Iron in PDB 1pc4: Crystal Structure of the P50A Mutant of Ferredoxin I at 1.65 A Resolution

The structure of Crystal Structure of the P50A Mutant of Ferredoxin I at 1.65 A Resolution, PDB code: 1pc4 was solved by R.Camba, Y.S.Jung, K.Chen, L.M.Hunsicker-Wang, B.K.Burgess, C.D.Stout, J.Hirst, F.A.Armstrong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 1.65
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	55.220, 55.220, 92.720, 90.00, 90.00, 90.00
R / Rfree (%)	15.9 / 23.8

The binding sites of Iron atom in the Crystal Structure of the P50A Mutant of Ferredoxin I at 1.65 A Resolution (pdb code 1pc4). 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 P50A Mutant of Ferredoxin I at 1.65 A Resolution, PDB code: 1pc4:
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 P50A Mutant of Ferredoxin I at 1.65 A Resolution


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 P50A Mutant of Ferredoxin I at 1.65 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe107 b:17.4 occ:1.00 FE1 A:SF4107 0.0 17.4 1.0 S2 A:SF4107 2.3 20.1 1.0 S3 A:SF4107 2.3 20.4 1.0 SG A:CYS39 2.3 21.6 1.0 S4 A:SF4107 2.3 19.5 1.0 FE4 A:SF4107 2.7 17.3 1.0 FE2 A:SF4107 2.7 15.6 1.0 FE3 A:SF4107 2.7 16.4 1.0 CB A:CYS39 3.4 21.8 1.0 CA A:CYS39 3.8 22.7 1.0 SG A:CYS24 3.9 28.7 1.0 S1 A:SF4107 4.0 20.4 1.0 N A:ILE40 4.0 25.3 1.0 N A:ASP41 4.1 23.8 1.0 C A:CYS39 4.3 25.8 1.0 CB A:PHE2 4.5 16.2 1.0 CG2 A:ILE34 4.6 24.4 1.0 N A:CYS42 4.6 23.9 1.0 CA A:ASP41 4.7 21.9 1.0 CD1 A:PHE2 4.8 21.2 1.0 SG A:CYS45 4.8 20.1 1.0 SG A:CYS20 4.9 25.4 1.0 SG A:CYS42 4.9 27.6 1.0 N A:PHE2 4.9 19.6 1.0 C A:ILE40 5.0 23.2 1.0 CG A:PHE2 5.0 18.8 1.0

Iron binding site 2 out of 7 in the Crystal Structure of the P50A Mutant of Ferredoxin I at 1.65 A Resolution


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 P50A Mutant of Ferredoxin I at 1.65 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe107 b:15.6 occ:1.00 FE2 A:SF4107 0.0 15.6 1.0 SG A:CYS42 2.2 27.6 1.0 S4 A:SF4107 2.3 19.5 1.0 S1 A:SF4107 2.4 20.4 1.0 S3 A:SF4107 2.4 20.4 1.0 FE4 A:SF4107 2.7 17.3 1.0 FE3 A:SF4107 2.7 16.4 1.0 FE1 A:SF4107 2.7 17.4 1.0 CB A:CYS42 3.5 24.6 1.0 N A:CYS42 3.6 23.9 1.0 N A:ALA43 3.8 23.3 1.0 S2 A:SF4107 3.9 20.1 1.0 CA A:CYS42 3.9 26.0 1.0 CD A:PRO21 4.1 26.6 1.0 C A:CYS42 4.2 24.7 1.0 N A:LEU44 4.3 22.4 1.0 N A:ASP41 4.6 23.8 1.0 SG A:CYS45 4.7 20.1 1.0 SG A:CYS20 4.7 25.4 1.0 C A:ASP41 4.7 21.1 1.0 SG A:CYS39 4.7 21.6 1.0 CA A:ALA43 4.8 24.2 1.0 CG A:PRO21 4.8 27.5 1.0 N A:CYS45 4.9 23.4 1.0 C A:ALA43 4.9 21.4 1.0 CG1 A:ILE40 4.9 26.0 1.0 N A:ILE40 5.0 25.3 1.0

