Nickel in PDB 2xdv: Crystal Structure of the Catalytic Domain of FLJ14393

The structure of Crystal Structure of the Catalytic Domain of FLJ14393, PDB code: 2xdv was solved by T.Krojer, J.R.C.Muniz, S.S.Ng, E.Pilka, K.Guo, A.C.W.Pike, P.Filippakopoulos, S.Knapp, K.L.Kavanagh, O.Gileadi, G.Bunkoczi, W.W.Yue, F.Niesen, F.Sobott, O.Fedorov, P.Savitsky, G.Kochan, M.Daniel, F.Vondelft, C.H.Arrowsmith, A.M.Edwards, J.Weigelt, C.Bountra, U.Oppermann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.28 / 2.57
Space group	P 43 3 2
Cell size a, b, c (Å), α, β, γ (°)	185.180, 185.180, 185.180, 90.00, 90.00, 90.00
R / Rfree (%)	19.7 / 22.9

The structure of Crystal Structure of the Catalytic Domain of FLJ14393 also contains other interesting chemical elements:

Cadmium	(Cd)	3 atoms
Manganese	(Mn)	1 atom

The binding sites of Nickel atom in the Crystal Structure of the Catalytic Domain of FLJ14393 (pdb code 2xdv). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 6 binding sites of Nickel where determined in the Crystal Structure of the Catalytic Domain of FLJ14393, PDB code: 2xdv:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6;

Nickel binding site 1 out of 6 in the Crystal Structure of the Catalytic Domain of FLJ14393


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 the Catalytic Domain of FLJ14393 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1466 b:43.8 occ:1.00 O2' A:OGA601 2.0 38.5 1.0 O2 A:OGA601 2.0 35.8 1.0 NE2 A:HIS179 2.2 41.9 1.0 NE2 A:HIS240 2.2 38.9 1.0 O A:HOH2148 2.4 53.3 1.0 OD2 A:ASP181 2.5 66.6 1.0 C2 A:OGA601 2.8 41.1 1.0 C1 A:OGA601 2.9 37.9 1.0 CE1 A:HIS240 3.0 38.2 1.0 CD2 A:HIS179 3.1 42.8 1.0 CE1 A:HIS179 3.1 42.4 1.0 OD1 A:ASP181 3.2 63.1 1.0 CG A:ASP181 3.2 61.4 1.0 CD2 A:HIS240 3.3 38.7 1.0 N1 A:OGA601 4.2 43.7 1.0 ND1 A:HIS240 4.2 39.1 1.0 O1 A:OGA601 4.2 36.9 1.0 CG A:HIS179 4.2 42.6 1.0 ND1 A:HIS179 4.3 44.1 1.0 CG A:HIS240 4.3 37.4 1.0 C4 A:OGA601 4.7 45.6 1.0 CB A:ASP181 4.7 42.5 1.0 OH A:TYR167 5.0 55.4 1.0

Nickel binding site 2 out of 6 in the Crystal Structure of the Catalytic Domain of FLJ14393


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 the Catalytic Domain of FLJ14393 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1467 b:43.9 occ:1.00 O A:HOH2086 1.8 41.0 1.0 OD1 A:ASP243 2.3 68.3 1.0 ND1 A:HIS195 2.3 46.6 1.0 OD2 A:ASP243 2.6 58.1 1.0 CG A:ASP243 2.8 60.4 1.0 CG A:HIS195 3.3 44.8 1.0 CE1 A:HIS195 3.3 45.7 1.0 CB A:HIS195 3.5 41.4 1.0 O A:HOH2085 4.2 48.9 1.0 CB A:ASP243 4.3 43.5 1.0 NE2 A:HIS195 4.4 45.7 1.0 CD2 A:HIS195 4.4 45.7 1.0 O A:ASP243 4.6 44.5 1.0 CA A:HIS195 5.0 40.0 1.0

Nickel binding site 3 out of 6 in the Crystal Structure of the Catalytic Domain of FLJ14393


