Nickel in PDB 3k2o: Structure of An Oxygenase

The structure of Structure of An Oxygenase, PDB code: 3k2o was solved by T.Krojer, M.A.Mcdonough, I.J.Clifton, M.Mantri, S.S.Ng, A.C.W.Pike, D.S.Butler, C.J.Webby, G.Kochan, C.Bhatia, J.E.Bray, A.Chaikuad, O.Gileadi, F.Von Delft, J.Weigelt, C.H.Arrowsmith, C.Bountra, A.M.Edwards, C.J.Schofield, K.L.Kavanagh, U.Oppermann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.85 / 1.75
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	49.440, 102.030, 98.218, 90.00, 95.89, 90.00
R / Rfree (%)	19.2 / 22.5

The structure of Structure of An Oxygenase also contains other interesting chemical elements:

Chlorine	(Cl)	6 atoms
Sodium	(Na)	2 atoms

The binding sites of Nickel atom in the Structure of An Oxygenase (pdb code 3k2o). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Structure of An Oxygenase, PDB code: 3k2o:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Structure of An Oxygenase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Structure of An Oxygenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni336 b:27.2 occ:1.00 O A:HOH715 2.3 25.4 1.0 NE2 A:HIS273 2.3 21.8 1.0 NE2 A:HIS187 2.3 22.3 1.0 OD1 A:ASP189 2.3 21.2 1.0 O A:HOH717 2.4 29.2 1.0 O A:HOH716 2.4 24.4 1.0 CE1 A:HIS273 3.1 23.8 1.0 CE1 A:HIS187 3.2 23.8 1.0 CG A:ASP189 3.3 22.1 1.0 CD2 A:HIS187 3.3 19.7 1.0 CD2 A:HIS273 3.4 21.0 1.0 OD2 A:ASP189 3.5 25.3 1.0 O A:HOH827 3.9 54.7 1.0 ND1 A:HIS273 4.3 17.3 1.0 ND1 A:HIS187 4.3 24.7 1.0 CG A:HIS187 4.4 21.7 1.0 CG A:HIS273 4.5 14.6 1.0 O A:HOH567 4.6 32.5 1.0 CB A:ASP189 4.7 17.5 1.0

Nickel binding site 2 out of 2 in the Structure of An Oxygenase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Structure of An Oxygenase within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni336 b:29.0 occ:1.00 O B:HOH356 2.3 29.2 1.0 O B:HOH354 2.3 26.1 1.0 NE2 B:HIS273 2.3 20.4 1.0 NE2 B:HIS187 2.3 25.3 1.0 OD1 B:ASP189 2.4 25.2 1.0 O B:HOH346 2.6 35.0 1.0 CE1 B:HIS273 3.2 21.6 1.0 CE1 B:HIS187 3.2 26.7 1.0 CG B:ASP189 3.3 25.9 1.0 CD2 B:HIS187 3.3 21.9 1.0 CD2 B:HIS273 3.4 22.3 1.0 OD2 B:ASP189 3.5 25.8 1.0 O B:HOH618 4.0 48.9 1.0 ND1 B:HIS273 4.3 16.9 1.0 ND1 B:HIS187 4.4 21.0 1.0 CG B:HIS273 4.4 13.1 1.0 CG B:HIS187 4.4 20.5 1.0 O B:HOH725 4.6 51.4 1.0 CL B:CL339 4.6 60.2 1.0 CB B:ASP189 4.7 21.8 1.0 O B:HOH603 4.9 56.9 1.0

M.Mantri, T.Krojer, E.A.Bagg, C.A.Webby, D.S.Butler, G.Kochan, K.L.Kavanagh, U.Oppermann, M.A.Mcdonough, C.J.Schofield. Crystal Structure of the 2-Oxoglutarate- and Fe(II)-Dependent Lysyl Hydroxylase JMJD6. J.Mol.Biol. V. 401 211 2010.
ISSN: ISSN 0022-2836
PubMed: 20685276
DOI: 10.1016/J.JMB.2010.05.054