Nickel 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:

Cadmium

(Cd)

4 atoms

The binding sites of Nickel atom in the Light-Sensitive Photoprotein (pdb code 5vp3). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total only one binding site of Nickel was determined in the Light-Sensitive Photoprotein, PDB code: 5vp3:

Nickel binding site 1 out of 1 in the Light-Sensitive Photoprotein


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Light-Sensitive Photoprotein within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni305 b:36.6 occ:1.00 ND1 A:HIS184 2.0 52.6 1.0 O A:HOH498 2.8 41.1 1.0 CE1 A:HIS184 2.9 41.9 1.0 HE1 A:HIS184 3.0 50.3 1.0 HB2 A:HIS184 3.0 35.2 1.0 CG A:HIS184 3.1 34.0 1.0 O A:HOH501 3.3 49.4 1.0 CB A:HIS184 3.6 29.3 1.0 NE2 A:HIS184 4.0 39.3 1.0 O A:HOH472 4.2 50.5 1.0 CD2 A:HIS184 4.2 41.9 1.0 HA A:HIS184 4.3 32.6 1.0 HB3 A:HIS184 4.3 35.2 1.0 CA A:HIS184 4.6 27.1 1.0 HE2 A:HIS184 4.8 47.2 1.0 O A:HOH459 4.9 32.6 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