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 the Catalytic Domain of FLJ14393 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1468 b:0.8 occ:1.00 NE2 A:HIS337 2.2 60.7 1.0 O A:HOH2127 2.8 68.3 1.0 CE1 A:HIS337 3.1 59.7 1.0 CD2 A:HIS337 3.4 59.5 1.0 O A:HOH2124 3.5 78.6 1.0 ND1 A:HIS337 4.3 58.6 1.0 CG A:HIS337 4.4 56.0 1.0

Nickel binding site 4 out of 6 in the Crystal Structure of the Catalytic Domain of FLJ14393


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 the Catalytic Domain of FLJ14393 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1469 b:0.6 occ:1.00 NE2 A:HIS423 2.4 82.0 1.0 CE1 A:HIS423 3.3 84.2 1.0 CD2 A:HIS423 3.4 80.7 1.0 CG A:GLU448 3.9 93.2 1.0 O A:GLU448 4.0 72.2 1.0 OE2 A:GLU448 4.1 0.8 1.0 CB A:SER451 4.3 67.6 1.0 CA A:GLU448 4.3 75.4 1.0 CB A:GLU448 4.4 79.3 1.0 ND1 A:HIS423 4.5 85.3 1.0 CD A:GLU448 4.5 0.4 1.0 CG A:HIS423 4.5 80.8 1.0 C A:GLU448 4.6 75.0 1.0 OG A:SER451 4.9 80.9 1.0 N A:LEU452 4.9 65.2 1.0

Nickel binding site 5 out of 6 in the Crystal Structure of the Catalytic Domain of FLJ14393


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Crystal Structure of the Catalytic Domain of FLJ14393 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1470 b:96.0 occ:1.00 OD1 A:ASP129 2.3 97.1 1.0 NE2 A:HIS138 2.4 59.2 1.0 OD2 A:ASP129 2.6 0.4 1.0 O A:HOH2024 2.6 79.7 1.0 CG A:ASP129 2.8 94.3 1.0 CE1 A:HIS138 3.3 56.7 1.0 CD2 A:HIS138 3.4 59.8 1.0 CB A:ASP129 4.2 80.3 1.0 ND1 A:HIS138 4.5 56.2 1.0 CG A:HIS138 4.5 55.6 1.0

Nickel binding site 6 out of 6 in the Crystal Structure of the Catalytic Domain of FLJ14393


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 6 of Crystal Structure of the Catalytic Domain of FLJ14393 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1471 b:91.8 occ:1.00 OE1 A:GLU459 2.5 68.9 1.0 O A:HOH2146 2.5 62.6 1.0 ND1 A:HIS415 2.6 0.9 1.0 OE2 A:GLU459 2.8 78.5 1.0 CD A:GLU459 3.0 71.5 1.0 CE1 A:HIS415 3.2 0.9 1.0 CG A:HIS415 3.8 99.9 1.0 CB A:HIS415 4.3 94.5 1.0 CG A:GLU459 4.5 58.6 1.0 NE2 A:HIS415 4.5 0.6 1.0 NE2 A:HIS395 4.5 61.0 1.0 O A:HOH2147 4.6 54.5 1.0 CD2 A:HIS415 4.8 0.9 1.0 CG A:LYS398 4.8 79.7 1.0 N A:GLY416 4.9 87.7 1.0 CE1 A:HIS395 5.0 60.2 1.0

R.Chowdhury, R.Sekirnik, N.C.Brissett, T.Krojer, C.H.Ho, S.S.Ng, I.J.Clifton, W.Ge, N.J.Kershaw, G.C.Fox, J.R.C.Muniz, M.Vollmar, C.Phillips, E.S.Pilka, K.L.Kavanagh, F.Von Delft, U.Oppermann, M.A.Mcdonough, A.J.Doherty, C.J.Schofield. Ribosomal Oxygenases Are Structurally Conserved From Prokaryotes to Humans. Nature V. 510 422 2014.
ISSN: ESSN 1476-4687
PubMed: 24814345
DOI: 10.1038/NATURE13263