Cadmium in PDB 5vju: De Novo Photosynthetic Reaction Center Protein Variant Equipped with His-Tyr H-Bond, Heme B, and Cd(II) Ions

The structure of De Novo Photosynthetic Reaction Center Protein Variant Equipped with His-Tyr H-Bond, Heme B, and Cd(II) Ions, PDB code: 5vju 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)	71.63 / 2.08
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	44.485, 25.876, 73.708, 90.00, 103.64, 90.00
R / Rfree (%)	18.3 / 24.3

The structure of De Novo Photosynthetic Reaction Center Protein Variant Equipped with His-Tyr H-Bond, Heme B, and Cd(II) Ions also contains other interesting chemical elements:

Iron

(Fe)

1 atom

The binding sites of Cadmium atom in the De Novo Photosynthetic Reaction Center Protein Variant Equipped with His-Tyr H-Bond, Heme B, and Cd(II) Ions (pdb code 5vju). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 7 binding sites of Cadmium where determined in the De Novo Photosynthetic Reaction Center Protein Variant Equipped with His-Tyr H-Bond, Heme B, and Cd(II) Ions, PDB code: 5vju:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7;

Cadmium binding site 1 out of 7 in the De Novo Photosynthetic Reaction Center Protein Variant Equipped with His-Tyr H-Bond, Heme B, and Cd(II) Ions


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 Variant Equipped with His-Tyr H-Bond, Heme B, and Cd(II) Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd202 b:23.5 occ:1.00 O A:HOH334 2.0 23.2 1.0 OE1 A:GLU64 2.3 25.8 1.0 OE1 A:GLU135 2.3 29.9 1.0 ND1 A:HIS67 2.3 24.6 1.0 OE2 A:GLU34 2.4 25.2 1.0 OE1 A:GLU34 2.4 22.8 1.0 CD A:GLU34 2.8 23.9 1.0 OE2 A:GLU135 2.8 18.5 1.0 CD A:GLU135 2.9 23.6 1.0 CE1 A:HIS67 3.2 24.8 1.0 CD A:GLU64 3.3 25.1 1.0 CG A:HIS67 3.3 24.1 1.0 CD A:CD203 3.6 22.1 1.0 CB A:HIS67 3.7 23.4 1.0 OE2 A:GLU64 3.9 30.1 1.0 O A:HOH363 4.0 29.4 1.0 CG A:GLU34 4.3 25.4 1.0 O A:HOH382 4.3 26.7 1.0 CA A:GLU64 4.3 26.4 1.0 CG A:GLU135 4.3 20.3 1.0 NE2 A:HIS67 4.4 24.2 1.0 CG A:GLU64 4.4 27.7 1.0 CD2 A:HIS67 4.4 24.2 1.0 CB A:GLU64 4.5 26.1 1.0 CG2 A:ILE131 4.6 21.2 1.0 OH A:TYR168 4.6 22.0 1.0 CE1 A:HIS138 4.8 18.5 1.0 ND1 A:HIS138 4.8 18.6 1.0 CE2 A:TYR168 5.0 18.9 1.0

Cadmium binding site 2 out of 7 in the De Novo Photosynthetic Reaction Center Protein Variant Equipped with His-Tyr H-Bond, Heme B, and Cd(II) Ions


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 Variant Equipped with His-Tyr H-Bond, Heme B, and Cd(II) Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd203 b:22.1 occ:1.00 OE1 A:GLU161 1.9 29.9 1.0 OE2 A:GLU64 2.2 30.1 1.0 OE2 A:GLU135 2.2 18.5 1.0 ND1 A:HIS138 2.4 18.6 1.0 O A:HOH334 2.6 23.2 1.0 OE2 A:GLU161 2.6 35.7 1.0 CD A:GLU161 2.6 32.0 1.0 OE1 A:GLU64 2.9 25.8 1.0 CD A:GLU64 2.9 25.1 1.0 CD A:GLU135 3.3 23.6 1.0 CE1 A:HIS138 3.3 18.5 1.0 CG A:HIS138 3.4 17.6 1.0 CD A:CD202 3.6 23.5 1.0 CB A:HIS138 3.7 17.6 1.0 OE1 A:GLU135 3.8 29.9 1.0 CG A:GLU161 4.1 29.1 1.0 CG A:GLU64 4.4 27.7 1.0 CA A:GLU135 4.4 18.2 1.0 CG A:GLU135 4.4 20.3 1.0 O A:HOH346 4.5 19.2 1.0 NE2 A:HIS138 4.5 16.8 1.0 CB A:GLU135 4.5 18.9 1.0 O A:HOH363 4.5 29.4 1.0 CD2 A:HIS138 4.5 16.0 1.0 CG2 A:ILE60 4.6 20.0 1.0 O A:HOH382 4.7 26.7 1.0 ND1 A:HIS67 4.9 24.6 1.0 CE1 A:HIS67 4.9 24.8 1.0

