Nickel in PDB 6u1a: Crystal Structure of Fluorescent Protein Fusionred

The structure of Crystal Structure of Fluorescent Protein Fusionred, PDB code: 6u1a was solved by S.Pletnev, L.Muslinkina, N.Pletneva, V.Z.Pletnev, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.52 / 1.09
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.015, 55.261, 89.347, 90.00, 90.00, 90.00
R / Rfree (%)	12.7 / 14.7

The structure of Crystal Structure of Fluorescent Protein Fusionred also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Nickel atom in the Crystal Structure of Fluorescent Protein Fusionred (pdb code 6u1a). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Crystal Structure of Fluorescent Protein Fusionred, PDB code: 6u1a:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in the Crystal Structure of Fluorescent Protein Fusionred


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of Fluorescent Protein Fusionred within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni301 b:11.7 occ:1.00 OE2 A:GLU36 2.2 18.7 1.0 O A:HOH634 2.4 18.9 1.0 O A:HOH545 2.5 18.5 1.0 OE1 A:GLU36 2.6 18.0 1.0 CD A:GLU36 2.7 16.0 1.0 CG A:GLU36 4.2 15.8 1.0 NZ A:LYS71 4.2 27.4 1.0 O A:HOH504 4.4 21.8 1.0 CE A:LYS71 4.5 53.4 1.0 O A:TYR35 4.5 17.9 1.0

Nickel binding site 2 out of 4 in the Crystal Structure of Fluorescent Protein Fusionred


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of Fluorescent Protein Fusionred within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni302 b:11.8 occ:1.00 OE2 A:GLU16 2.0 13.5 1.0 NE2 A:HIS23 2.1 11.7 1.0 CD2 A:HIS23 3.1 11.2 1.0 CE1 A:HIS23 3.1 13.4 1.0 CD A:GLU16 3.1 13.9 1.0 CG A:GLU16 3.6 12.0 1.0 OE1 A:GLU16 4.2 19.9 1.0 ND1 A:HIS23 4.2 12.5 1.0 CG A:HIS23 4.2 11.2 1.0 O A:HOH470 4.6 43.0 1.0 O A:HOH517 4.8 44.0 1.0 CB A:GLU16 5.0 10.8 1.0

Nickel binding site 3 out of 4 in the Crystal Structure of Fluorescent Protein Fusionred


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Crystal Structure of Fluorescent Protein Fusionred within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni303 b:12.6 occ:0.60 NI A:NI304 1.3 50.1 0.4 ND1 A:HIS22 1.6 27.1 0.5 CE1 A:HIS22 1.8 14.0 0.5 O A:HOH408 2.3 39.0 0.5 ND1 A:HIS22 2.5 69.8 0.5 CG A:HIS22 2.8 14.1 0.5 NE2 A:HIS22 2.9 19.3 0.5 CG A:HIS22 3.2 19.4 0.5 CB A:HIS22 3.4 13.0 0.5 CD2 A:HIS22 3.4 17.7 0.5 CE1 A:HIS22 3.6 0.2 0.5 CB A:HIS22 3.7 11.1 0.5 CA A:HIS22 4.0 11.0 0.5 CA A:HIS22 4.0 10.8 0.5 O A:HOH621 4.3 37.2 1.0 CD2 A:HIS22 4.4 30.6 0.5 N A:HIS23 4.5 10.1 1.0 O A:HOH558 4.5 29.8 1.0 O A:HOH663 4.5 41.6 1.0 O A:HIS23 4.6 11.8 1.0 NE2 A:HIS22 4.6 55.4 0.5 C A:HIS22 4.7 11.2 0.5 O A:GLY48 4.7 18.0 1.0 C A:HIS22 4.7 10.9 0.5 O A:HOH642 4.7 38.9 1.0

Nickel binding site 4 out of 4 in the Crystal Structure of Fluorescent Protein Fusionred


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Crystal Structure of Fluorescent Protein Fusionred within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni304 b:50.1 occ:0.40 NI A:NI303 1.3 12.6 0.6 ND1 A:HIS22 1.8 69.8 0.5 ND1 A:HIS22 2.2 27.1 0.5 O A:HOH408 2.3 39.0 0.5 CE1 A:HIS22 2.6 0.2 0.5 CE1 A:HIS22 2.7 14.0 0.5 CG A:HIS22 3.0 19.4 0.5 CG A:HIS22 3.5 14.1 0.5 CB A:HIS22 3.7 13.0 0.5 NE2 A:HIS22 3.8 55.4 0.5 NE2 A:HIS22 3.9 19.3 0.5 O A:HOH642 4.0 38.9 1.0 CD2 A:HIS22 4.0 30.6 0.5 CB A:HIS22 4.1 11.1 0.5 CD2 A:HIS22 4.3 17.7 0.5 CA A:HIS22 4.4 11.0 0.5 CA A:HIS22 4.5 10.8 0.5 O A:HOH558 4.8 29.8 1.0 CG A:PRO52 4.9 16.7 1.0

L.Muslinkina, V.Z.Pletnev, N.V.Pletneva, D.A.Ruchkin, D.V.Kolesov, A.M.Bogdanov, L.A.Kost, T.V.Rakitina, Y.K.Agapova, I.I.Shemyakina, D.M.Chudakov, S.Pletnev. Two Independent Routes of Post-Translational Chemistry in Fluorescent Protein Fusionred. Int.J.Biol.Macromol. V. 155 551 2020.
ISSN: ISSN 0141-8130
PubMed: 32243936
DOI: 10.1016/J.IJBIOMAC.2020.03.244