Iron in PDB 1vf5: Crystal Structure of Cytochrome B6F Complex From M.Laminosus

The structure of Crystal Structure of Cytochrome B6F Complex From M.Laminosus, PDB code: 1vf5 was solved by G.Kurisu, H.Zhang, J.L.Smith, W.A.Cramer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.16 / 3.00
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	157.536, 157.536, 360.347, 90.00, 90.00, 120.00
R / Rfree (%)	25.8 / 34.6

The structure of Crystal Structure of Cytochrome B6F Complex From M.Laminosus also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Iron atom in the Crystal Structure of Cytochrome B6F Complex From M.Laminosus (pdb code 1vf5). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 12 binding sites of Iron where determined in the Crystal Structure of Cytochrome B6F Complex From M.Laminosus, PDB code: 1vf5:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 12 in the Crystal Structure of Cytochrome B6F Complex From M.Laminosus


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 Cytochrome B6F Complex From M.Laminosus within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:45.1 occ:1.00 FE A:HEM301 0.0 45.1 1.0 ND A:HEM301 2.0 46.0 1.0 NB A:HEM301 2.0 46.0 1.0 NA A:HEM301 2.1 46.0 1.0 NC A:HEM301 2.1 46.0 1.0 NE2 A:HIS86 2.1 28.8 1.0 NE2 A:HIS187 2.3 50.3 1.0 CE1 A:HIS86 2.9 28.8 1.0 C4D A:HEM301 3.0 46.0 1.0 C4B A:HEM301 3.0 46.0 1.0 C1B A:HEM301 3.1 46.0 1.0 C4A A:HEM301 3.1 46.0 1.0 C1C A:HEM301 3.1 46.0 1.0 C4C A:HEM301 3.1 46.0 1.0 C1D A:HEM301 3.1 46.0 1.0 C1A A:HEM301 3.1 46.0 1.0 CD2 A:HIS187 3.2 50.3 1.0 CD2 A:HIS86 3.2 28.8 1.0 CE1 A:HIS187 3.3 50.3 1.0 CHC A:HEM301 3.4 46.0 1.0 CHB A:HEM301 3.4 46.0 1.0 CHA A:HEM301 3.4 46.0 1.0 CHD A:HEM301 3.5 46.0 1.0 ND1 A:HIS86 4.1 28.8 1.0 CG A:HIS86 4.3 28.8 1.0 C2B A:HEM301 4.3 46.0 1.0 C3D A:HEM301 4.3 46.0 1.0 C3B A:HEM301 4.3 46.0 1.0 C2C A:HEM301 4.3 46.0 1.0 C3C A:HEM301 4.3 46.0 1.0 C2D A:HEM301 4.4 46.0 1.0 C3A A:HEM301 4.4 46.0 1.0 C2A A:HEM301 4.4 46.0 1.0 ND1 A:HIS187 4.4 50.3 1.0 CG A:HIS187 4.4 50.3 1.0 CA A:GLY51 4.8 52.3 1.0 CG A:GLN47 4.9 51.9 1.0

Iron binding site 2 out of 12 in the Crystal Structure of Cytochrome B6F Complex From M.Laminosus


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 Cytochrome B6F Complex From M.Laminosus within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe302 b:62.8 occ:1.00 FE A:HEM302 0.0 62.8 1.0 NA A:HEM302 2.0 62.6 1.0 ND A:HEM302 2.0 62.6 1.0 NC A:HEM302 2.1 62.6 1.0 NB A:HEM302 2.1 62.6 1.0 NE2 A:HIS202 2.3 36.3 1.0 NE2 A:HIS100 2.5 45.4 1.0 CD2 A:HIS100 2.9 45.4 1.0 C1A A:HEM302 3.0 62.6 1.0 C4D A:HEM302 3.0 62.6 1.0 C4A A:HEM302 3.0 62.6 1.0 C1D A:HEM302 3.1 62.6 1.0 C4C A:HEM302 3.1 62.6 1.0 C1C A:HEM302 3.1 62.6 1.0 C1B A:HEM302 3.1 62.6 1.0 C4B A:HEM302 3.1 62.6 1.0 CE1 A:HIS202 3.2 36.3 1.0 CD2 A:HIS202 3.3 36.3 1.0 CHA A:HEM302 3.4 62.6 1.0 CHB A:HEM302 3.4 62.6 1.0 CHD A:HEM302 3.4 62.6 1.0 CHC A:HEM302 3.5 62.6 1.0 CE1 A:HIS100 3.8 45.4 1.0 CG A:HIS100 4.2 45.4 1.0 C2A A:HEM302 4.2 62.6 1.0 C3A A:HEM302 4.3 62.6 1.0 C3D A:HEM302 4.3 62.6 1.0 ND1 A:HIS202 4.3 36.3 1.0 C3C A:HEM302 4.3 62.6 1.0 C2C A:HEM302 4.3 62.6 1.0 C2D A:HEM302 4.3 62.6 1.0 C2B A:HEM302 4.4 62.6 1.0 CG A:HIS202 4.4 36.3 1.0 C3B A:HEM302 4.4 62.6 1.0 ND1 A:HIS100 4.6 45.4 1.0

