Iron in PDB 1fdd: Azotobacter Vinelandii Ferredoxin I: Aspartate 15 Facilitates Proton Transfer to the Reduced [3FE-4S] Cluster

The structure of Azotobacter Vinelandii Ferredoxin I: Aspartate 15 Facilitates Proton Transfer to the Reduced [3FE-4S] Cluster, PDB code: 1fdd was solved by C.D.Stout, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 1.90
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	55.600, 55.600, 95.900, 90.00, 90.00, 90.00
R / Rfree (%)	20.7 / n/a

The binding sites of Iron atom in the Azotobacter Vinelandii Ferredoxin I: Aspartate 15 Facilitates Proton Transfer to the Reduced [3FE-4S] Cluster (pdb code 1fdd). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 7 binding sites of Iron where determined in the Azotobacter Vinelandii Ferredoxin I: Aspartate 15 Facilitates Proton Transfer to the Reduced [3FE-4S] Cluster, PDB code: 1fdd:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7;

Iron binding site 1 out of 7 in the Azotobacter Vinelandii Ferredoxin I: Aspartate 15 Facilitates Proton Transfer to the Reduced [3FE-4S] Cluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Azotobacter Vinelandii Ferredoxin I: Aspartate 15 Facilitates Proton Transfer to the Reduced [3FE-4S] Cluster within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe107 b:14.3 occ:1.00 FE1 A:SF4107 0.0 14.3 1.0 S4 A:SF4107 2.3 14.9 1.0 S2 A:SF4107 2.3 15.4 1.0 S3 A:SF4107 2.3 14.8 1.0 SG A:CYS39 2.3 12.6 1.0 FE3 A:SF4107 2.7 14.1 1.0 FE2 A:SF4107 2.7 16.4 1.0 FE4 A:SF4107 2.7 16.7 1.0 CB A:CYS39 3.3 11.2 1.0 CA A:CYS39 3.8 11.9 1.0 S1 A:SF4107 3.8 13.6 1.0 SG A:CYS24 4.0 14.2 1.0 N A:ASP41 4.1 12.1 1.0 N A:ILE40 4.1 13.5 1.0 C A:CYS39 4.4 13.4 1.0 CB A:PHE2 4.4 11.8 1.0 CA A:ASP41 4.6 14.2 1.0 CG2 A:ILE34 4.7 6.3 1.0 CD1 A:PHE2 4.7 15.4 1.0 N A:CYS42 4.7 14.9 1.0 SG A:CYS45 4.8 14.0 1.0 CG A:PHE2 4.8 13.4 1.0 SG A:CYS20 4.9 14.3 1.0 SG A:CYS42 4.9 15.0 1.0 N A:PHE2 5.0 11.7 1.0 C A:ILE40 5.0 14.2 1.0

Iron binding site 2 out of 7 in the Azotobacter Vinelandii Ferredoxin I: Aspartate 15 Facilitates Proton Transfer to the Reduced [3FE-4S] Cluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Azotobacter Vinelandii Ferredoxin I: Aspartate 15 Facilitates Proton Transfer to the Reduced [3FE-4S] Cluster within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe107 b:16.4 occ:1.00 FE2 A:SF4107 0.0 16.4 1.0 S3 A:SF4107 2.3 14.8 1.0 S1 A:SF4107 2.3 13.6 1.0 S4 A:SF4107 2.3 14.9 1.0 SG A:CYS42 2.3 15.0 1.0 FE3 A:SF4107 2.7 14.1 1.0 FE1 A:SF4107 2.7 14.3 1.0 FE4 A:SF4107 2.7 16.7 1.0 CB A:CYS42 3.6 15.0 1.0 N A:CYS42 3.6 14.9 1.0 S2 A:SF4107 3.9 15.4 1.0 N A:ALA43 3.9 12.7 1.0 CA A:CYS42 4.0 15.2 1.0 CD A:PRO21 4.1 14.0 1.0 N A:LEU44 4.2 13.4 1.0 C A:CYS42 4.2 13.3 1.0 CB A:LEU44 4.6 14.7 1.0 SG A:CYS45 4.6 14.0 1.0 C A:ASP41 4.6 14.9 1.0 SG A:CYS39 4.7 12.6 1.0 CG A:PRO21 4.7 12.8 1.0 N A:ASP41 4.7 12.1 1.0 CA A:ALA43 4.8 12.6 1.0 SG A:CYS20 4.8 14.3 1.0 CG1 A:ILE40 4.8 14.0 1.0 N A:CYS45 4.9 14.7 1.0 C A:ALA43 4.9 13.4 1.0 CA A:ASP41 4.9 14.2 1.0 CA A:LEU44 5.0 15.7 1.0

