Cadmium in PDB 5vp3: Light-Sensitive Photoprotein

The structure of Light-Sensitive Photoprotein, PDB code: 5vp3 was solved by M.A.Gorman, M.W.Parker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.18 / 2.15
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	72.614, 72.614, 81.429, 90.00, 90.00, 120.00
R / Rfree (%)	16.1 / 20.3

The structure of Light-Sensitive Photoprotein also contains other interesting chemical elements:

Nickel

(Ni)

1 atom

The binding sites of Cadmium atom in the Light-Sensitive Photoprotein (pdb code 5vp3). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 4 binding sites of Cadmium where determined in the Light-Sensitive Photoprotein, PDB code: 5vp3:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in the Light-Sensitive Photoprotein


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Light-Sensitive Photoprotein within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd301 b:34.1 occ:1.00 OD1 A:ASP44 2.2 34.0 1.0 OD1 A:ASP46 2.3 44.4 1.0 O A:LYS50 2.3 31.7 1.0 OE2 A:GLU55 2.4 34.6 1.0 OD1 A:ASP48 2.4 37.4 1.0 O A:HOH424 2.5 39.6 1.0 OE1 A:GLU55 2.8 33.9 1.0 CD A:GLU55 2.9 33.3 1.0 CG A:ASP48 3.1 45.0 1.0 CG A:ASP46 3.2 42.0 1.0 CG A:ASP44 3.2 38.6 1.0 OD2 A:ASP48 3.4 41.5 1.0 H A:LYS50 3.4 43.5 1.0 H A:ASP48 3.4 49.2 1.0 C A:LYS50 3.4 31.7 1.0 OD2 A:ASP46 3.5 45.1 1.0 HA A:ASP44 3.5 42.3 1.0 H A:ASP46 3.5 46.1 1.0 HB3 A:LYS50 3.7 49.5 1.0 HA A:MET51 3.9 39.6 1.0 OD2 A:ASP44 4.0 31.0 1.0 HG23 A:THR52 4.1 40.5 1.0 CA A:ASP44 4.1 35.2 1.0 N A:LYS50 4.1 36.2 1.0 CB A:ASP44 4.2 36.5 1.0 H A:LEU45 4.2 54.1 1.0 CA A:LYS50 4.2 33.6 1.0 H A:THR47 4.2 58.7 1.0 N A:ASP48 4.3 41.0 1.0 CB A:ASP48 4.3 40.9 1.0 C A:ASP44 4.3 46.3 1.0 N A:ASP46 4.4 38.4 1.0 HB3 A:ASP48 4.4 49.2 1.0 CG A:GLU55 4.4 37.3 1.0 HB2 A:ASP44 4.4 43.9 1.0 CB A:LYS50 4.4 41.3 1.0 N A:LEU45 4.4 45.0 1.0 N A:MET51 4.4 29.5 1.0 H A:THR52 4.5 37.0 1.0 CB A:ASP46 4.5 44.4 1.0 N A:THR47 4.6 48.9 1.0 CA A:MET51 4.6 33.0 1.0 HG3 A:GLU55 4.7 44.8 1.0 HG2 A:GLU55 4.7 44.8 1.0 CA A:ASP48 4.8 33.8 1.0 H A:GLY49 4.8 34.5 1.0 HE2 A:LYS50 4.8 56.5 1.0 CA A:ASP46 4.8 36.8 1.0 O A:ASP44 4.9 41.7 1.0 HG2 A:LYS50 4.9 48.3 1.0 C A:ASP46 5.0 48.5 1.0 N A:GLY49 5.0 28.8 1.0 N A:THR52 5.0 30.8 1.0 CG2 A:THR52 5.0 33.7 1.0 HB3 A:ASP46 5.0 53.3 1.0

