Iron in PDB 1fer: Structure at pH 6.5 of Ferredoxin I From Azotobacter Vinelandii at 2.3 Angstroms Resolution

The structure of Structure at pH 6.5 of Ferredoxin I From Azotobacter Vinelandii at 2.3 Angstroms Resolution, PDB code: 1fer was solved by E.A.Merritt, G.H.Stout, S.Turley, L.C.Sieker, L.H.Jensen, W.H.Orme-Johnson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	N/A / 2.30
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	55.550, 55.550, 95.650, 90.00, 90.00, 90.00
R / Rfree (%)	17 / n/a

The binding sites of Iron atom in the Structure at pH 6.5 of Ferredoxin I From Azotobacter Vinelandii at 2.3 Angstroms Resolution (pdb code 1fer). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 7 binding sites of Iron where determined in the Structure at pH 6.5 of Ferredoxin I From Azotobacter Vinelandii at 2.3 Angstroms Resolution, PDB code: 1fer:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7;

Iron binding site 1 out of 7 in the Structure at pH 6.5 of Ferredoxin I From Azotobacter Vinelandii at 2.3 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure at pH 6.5 of Ferredoxin I From Azotobacter Vinelandii at 2.3 Angstroms Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe107 b:11.8 occ:1.00 FE1 A:F3S107 0.0 11.8 1.0 S2 A:F3S107 2.2 13.2 1.0 SG A:CYS8 2.2 12.6 1.0 S3 A:F3S107 2.3 13.7 1.0 S1 A:F3S107 2.3 14.4 1.0 FE4 A:F3S107 2.6 13.1 1.0 FE3 A:F3S107 2.7 14.1 1.0 CB A:CYS8 3.2 9.3 1.0 S4 A:F3S107 3.8 15.1 1.0 CA A:CYS8 3.9 12.4 1.0 CA A:LYS12 4.1 12.8 1.0 N A:TYR13 4.3 14.5 1.0 CG1 A:VAL4 4.4 3.3 1.0 N A:LYS12 4.4 11.4 1.0 C A:LYS12 4.6 14.5 1.0 O A:CYS8 4.6 15.3 1.0 SG A:CYS49 4.7 15.1 1.0 C A:CYS8 4.7 13.3 1.0 CB A:LEU32 4.7 12.8 1.0 SG A:CYS16 4.8 16.4 1.0 N A:THR14 4.9 13.2 1.0 N A:LEU32 5.0 13.8 1.0

Iron binding site 2 out of 7 in the Structure at pH 6.5 of Ferredoxin I From Azotobacter Vinelandii at 2.3 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure at pH 6.5 of Ferredoxin I From Azotobacter Vinelandii at 2.3 Angstroms Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe107 b:14.1 occ:1.00 FE3 A:F3S107 0.0 14.1 1.0 S4 A:F3S107 2.2 15.1 1.0 SG A:CYS16 2.2 16.4 1.0 S3 A:F3S107 2.3 13.7 1.0 S1 A:F3S107 2.3 14.4 1.0 FE4 A:F3S107 2.7 13.1 1.0 FE1 A:F3S107 2.7 11.8 1.0 CB A:CYS16 3.3 14.0 1.0 S2 A:F3S107 3.9 13.2 1.0 N A:CYS16 4.0 17.9 1.0 N A:THR14 4.1 13.2 1.0 CA A:THR14 4.1 15.5 1.0 CA A:CYS16 4.3 14.0 1.0 CD2 A:LEU32 4.4 14.0 1.0 N A:ASP15 4.5 20.5 1.0 CD1 A:ILE54 4.5 9.6 1.0 C A:THR14 4.6 16.9 1.0 SG A:CYS49 4.7 15.1 1.0 SG A:CYS8 4.7 12.6 1.0 CB A:LEU32 4.9 12.8 1.0 CE2 A:PHE25 4.9 11.3 1.0 CB A:CYS49 5.0 15.4 1.0

