Cadmium in PDB 8d9o: De Novo Photosynthetic Reaction Center Protein in Apo-State

The structure of De Novo Photosynthetic Reaction Center Protein in Apo-State, PDB code: 8d9o 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)	18.46 / 1.78
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	89.692, 23.693, 72.756, 90, 99.93, 90
R / Rfree (%)	18.3 / 20.9

Pages:

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

Binding sites:

The binding sites of Cadmium atom in the De Novo Photosynthetic Reaction Center Protein in Apo-State (pdb code 8d9o). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 11 binding sites of Cadmium where determined in the De Novo Photosynthetic Reaction Center Protein in Apo-State, PDB code: 8d9o:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 11 in the De Novo Photosynthetic Reaction Center Protein in Apo-State


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of De Novo Photosynthetic Reaction Center Protein in Apo-State within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd201 b:17.9 occ:1.00 OE1 A:GLU8 2.4 17.3 1.0 O A:HOH325 2.5 9.2 1.0 OE2 A:GLU8 2.5 18.2 1.0 O A:HOH384 2.5 4.7 1.0 CD A:GLU8 2.8 16.3 1.0 O A:HOH318 4.2 30.7 1.0 CG A:GLU8 4.3 15.0 1.0 CE A:LYS184 4.5 30.6 1.0 NZ A:LYS184 4.6 33.6 1.0 NZ A:LYS191 4.7 35.1 1.0 CG2 A:THR188 4.8 13.4 1.0

Cadmium binding site 2 out of 11 in the De Novo Photosynthetic Reaction Center Protein in Apo-State


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of De Novo Photosynthetic Reaction Center Protein in Apo-State within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd202 b:17.8 occ:1.00 OE2 A:GLU4 2.3 23.3 1.0 OE1 A:GLU4 2.4 13.8 1.0 CD A:GLU4 2.7 18.0 1.0 CG A:GLU4 4.2 17.8 1.0 CD A:PRO3 4.4 15.9 1.0 O A:HOH321 4.7 29.9 1.0 CG A:PRO3 4.9 17.7 1.0 CB A:SER2 4.9 17.0 1.0

Cadmium binding site 3 out of 11 in the De Novo Photosynthetic Reaction Center Protein in Apo-State


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of De Novo Photosynthetic Reaction Center Protein in Apo-State within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd203 b:20.4 occ:1.00 OE2 A:GLU161 2.3 29.8 1.0 OE2 A:GLU64 2.3 29.4 1.0 ND1 A:HIS138 2.4 22.2 1.0 OE1 A:GLU161 2.4 33.1 1.0 OE1 A:GLU135 2.4 22.9 1.0 O A:HOH344 2.5 19.9 1.0 CD A:GLU161 2.6 27.5 1.0 CD A:GLU64 3.0 25.4 1.0 OE1 A:GLU64 3.0 27.6 1.0 CD A:GLU135 3.3 21.2 1.0 CE1 A:HIS138 3.3 20.0 1.0 CG A:HIS138 3.4 19.8 1.0 CD A:CD204 3.6 16.7 1.0 CB A:HIS138 3.7 20.1 1.0 OE2 A:GLU135 3.7 30.0 1.0 O A:HOH357 3.7 41.6 1.0 CG A:GLU161 4.1 26.9 1.0 O A:HOH362 4.3 26.5 1.0 O A:HOH347 4.3 33.8 1.0 CG A:GLU135 4.4 18.1 1.0 NE2 A:HIS138 4.4 21.7 1.0 CG2 A:ILE60 4.5 25.2 1.0 CG A:GLU64 4.5 23.6 1.0 CA A:GLU135 4.5 16.1 1.0 CD2 A:HIS138 4.5 21.5 1.0 CB A:GLU135 4.7 17.3 1.0 ND1 A:HIS67 4.8 14.1 1.0 CE1 A:HIS67 4.9 15.8 1.0 CB A:GLU161 5.0 25.6 1.0

Cadmium binding site 4 out of 11 in the De Novo Photosynthetic Reaction Center Protein in Apo-State


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of De Novo Photosynthetic Reaction Center Protein in Apo-State within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd204 b:16.7 occ:1.00 OE2 A:GLU34 2.2 20.6 1.0 ND1 A:HIS67 2.3 14.1 1.0 OE2 A:GLU135 2.3 30.0 1.0 OE1 A:GLU34 2.4 16.4 1.0 OE1 A:GLU64 2.4 27.6 1.0 O A:HOH344 2.5 19.9 1.0 CD A:GLU34 2.6 18.2 1.0 OE1 A:GLU135 2.8 22.9 1.0 CD A:GLU135 2.9 21.2 1.0 CE1 A:HIS67 3.2 15.8 1.0 CG A:HIS67 3.3 14.7 1.0 CD A:GLU64 3.4 25.4 1.0 CD A:CD203 3.6 20.4 1.0 CB A:HIS67 3.6 14.1 1.0 OE2 A:GLU64 3.9 29.4 1.0 O A:HOH347 4.0 33.8 1.0 CG A:GLU34 4.1 19.4 1.0 O A:HOH338 4.2 25.8 1.0 CG A:GLU135 4.4 18.1 1.0 NE2 A:HIS67 4.4 13.9 1.0 CD2 A:HIS67 4.5 14.3 1.0 CG2 A:ILE131 4.5 14.7 1.0 CG A:GLU64 4.6 23.6 1.0 O A:HOH357 4.6 41.6 1.0 CA A:GLU64 4.6 20.5 1.0 OH A:TYR168 4.7 17.2 1.0 CB A:GLU64 4.8 22.9 1.0 CE1 A:HIS138 4.8 20.0 1.0 ND1 A:HIS138 4.8 22.2 1.0 CE2 A:TYR168 4.9 15.7 1.0 CB A:GLU34 5.0 18.4 1.0

