Manganese in PDB 8d9p: De Novo Photosynthetic Reaction Center Protein Equipped with Heme B and Mn(II) Cations

The structure of De Novo Photosynthetic Reaction Center Protein Equipped with Heme B and Mn(II) Cations, PDB code: 8d9p was solved by N.M.Ennist, S.E.Stayrook, P.L.Dutton, C.C.Moser, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.25 / 1.90
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	44.968, 44.968, 238.295, 90, 90, 90
R / Rfree (%)	21.9 / 24.3

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

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

The binding sites of Manganese atom in the De Novo Photosynthetic Reaction Center Protein Equipped with Heme B and Mn(II) Cations (pdb code 8d9p). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the De Novo Photosynthetic Reaction Center Protein Equipped with Heme B and Mn(II) Cations, PDB code: 8d9p:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the De Novo Photosynthetic Reaction Center Protein Equipped with Heme B and Mn(II) Cations


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of De Novo Photosynthetic Reaction Center Protein Equipped with Heme B and Mn(II) Cations within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn202 b:70.0 occ:1.00 OE1 A:GLU161 2.0 118.3 1.0 OE2 A:GLU161 2.0 104.4 1.0 OE2 A:GLU64 2.0 118.7 1.0 OE1 A:GLU135 2.0 55.0 1.0 ND1 A:HIS138 2.0 22.2 1.0 CD A:GLU161 2.3 42.0 1.0 CE1 A:HIS138 2.9 17.9 1.0 CD A:GLU135 3.0 22.5 1.0 CG A:HIS138 3.1 22.1 1.0 CD A:GLU64 3.3 31.3 1.0 OE2 A:GLU135 3.5 99.3 1.0 CB A:HIS138 3.5 21.1 1.0 CG A:GLU161 3.8 50.3 1.0 CA A:GLU135 4.0 15.1 1.0 OE1 A:GLU64 4.0 39.3 1.0 CG2 A:ILE60 4.0 19.9 1.0 NE2 A:HIS138 4.1 22.7 1.0 CG A:GLU135 4.2 44.0 1.0 CD2 A:HIS138 4.2 26.8 1.0 CG A:GLU64 4.3 36.6 1.0 CB A:GLU135 4.3 21.9 1.0 O A:GLU135 4.5 21.9 1.0 CB A:GLU161 4.7 21.4 1.0 C A:GLU135 4.8 22.8 1.0 N A:GLU135 4.9 13.1 1.0 O A:HOH336 4.9 28.5 1.0 MN A:MN203 5.0 81.6 0.4 O A:ASP134 5.0 23.6 1.0

Manganese binding site 2 out of 2 in the De Novo Photosynthetic Reaction Center Protein Equipped with Heme B and Mn(II) Cations


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of De Novo Photosynthetic Reaction Center Protein Equipped with Heme B and Mn(II) Cations within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn203 b:81.6 occ:0.42 OE1 A:GLU64 2.0 39.3 1.0 OE2 A:GLU34 2.0 107.4 1.0 OE2 A:GLU135 2.0 99.3 1.0 OE1 A:GLU34 2.0 171.3 1.0 ND1 A:HIS67 2.0 21.4 1.0 CD A:GLU34 2.3 93.2 1.0 CG A:HIS67 3.0 22.6 1.0 CE1 A:HIS67 3.1 30.7 1.0 CD A:GLU64 3.1 31.3 1.0 CB A:HIS67 3.2 27.1 1.0 CD A:GLU135 3.3 22.5 1.0 OE2 A:GLU64 3.6 118.7 1.0 OH A:TYR168 3.7 38.4 1.0 CG A:GLU34 3.9 49.4 1.0 OE1 A:GLU135 4.1 55.0 1.0 CD2 A:HIS67 4.1 18.6 1.0 NE2 A:HIS67 4.2 19.1 1.0 CG A:GLU135 4.2 44.0 1.0 CA A:GLU64 4.2 14.7 1.0 CG2 A:ILE131 4.3 24.5 1.0 CG A:GLU64 4.3 36.6 1.0 CB A:GLU64 4.5 20.7 1.0 CZ A:TYR168 4.5 31.7 1.0 CE2 A:TYR168 4.7 31.8 1.0 CA A:HIS67 4.7 25.2 1.0 O A:GLU64 4.8 19.6 1.0 CB A:GLU34 4.8 31.1 1.0 MN A:MN202 5.0 70.0 1.0

N.M.Ennist, S.E.Stayrook, P.L.Dutton, C.C.Moser. Rational Design of Photosynthetic Reaction Center Protein Maquettes. Front Mol Biosci V. 9 97295 2022.
ISSN: ESSN 2296-889X
PubMed: 36213121
DOI: 10.3389/FMOLB.2022.997295