 HB3 A:CYS45 3.0 13.4 1.0 CB A:CYS45 3.2 11.2 1.0 H A:CYS45 3.3 12.2 1.0 HB2 A:PHE2 3.8 16.5 1.0 S4 A:SF4107 3.9 9.4 1.0 HE1 A:PHE25 3.9 13.9 1.0 HZ A:PHE25 3.9 10.7 1.0 HB2 A:CYS45 3.9 13.4 1.0 N A:CYS45 4.0 10.2 1.0 CA A:CYS45 4.2 10.6 1.0 HD11 A:ILE34 4.3 12.0 1.0 H A:ALA43 4.4 12.8 1.0 CE1 A:PHE25 4.4 11.6 1.0 HD12 A:ILE34 4.4 12.0 1.0 CZ A:PHE25 4.4 8.9 1.0 H A:LEU44 4.5 12.1 1.0 CB A:PHE2 4.5 13.8 1.0 HA A:ALA43 4.6 14.9 1.0 HB3 A:PHE2 4.6 16.5 1.0 SG A:CYS42 4.6 11.9 1.0 HG12 A:ILE34 4.7 9.7 1.0 SG A:CYS39 4.8 10.8 1.0 N A:LEU44 4.8 10.1 1.0 HB2 A:CYS20 4.8 15.8 1.0 CG A:PHE2 4.8 11.8 1.0 CD1 A:ILE34 4.8 8.0 1.0 HD12 A:ILE54 4.8 17.4 1.0 SG A:CYS20 4.9 12.1 1.0 HG23 A:ILE54 4.9 16.5 1.0 HA A:CYS20 4.9 13.3 1.0 H A:GLU46 4.9 16.4 1.0 HA A:CYS45 4.9 12.8 1.0 N A:ALA43 4.9 10.7 1.0

Iron binding site 5 out of 7 in the 7-Fe Ferredoxin From Azotobacter Vinelandii at 100K, Na Dithionite Reduced at pH 8.5, Resolution 1.4 A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of 7-Fe Ferredoxin From Azotobacter Vinelandii at 100K, Na Dithionite Reduced at pH 8.5, Resolution 1.4 A within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe108 b:10.7 occ:1.00 FE1 A:F3S108 0.0 10.7 1.0 S2 A:F3S108 2.2 11.3 1.0 SG A:CYS49 2.3 11.4 1.0 S1 A:F3S108 2.3 12.1 1.0 S3 A:F3S108 2.3 10.2 1.0 FE3 A:F3S108 2.6 11.4 1.0 FE4 A:F3S108 2.7 11.1 1.0 HB2 A:CYS49 3.0 14.4 1.0 CB A:CYS49 3.2 12.0 1.0 HA A:CYS49 3.6 15.3 1.0 HD2 A:PRO50 3.7 16.9 1.0 HB2 A:ALA51 3.7 15.8 1.0 HB2 A:TYR13 3.7 15.1 1.0 S4 A:F3S108 3.8 10.5 1.0 HD2 A:TYR13 3.8 12.2 1.0 H A:ALA51 3.9 17.3 1.0 HB2 A:ALA53 4.0 25.6 1.0 CA A:CYS49 4.0 12.8 1.0 HB3 A:CYS49 4.0 14.4 1.0 H A:TYR13 4.0 14.2 1.0 H A:THR14 4.3 16.1 1.0 HB3 A:CYS16 4.3 15.9 1.0 HB2 A:CYS8 4.4 13.6 1.0 HG13 A:ILE54 4.4 15.1 1.0 CD A:PRO50 4.4 14.1 1.0 HA A:CYS8 4.5 10.5 1.0 H A:ALA53 4.5 12.8 1.0 CB A:ALA51 4.5 10.6 1.0 HD3 A:PRO50 4.5 16.9 1.0 C A:CYS49 4.6 17.9 1.0 HB1 A:ALA51 4.6 15.8 1.0 CB A:TYR13 4.7 12.6 1.0 N A:PRO50 4.7 12.1 1.0 CD2 A:TYR13 4.7 10.2 1.0 H A:CYS16 4.7 17.8 1.0 HD13 A:ILE54 4.7 17.4 1.0 SG A:CYS8 4.7 9.7 1.0 SG A:CYS16 4.7 11.7 1.0 N A:TYR13 4.7 11.8 1.0 N A:ALA51 4.7 14.4 1.0 HB1 A:ALA53 4.7 25.6 1.0 CB A:ALA53 4.8 17.0 1.0 HD11 A:ILE54 4.8 17.4 1.0 H A:ASP15 4.9 16.3 1.0 CB A:CYS8 4.9 11.3 1.0 HG12 A:VAL4 5.0 18.8 1.0 HA A:LYS12 5.0 12.1 1.0