Iron binding site 3 out of 7 in the Structure at pH 6.5 of Ferredoxin I From Azotobacter Vinelandii at 2.3 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure at pH 6.5 of Ferredoxin I From Azotobacter Vinelandii at 2.3 Angstroms Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe107 b:13.1 occ:1.00 FE4 A:F3S107 0.0 13.1 1.0 S3 A:F3S107 2.2 13.7 1.0 S2 A:F3S107 2.2 13.2 1.0 S4 A:F3S107 2.3 15.1 1.0 SG A:CYS49 2.3 15.1 1.0 FE1 A:F3S107 2.6 11.8 1.0 FE3 A:F3S107 2.7 14.1 1.0 CB A:CYS49 3.3 15.4 1.0 CA A:CYS49 3.8 18.6 1.0 S1 A:F3S107 3.8 14.4 1.0 CD A:PRO50 4.3 17.4 1.0 C A:CYS49 4.5 18.5 1.0 CB A:ALA51 4.6 17.7 1.0 N A:PRO50 4.6 18.1 1.0 SG A:CYS8 4.7 12.6 1.0 SG A:CYS16 4.7 16.4 1.0 N A:ALA51 4.7 20.0 1.0 CB A:ALA53 4.7 16.1 1.0 CB A:TYR13 4.8 12.8 1.0 CB A:CYS8 4.9 9.3 1.0 N A:TYR13 4.9 14.5 1.0 CD2 A:TYR13 4.9 13.6 1.0 CD1 A:ILE54 4.9 9.6 1.0 N A:CYS49 5.0 21.5 1.0 CG1 A:ILE54 5.0 9.8 1.0 CB A:CYS16 5.0 14.0 1.0

Iron binding site 4 out of 7 in the Structure at pH 6.5 of Ferredoxin I From Azotobacter Vinelandii at 2.3 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure at pH 6.5 of Ferredoxin I From Azotobacter Vinelandii at 2.3 Angstroms Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe108 b:15.3 occ:1.00 FE1 A:SF4108 0.0 15.3 1.0 S3 A:SF4108 2.2 14.3 1.0 S4 A:SF4108 2.2 14.1 1.0 S2 A:SF4108 2.2 15.4 1.0 SG A:CYS45 2.3 13.2 1.0 FE2 A:SF4108 2.6 14.2 1.0 FE3 A:SF4108 2.7 15.6 1.0 FE4 A:SF4108 2.8 16.1 1.0 CB A:CYS45 3.4 14.0 1.0 S1 A:SF4108 3.8 14.0 1.0 N A:CYS45 4.1 17.5 1.0 CA A:CYS45 4.3 15.2 1.0 CB A:PHE2 4.4 13.7 1.0 CD1 A:ILE34 4.5 8.6 1.0 CZ A:PHE25 4.5 12.3 1.0 CE1 A:PHE25 4.5 13.1 1.0 SG A:CYS39 4.6 14.1 1.0 SG A:CYS42 4.6 19.8 1.0 CG A:PHE2 4.7 13.8 1.0 N A:LEU44 4.9 17.0 1.0 SG A:CYS20 4.9 16.5 1.0 N A:ALA43 4.9 17.6 1.0

Iron binding site 5 out of 7 in the Structure at pH 6.5 of Ferredoxin I From Azotobacter Vinelandii at 2.3 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Structure at pH 6.5 of Ferredoxin I From Azotobacter Vinelandii at 2.3 Angstroms Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe108 b:14.2 occ:1.00 FE2 A:SF4108 0.0 14.2 1.0 S3 A:SF4108 2.2 14.3 1.0 SG A:CYS39 2.2 14.1 1.0 S1 A:SF4108 2.3 14.0 1.0 S4 A:SF4108 2.3 14.1 1.0 FE1 A:SF4108 2.6 15.3 1.0 FE4 A:SF4108 2.7 16.1 1.0 FE3 A:SF4108 2.7 15.6 1.0 CB A:CYS39 3.4 13.4 1.0 S2 A:SF4108 3.8 15.4 1.0 CA A:CYS39 3.9 16.5 1.0 SG A:CYS24 4.0 17.1 1.0 N A:ILE40 4.1 18.8 1.0 N A:ASP41 4.1 19.4 1.0 C A:CYS39 4.4 15.8 1.0 CB A:PHE2 4.5 13.7 1.0 CG2 A:ILE34 4.5 6.4 1.0 CA A:ASP41 4.6 21.0 1.0 SG A:CYS45 4.7 13.2 1.0 N A:CYS42 4.7 21.4 1.0 CD1 A:PHE2 4.7 15.3 1.0 SG A:CYS20 4.8 16.5 1.0 CG A:PHE2 4.9 13.8 1.0 N A:PHE2 4.9 12.4 1.0 SG A:CYS42 4.9 19.8 1.0 CD1 A:ILE34 4.9 8.6 1.0

