Iron in PDB 6vjv: Crystal Structure of the Prochlorococcus Phage (Myovirus P-SSM2) Ferredoxin at 1.6 Angstroms

The structure of Crystal Structure of the Prochlorococcus Phage (Myovirus P-SSM2) Ferredoxin at 1.6 Angstroms, PDB code: 6vjv was solved by J.L.Olmos Jr., I.J.Campbell, M.D.Miller, W.Xu, D.Kahanda, J.T.Atkinson, N.Sparks, G.N.Bennett, J.J.Silberg, G.N.Phillips Jr., with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.06 / 1.59
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	52.619, 31.446, 61.288, 90.00, 92.48, 90.00
R / Rfree (%)	17.8 / 21.3

The structure of Crystal Structure of the Prochlorococcus Phage (Myovirus P-SSM2) Ferredoxin at 1.6 Angstroms also contains other interesting chemical elements:

Zinc

(Zn)

15 atoms

The binding sites of Iron atom in the Crystal Structure of the Prochlorococcus Phage (Myovirus P-SSM2) Ferredoxin at 1.6 Angstroms (pdb code 6vjv). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of the Prochlorococcus Phage (Myovirus P-SSM2) Ferredoxin at 1.6 Angstroms, PDB code: 6vjv:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of the Prochlorococcus Phage (Myovirus P-SSM2) Ferredoxin at 1.6 Angstroms


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 Prochlorococcus Phage (Myovirus P-SSM2) Ferredoxin at 1.6 Angstroms within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe101 b:17.7 occ:1.00 FE1 A:FES101 0.0 17.7 1.0 S1 A:FES101 2.2 18.4 1.0 S2 A:FES101 2.2 18.5 1.0 SG A:CYS78 2.3 17.4 1.0 SG A:CYS48 2.3 16.5 1.0 FE2 A:FES101 2.8 19.5 1.0 HB3 A:CYS78 2.9 22.3 1.0 HB3 A:CYS48 3.2 15.7 1.0 CB A:CYS78 3.2 18.6 1.0 HB3 A:LEU76 3.4 22.1 1.0 CB A:CYS48 3.4 13.1 1.0 H A:CYS78 3.5 18.7 1.0 H A:GLY43 3.5 24.4 1.0 H A:CYS48 3.5 20.4 1.0 HA A:ARG41 3.7 25.7 1.0 HB2 A:CYS78 3.9 22.3 1.0 H A:ARG41 3.9 24.6 1.0 HA2 A:GLY43 3.9 23.9 1.0 HD22 A:LEU76 4.0 22.4 1.0 HB2 A:CYS48 4.0 15.7 1.0 N A:CYS78 4.2 15.6 1.0 N A:CYS48 4.2 17.0 1.0 N A:GLY43 4.3 20.3 1.0 H A:ALA42 4.3 25.5 1.0 CA A:CYS78 4.3 14.4 1.0 CB A:LEU76 4.3 18.4 1.0 SG A:CYS40 4.4 21.2 1.0 CA A:CYS48 4.4 13.3 1.0 N A:ARG41 4.4 20.5 1.0 CA A:ARG41 4.5 21.4 1.0 HD13 A:LEU76 4.5 21.2 1.0 H A:CYS45 4.5 26.4 1.0 H A:SER39 4.6 24.4 1.0 CA A:GLY43 4.6 19.9 1.0 HA A:LEU76 4.7 16.6 1.0 SG A:CYS45 4.7 20.1 1.0 HB2 A:SER38 4.7 22.4 1.0 H A:ALA47 4.7 20.8 1.0 N A:ALA42 4.7 21.2 1.0 HA A:SER38 4.8 22.3 1.0 CD2 A:LEU76 4.8 18.7 1.0 HB2 A:LEU76 4.9 22.1 1.0 C A:ARG41 4.9 23.5 1.0 CA A:LEU76 4.9 13.8 1.0 HB3 A:ALA47 4.9 22.8 1.0 H A:ALA44 4.9 27.0 1.0 C A:LEU76 4.9 15.3 1.0 H A:LEU77 4.9 16.9 1.0 H A:CYS40 5.0 26.4 1.0

Iron binding site 2 out of 4 in the Crystal Structure of the Prochlorococcus Phage (Myovirus P-SSM2) Ferredoxin at 1.6 Angstroms