Iron binding site 3 out of 7 in the Crystal Structure of the P50A Mutant of Ferredoxin I at 1.65 A Resolution


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 P50A Mutant of Ferredoxin I at 1.65 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe107 b:16.4 occ:1.00 FE3 A:SF4107 0.0 16.4 1.0 S1 A:SF4107 2.3 20.4 1.0 SG A:CYS45 2.3 20.1 1.0 S2 A:SF4107 2.3 20.1 1.0 S4 A:SF4107 2.3 19.5 1.0 FE2 A:SF4107 2.7 15.6 1.0 FE1 A:SF4107 2.7 17.4 1.0 FE4 A:SF4107 2.8 17.3 1.0 CB A:CYS45 3.3 21.1 1.0 S3 A:SF4107 4.0 20.4 1.0 N A:CYS45 4.0 23.4 1.0 CE1 A:PHE25 4.3 20.2 1.0 CZ A:PHE25 4.3 20.0 1.0 CA A:CYS45 4.3 20.2 1.0 CB A:PHE2 4.5 16.2 1.0 CD1 A:ILE34 4.6 18.9 1.0 SG A:CYS42 4.6 27.6 1.0 SG A:CYS39 4.7 21.6 1.0 SG A:CYS20 4.8 25.4 1.0 CG A:PHE2 4.8 18.8 1.0 N A:LEU44 4.8 22.4 1.0 N A:ALA43 4.9 23.3 1.0

Iron binding site 4 out of 7 in the Crystal Structure of the P50A Mutant of Ferredoxin I at 1.65 A Resolution


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 P50A Mutant of Ferredoxin I at 1.65 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe107 b:17.3 occ:1.00 FE4 A:SF4107 0.0 17.3 1.0 S2 A:SF4107 2.3 20.1 1.0 SG A:CYS20 2.3 25.4 1.0 S3 A:SF4107 2.4 20.4 1.0 S1 A:SF4107 2.4 20.4 1.0 FE1 A:SF4107 2.7 17.4 1.0 FE2 A:SF4107 2.7 15.6 1.0 FE3 A:SF4107 2.8 16.4 1.0 CB A:CYS20 3.4 26.9 1.0 SG A:CYS24 3.5 28.7 1.0 CA A:CYS20 3.9 29.0 1.0 S4 A:SF4107 3.9 19.5 1.0 CE1 A:PHE25 4.1 20.2 1.0 CD A:PRO21 4.3 26.6 1.0 CG2 A:VAL22 4.4 27.7 1.0 C A:CYS20 4.6 30.9 1.0 SG A:CYS42 4.6 27.6 1.0 CD1 A:PHE25 4.7 23.3 1.0 N A:PRO21 4.7 28.4 1.0 SG A:CYS45 4.8 20.1 1.0 SG A:CYS39 4.9 21.6 1.0 CZ A:PHE25 4.9 20.0 1.0

Iron binding site 5 out of 7 in the Crystal Structure of the P50A Mutant of Ferredoxin I at 1.65 A Resolution


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 P50A Mutant of Ferredoxin I at 1.65 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe108 b:16.9 occ:1.00 FE1 A:F3S108 0.0 16.9 1.0 S3 A:F3S108 2.2 18.1 1.0 SG A:CYS16 2.2 21.6 1.0 S1 A:F3S108 2.3 22.7 1.0 S2 A:F3S108 2.4 22.2 1.0 FE4 A:F3S108 2.7 16.5 1.0 FE3 A:F3S108 2.7 15.4 1.0 CB A:CYS16 3.2 24.0 1.0 S4 A:F3S108 3.9 19.2 1.0 CA A:THR14 4.0 24.0 1.0 N A:THR14 4.0 26.3 1.0 N A:CYS16 4.0 25.0 1.0 CA A:CYS16 4.3 23.2 1.0 CD2 A:LEU32 4.4 20.5 1.0 C A:THR14 4.4 21.6 1.0 N A:ASP15 4.5 23.4 1.0 SG A:CYS49 4.7 24.4 1.0 SG A:CYS8 4.7 21.0 1.0 CB A:CYS49 4.8 18.6 1.0 CD1 A:ILE54 4.8 19.8 1.0 CB A:LEU32 4.8 18.8 1.0

