Chlorine 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:

Nickel	(Ni)	2 atoms
Sodium	(Na)	2 atoms

The binding sites of Chlorine atom in the Structure of An Oxygenase (pdb code 3k2o). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Structure of An Oxygenase, PDB code: 3k2o:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in the Structure of An Oxygenase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of An Oxygenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl338 b:75.2 occ:1.00 NA A:NA337 3.5 43.4 1.0 CB A:LYS154 4.1 26.2 1.0 NZ A:LYS151 4.3 68.3 1.0 CD A:LYS154 4.3 32.2 1.0 CG A:LYS154 4.5 26.4 1.0

Chlorine binding site 2 out of 6 in the Structure of An Oxygenase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of An Oxygenase within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl337 b:86.2 occ:1.00 NZ B:LYS4 3.0 74.2 1.0 O B:HOH617 3.7 53.5 1.0 ND1 B:HIS3 4.1 44.0 1.0 CE B:LYS4 4.2 68.1 1.0 CB B:LYS4 4.6 37.5 1.0 CE1 B:HIS3 4.6 40.2 1.0 O B:HOH634 4.7 68.0 1.0 CA B:LYS4 4.8 37.8 1.0 CD B:LYS7 4.8 57.6 1.0 NZ B:LYS7 4.9 72.3 1.0 CG B:LYS4 4.9 46.8 1.0

Chlorine binding site 3 out of 6 in the Structure of An Oxygenase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structure of An Oxygenase within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl339 b:60.2 occ:1.00 ND2 B:ASN197 3.2 23.2 1.0 OG1 B:THR285 3.3 25.8 1.0 O B:HOH356 3.3 29.2 1.0 O B:HOH354 3.4 26.1 1.0 CH3 B:ACT345 3.7 32.0 1.0 CB B:ASN197 3.9 20.4 1.0 CG B:ASN197 4.0 21.8 1.0 CB B:THR285 4.2 22.5 1.0 CH2 B:TRP206 4.2 18.9 1.0 CG2 B:THR285 4.4 18.9 1.0 O B:HOH530 4.4 41.7 1.0 NI B:NI336 4.6 29.0 1.0 C B:ACT345 4.8 33.2 1.0 OXT B:ACT345 4.9 25.1 1.0 CZ3 B:TRP206 5.0 17.1 1.0 CA B:ASN197 5.0 16.1 1.0 CB B:ALA195 5.0 15.1 1.0 O B:HOH618 5.0 48.9 1.0

Chlorine binding site 4 out of 6 in the Structure of An Oxygenase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Structure of An Oxygenase within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl340 b:57.0 occ:1.00 N B:GLU88 3.2 32.9 1.0 O B:HOH490 3.4 34.6 1.0 N B:LEU87 3.6 26.6 1.0 CB B:GLU88 3.6 48.1 1.0 CB B:THR86 3.9 34.6 1.0 OG1 B:THR86 4.0 32.7 1.0 CB B:LEU87 4.0 31.5 1.0 CA B:LEU87 4.0 29.4 1.0 CA B:GLU88 4.0 36.1 1.0 C B:LEU87 4.1 32.0 1.0 C B:THR86 4.3 27.0 1.0 CA B:THR86 4.7 28.8 1.0 OE1 B:GLU88 4.8 76.2 1.0 CG B:LEU87 4.8 38.1 1.0

Chlorine binding site 5 out of 6 in the Structure of An Oxygenase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Structure of An Oxygenase within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl342 b:56.3 occ:1.00 N B:VAL56 3.3 20.9 1.0 O B:HOH644 3.3 67.7 1.0 O B:HOH511 3.7 32.6 1.0 CG2 B:VAL56 3.7 28.8 1.0 CA B:SER55 3.9 25.6 1.0 CB B:SER55 3.9 28.3 1.0 CE B:LYS154 3.9 40.9 1.0 CB B:VAL56 4.0 30.0 1.0 C B:SER55 4.0 26.0 1.0 CA B:VAL56 4.2 24.0 1.0 CD B:LYS154 4.5 31.1 1.0

Chlorine binding site 6 out of 6 in the Structure of An Oxygenase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Structure of An Oxygenase within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl343 b:65.6 occ:1.00 O B:HOH665 3.1 55.7 1.0 O B:HOH676 3.1 64.8 1.0 N B:LYS98 3.3 25.7 1.0 OE1 B:GLN97 3.5 35.2 0.5 CA B:GLN97 3.9 30.4 0.5 CA B:GLN97 3.9 30.5 0.5 CD B:GLN97 4.1 32.7 0.5 C B:GLN97 4.1 26.1 1.0 CB B:LYS98 4.1 26.8 1.0 O B:HOH661 4.2 51.6 1.0 CA B:LYS98 4.2 21.8 1.0 CG B:LYS98 4.3 30.9 1.0 CB B:GLN97 4.3 29.5 0.5 CB B:GLN97 4.4 28.9 0.5 CG B:GLN97 4.4 31.1 0.5 O B:LYS98 4.5 24.4 1.0 NE2 B:GLN97 4.6 34.5 0.5 O B:ASN96 4.6 33.4 1.0 NE B:ARG143 4.8 33.7 1.0 CG B:GLN97 4.9 30.6 0.5 C B:LYS98 4.9 25.4 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