Zinc in PDB 4n7k: Zinc Substituted Reaction Center of the Rhodobacter Sphaeroides

The structure of Zinc Substituted Reaction Center of the Rhodobacter Sphaeroides, PDB code: 4n7k was solved by A.Hardjasa, M.E.P.Murphy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.91 / 2.85
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	139.450, 139.450, 184.181, 90.00, 90.00, 120.00
R / Rfree (%)	18.2 / 24.3

The structure of Zinc Substituted Reaction Center of the Rhodobacter Sphaeroides also contains other interesting chemical elements:

Iron

(Fe)

1 atom

The binding sites of Zinc atom in the Zinc Substituted Reaction Center of the Rhodobacter Sphaeroides (pdb code 4n7k). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Zinc Substituted Reaction Center of the Rhodobacter Sphaeroides, PDB code: 4n7k:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Zinc Substituted Reaction Center of the Rhodobacter Sphaeroides


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Zinc Substituted Reaction Center of the Rhodobacter Sphaeroides within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn301 b:39.3 occ:1.00 ZN L:2GO301 0.0 39.3 1.0 NA L:2GO301 2.0 30.5 1.0 NC L:2GO301 2.0 35.4 1.0 ND L:2GO301 2.0 29.4 1.0 NB L:2GO301 2.0 33.5 1.0 NE2 L:HIS153 2.4 46.5 1.0 C4D L:2GO301 2.9 29.4 1.0 C1A L:2GO301 2.9 31.0 1.0 C4A L:2GO301 3.0 30.2 1.0 C4C L:2GO301 3.0 36.4 1.0 C1C L:2GO301 3.0 39.2 1.0 C1B L:2GO301 3.0 33.2 1.0 C4B L:2GO301 3.1 34.5 1.0 C1D L:2GO301 3.1 31.4 1.0 CD2 L:HIS153 3.3 49.2 1.0 CE1 L:HIS153 3.3 46.5 1.0 CHB L:2GO301 3.4 29.9 1.0 CHA L:2GO301 3.4 29.7 1.0 CHC L:2GO301 3.4 35.9 1.0 CHD L:2GO301 3.5 32.7 1.0 C3D L:2GO301 4.2 32.6 1.0 C2A L:2GO301 4.3 30.9 1.0 C3A L:2GO301 4.3 29.4 1.0 C3C L:2GO301 4.3 38.2 1.0 C2C L:2GO301 4.4 39.9 1.0 C2D L:2GO301 4.4 32.5 1.0 C3B L:2GO301 4.4 37.1 1.0 C2B L:2GO301 4.4 34.7 1.0 CE2 M:TYR210 4.4 46.6 1.0 ND1 L:HIS153 4.4 55.0 1.0 CG L:HIS153 4.4 55.7 1.0 OBB L:2GO305 4.5 56.6 1.0 CBA L:2GO301 4.6 40.0 1.0 C20 L:2GO305 4.8 37.8 1.0 CBD L:2GO301 4.9 33.5 1.0 CD1 L:LEU154 4.9 48.6 1.0

Zinc binding site 2 out of 6 in the Zinc Substituted Reaction Center of the Rhodobacter Sphaeroides


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Zinc Substituted Reaction Center of the Rhodobacter Sphaeroides within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn305 b:58.3 occ:1.00 ZN L:2GO305 0.0 58.3 1.0 NA L:2GO305 2.0 48.2 1.0 NC L:2GO305 2.0 55.0 1.0 ND L:2GO305 2.0 52.0 1.0 NB L:2GO305 2.1 51.3 1.0 C4D L:2GO305 3.0 48.0 1.0 C4A L:2GO305 3.0 44.7 1.0 C1A L:2GO305 3.0 46.4 1.0 C4C L:2GO305 3.0 51.8 1.0 C1B L:2GO305 3.0 49.0 1.0 C1C L:2GO305 3.1 52.3 1.0 C4B L:2GO305 3.1 51.6 1.0 C1D L:2GO305 3.2 51.2 1.0 CD1 M:LEU214 3.2 39.4 1.0 CHB L:2GO305 3.3 46.7 1.0 CHA L:2GO305 3.4 46.5 1.0 CHC L:2GO305 3.4 50.0 1.0 CHD L:2GO305 3.5 50.1 1.0 CB L:ALA124 4.1 39.5 1.0 CG M:LEU214 4.2 46.4 1.0 C3D L:2GO305 4.2 48.1 1.0 C3A L:2GO305 4.3 39.5 1.0 C2A L:2GO305 4.4 43.9 1.0 C3C L:2GO305 4.4 48.8 1.0 CB M:LEU214 4.4 48.1 1.0 C3B L:2GO305 4.4 49.7 1.0 C2D L:2GO305 4.4 51.1 1.0 C2B L:2GO305 4.4 47.7 1.0 C2C L:2GO305 4.4 47.5 1.0 CE1 L:PHE121 4.4 49.7 1.0 CD2 M:LEU214 4.5 45.6 1.0 CD1 L:PHE121 4.5 51.6 1.0 C7 L:2GO307 4.8 37.7 1.0 CBD L:2GO305 4.9 46.0 1.0 CMA L:2GO305 5.0 31.2 1.0

