Zinc in PDB 5vjs: De Novo Photosynthetic Reaction Center Protein Equipped with Heme B, A Synthetic Zn Porphyrin, and Zn(II) Cations

The structure of De Novo Photosynthetic Reaction Center Protein Equipped with Heme B, A Synthetic Zn Porphyrin, and Zn(II) Cations, PDB code: 5vjs was solved by N.M.Ennist, P.L.Dutton, S.E.Stayrook, C.C.Moser, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	61.43 / 2.00
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	43.749, 43.749, 245.737, 90.00, 90.00, 90.00
R / Rfree (%)	23.5 / 27.8

The structure of De Novo Photosynthetic Reaction Center Protein Equipped with Heme B, A Synthetic Zn Porphyrin, and Zn(II) Cations also contains other interesting chemical elements:

Iron	(Fe)	1 atom
Chlorine	(Cl)	3 atoms

The binding sites of Zinc atom in the De Novo Photosynthetic Reaction Center Protein Equipped with Heme B, A Synthetic Zn Porphyrin, and Zn(II) Cations (pdb code 5vjs). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the De Novo Photosynthetic Reaction Center Protein Equipped with Heme B, A Synthetic Zn Porphyrin, and Zn(II) Cations, PDB code: 5vjs:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the De Novo Photosynthetic Reaction Center Protein Equipped with Heme B, A Synthetic Zn Porphyrin, and Zn(II) Cations


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of De Novo Photosynthetic Reaction Center Protein Equipped with Heme B, A Synthetic Zn Porphyrin, and Zn(II) Cations within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:33.9 occ:0.70 ZN A:9D7202 0.0 33.9 0.7 CD2 A:HIS124 1.9 29.6 1.0 NB A:9D7202 2.1 41.4 0.7 NC A:9D7202 2.1 37.6 0.7 NE2 A:HIS124 2.1 32.0 1.0 ND A:9D7202 2.1 35.6 0.7 NA A:9D7202 2.1 38.2 0.7 C4C A:9D7202 3.1 35.4 0.7 C1B A:9D7202 3.1 42.6 0.7 C4A A:9D7202 3.1 39.6 0.7 C1C A:9D7202 3.1 35.0 0.7 C4B A:9D7202 3.1 39.3 0.7 C1D A:9D7202 3.1 38.9 0.7 C4D A:9D7202 3.2 37.3 0.7 C1A A:9D7202 3.2 34.1 0.7 CG A:HIS124 3.2 33.6 1.0 CE1 A:HIS124 3.4 33.5 1.0 CD2 A:LEU171 3.4 62.6 1.0 CHB A:9D7202 3.5 41.0 0.7 CHD A:9D7202 3.5 36.6 0.7 CHC A:9D7202 3.5 39.3 0.7 CHA A:9D7202 3.6 37.0 0.7 CG2 A:ILE23 3.8 37.8 1.0 ND1 A:HIS124 3.9 37.6 1.0 CB A:HIS124 4.3 40.0 1.0 CD2 A:LEU74 4.3 42.8 1.0 C3C A:9D7202 4.3 40.4 0.7 C2C A:9D7202 4.3 36.6 0.7 C2B A:9D7202 4.3 39.3 0.7 C3B A:9D7202 4.4 40.1 0.7 C3A A:9D7202 4.4 41.0 0.7 C2A A:9D7202 4.4 39.7 0.7 C3D A:9D7202 4.4 37.7 0.7 C2D A:9D7202 4.4 38.0 0.7 CG A:LEU171 4.7 59.3 1.0 CD1 A:LEU171 4.8 59.7 1.0 O A:HIS124 4.8 45.5 1.0 CBE A:9D7202 5.0 40.7 0.7

Zinc binding site 2 out of 3 in the De Novo Photosynthetic Reaction Center Protein Equipped with Heme B, A Synthetic Zn Porphyrin, and Zn(II) Cations


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of De Novo Photosynthetic Reaction Center Protein Equipped with Heme B, A Synthetic Zn Porphyrin, and Zn(II) Cations within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:30.5 occ:1.00 NE2 A:HIS138 2.0 21.0 1.0 OD2 A:ASP63 2.0 34.2 1.0 OD1 A:ASP134 2.0 34.4 1.0 CL A:CL207 2.4 34.9 1.0 CG A:ASP134 2.8 35.9 1.0 CG A:ASP63 2.9 30.2 1.0 CD2 A:HIS138 2.9 24.3 1.0 OD2 A:ASP134 2.9 36.6 1.0 CE1 A:HIS138 3.0 25.9 1.0 CB A:ASP63 3.1 26.7 1.0 CG A:HIS138 4.0 24.8 1.0 OD1 A:ASP63 4.0 35.1 1.0 O A:ASP134 4.1 25.1 1.0 ND1 A:HIS138 4.1 23.5 1.0 CE A:LYS59 4.1 37.5 1.0 CB A:ASP134 4.1 29.7 1.0 CA A:ASP134 4.5 24.2 1.0 C A:ASP134 4.6 22.4 1.0 NZ A:LYS59 4.7 40.1 1.0 CA A:ASP63 4.7 24.6 1.0 O A:LYS59 4.8 22.5 1.0 CD A:LYS59 4.9 38.5 1.0 CB A:LYS137 4.9 32.2 1.0

Zinc binding site 3 out of 3 in the De Novo Photosynthetic Reaction Center Protein Equipped with Heme B, A Synthetic Zn Porphyrin, and Zn(II) Cations


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of De Novo Photosynthetic Reaction Center Protein Equipped with Heme B, A Synthetic Zn Porphyrin, and Zn(II) Cations within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn204 b:53.6 occ:1.00 OE1 A:GLU34 2.0 50.8 1.0 OE1 A:GLU64 2.0 37.6 1.0 OE1 A:GLU135 2.1 45.1 1.0 ND1 A:HIS67 2.1 32.1 1.0 CD A:GLU34 2.7 51.6 1.0 OE2 A:GLU34 2.9 59.2 1.0 CD A:GLU64 3.0 34.5 1.0 CE1 A:HIS67 3.0 31.9 1.0 CD A:GLU135 3.0 40.9 1.0 CG A:HIS67 3.2 29.6 1.0 OE2 A:GLU64 3.3 43.9 1.0 OE2 A:GLU135 3.3 49.3 1.0 CB A:HIS67 3.6 27.0 1.0 OH A:TYR168 3.9 53.9 1.0 O A:HOH305 4.1 39.8 1.0 CG A:GLU34 4.1 45.7 1.0 NE2 A:HIS67 4.1 28.6 1.0 CD2 A:HIS67 4.2 29.2 1.0 CG A:GLU64 4.3 31.0 1.0 CG A:GLU135 4.4 37.8 1.0 CG2 A:ILE131 4.5 29.9 1.0 CA A:GLU64 4.5 24.4 1.0 CE2 A:TYR168 4.6 44.9 1.0 CZ A:TYR168 4.6 52.0 1.0 CB A:GLU64 4.6 26.8 1.0 O A:GLU64 4.8 22.6 1.0 CB A:GLU135 4.8 28.4 1.0 OE2 A:GLU161 4.9 61.3 1.0

N.M.Ennist, Z.Zhao, S.E.Stayrook, P.L.Dutton, C.C.Moser. Design, Structure, and Action of An Artificial Photosynthetic Reaction Center Protein To Be Published.