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 Prochlorococcus Phage (Myovirus P-SSM2) Ferredoxin at 1.6 Angstroms within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe101 b:19.5 occ:1.00 FE2 A:FES101 0.0 19.5 1.0 S1 A:FES101 2.2 18.4 1.0 S2 A:FES101 2.3 18.5 1.0 SG A:CYS45 2.3 20.1 1.0 SG A:CYS40 2.3 21.2 1.0 FE1 A:FES101 2.8 17.7 1.0 H A:CYS40 2.8 26.4 1.0 H A:CYS45 2.9 26.4 1.0 H A:ARG41 3.2 24.6 1.0 CB A:CYS45 3.4 26.1 1.0 N A:CYS45 3.5 22.0 1.0 N A:CYS40 3.5 22.1 1.0 CB A:CYS40 3.5 23.6 1.0 HB3 A:CYS45 3.5 31.3 1.0 HB3 A:CYS40 3.6 28.3 1.0 H A:ALA47 3.6 20.8 1.0 H A:ALA42 3.7 25.5 1.0 H A:ALA44 3.7 27.0 1.0 N A:ARG41 3.8 20.5 1.0 H A:GLY43 3.8 24.4 1.0 CA A:CYS45 3.8 22.5 1.0 H A:SER39 3.8 24.4 1.0 CA A:CYS40 3.9 24.5 1.0 C A:CYS45 4.0 24.3 1.0 HB3 A:SER39 4.0 27.8 1.0 HB3 A:ALA47 4.0 22.8 1.0 H A:CYS48 4.2 20.4 1.0 C A:CYS40 4.2 22.6 1.0 HB2 A:CYS45 4.3 31.3 1.0 O A:CYS45 4.3 23.5 1.0 N A:ALA44 4.3 22.5 1.0 HB2 A:CYS40 4.4 28.3 1.0 N A:ALA47 4.4 17.3 1.0 HA A:ARG41 4.4 25.7 1.0 SG A:CYS78 4.4 17.4 1.0 N A:GLY43 4.4 20.3 1.0 N A:SER46 4.5 24.1 1.0 N A:ALA42 4.5 21.2 1.0 C A:ALA44 4.5 24.6 1.0 C A:SER39 4.5 22.7 1.0 N A:SER39 4.6 20.3 1.0 HA2 A:GLY43 4.6 23.9 1.0 SG A:CYS48 4.6 16.5 1.0 CA A:ARG41 4.7 21.4 1.0 H A:SER46 4.7 29.0 1.0 HA A:CYS45 4.7 27.0 1.0 CB A:ALA47 4.8 19.0 1.0 HB2 A:ALA47 4.9 22.8 1.0 HA A:CYS40 4.9 29.4 1.0 CB A:SER39 4.9 23.2 1.0 CA A:GLY43 4.9 19.9 1.0 CA A:SER39 4.9 25.4 1.0 HD22 A:LEU76 4.9 22.4 1.0 HD13 A:LEU76 4.9 21.2 1.0 HB3 A:CYS48 4.9 15.7 1.0 C A:GLY43 5.0 24.6 1.0 N A:CYS48 5.0 17.0 1.0 CA A:ALA44 5.0 25.0 1.0

Iron binding site 3 out of 4 in the Crystal Structure of the Prochlorococcus Phage (Myovirus P-SSM2) Ferredoxin at 1.6 Angstroms