Iron binding site 6 out of 7 in the Structure at pH 6.5 of Ferredoxin I From Azotobacter Vinelandii at 2.3 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Structure at pH 6.5 of Ferredoxin I From Azotobacter Vinelandii at 2.3 Angstroms Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe108 b:15.6 occ:1.00 FE3 A:SF4108 0.0 15.6 1.0 S2 A:SF4108 2.2 15.4 1.0 S1 A:SF4108 2.2 14.0 1.0 S4 A:SF4108 2.3 14.1 1.0 SG A:CYS42 2.3 19.8 1.0 FE4 A:SF4108 2.7 16.1 1.0 FE1 A:SF4108 2.7 15.3 1.0 FE2 A:SF4108 2.7 14.2 1.0 CB A:CYS42 3.5 17.4 1.0 N A:CYS42 3.6 21.4 1.0 S3 A:SF4108 3.8 14.3 1.0 CA A:CYS42 4.0 19.0 1.0 N A:ALA43 4.0 17.6 1.0 CD A:PRO21 4.1 17.1 1.0 C A:CYS42 4.3 18.8 1.0 N A:LEU44 4.4 17.0 1.0 CG A:PRO21 4.5 17.9 1.0 SG A:CYS20 4.6 16.5 1.0 C A:ASP41 4.6 22.4 1.0 SG A:CYS39 4.6 14.1 1.0 SG A:CYS45 4.7 13.2 1.0 CG1 A:ILE40 4.7 19.1 1.0 N A:ASP41 4.7 19.4 1.0 CB A:LEU44 4.9 16.5 1.0 CA A:ALA43 4.9 16.4 1.0 CA A:ASP41 4.9 21.0 1.0 N A:CYS45 5.0 17.5 1.0 CA A:CYS20 5.0 20.6 1.0

Iron binding site 7 out of 7 in the Structure at pH 6.5 of Ferredoxin I From Azotobacter Vinelandii at 2.3 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Structure at pH 6.5 of Ferredoxin I From Azotobacter Vinelandii at 2.3 Angstroms Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe108 b:16.1 occ:1.00 FE4 A:SF4108 0.0 16.1 1.0 S3 A:SF4108 2.3 14.3 1.0 S1 A:SF4108 2.3 14.0 1.0 S2 A:SF4108 2.3 15.4 1.0 SG A:CYS20 2.3 16.5 1.0 FE3 A:SF4108 2.7 15.6 1.0 FE2 A:SF4108 2.7 14.2 1.0 FE1 A:SF4108 2.8 15.3 1.0 CB A:CYS20 3.4 18.7 1.0 SG A:CYS24 3.5 17.1 1.0 CA A:CYS20 3.8 20.6 1.0 S4 A:SF4108 3.9 14.1 1.0 CE1 A:PHE25 4.2 13.1 1.0 CD A:PRO21 4.2 17.1 1.0 CG2 A:VAL22 4.4 14.5 1.0 C A:CYS20 4.6 22.5 1.0 SG A:CYS42 4.6 19.8 1.0 N A:PRO21 4.6 19.9 1.0 SG A:CYS45 4.8 13.2 1.0 SG A:CYS39 4.8 14.1 1.0 CD1 A:PHE25 4.9 14.5 1.0 N A:CYS20 4.9 20.8 1.0 CZ A:PHE25 5.0 12.3 1.0

E.A.Merritt, G.H.Stout, S.Turley, L.C.Sieker, L.H.Jehsen, W.H.Orme-Johnson. Structure at pH 6.5 of Ferredoxin I From Azotobacter Vinelandii at 2.3 A Resolution. Acta Crystallogr.,Sect.D V. 49 272 1993.
ISSN: ISSN 0907-4449
PubMed: 15299532
DOI: 10.1107/S0907444992007248