Iron binding site 3 out of 7 in the Azotobacter Vinelandii Ferredoxin I: Aspartate 15 Facilitates Proton Transfer to the Reduced [3FE-4S] Cluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Azotobacter Vinelandii Ferredoxin I: Aspartate 15 Facilitates Proton Transfer to the Reduced [3FE-4S] Cluster within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe107 b:14.1 occ:1.00 FE3 A:SF4107 0.0 14.1 1.0 S4 A:SF4107 2.3 14.9 1.0 S1 A:SF4107 2.3 13.6 1.0 SG A:CYS45 2.3 14.0 1.0 S2 A:SF4107 2.3 15.4 1.0 FE1 A:SF4107 2.7 14.3 1.0 FE2 A:SF4107 2.7 16.4 1.0 FE4 A:SF4107 2.8 16.7 1.0 CB A:CYS45 3.3 13.2 1.0 S3 A:SF4107 3.9 14.8 1.0 N A:CYS45 4.0 14.7 1.0 CA A:CYS45 4.3 13.5 1.0 CE1 A:PHE25 4.4 10.3 1.0 CB A:PHE2 4.4 11.8 1.0 CZ A:PHE25 4.4 9.7 1.0 CG A:PHE2 4.6 13.4 1.0 SG A:CYS42 4.7 15.0 1.0 SG A:CYS39 4.7 12.6 1.0 CD1 A:ILE34 4.7 8.4 1.0 N A:LEU44 4.7 13.4 1.0 SG A:CYS20 4.9 14.3 1.0 N A:ALA43 5.0 12.7 1.0

Iron binding site 4 out of 7 in the Azotobacter Vinelandii Ferredoxin I: Aspartate 15 Facilitates Proton Transfer to the Reduced [3FE-4S] Cluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Azotobacter Vinelandii Ferredoxin I: Aspartate 15 Facilitates Proton Transfer to the Reduced [3FE-4S] Cluster within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe107 b:16.7 occ:1.00 FE4 A:SF4107 0.0 16.7 1.0 S1 A:SF4107 2.3 13.6 1.0 S2 A:SF4107 2.3 15.4 1.0 S3 A:SF4107 2.3 14.8 1.0 SG A:CYS20 2.3 14.3 1.0 FE1 A:SF4107 2.7 14.3 1.0 FE2 A:SF4107 2.7 16.4 1.0 FE3 A:SF4107 2.8 14.1 1.0 CB A:CYS20 3.4 15.0 1.0 SG A:CYS24 3.5 14.2 1.0 CA A:CYS20 3.7 15.5 1.0 S4 A:SF4107 3.9 14.9 1.0 CE1 A:PHE25 4.1 10.3 1.0 CD A:PRO21 4.3 14.0 1.0 C A:CYS20 4.5 17.0 1.0 CG2 A:VAL22 4.5 11.1 1.0 N A:PRO21 4.6 14.4 1.0 SG A:CYS42 4.7 15.0 1.0 CD1 A:PHE25 4.8 10.9 1.0 SG A:CYS45 4.8 14.0 1.0 N A:CYS20 4.9 16.6 1.0 SG A:CYS39 4.9 12.6 1.0 CZ A:PHE25 4.9 9.7 1.0

Iron binding site 5 out of 7 in the Azotobacter Vinelandii Ferredoxin I: Aspartate 15 Facilitates Proton Transfer to the Reduced [3FE-4S] Cluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Azotobacter Vinelandii Ferredoxin I: Aspartate 15 Facilitates Proton Transfer to the Reduced [3FE-4S] Cluster within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe108 b:15.4 occ:1.00 FE1 A:F3S108 0.0 15.4 1.0 S2 A:F3S108 2.2 14.9 1.0 SG A:CYS16 2.3 15.0 1.0 S3 A:F3S108 2.3 13.2 1.0 S1 A:F3S108 2.3 13.7 1.0 FE4 A:F3S108 2.6 14.4 1.0 FE3 A:F3S108 2.7 14.4 1.0 CB A:CYS16 3.3 13.6 1.0 S4 A:F3S108 3.9 13.6 1.0 N A:CYS16 4.0 14.2 1.0 CA A:THR14 4.1 14.3 1.0 N A:THR14 4.1 13.8 1.0 CA A:CYS16 4.3 13.2 1.0 C A:THR14 4.5 13.6 1.0 CD1 A:LEU32 4.5 14.2 1.0 N A:ASN15 4.6 14.8 1.0 SG A:CYS49 4.7 13.8 1.0 CG A:LEU32 4.7 14.4 1.0 CD1 A:ILE54 4.7 9.9 1.0 SG A:CYS8 4.8 10.2 1.0 CB A:LEU32 5.0 10.8 1.0 CE2 A:PHE25 5.0 9.7 1.0