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 Prochlorococcus Phage (Myovirus P-SSM2) Ferredoxin at 1.6 Angstroms within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe101 b:28.2 occ:0.52 FE1 B:FES101 0.0 28.2 0.5 ZN B:ZN110 1.4 34.9 0.5 O B:HOH260 2.0 33.5 0.5 SG B:CYS78 2.1 44.1 0.5 S1 B:FES101 2.2 35.2 0.5 S2 B:FES101 2.2 37.5 0.5 SG B:CYS78 2.2 44.4 0.5 SG B:CYS48 2.3 40.0 0.5 O B:HOH216 2.6 34.6 0.5 SG B:CYS48 2.8 52.6 0.5 FE2 B:FES101 2.9 34.7 0.5 HB3 B:LEU76 3.0 51.9 1.0 HB3 B:CYS78 3.0 48.3 0.5 HB3 B:CYS78 3.1 48.3 0.5 HB3 B:CYS48 3.3 45.5 0.5 CB B:CYS78 3.3 40.3 0.5 CB B:CYS78 3.3 40.2 0.5 O B:HOH207 3.4 35.6 0.5 O B:HOH206 3.4 31.7 0.5 H B:CYS78 3.4 41.7 0.5 H B:CYS78 3.4 41.7 0.5 H B:GLY43 3.4 69.8 1.0 CB B:CYS48 3.4 37.9 0.5 HD22 B:LEU76 3.6 55.1 1.0 H B:CYS48 3.6 50.7 0.5 H B:CYS48 3.6 50.8 0.5 HA B:ARG41 3.7 84.7 1.0 HB2 B:CYS48 3.7 44.8 0.5 H B:ARG41 3.8 84.5 1.0 HA2 B:GLY43 3.8 69.1 1.0 CB B:CYS48 3.9 37.3 0.5 CB B:LEU76 3.9 43.2 1.0 HB2 B:CYS78 3.9 48.3 0.5 HB2 B:CYS78 3.9 48.3 0.5 HB2 B:CYS48 4.0 45.5 0.5 N B:CYS78 4.1 34.8 0.5 N B:CYS78 4.2 34.8 0.5 N B:GLY43 4.2 58.2 1.0 H B:ALA42 4.3 87.1 1.0 CA B:CYS78 4.3 36.4 0.5 CA B:CYS78 4.3 36.4 0.5 HA B:LEU76 4.3 46.5 1.0 N B:CYS48 4.3 42.3 0.5 N B:CYS48 4.3 42.3 0.5 CA B:ARG41 4.4 70.5 1.0 N B:ARG41 4.4 70.4 1.0 HB2 B:LEU76 4.4 51.9 1.0 CD2 B:LEU76 4.4 45.9 1.0 SG B:CYS40 4.4 62.2 0.5 CA B:GLY43 4.5 57.6 1.0 O B:CYS45 4.5 65.8 0.5 CA B:CYS48 4.5 38.1 0.5 CA B:LEU76 4.5 38.8 1.0 O B:CYS45 4.6 66.0 0.5 H B:CYS45 4.6 84.5 0.5 H B:CYS45 4.6 84.5 0.5 HD12 B:LEU76 4.6 62.1 1.0 CA B:CYS48 4.6 37.9 0.5 CG B:LEU76 4.6 46.5 1.0 HB3 B:CYS48 4.6 44.8 0.5 N B:ALA42 4.7 72.6 1.0 C B:LEU76 4.7 35.9 1.0 HD13 B:LEU76 4.7 62.1 1.0 SG B:CYS40 4.7 63.6 0.5 H B:SER39 4.7 86.6 1.0 HG22 B:VAL79 4.8 54.2 1.0 SG B:CYS45 4.8 74.2 0.5 H B:VAL79 4.8 45.4 1.0 SG B:CYS45 4.8 70.2 0.5 C B:ARG41 4.8 69.6 1.0 HB2 B:SER38 4.8 65.5 1.0 H B:ALA44 4.8 84.2 1.0 H B:LEU77 4.8 39.9 1.0 N B:LEU77 4.9 33.2 1.0 CD1 B:LEU76 4.9 51.8 1.0 HD23 B:LEU76 4.9 55.1 1.0 HB3 B:ALA47 4.9 62.6 1.0 H B:ALA47 5.0 61.7 1.0

Iron binding site 4 out of 4 in the Crystal Structure of the Prochlorococcus Phage (Myovirus P-SSM2) Ferredoxin at 1.6 Angstroms


