Manganese in PDB 5nfo: Human JMJD7 in Complex with Mn and 2OG in the P21212 Form

The structure of Human JMJD7 in Complex with Mn and 2OG in the P21212 Form, PDB code: 5nfo was solved by R.Chowdhury, S.Markolovic, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.78 / 2.17
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	137.315, 61.020, 86.055, 90.00, 90.00, 90.00
R / Rfree (%)	17.1 / 18.9

The binding sites of Manganese atom in the Human JMJD7 in Complex with Mn and 2OG in the P21212 Form (pdb code 5nfo). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Human JMJD7 in Complex with Mn and 2OG in the P21212 Form, PDB code: 5nfo:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Human JMJD7 in Complex with Mn and 2OG in the P21212 Form


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Human JMJD7 in Complex with Mn and 2OG in the P21212 Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:35.2 occ:1.00 NE2 A:HIS178 2.0 40.7 1.0 NE2 A:HIS277 2.1 43.4 1.0 O2 A:AKG502 2.1 33.4 1.0 O5 A:AKG502 2.1 36.5 1.0 OD2 A:ASP180 2.1 44.2 1.0 O A:HOH680 2.5 34.8 1.0 C2 A:AKG502 2.8 39.3 1.0 C1 A:AKG502 2.8 41.8 1.0 CE1 A:HIS277 2.8 40.1 1.0 CE1 A:HIS178 2.9 34.5 1.0 CG A:ASP180 3.1 41.9 1.0 CD2 A:HIS178 3.1 34.9 1.0 CD2 A:HIS277 3.2 42.5 1.0 OD1 A:ASP180 3.4 45.5 1.0 O A:HOH662 3.9 30.8 1.0 O1 A:AKG502 4.0 41.5 1.0 ND1 A:HIS277 4.0 38.6 1.0 ND1 A:HIS178 4.0 33.6 1.0 O A:HOH733 4.0 47.9 1.0 CG A:HIS178 4.2 35.1 1.0 CG A:HIS277 4.2 39.1 1.0 C3 A:AKG502 4.2 42.0 1.0 CZ2 A:TRP291 4.3 51.9 1.0 CB A:ASP180 4.5 45.3 1.0 C4 A:AKG502 4.8 43.0 1.0

Manganese binding site 2 out of 2 in the Human JMJD7 in Complex with Mn and 2OG in the P21212 Form


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Human JMJD7 in Complex with Mn and 2OG in the P21212 Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn501 b:42.4 occ:1.00 O5 B:AKG502 2.1 51.7 1.0 O2 B:AKG502 2.1 45.2 1.0 OD2 B:ASP180 2.1 58.3 1.0 NE2 B:HIS178 2.2 35.2 1.0 NE2 B:HIS277 2.2 39.4 1.0 O B:HOH680 2.3 41.8 1.0 C1 B:AKG502 2.8 51.0 1.0 C2 B:AKG502 2.8 52.5 1.0 CE1 B:HIS178 3.1 35.1 1.0 CG B:ASP180 3.1 54.3 1.0 CE1 B:HIS277 3.1 36.6 1.0 CD2 B:HIS178 3.2 35.4 1.0 CD2 B:HIS277 3.3 38.5 1.0 OD1 B:ASP180 3.3 58.0 1.0 O B:HOH645 3.9 34.2 1.0 O1 B:AKG502 4.0 50.1 1.0 O B:HOH712 4.0 38.9 1.0 ND1 B:HIS178 4.2 35.2 1.0 ND1 B:HIS277 4.3 37.9 1.0 CZ2 B:TRP291 4.3 61.4 1.0 C3 B:AKG502 4.3 54.3 1.0 CG B:HIS178 4.3 35.4 1.0 CG B:HIS277 4.4 37.4 1.0 CB B:ASP180 4.5 50.5 1.0 C4 B:AKG502 4.9 55.1 1.0

S.Markolovic, Q.Zhuang, S.E.Wilkins, C.Eaton, M.J.Katz, H.E.Smith, R.K.Lesniak, C.Hall, W.B.Struwe, R.Konietzny, S.Davis, M.Yang, W.Ge, J.L.Benesch, B.M.Kessler, P.J.Ratcliffe, M.E.Cockman, R.Fischer, P.Wappner, R.Chowdhury, M.L.Coleman, C.J.Schofield. (3S)-Lysyl Hydroxylation of Trafac Gtpases Is Catalyzed By the Human Jumonji-C Oxygenase JMJD7. To Be Published.