Zinc binding site 3 out of 6 in the Zinc Substituted Reaction Center of the Rhodobacter Sphaeroides


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Zinc Substituted Reaction Center of the Rhodobacter Sphaeroides within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn307 b:49.6 occ:1.00 ZN L:2GO307 0.0 49.6 1.0 NC L:2GO307 2.0 49.5 1.0 NA L:2GO307 2.0 52.3 1.0 ND L:2GO307 2.0 53.3 1.0 NB L:2GO307 2.0 48.5 1.0 NE2 L:HIS173 2.1 34.6 1.0 C4D L:2GO307 3.0 51.2 1.0 C1C L:2GO307 3.0 47.8 1.0 C1A L:2GO307 3.0 50.9 1.0 C4C L:2GO307 3.0 46.5 1.0 C4A L:2GO307 3.0 48.9 1.0 C1B L:2GO307 3.1 48.6 1.0 C4B L:2GO307 3.1 46.3 1.0 CD2 L:HIS173 3.1 38.2 1.0 CE1 L:HIS173 3.1 35.5 1.0 C1D L:2GO307 3.1 51.3 1.0 OBB M:2GO402 3.3 64.0 1.0 CHC L:2GO307 3.4 47.0 1.0 CHB L:2GO307 3.4 44.9 1.0 CHA L:2GO307 3.4 50.6 1.0 CHD L:2GO307 3.5 48.6 1.0 CAB M:2GO402 3.6 59.3 1.0 CBB M:2GO402 3.9 60.4 1.0 C3D L:2GO307 4.2 53.6 1.0 ND1 L:HIS173 4.2 37.0 1.0 CG L:HIS173 4.3 40.3 1.0 C2A L:2GO307 4.3 49.3 1.0 C3C L:2GO307 4.3 44.0 1.0 C3A L:2GO307 4.4 49.5 1.0 C3B L:2GO307 4.4 48.8 1.0 C2C L:2GO307 4.4 43.4 1.0 C2D L:2GO307 4.4 51.8 1.0 C2B L:2GO307 4.4 50.6 1.0 C3B M:2GO402 4.5 55.8 1.0 CD1 L:PHE167 4.7 48.0 1.0 CBD L:2GO307 4.9 53.0 1.0

Zinc binding site 4 out of 6 in the Zinc Substituted Reaction Center of the Rhodobacter Sphaeroides


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Zinc Substituted Reaction Center of the Rhodobacter Sphaeroides within 5.0Å range: probe atom residue distance (Å) B Occ M:Zn401 b:44.5 occ:1.00 ZN M:2GO401 0.0 44.5 1.0 NC M:2GO401 2.0 44.4 1.0 ND M:2GO401 2.0 41.7 1.0 NA M:2GO401 2.0 42.7 1.0 NB M:2GO401 2.0 44.7 1.0 NE2 M:HIS182 2.2 43.7 1.0 C4D M:2GO401 2.9 41.3 1.0 C1C M:2GO401 3.0 43.0 1.0 C1A M:2GO401 3.0 43.0 1.0 C4C M:2GO401 3.0 42.2 1.0 C4A M:2GO401 3.0 42.6 1.0 C4B M:2GO401 3.0 44.5 1.0 C1B M:2GO401 3.0 45.0 1.0 CE1 M:HIS182 3.1 44.7 1.0 C1D M:2GO401 3.1 44.0 1.0 CD2 M:HIS182 3.2 47.3 1.0 CHC M:2GO401 3.3 42.2 1.0 CHB M:2GO401 3.4 43.2 1.0 CHA M:2GO401 3.4 41.1 1.0 CHD M:2GO401 3.5 41.7 1.0 C3D M:2GO401 4.2 45.3 1.0 ND1 M:HIS182 4.2 45.2 1.0 CG M:HIS182 4.3 48.8 1.0 C3C M:2GO401 4.3 40.4 1.0 C2A M:2GO401 4.3 43.5 1.0 C3B M:2GO401 4.3 50.9 1.0 C2D M:2GO401 4.3 45.5 1.0 C2C M:2GO401 4.4 39.1 1.0 C3A M:2GO401 4.4 41.7 1.0 C2B M:2GO401 4.4 46.4 1.0 OBB M:2GO406 4.7 68.6 1.0 CE2 L:PHE181 4.8 51.7 1.0 CBD M:2GO401 4.9 43.5 1.0

Zinc binding site 5 out of 6 in the Zinc Substituted Reaction Center of the Rhodobacter Sphaeroides