Cadmium binding site 3 out of 7 in the De Novo Photosynthetic Reaction Center Protein Variant Equipped with His-Tyr H-Bond, Heme B, and Cd(II) Ions


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 Variant Equipped with His-Tyr H-Bond, Heme B, and Cd(II) Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd204 b:26.9 occ:1.00 OE2 A:GLU133 2.3 22.7 1.0 O A:HOH377 2.3 22.7 1.0 OE1 A:GLU136 2.4 20.3 1.0 OE2 A:GLU136 2.5 24.6 1.0 OE1 A:GLU133 2.5 20.3 1.0 CD A:GLU136 2.8 21.8 1.0 CD A:GLU133 2.8 21.0 1.0 CG A:GLU136 4.3 20.6 1.0 CG A:GLU133 4.3 20.7 1.0 O A:HOH315 4.5 29.2 1.0 NH2 A:ARG169 4.6 31.4 1.0 CG A:LEU132 4.8 19.3 1.0 CA A:GLU133 4.8 18.6 1.0 CD2 A:LEU132 4.9 19.4 1.0 CB A:GLU136 5.0 18.8 1.0

Cadmium binding site 4 out of 7 in the De Novo Photosynthetic Reaction Center Protein Variant Equipped with His-Tyr H-Bond, Heme B, and Cd(II) Ions


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 Variant Equipped with His-Tyr H-Bond, Heme B, and Cd(II) Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd205 b:50.5 occ:1.00 OE1 A:GLN97 2.3 42.6 1.0 OE2 A:GLU94 2.7 43.9 1.0 OE1 A:GLU94 2.9 41.8 1.0 CD A:GLU94 3.1 38.8 1.0 CD A:GLN97 3.2 37.5 1.0 NE2 A:GLN97 3.4 41.0 1.0 CG A:GLU94 4.5 37.8 1.0 CG A:GLN97 4.5 36.3 1.0 CB A:GLN97 4.9 30.3 1.0

Cadmium binding site 5 out of 7 in the De Novo Photosynthetic Reaction Center Protein Variant Equipped with His-Tyr H-Bond, Heme B, and Cd(II) Ions


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 Variant Equipped with His-Tyr H-Bond, Heme B, and Cd(II) Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd206 b:32.6 occ:1.00 OE1 A:GLU140 2.4 25.3 1.0 OE2 A:GLU140 2.4 24.8 1.0 OE1 A:GLU143 2.5 24.6 1.0 CD A:GLU140 2.8 23.4 1.0 CD A:GLU143 3.6 25.1 1.0 OE2 A:GLU143 3.8 25.5 1.0 CG A:GLU140 4.3 21.6 1.0 O A:HOH309 4.5 18.5 1.0 O A:HOH337 4.7 31.7 1.0 CG2 A:ILE139 4.7 25.3 1.0 CA A:GLU140 4.8 19.6 1.0 CG A:GLU143 4.9 21.5 1.0

Cadmium binding site 6 out of 7 in the De Novo Photosynthetic Reaction Center Protein Variant Equipped with His-Tyr H-Bond, Heme B, and Cd(II) Ions


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 Variant Equipped with His-Tyr H-Bond, Heme B, and Cd(II) Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd207 b:46.5 occ:1.00 OE2 A:GLU43 2.0 48.6 1.0 OE1 A:GLU46 2.3 38.3 1.0 OE2 A:GLU46 2.5 41.6 1.0 CD A:GLU46 2.8 38.5 1.0 CD A:GLU43 3.1 48.2 1.0 OE1 A:GLU43 3.6 56.5 1.0 O A:HOH354 3.9 32.8 1.0 CG A:GLU43 4.2 42.9 1.0 CG A:GLU46 4.3 39.1 1.0 NZ A:LYS39 4.6 47.1 1.0 CA A:GLU43 4.8 36.3 1.0 CB A:GLU46 5.0 37.2 1.0

Cadmium binding site 7 out of 7 in the De Novo Photosynthetic Reaction Center Protein Variant Equipped with His-Tyr H-Bond, Heme B, and Cd(II) Ions


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 Variant Equipped with His-Tyr H-Bond, Heme B, and Cd(II) Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd208 b:37.5 occ:1.00 OE2 A:GLU8 2.3 26.1 1.0 OE1 A:GLU8 2.5 21.9 1.0 O A:HOH375 2.6 15.1 1.0 O A:HOH386 2.6 21.0 1.0 CD A:GLU8 2.8 22.6 1.0 NZ A:LYS184 4.1 49.4 1.0 CE A:LYS184 4.3 48.2 1.0 CG A:GLU8 4.3 22.5 1.0 CD2 A:LEU5 4.6 37.3 1.0 CG2 A:THR188 4.8 21.3 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.