Manganese in PDB 5nfn: JMJD7 in Complex with Mn and 2OG in the H32 Form

The structure of JMJD7 in Complex with Mn and 2OG in the H32 Form, PDB code: 5nfn 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)	48.46 / 2.98
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	207.220, 207.220, 211.788, 90.00, 90.00, 120.00
R / Rfree (%)	24.9 / 25.1

The binding sites of Manganese atom in the JMJD7 in Complex with Mn and 2OG in the H32 Form (pdb code 5nfn). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the JMJD7 in Complex with Mn and 2OG in the H32 Form, PDB code: 5nfn:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the JMJD7 in Complex with Mn and 2OG in the H32 Form


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of JMJD7 in Complex with Mn and 2OG in the H32 Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:72.6 occ:1.00 OD2 A:ASP180 1.9 0.8 1.0 O2 A:AKG502 2.1 90.1 1.0 O5 A:AKG502 2.1 95.7 1.0 NE2 A:HIS178 2.1 83.8 1.0 NE2 A:HIS277 2.1 81.8 1.0 O A:HOH632 2.2 86.1 1.0 C2 A:AKG502 2.7 92.5 1.0 C1 A:AKG502 2.7 91.2 1.0 CE1 A:HIS178 2.9 85.3 1.0 CG A:ASP180 3.0 90.2 1.0 CE1 A:HIS277 3.0 83.8 1.0 CD2 A:HIS277 3.2 87.8 1.0 CD2 A:HIS178 3.2 82.6 1.0 OD1 A:ASP180 3.4 90.6 1.0 O A:HOH601 3.7 88.1 1.0 O1 A:AKG502 3.9 94.0 1.0 ND1 A:HIS178 4.0 84.1 1.0 C3 A:AKG502 4.1 95.4 1.0 ND1 A:HIS277 4.1 81.4 1.0 CG A:HIS178 4.2 83.1 1.0 CG A:HIS277 4.3 82.8 1.0 CB A:ASP180 4.3 88.0 1.0 CZ2 A:TRP291 4.5 97.0 1.0 C4 A:AKG502 4.7 96.5 1.0

Manganese binding site 2 out of 4 in the JMJD7 in Complex with Mn and 2OG in the H32 Form


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of JMJD7 in Complex with Mn and 2OG in the H32 Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn501 b:68.6 occ:1.00 O1 B:AKG502 2.1 90.1 1.0 NE2 B:HIS178 2.1 83.3 1.0 O5 B:AKG502 2.1 0.1 1.0 NE2 B:HIS277 2.2 84.8 1.0 OD2 B:ASP180 2.2 97.1 1.0 O B:HOH637 2.5 84.0 1.0 C1 B:AKG502 2.7 92.1 1.0 C2 B:AKG502 2.7 99.9 1.0 CE1 B:HIS178 2.8 89.2 1.0 CE1 B:HIS277 2.9 86.0 1.0 CG B:ASP180 3.1 88.2 1.0 CD2 B:HIS178 3.2 85.8 1.0 CD2 B:HIS277 3.4 86.9 1.0 OD1 B:ASP180 3.4 87.4 1.0 O2 B:AKG502 3.9 92.3 1.0 ND1 B:HIS178 4.0 89.1 1.0 ND1 B:HIS277 4.1 84.5 1.0 CG B:HIS178 4.2 85.3 1.0 C3 B:AKG502 4.2 94.3 1.0 CZ2 B:TRP291 4.4 0.6 1.0 CG B:HIS277 4.4 86.0 1.0 O B:HOH659 4.4 83.4 1.0 CB B:ASP180 4.5 89.1 1.0 ND2 B:ASN184 4.7 91.3 1.0 C4 B:AKG502 4.8 94.2 1.0

Manganese binding site 3 out of 4 in the JMJD7 in Complex with Mn and 2OG in the H32 Form


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of JMJD7 in Complex with Mn and 2OG in the H32 Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn501 b:0.5 occ:1.00 NE2 C:HIS178 1.9 0.3 1.0 OD2 C:ASP180 2.1 0.6 1.0 O C:HOH622 2.3 0.3 1.0 NE2 C:HIS277 2.7 0.3 1.0 CE1 C:HIS178 2.8 0.3 1.0 CD2 C:HIS178 2.9 0.7 1.0 CG C:ASP180 3.1 0.8 1.0 CE1 C:HIS277 3.3 0.5 1.0 OD1 C:ASP180 3.5 0.9 1.0 CD2 C:HIS277 3.8 0.0 1.0 ND1 C:HIS178 3.9 0.3 1.0 CG C:HIS178 4.0 0.6 1.0 CB C:ASP180 4.4 0.6 1.0 O C:HOH646 4.4 0.4 1.0 CZ2 C:TRP291 4.5 0.9 1.0 ND1 C:HIS277 4.6 0.3 1.0 CG C:HIS277 4.8 0.5 1.0 O C:HOH644 5.0 0.1 1.0

Manganese binding site 4 out of 4 in the JMJD7 in Complex with Mn and 2OG in the H32 Form


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of JMJD7 in Complex with Mn and 2OG in the H32 Form within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn501 b:70.2 occ:1.00 OD2 D:ASP180 2.0 0.4 1.0 O2 D:AKG502 2.1 97.1 1.0 NE2 D:HIS178 2.1 91.1 1.0 O5 D:AKG502 2.1 0.4 1.0 NE2 D:HIS277 2.3 91.0 1.0 O D:HOH625 2.4 97.4 1.0 C2 D:AKG502 2.7 0.9 1.0 C1 D:AKG502 2.7 0.5 1.0 CG D:ASP180 2.9 0.9 1.0 CE1 D:HIS178 3.0 92.3 1.0 CE1 D:HIS277 3.0 90.1 1.0 CD2 D:HIS178 3.0 88.7 1.0 OD1 D:ASP180 3.1 0.6 1.0 CD2 D:HIS277 3.5 90.8 1.0 O1 D:AKG502 3.9 0.4 1.0 ND1 D:HIS178 4.1 90.8 1.0 CG D:HIS178 4.2 87.7 1.0 C3 D:AKG502 4.2 0.6 1.0 ND1 D:HIS277 4.3 88.6 1.0 CB D:ASP180 4.3 98.8 1.0 CG D:HIS277 4.5 88.1 1.0 CZ2 D:TRP291 4.6 0.1 1.0 C4 D:AKG502 4.7 0.8 1.0 O D:HOH648 4.9 89.1 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.