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 Prochlorococcus Phage (Myovirus P-SSM2) Ferredoxin at 1.6 Angstroms within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe101 b:34.7 occ:0.52 FE2 B:FES101 0.0 34.7 0.5 O B:HOH260 1.2 33.5 0.5 O B:HOH206 1.4 31.7 0.5 S2 B:FES101 2.1 37.5 0.5 SG B:CYS45 2.2 74.2 0.5 S1 B:FES101 2.2 35.2 0.5 SG B:CYS45 2.3 70.2 0.5 SG B:CYS40 2.3 62.2 0.5 SG B:CYS40 2.4 63.6 0.5 HG B:CYS45 2.8 89.1 0.5 ZN B:ZN110 2.9 34.9 0.5 FE1 B:FES101 2.9 28.2 0.5 H B:ARG41 2.9 84.5 1.0 H B:CYS40 2.9 76.4 0.5 H B:CYS40 3.0 76.4 0.5 HG B:CYS40 3.0 76.4 0.5 O B:HOH216 3.1 34.6 0.5 H B:CYS45 3.1 84.5 0.5 H B:CYS45 3.1 84.5 0.5 O B:HOH207 3.3 35.6 0.5 HB3 B:CYS40 3.4 80.5 0.5 CB B:CYS40 3.4 67.1 0.5 CB B:CYS45 3.5 75.5 0.5 CB B:CYS45 3.5 75.5 0.5 N B:CYS45 3.5 70.4 0.5 N B:CYS45 3.5 70.4 0.5 H B:ALA42 3.5 87.1 1.0 H B:ALA44 3.5 84.2 1.0 N B:CYS40 3.5 63.7 0.5 N B:ARG41 3.5 70.4 1.0 N B:CYS40 3.5 63.7 0.5 CB B:CYS40 3.6 68.0 0.5 HB3 B:CYS45 3.7 90.5 0.5 HB3 B:CYS45 3.8 90.5 0.5 CA B:CYS45 3.8 72.8 0.5 HB3 B:CYS40 3.8 81.6 0.5 CA B:CYS45 3.8 72.8 0.5 H B:ALA47 3.9 61.7 1.0 CA B:CYS40 3.9 65.9 0.5 H B:GLY43 3.9 69.8 1.0 O B:CYS45 3.9 65.8 0.5 H B:SER39 3.9 86.6 1.0 C B:CYS45 3.9 68.3 0.5 C B:CYS45 3.9 68.4 0.5 CA B:CYS40 3.9 66.0 0.5 O B:CYS45 4.0 66.0 0.5 HB3 B:SER39 4.0 0.1 1.0 C B:CYS40 4.1 61.5 0.5 C B:CYS40 4.1 61.5 0.5 N B:ALA44 4.2 70.1 1.0 HB3 B:ALA47 4.2 62.6 1.0 HB2 B:CYS40 4.2 80.5 0.5 HB2 B:CYS45 4.2 90.5 0.5 HA B:ARG41 4.2 84.7 1.0 H B:CYS48 4.3 50.7 0.5 SG B:CYS48 4.3 52.6 0.5 HB2 B:CYS45 4.3 90.5 0.5 N B:ALA42 4.3 72.6 1.0 H B:CYS48 4.3 50.8 0.5 C B:ALA44 4.3 75.3 1.0 SG B:CYS78 4.4 44.1 0.5 SG B:CYS78 4.4 44.4 0.5 HB2 B:CYS40 4.4 81.6 0.5 N B:GLY43 4.4 58.2 1.0 CA B:ARG41 4.4 70.5 1.0 HB2 B:ALA47 4.5 62.6 1.0 C B:SER39 4.6 77.6 1.0 N B:ALA47 4.6 51.4 1.0 N B:SER46 4.6 68.0 1.0 N B:SER39 4.7 72.1 1.0 HA2 B:GLY43 4.7 69.1 1.0 SG B:CYS48 4.7 40.0 0.5 HA B:CYS45 4.8 87.4 0.5 CB B:ALA47 4.8 52.2 1.0 HA B:CYS45 4.8 87.4 0.5 HA B:CYS40 4.8 79.1 0.5 HD22 B:LEU76 4.8 55.1 1.0 CA B:ALA44 4.9 74.8 1.0 C B:GLY43 4.9 62.2 1.0 CA B:GLY43 4.9 57.6 1.0 HA B:CYS40 4.9 79.2 0.5 H B:SER46 4.9 81.6 1.0 CB B:SER39 4.9 84.2 1.0 C B:ARG41 4.9 69.6 1.0 CA B:SER39 5.0 79.2 1.0 HB3 B:CYS48 5.0 45.5 0.5

I.J.Campbell, J.L.Olmos Jr., W.Xu, D.Kahanda, J.T.Atkinson, N.Sparks, M.D.Miller, G.N.Phillips Jr., G.N.Bennett, J.J.Silberg. Prochlorococcus Phage Ferredoxin: Structural Characterization and Interactions with Cyanobacterial Sulfite Reductases To Be Published.