Iron binding site 6 out of 7 in the Azotobacter Vinelandii Ferredoxin I: Aspartate 15 Facilitates Proton Transfer to the Reduced [3FE-4S] Cluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Azotobacter Vinelandii Ferredoxin I: Aspartate 15 Facilitates Proton Transfer to the Reduced [3FE-4S] Cluster within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe108 b:14.4 occ:1.00 FE3 A:F3S108 0.0 14.4 1.0 S1 A:F3S108 2.3 13.7 1.0 S4 A:F3S108 2.3 13.6 1.0 SG A:CYS8 2.3 10.2 1.0 S3 A:F3S108 2.3 13.2 1.0 FE4 A:F3S108 2.6 14.4 1.0 FE1 A:F3S108 2.7 15.4 1.0 CB A:CYS8 3.2 7.5 1.0 S2 A:F3S108 3.9 14.9 1.0 CA A:CYS8 3.9 9.5 1.0 CA A:LYS12 4.1 13.0 1.0 N A:TYR13 4.4 14.1 1.0 N A:LYS12 4.4 13.1 1.0 CG1 A:VAL4 4.5 6.8 1.0 O A:CYS8 4.6 12.4 1.0 SG A:CYS49 4.6 13.8 1.0 C A:LYS12 4.7 12.6 1.0 C A:CYS8 4.7 12.3 1.0 CB A:LEU32 4.7 10.8 1.0 CG A:LEU32 4.8 14.4 1.0 SG A:CYS16 4.8 15.0 1.0 N A:LEU32 5.0 7.4 1.0 N A:THR14 5.0 13.8 1.0

Iron binding site 7 out of 7 in the Azotobacter Vinelandii Ferredoxin I: Aspartate 15 Facilitates Proton Transfer to the Reduced [3FE-4S] Cluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Azotobacter Vinelandii Ferredoxin I: Aspartate 15 Facilitates Proton Transfer to the Reduced [3FE-4S] Cluster within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe108 b:14.4 occ:1.00 FE4 A:F3S108 0.0 14.4 1.0 S4 A:F3S108 2.3 13.6 1.0 SG A:CYS49 2.3 13.8 1.0 S2 A:F3S108 2.3 14.9 1.0 S3 A:F3S108 2.3 13.2 1.0 FE1 A:F3S108 2.6 15.4 1.0 FE3 A:F3S108 2.6 14.4 1.0 CB A:CYS49 3.3 12.9 1.0 S1 A:F3S108 3.9 13.7 1.0 CA A:CYS49 3.9 14.4 1.0 CD A:PRO50 4.4 13.8 1.0 C A:CYS49 4.6 14.3 1.0 CB A:ALA51 4.6 15.0 1.0 SG A:CYS16 4.7 15.0 1.0 SG A:CYS8 4.7 10.2 1.0 N A:ALA51 4.7 15.1 1.0 CB A:ALA53 4.7 9.2 1.0 N A:PRO50 4.7 15.0 1.0 CD2 A:TYR13 4.8 11.1 1.0 CB A:CYS8 4.9 7.5 1.0 CB A:TYR13 4.9 12.0 1.0 CB A:CYS16 4.9 13.6 1.0 N A:TYR13 5.0 14.1 1.0

B.Shen, L.L.Martin, J.N.Butt, F.A.Armstrong, C.D.Stout, G.M.Jensen, P.J.Stephens, G.N.La Mar, C.M.Gorst, B.K.Burgess. Azotobacter Vinelandii Ferredoxin I. Aspartate 15 Facilitates Proton Transfer to the Reduced [3FE-4S] Cluster. J.Biol.Chem. V. 268 25928 1993.
ISSN: ISSN 0021-9258
PubMed: 8245026