Iron binding site 3 out of 12 in the Crystal Structure of Cytochrome B6F Complex From M.Laminosus


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 Cytochrome B6F Complex From M.Laminosus within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe303 b:55.5 occ:1.00 FE A:HEM303 0.0 55.5 1.0 NA A:HEM303 2.0 81.0 1.0 NB A:HEM303 2.0 81.0 1.0 ND A:HEM303 2.0 81.0 1.0 NC A:HEM303 2.0 81.0 1.0 O A:HOH306 2.5 26.1 1.0 C4A A:HEM303 3.0 81.0 1.0 C1D A:HEM303 3.0 81.0 1.0 C1B A:HEM303 3.0 81.0 1.0 C4B A:HEM303 3.1 81.0 1.0 C1A A:HEM303 3.1 81.0 1.0 C4D A:HEM303 3.1 81.0 1.0 C4C A:HEM303 3.1 81.0 1.0 C1C A:HEM303 3.1 81.0 1.0 CHB A:HEM303 3.3 81.0 1.0 CHD A:HEM303 3.4 81.0 1.0 CHC A:HEM303 3.5 81.0 1.0 CHA A:HEM303 3.5 81.0 1.0 CZ B:PHE40 3.9 83.2 1.0 CE2 B:PHE40 3.9 83.2 1.0 C2D A:HEM303 4.2 81.0 1.0 C2B A:HEM303 4.3 81.0 1.0 C2A A:HEM303 4.3 81.0 1.0 C3A A:HEM303 4.3 81.0 1.0 C3B A:HEM303 4.3 81.0 1.0 C3C A:HEM303 4.3 81.0 1.0 C2C A:HEM303 4.3 81.0 1.0 CMA A:HEM302 4.3 62.6 1.0 C3D A:HEM303 4.3 81.0 1.0 N A:GLY38 4.6 71.7 1.0 CAA A:HEM302 4.8 62.6 1.0 CA A:GLY38 4.8 71.7 1.0 O A:TYR34 4.8 64.1 1.0 CGA A:HEM302 4.9 62.6 1.0 CBA A:HEM302 4.9 62.6 1.0 CE1 B:PHE40 5.0 83.2 1.0

Iron binding site 4 out of 12 in the Crystal Structure of Cytochrome B6F Complex From M.Laminosus


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 Cytochrome B6F Complex From M.Laminosus within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe301 b:62.2 occ:1.00 FE C:HEM301 0.0 62.2 1.0 ND C:HEM301 2.0 83.2 1.0 NA C:HEM301 2.0 83.2 1.0 NB C:HEM301 2.1 83.2 1.0 NC C:HEM301 2.1 83.2 1.0 N C:TYR1 2.3 53.4 1.0 NE2 C:HIS26 2.4 71.3 1.0 C4D C:HEM301 3.0 83.2 1.0 C4A C:HEM301 3.0 83.2 1.0 C1A C:HEM301 3.1 83.2 1.0 C1D C:HEM301 3.1 83.2 1.0 C1B C:HEM301 3.1 83.2 1.0 C4C C:HEM301 3.1 83.2 1.0 C4B C:HEM301 3.1 83.2 1.0 C1C C:HEM301 3.1 83.2 1.0 CA C:TYR1 3.2 53.4 1.0 CE1 C:HIS26 3.3 71.3 1.0 CD2 C:HIS26 3.4 71.3 1.0 CHB C:HEM301 3.4 83.2 1.0 CHA C:HEM301 3.4 83.2 1.0 CHD C:HEM301 3.5 83.2 1.0 CHC C:HEM301 3.5 83.2 1.0 C C:TYR1 3.9 53.4 1.0 O C:TYR1 4.2 53.4 1.0 C3A C:HEM301 4.3 83.2 1.0 C2A C:HEM301 4.3 83.2 1.0 C3D C:HEM301 4.3 83.2 1.0 C2D C:HEM301 4.3 83.2 1.0 C2B C:HEM301 4.3 83.2 1.0 ND1 C:HIS26 4.3 71.3 1.0 C2C C:HEM301 4.4 83.2 1.0 C3B C:HEM301 4.4 83.2 1.0 C3C C:HEM301 4.4 83.2 1.0 CG C:HIS26 4.4 71.3 1.0 CB C:TYR1 4.6 86.2 1.0 N C:PRO2 4.7 73.0 1.0 CG C:TYR1 4.9 86.2 1.0 CD1 C:TYR1 4.9 86.2 1.0 ND2 C:ASN154 5.0 88.9 1.0