Cadmium binding site 2 out of 4 in the Light-Sensitive Photoprotein


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Light-Sensitive Photoprotein within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd302 b:28.5 occ:1.00 HB2 A:ASP138 2.1 39.7 1.0 OE2 A:GLU147 2.2 27.4 1.0 OD1 A:ASP136 2.2 32.3 1.0 OD1 A:ASP140 2.3 38.4 1.0 O A:THR142 2.4 27.3 1.0 OE1 A:GLU147 2.4 29.1 1.0 CD A:GLU147 2.7 31.4 1.0 O A:HOH402 2.7 25.1 1.0 CB A:ASP138 3.0 33.1 1.0 CG A:ASP140 3.1 35.2 1.0 HA A:ASP136 3.1 39.5 1.0 OD2 A:ASP138 3.3 46.6 1.0 CG A:ASP136 3.3 33.1 1.0 H A:ASP140 3.4 45.2 1.0 H A:ASP138 3.4 54.4 1.0 CG A:ASP138 3.4 33.2 1.0 OD2 A:ASP140 3.4 33.6 1.0 C A:THR142 3.5 29.2 1.0 H A:THR142 3.5 30.8 1.0 HB3 A:ASP138 3.5 39.7 1.0 HA A:VAL143 3.5 33.6 1.0 HG1 A:THR142 3.8 46.1 1.0 H A:ASP144 3.8 31.4 1.0 CA A:ASP136 3.8 32.9 1.0 CB A:ASP136 4.0 29.5 1.0 N A:ASP138 4.0 45.3 1.0 HB2 A:ASP136 4.0 35.5 1.0 OG1 A:THR142 4.1 38.4 1.0 CA A:ASP138 4.1 45.6 1.0 N A:ASP140 4.2 37.6 1.0 OD2 A:ASP136 4.2 33.8 1.0 CG A:GLU147 4.2 23.1 1.0 N A:THR142 4.2 25.7 1.0 C A:ASP136 4.2 33.6 1.0 H A:GLY139 4.3 43.2 1.0 N A:VAL143 4.3 22.6 1.0 CA A:VAL143 4.3 28.0 1.0 CB A:ASP140 4.3 30.9 1.0 CA A:THR142 4.4 30.7 1.0 N A:ASP144 4.4 26.1 1.0 OD1 A:ASP138 4.4 59.9 1.0 HB3 A:ASP140 4.5 37.2 1.0 HG3 A:GLU147 4.5 27.7 1.0 H A:GLY141 4.6 44.2 1.0 N A:GLY139 4.6 36.0 1.0 N A:ASP137 4.6 33.1 1.0 H A:ASP137 4.6 39.7 1.0 HB3 A:ASP144 4.6 37.2 1.0 HG2 A:GLU147 4.7 27.7 1.0 O A:ASP136 4.7 27.7 1.0 CA A:ASP140 4.7 34.6 1.0 C A:ASP138 4.8 42.3 1.0 HB2 A:GLU147 4.8 34.2 1.0 C A:VAL143 4.8 30.3 1.0 N A:GLY141 4.8 36.8 1.0 HB3 A:ASP136 4.9 35.5 1.0 HA A:ASP138 4.9 54.7 1.0 CB A:THR142 4.9 34.9 1.0 C A:ASP140 4.9 41.0 1.0 CG A:ASP144 5.0 37.4 1.0