Cadmium binding site 5 out of 11 in the De Novo Photosynthetic Reaction Center Protein in Apo-State


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of De Novo Photosynthetic Reaction Center Protein in Apo-State within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd205 b:21.8 occ:1.00 NE2 A:HIS110 2.1 13.4 1.0 NE2 A:HIS9 2.1 10.9 1.0 O A:HOH386 2.2 3.6 1.0 O A:HOH376 2.3 4.2 1.0 CE1 A:HIS110 2.9 14.2 1.0 CD2 A:HIS9 2.9 12.5 1.0 CD2 A:HIS110 3.2 14.5 1.0 CE1 A:HIS9 3.2 12.3 1.0 ND1 A:HIS110 4.1 14.0 1.0 CG A:HIS9 4.1 11.2 1.0 ND1 A:HIS9 4.2 11.5 1.0 CG A:HIS110 4.3 12.7 1.0 CA A:GLY92 4.3 13.0 1.0 NE1 A:TRP193 4.4 19.6 1.0 O A:LEU88 4.7 10.6 1.0 CD1 A:LEU88 4.7 14.2 1.0 CG A:LEU88 4.7 13.7 1.0 O A:HOH322 4.8 23.7 1.0 N A:GLY92 4.9 12.1 1.0 CD1 A:TRP193 4.9 20.0 1.0

Cadmium binding site 6 out of 11 in the De Novo Photosynthetic Reaction Center Protein in Apo-State


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of De Novo Photosynthetic Reaction Center Protein in Apo-State within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd206 b:28.7 occ:1.00 O A:HOH307 2.2 25.9 1.0 OE2 A:GLU87 2.4 16.4 1.0 O A:HOH367 3.1 34.5 1.0 CD A:GLU87 3.2 15.2 1.0 OE1 A:GLU87 3.3 15.1 1.0 O A:HOH336 4.2 25.2 1.0 CE A:LYS109 4.2 15.0 1.0 NZ A:LYS109 4.5 13.9 1.0 CG A:GLU87 4.6 13.6 1.0 CD2 A:LEU113 4.9 14.0 1.0

Cadmium binding site 7 out of 11 in the De Novo Photosynthetic Reaction Center Protein in Apo-State


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of De Novo Photosynthetic Reaction Center Protein in Apo-State within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd207 b:32.3 occ:0.30 OE1 A:GLN83 2.0 35.7 1.0 O A:HOH365 2.8 35.3 1.0 CD A:GLN83 3.2 29.2 1.0 NE2 A:GLN83 3.8 30.2 1.0 CG A:GLN83 4.4 21.9 1.0 CG A:GLU80 4.4 22.2 1.0 CB A:GLN83 4.8 17.1 1.0 CB A:GLU80 5.0 18.1 1.0

Cadmium binding site 8 out of 11 in the De Novo Photosynthetic Reaction Center Protein in Apo-State


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of De Novo Photosynthetic Reaction Center Protein in Apo-State within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd208 b:33.5 occ:1.00 OE1 A:GLU170 2.3 21.5 1.0 OE2 A:GLU170 2.4 24.2 1.0 O A:HOH370 2.4 17.5 1.0 CD A:GLU170 2.6 18.6 1.0 O A:HOH378 3.9 26.6 1.0 CG A:GLU170 4.1 17.1 1.0 CD1 A:LEU26 4.5 14.2 1.0 CB A:GLU170 4.8 14.3 1.0 CD2 A:LEU26 5.0 13.5 1.0

Cadmium binding site 9 out of 11 in the De Novo Photosynthetic Reaction Center Protein in Apo-State


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of De Novo Photosynthetic Reaction Center Protein in Apo-State within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd209 b:44.2 occ:1.00 NE2 A:GLN18 4.9 28.0 1.0

Cadmium binding site 10 out of 11 in the De Novo Photosynthetic Reaction Center Protein in Apo-State


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of De Novo Photosynthetic Reaction Center Protein in Apo-State within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd210 b:60.3 occ:1.00 O A:HOH306 2.1 33.0 1.0 OE1 A:GLU62 2.5 41.0 1.0 OE1 A:GLU65 2.5 37.9 1.0 OE2 A:GLU62 2.8 47.7 1.0 CD A:GLU62 2.9 41.0 1.0 CD A:GLU65 3.7 36.5 1.0 OE2 A:GLU65 4.1 46.6 1.0 CG A:GLU62 4.4 37.0 1.0 CA A:GLU62 4.7 26.1 1.0 CB A:GLU62 4.9 32.5 1.0 CG A:GLU65 4.9 29.4 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