Iron binding site 5 out of 12 in the Crystal Structure of Cytochrome B6F Complex From M.Laminosus


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 Cytochrome B6F Complex From M.Laminosus within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe200 b:0.3 occ:1.00 FE1 D:FES200 0.0 0.3 1.0 S1 D:FES200 2.2 0.6 1.0 S2 D:FES200 2.2 0.6 1.0 SG D:CYS108 2.3 0.9 1.0 SG D:CYS126 2.3 0.0 1.0 FE2 D:FES200 2.7 0.3 1.0 CB D:CYS126 3.4 0.0 1.0 CB D:CYS108 3.8 0.9 1.0 CB D:CYS113 4.1 99.2 1.0 O D:CYS113 4.2 0.1 1.0 ND1 D:HIS129 4.4 0.4 1.0 ND1 D:HIS110 4.5 0.4 1.0 CB D:SER131 4.5 80.4 1.0 CB D:HIS110 4.5 0.4 1.0 C D:CYS113 4.5 0.1 1.0 OG D:SER131 4.6 80.4 1.0 CB D:CYS128 4.6 94.3 1.0 N D:CYS113 4.6 0.1 1.0 O D:CYS108 4.6 0.6 1.0 CA D:CYS113 4.7 0.1 1.0 CA D:CYS126 4.7 0.8 1.0 CG D:HIS110 5.0 0.4 1.0 N D:HIS129 5.0 0.2 1.0

Iron binding site 6 out of 12 in the Crystal Structure of Cytochrome B6F Complex From M.Laminosus


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 Cytochrome B6F Complex From M.Laminosus within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe200 b:0.3 occ:1.00 FE2 D:FES200 0.0 0.3 1.0 S1 D:FES200 2.2 0.6 1.0 S2 D:FES200 2.2 0.6 1.0 ND1 D:HIS129 2.3 0.4 1.0 ND1 D:HIS110 2.3 0.4 1.0 FE1 D:FES200 2.7 0.3 1.0 CG D:HIS129 3.1 0.4 1.0 CE1 D:HIS110 3.2 0.4 1.0 CB D:HIS129 3.2 0.4 1.0 CG D:HIS110 3.3 0.4 1.0 CE1 D:HIS129 3.3 0.4 1.0 CB D:HIS110 3.6 0.4 1.0 N D:LEU111 3.7 93.5 1.0 N D:HIS129 3.9 0.2 1.0 CA D:HIS129 4.1 0.2 1.0 CB D:LEU111 4.1 0.2 1.0 CB D:CYS128 4.3 94.3 1.0 CD2 D:HIS129 4.3 0.4 1.0 NE2 D:HIS110 4.3 0.4 1.0 NE2 D:HIS129 4.4 0.4 1.0 CD2 D:HIS110 4.4 0.4 1.0 CA D:LEU111 4.4 93.5 1.0 SG D:CYS108 4.4 0.9 1.0 OG D:SER131 4.5 80.4 1.0 C D:CYS128 4.6 0.0 1.0 C D:HIS129 4.7 0.2 1.0 C D:HIS110 4.7 0.7 1.0 CA D:HIS110 4.7 0.7 1.0 SG D:CYS126 4.8 0.0 1.0 C D:LEU111 4.9 93.5 1.0

Iron binding site 7 out of 12 in the Crystal Structure of Cytochrome B6F Complex From M.Laminosus