Cadmium binding site 3 out of 4 in the Light-Sensitive Photoprotein


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Light-Sensitive Photoprotein within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd303 b:26.2 occ:1.00 HB2 A:ASP172 2.1 31.3 1.0 OE1 A:GLU178 2.2 25.9 1.0 OD1 A:ASP170 2.2 28.3 1.0 OE1 A:GLU181 2.4 24.7 1.0 O A:LYS176 2.4 29.6 1.0 HG1 A:THR174 2.5 34.3 1.0 OG1 A:THR174 2.5 28.5 1.0 HB3 A:ASP172 2.6 31.3 1.0 CB A:ASP172 2.7 26.1 1.0 OE2 A:GLU181 2.9 22.2 1.0 CD A:GLU181 2.9 24.3 1.0 H A:THR174 3.1 38.0 1.0 OD2 A:ASP172 3.2 54.2 1.0 CD A:GLU178 3.2 38.6 1.0 HA A:ASP170 3.3 34.8 1.0 CG A:ASP170 3.3 34.6 1.0 CG A:ASP172 3.4 26.5 1.0 H A:GLU178 3.4 25.2 1.0 OE2 A:GLU178 3.5 31.2 1.0 C A:LYS176 3.6 29.9 1.0 HG23 A:THR174 3.6 41.5 1.0 HA A:LEU177 3.6 36.6 1.0 CB A:THR174 3.7 37.4 1.0 H A:LYS176 3.7 30.0 1.0 H A:ASP172 3.9 36.4 1.0 N A:THR174 3.9 31.7 1.0 HG21 A:THR174 4.0 41.5 1.0 CG2 A:THR174 4.0 34.6 1.0 CA A:ASP170 4.0 29.0 1.0 CB A:ASP170 4.1 26.8 1.0 CA A:ASP172 4.1 40.5 1.0 HB2 A:ASP170 4.1 32.2 1.0 OD2 A:ASP170 4.2 30.1 1.0 N A:GLU178 4.2 21.0 1.0 N A:ASP172 4.3 30.3 1.0 H A:LYS173 4.4 44.4 1.0 HD23 A:LEU177 4.4 31.9 1.0 CA A:THR174 4.4 34.8 1.0 CG A:GLU181 4.4 26.8 1.0 CA A:LEU177 4.4 30.5 1.0 N A:LYS176 4.4 25.0 1.0 HB A:THR174 4.4 44.9 1.0 C A:ASP170 4.4 30.8 1.0 N A:LEU177 4.5 35.5 1.0 HB2 A:GLU178 4.5 34.2 1.0 HB2 A:LYS176 4.5 34.8 1.0 N A:LYS173 4.5 37.0 1.0 CG A:GLU178 4.6 30.7 1.0 C A:ASP172 4.6 42.0 1.0 CA A:LYS176 4.6 27.6 1.0 HG3 A:GLU181 4.6 32.2 1.0 OD1 A:ASP172 4.6 61.0 1.0 HB2 A:GLU181 4.8 33.2 1.0 HA A:ASP172 4.8 48.6 1.0 H A:GLY175 4.8 38.7 1.0 C A:LEU177 4.8 26.6 1.0 N A:THR171 4.9 28.1 1.0 H A:THR171 4.9 33.8 1.0 O A:ASP170 4.9 32.8 1.0 HG22 A:THR174 4.9 41.5 1.0 HG2 A:GLU181 4.9 32.2 1.0 CB A:GLU178 4.9 28.5 1.0 HB3 A:ASP170 5.0 32.2 1.0 C A:THR174 5.0 27.7 1.0 HG2 A:GLU178 5.0 36.9 1.0

Cadmium binding site 4 out of 4 in the Light-Sensitive Photoprotein


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Light-Sensitive Photoprotein within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd304 b:31.1 occ:0.70 O A:HOH496 2.6 31.4 1.0 OE1 A:GLU192 2.6 31.6 1.0 O A:HOH495 2.7 27.6 1.0 OE2 A:GLU192 2.7 35.0 1.0 CD A:GLU192 3.0 39.3 1.0 HZ2 A:LYS188 3.5 64.2 1.0 HH11 A:ARG187 3.7 52.5 1.0 O A:HOH501 3.7 49.4 1.0 HZ3 A:LYS188 3.9 64.2 1.0 O A:HOH500 4.0 39.3 1.0 HD3 A:ARG187 4.0 39.4 1.0 NZ A:LYS188 4.1 53.4 1.0 NH1 A:ARG187 4.4 43.8 1.0 CG A:GLU192 4.4 45.3 1.0 HH12 A:ARG187 4.5 52.5 1.0 HG2 A:GLU192 4.6 54.4 1.0 HZ1 A:LYS188 4.6 64.2 1.0 HB3 A:ARG187 4.8 31.6 1.0 HE2 A:LYS188 4.9 60.2 1.0 HG3 A:GLU192 4.9 54.4 1.0 CD A:ARG187 5.0 32.8 1.0

M.Molakarimi, M.A.Gorman, A.Mohseni, Z.Pashandi, M.Taghdir, H.Naderi-Manesh, R.H.Sajedi, M.W.Parker. Reaction Mechanism of the Bioluminescent Protein MNEMIOPSIN1 Revealed By X-Ray Crystallography and Qm/Mm Simulations. J. Biol. Chem. V. 294 20 2019.
ISSN: ESSN 1083-351X
PubMed: 30420427
DOI: 10.1074/JBC.RA118.006053