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Zinc Substituted Reaction Center of the Rhodobacter Sphaeroides within 5.0Å range: probe atom residue distance (Å) B Occ M:Zn402 b:50.2 occ:1.00 ZN M:2GO402 0.0 50.2 1.0 NC M:2GO402 2.0 50.3 1.0 ND M:2GO402 2.0 45.8 1.0 NA M:2GO402 2.0 50.8 1.0 NB M:2GO402 2.0 49.4 1.0 NE2 M:HIS202 2.1 37.0 1.0 C4D M:2GO402 2.9 44.3 1.0 C4C M:2GO402 3.0 48.9 1.0 C1C M:2GO402 3.0 51.3 1.0 C1A M:2GO402 3.0 46.1 1.0 C4B M:2GO402 3.0 51.6 1.0 C4A M:2GO402 3.0 48.4 1.0 C1B M:2GO402 3.1 47.7 1.0 CD2 M:HIS202 3.1 41.1 1.0 C1D M:2GO402 3.1 47.0 1.0 CE1 M:HIS202 3.1 40.2 1.0 CBB L:2GO307 3.3 47.8 1.0 CHC M:2GO402 3.4 53.7 1.0 CHA M:2GO402 3.4 44.9 1.0 CHB M:2GO402 3.4 45.0 1.0 CHD M:2GO402 3.5 48.7 1.0 CAB L:2GO307 3.7 47.3 1.0 OBB L:2GO307 3.9 46.2 1.0 C3D M:2GO402 4.2 43.7 1.0 ND1 M:HIS202 4.2 39.6 1.0 CG M:HIS202 4.3 39.8 1.0 C3C M:2GO402 4.3 45.6 1.0 C2C M:2GO402 4.3 46.3 1.0 C3B M:2GO402 4.3 55.8 1.0 C2A M:2GO402 4.4 45.3 1.0 C3A M:2GO402 4.4 47.2 1.0 C2D M:2GO402 4.4 45.6 1.0 C2B M:2GO402 4.4 51.9 1.0 C3B L:2GO307 4.5 48.8 1.0 CBD M:2GO402 4.9 44.5 1.0 O2D M:2GO402 4.9 48.3 1.0 CMC M:2GO402 5.0 46.5 1.0 CD1 M:LEU196 5.0 48.1 1.0

Zinc binding site 6 out of 6 in the Zinc Substituted Reaction Center of the Rhodobacter Sphaeroides


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Zinc Substituted Reaction Center of the Rhodobacter Sphaeroides within 5.0Å range: probe atom residue distance (Å) B Occ M:Zn406 b:86.5 occ:1.00 ZN M:2GO406 0.0 86.5 1.0 NA M:2GO406 2.0 85.7 1.0 NC M:2GO406 2.0 80.0 1.0 ND M:2GO406 2.1 77.0 1.0 NB M:2GO406 2.1 81.2 1.0 C4D M:2GO406 3.0 70.1 1.0 C4A M:2GO406 3.0 80.7 1.0 C1A M:2GO406 3.0 77.8 1.0 C4C M:2GO406 3.0 76.9 1.0 C1B M:2GO406 3.1 76.5 1.0 C1C M:2GO406 3.1 75.7 1.0 C4B M:2GO406 3.1 76.3 1.0 C1D M:2GO406 3.2 75.5 1.0 CHB M:2GO406 3.4 78.6 1.0 CHA M:2GO406 3.4 70.8 1.0 CHC M:2GO406 3.4 75.2 1.0 CHD M:2GO406 3.5 78.5 1.0 CD2 L:LEU185 3.7 42.2 1.0 CD1 L:LEU185 3.7 45.2 1.0 CG L:LEU185 4.2 42.6 1.0 C3D M:2GO406 4.2 69.5 1.0 CB M:ALA153 4.3 39.5 1.0 C3A M:2GO406 4.3 71.2 1.0 C3B M:2GO406 4.4 72.9 1.0 C2A M:2GO406 4.4 68.4 1.0 C3C M:2GO406 4.4 72.2 1.0 CB L:LEU185 4.4 42.8 1.0 C2B M:2GO406 4.4 71.0 1.0 C2D M:2GO406 4.4 72.9 1.0 C2C M:2GO406 4.4 70.5 1.0 C7 M:2GO402 4.5 60.1 1.0 CE1 M:PHE150 4.7 51.2 1.0 CD1 M:PHE150 4.8 53.2 1.0 C10 M:2GO402 4.8 54.7 1.0 CBD M:2GO406 4.9 66.2 1.0 CMA M:2GO406 5.0 60.9 1.0

R.G.Saer, J.Pan, A.Hardjasa, S.Lin, F.Rosell, A.G.Mauk, N.W.Woodbury, M.E.Murphy, J.T.Beatty. Structural and Kinetic Properties of Rhodobacter Sphaeroides Photosynthetic Reaction Centers Containing Exclusively Zn-Coordinated Bacteriochlorophyll As Bacteriochlorin Cofactors. Biochim.Biophys.Acta V.1837 366 2013.
ISSN: ISSN 0006-3002
PubMed: 24316146
DOI: 10.1016/J.BBABIO.2013.11.015