Iron binding site 6 out of 7 in the Crystal Structure of the P50A Mutant of Ferredoxin I at 1.65 A Resolution


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 P50A Mutant of Ferredoxin I at 1.65 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe108 b:15.4 occ:1.00 FE3 A:F3S108 0.0 15.4 1.0 SG A:CYS8 2.2 21.0 1.0 S4 A:F3S108 2.2 19.2 1.0 S1 A:F3S108 2.2 22.7 1.0 S3 A:F3S108 2.3 18.1 1.0 FE4 A:F3S108 2.7 16.5 1.0 FE1 A:F3S108 2.7 16.9 1.0 CB A:CYS8 3.2 20.5 1.0 CA A:CYS8 3.9 20.3 1.0 S2 A:F3S108 3.9 22.2 1.0 CA A:LYS12 4.0 20.4 1.0 N A:TYR13 4.3 22.2 1.0 N A:LYS12 4.4 20.0 1.0 CG1 A:VAL4 4.5 20.0 1.0 CB A:LEU32 4.5 18.8 1.0 O A:CYS8 4.5 19.0 1.0 C A:LYS12 4.6 21.0 1.0 C A:CYS8 4.6 21.1 1.0 SG A:CYS49 4.7 24.4 1.0 SG A:CYS16 4.8 21.6 1.0 N A:THR14 4.9 26.3 1.0

Iron binding site 7 out of 7 in the Crystal Structure of the P50A Mutant of Ferredoxin I at 1.65 A Resolution


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 P50A Mutant of Ferredoxin I at 1.65 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe108 b:16.5 occ:1.00 FE4 A:F3S108 0.0 16.5 1.0 S4 A:F3S108 2.2 19.2 1.0 S2 A:F3S108 2.2 22.2 1.0 SG A:CYS49 2.3 24.4 1.0 S3 A:F3S108 2.3 18.1 1.0 FE3 A:F3S108 2.7 15.4 1.0 FE1 A:F3S108 2.7 16.9 1.0 CB A:CYS49 3.1 18.6 1.0 S1 A:F3S108 3.8 22.7 1.0 CA A:CYS49 3.8 22.7 1.0 C A:CYS49 4.5 24.9 1.0 CD2 A:TYR13 4.5 22.7 1.0 CB A:ALA51 4.6 25.2 1.0 SG A:CYS8 4.7 21.0 1.0 N A:ALA51 4.7 24.2 1.0 SG A:CYS16 4.7 21.6 1.0 N A:ALA50 4.7 24.7 1.0 CB A:TYR13 4.7 21.2 1.0 N A:TYR13 4.8 22.2 1.0 CB A:CYS8 4.8 20.5 1.0 CB A:ALA53 4.9 19.5 1.0 CB A:CYS16 4.9 24.0 1.0

R.Camba, Y.S.Jung, L.M.Hunsicker-Wang, B.K.Burgess, C.D.Stout, J.Hirst, F.A.Armstrong. Mechanisms of Redox-Coupled Proton Transfer in Proteins: Role of the Proximal Proline in Reactions of the [3FE-4S] Cluster in Azotobacter Vinelandii Ferredoxin I Biochemistry V. 42 10589 2003.
ISSN: ISSN 0006-2960
PubMed: 12962482
DOI: 10.1021/BI035021V