Iron binding site 6 out of 7 in the 7-Fe Ferredoxin From Azotobacter Vinelandii at 100K, Na Dithionite Reduced at pH 8.5, Resolution 1.4 A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of 7-Fe Ferredoxin From Azotobacter Vinelandii at 100K, Na Dithionite Reduced at pH 8.5, Resolution 1.4 A within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe108 b:11.4 occ:1.00 FE3 A:F3S108 0.0 11.4 1.0 S4 A:F3S108 2.2 10.5 1.0 SG A:CYS16 2.3 11.7 1.0 S1 A:F3S108 2.3 12.1 1.0 S3 A:F3S108 2.3 10.2 1.0 FE1 A:F3S108 2.6 10.7 1.0 FE4 A:F3S108 2.7 11.1 1.0 HB3 A:CYS16 3.1 15.9 1.0 H A:THR14 3.3 16.1 1.0 H A:CYS16 3.3 17.8 1.0 HA A:THR14 3.3 19.1 1.0 CB A:CYS16 3.3 13.2 1.0 HD23 A:LEU32 3.6 19.4 1.0 S2 A:F3S108 3.8 11.3 1.0 N A:THR14 3.9 13.4 1.0 CA A:THR14 4.0 15.9 1.0 N A:CYS16 4.0 14.8 1.0 H A:ASP15 4.0 16.3 1.0 HD13 A:ILE54 4.0 17.4 1.0 HB2 A:CYS16 4.0 15.9 1.0 HB2 A:CYS49 4.1 14.4 1.0 HB2 A:LEU32 4.2 13.6 1.0 CA A:CYS16 4.3 11.7 1.0 N A:ASP15 4.3 13.6 1.0 CD2 A:LEU32 4.4 12.9 1.0 HB2 A:TYR13 4.5 15.1 1.0 HD21 A:LEU32 4.5 19.4 1.0 C A:THR14 4.5 12.3 1.0 H A:TYR13 4.5 14.2 1.0 SG A:CYS49 4.6 11.4 1.0 H A:VAL17 4.7 16.8 1.0 HA A:LYS12 4.8 12.1 1.0 HE2 A:PHE25 4.8 14.9 1.0 HD11 A:ILE54 4.8 17.4 1.0 SG A:CYS8 4.8 9.7 1.0 CD1 A:ILE54 4.8 11.6 1.0 HB3 A:LEU32 4.8 13.6 1.0 HG12 A:VAL17 4.8 16.8 1.0 CB A:CYS49 4.8 12.0 1.0 N A:TYR13 4.8 11.8 1.0 HA A:CYS49 4.9 15.3 1.0 CB A:LEU32 4.9 11.3 1.0 HA A:CYS16 5.0 14.0 1.0 HG13 A:ILE54 5.0 15.1 1.0 HG21 A:THR14 5.0 29.5 1.0 C A:TYR13 5.0 12.6 1.0

Iron binding site 7 out of 7 in the 7-Fe Ferredoxin From Azotobacter Vinelandii at 100K, Na Dithionite Reduced at pH 8.5, Resolution 1.4 A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of 7-Fe Ferredoxin From Azotobacter Vinelandii at 100K, Na Dithionite Reduced at pH 8.5, Resolution 1.4 A within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe108 b:11.1 occ:1.00 FE4 A:F3S108 0.0 11.1 1.0 S3 A:F3S108 2.2 10.2 1.0 S2 A:F3S108 2.2 11.3 1.0 S4 A:F3S108 2.2 10.5 1.0 SG A:CYS8 2.3 9.7 1.0 FE1 A:F3S108 2.7 10.7 1.0 FE3 A:F3S108 2.7 11.4 1.0 HA A:LYS12 3.1 12.1 1.0 HB2 A:CYS8 3.1 13.6 1.0 CB A:CYS8 3.2 11.3 1.0 HA A:CYS8 3.5 10.5 1.0 H A:TYR13 3.7 14.2 1.0 HB2 A:LEU32 3.7 13.6 1.0 HG13 A:VAL4 3.9 18.8 1.0 CA A:CYS8 3.9 8.8 1.0 H A:LYS12 4.0 15.3 1.0 CA A:LYS12 4.0 10.1 1.0 S1 A:F3S108 4.0 12.1 1.0 HB3 A:CYS8 4.0 13.6 1.0 H A:THR14 4.0 16.1 1.0 HG12 A:VAL4 4.1 18.8 1.0 N A:TYR13 4.2 11.8 1.0 N A:LYS12 4.3 12.7 1.0 H A:LEU32 4.4 13.1 1.0 CG1 A:VAL4 4.4 12.5 1.0 HB2 A:ALA53 4.5 25.6 1.0 C A:LYS12 4.5 13.6 1.0 HG3 A:LYS12 4.6 14.4 1.0 O A:CYS8 4.6 10.9 1.0 HD23 A:LEU32 4.6 19.4 1.0 CB A:LEU32 4.6 11.3 1.0 SG A:CYS49 4.6 11.4 1.0 C A:CYS8 4.7 7.8 1.0 HB2 A:TYR13 4.8 15.1 1.0 SG A:CYS16 4.8 11.7 1.0 HG11 A:VAL4 4.8 18.8 1.0 HB3 A:LEU32 4.9 13.6 1.0 HD12 A:LEU32 4.9 22.1 1.0 N A:THR14 4.9 13.4 1.0 HB2 A:ALA51 4.9 15.8 1.0 N A:LEU32 5.0 10.9 1.0 HD2 A:TYR13 5.0 12.2 1.0 HA A:THR14 5.0 19.1 1.0

C.G.Schipke, D.B.Goodin, D.E.Mcree, C.D.Stout. Oxidized and Reduced Azotobacter Vinelandii Ferredoxin I at 1.4 A Resolution: Conformational Change of Surface Residues Without Significant Change in the [3FE-4S]+/0 Cluster. Biochemistry V. 38 8228 1999.
ISSN: ISSN 0006-2960
PubMed: 10387068
DOI: 10.1021/BI983008I