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 Cytochrome B6F Complex From M.Laminosus within 5.0Å range: probe atom residue distance (Å) B Occ N:Fe301 b:41.9 occ:1.00 FE N:HEM301 0.0 41.9 1.0 ND N:HEM301 2.0 50.3 1.0 NA N:HEM301 2.1 50.3 1.0 NC N:HEM301 2.1 50.3 1.0 NB N:HEM301 2.1 50.3 1.0 NE2 N:HIS187 2.1 44.5 1.0 NE2 N:HIS86 2.3 58.1 1.0 C4D N:HEM301 3.0 50.3 1.0 CE1 N:HIS187 3.0 44.5 1.0 C1D N:HEM301 3.1 50.3 1.0 C4A N:HEM301 3.1 50.3 1.0 C1A N:HEM301 3.1 50.3 1.0 C4C N:HEM301 3.1 50.3 1.0 C4B N:HEM301 3.1 50.3 1.0 C1C N:HEM301 3.1 50.3 1.0 C1B N:HEM301 3.1 50.3 1.0 CD2 N:HIS187 3.1 44.5 1.0 CE1 N:HIS86 3.2 58.1 1.0 CD2 N:HIS86 3.3 58.1 1.0 CHA N:HEM301 3.4 50.3 1.0 CHB N:HEM301 3.4 50.3 1.0 CHC N:HEM301 3.4 50.3 1.0 CHD N:HEM301 3.4 50.3 1.0 ND1 N:HIS187 4.1 44.5 1.0 CG N:HIS187 4.2 44.5 1.0 C3D N:HEM301 4.3 50.3 1.0 C2D N:HEM301 4.3 50.3 1.0 C2A N:HEM301 4.3 50.3 1.0 C3A N:HEM301 4.3 50.3 1.0 C2C N:HEM301 4.3 50.3 1.0 C2B N:HEM301 4.3 50.3 1.0 C3C N:HEM301 4.3 50.3 1.0 ND1 N:HIS86 4.4 58.1 1.0 C3B N:HEM301 4.4 50.3 1.0 CG N:HIS86 4.4 58.1 1.0 CA N:GLY135 4.9 57.6 1.0

Iron binding site 8 out of 12 in the Crystal Structure of Cytochrome B6F Complex From M.Laminosus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of Cytochrome B6F Complex From M.Laminosus within 5.0Å range: probe atom residue distance (Å) B Occ N:Fe302 b:48.1 occ:1.00 FE N:HEM302 0.0 48.1 1.0 NA N:HEM302 2.0 56.1 1.0 ND N:HEM302 2.0 56.1 1.0 NC N:HEM302 2.1 56.1 1.0 NB N:HEM302 2.1 56.1 1.0 NE2 N:HIS202 2.2 55.8 1.0 NE2 N:HIS100 2.6 57.2 1.0 CD2 N:HIS100 2.9 57.2 1.0 C1A N:HEM302 3.0 56.1 1.0 C4D N:HEM302 3.0 56.1 1.0 C4A N:HEM302 3.0 56.1 1.0 C1D N:HEM302 3.1 56.1 1.0 CE1 N:HIS202 3.1 55.8 1.0 C4C N:HEM302 3.1 56.1 1.0 C1C N:HEM302 3.1 56.1 1.0 C1B N:HEM302 3.1 56.1 1.0 C4B N:HEM302 3.1 56.1 1.0 CD2 N:HIS202 3.3 55.8 1.0 CHA N:HEM302 3.4 56.1 1.0 CHB N:HEM302 3.4 56.1 1.0 CHD N:HEM302 3.4 56.1 1.0 CHC N:HEM302 3.5 56.1 1.0 CE1 N:HIS100 3.9 57.2 1.0 C2A N:HEM302 4.2 56.1 1.0 ND1 N:HIS202 4.2 55.8 1.0 C3A N:HEM302 4.2 56.1 1.0 CG N:HIS100 4.3 57.2 1.0 C3D N:HEM302 4.3 56.1 1.0 C2D N:HEM302 4.3 56.1 1.0 CG N:HIS202 4.3 55.8 1.0 C3C N:HEM302 4.3 56.1 1.0 C2C N:HEM302 4.3 56.1 1.0 C2B N:HEM302 4.4 56.1 1.0 C3B N:HEM302 4.4 56.1 1.0 ND1 N:HIS100 4.7 57.2 1.0

Iron binding site 9 out of 12 in the Crystal Structure of Cytochrome B6F Complex From M.Laminosus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Crystal Structure of Cytochrome B6F Complex From M.Laminosus within 5.0Å range: probe atom residue distance (Å) B Occ N:Fe303 b:64.8 occ:1.00 FE N:HEM303 0.0 64.8 1.0 NB N:HEM303 2.0 61.9 1.0 NA N:HEM303 2.0 61.9 1.0 ND N:HEM303 2.0 61.9 1.0 NC N:HEM303 2.0 61.9 1.0 O N:HOH1307 2.3 22.9 1.0 C4D N:HEM303 3.0 61.9 1.0 C1C N:HEM303 3.0 61.9 1.0 C4B N:HEM303 3.0 61.9 1.0 C4C N:HEM303 3.1 61.9 1.0 C1D N:HEM303 3.1 61.9 1.0 C1A N:HEM303 3.1 61.9 1.0 C4A N:HEM303 3.1 61.9 1.0 C1B N:HEM303 3.1 61.9 1.0 CHC N:HEM303 3.4 61.9 1.0 CHD N:HEM303 3.4 61.9 1.0 CHA N:HEM303 3.4 61.9 1.0 CHB N:HEM303 3.5 61.9 1.0 O2A N:HEM302 3.6 56.1 1.0 CZ O:PHE40 3.6 63.5 1.0 CE2 O:PHE40 3.7 63.5 1.0 O N:TYR34 4.2 57.2 1.0 C2C N:HEM303 4.3 61.9 1.0 C3C N:HEM303 4.3 61.9 1.0 C2D N:HEM303 4.3 61.9 1.0 C3B N:HEM303 4.3 61.9 1.0 C2B N:HEM303 4.3 61.9 1.0 C3D N:HEM303 4.3 61.9 1.0 C2A N:HEM303 4.3 61.9 1.0 C3A N:HEM303 4.3 61.9 1.0 CE1 O:PHE40 4.6 63.5 1.0 N N:GLY38 4.6 48.7 1.0 CA N:GLY38 4.6 48.7 1.0 CD2 O:PHE40 4.6 63.5 1.0 CGA N:HEM302 4.7 56.1 1.0

Iron binding site 10 out of 12 in the Crystal Structure of Cytochrome B6F Complex From M.Laminosus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Crystal Structure of Cytochrome B6F Complex From M.Laminosus within 5.0Å range: probe atom residue distance (Å) B Occ P:Fe301 b:47.2 occ:1.00 FE P:HEM301 0.0 47.2 1.0 ND P:HEM301 2.0 56.5 1.0 NA P:HEM301 2.0 56.5 1.0 NC P:HEM301 2.1 56.5 1.0 NB P:HEM301 2.1 56.5 1.0 N P:TYR1 2.3 49.9 1.0 NE2 P:HIS26 2.5 72.2 1.0 C4D P:HEM301 3.0 56.5 1.0 C1D P:HEM301 3.1 56.5 1.0 C4A P:HEM301 3.1 56.5 1.0 C1A P:HEM301 3.1 56.5 1.0 C4C P:HEM301 3.1 56.5 1.0 C1B P:HEM301 3.1 56.5 1.0 C1C P:HEM301 3.1 56.5 1.0 C4B P:HEM301 3.1 56.5 1.0 CA P:TYR1 3.2 49.9 1.0 CE1 P:HIS26 3.3 72.2 1.0 CHB P:HEM301 3.4 56.5 1.0 CD2 P:HIS26 3.4 72.2 1.0 CHD P:HEM301 3.4 56.5 1.0 CHA P:HEM301 3.4 56.5 1.0 CHC P:HEM301 3.5 56.5 1.0 C P:TYR1 3.8 49.9 1.0 O P:TYR1 4.0 49.9 1.0 C3D P:HEM301 4.3 56.5 1.0 C2D P:HEM301 4.3 56.5 1.0 C3A P:HEM301 4.3 56.5 1.0 C2A P:HEM301 4.3 56.5 1.0 C2C P:HEM301 4.4 56.5 1.0 C3C P:HEM301 4.4 56.5 1.0 C2B P:HEM301 4.4 56.5 1.0 ND1 P:HIS26 4.4 72.2 1.0 C3B P:HEM301 4.4 56.5 1.0 CG P:HIS26 4.5 72.2 1.0 CB P:TYR1 4.5 98.0 1.0 N P:PRO2 4.7 59.1 1.0 CG P:TYR1 4.9 98.0 1.0 CD1 P:TYR1 4.9 98.0 1.0

G.Kurisu, H.Zhang, J.L.Smith, W.A.Cramer. Structure of the Cytochrome B6F Complex of Oxygenic Photosynthesis: Tuning the Cavity Science V. 302 1009 2003.
ISSN: ISSN 0036-8075
PubMed: 14526088
DOI: 10.1126/SCIENCE.1090165