Manganese in PDB 6f4o: Human JMJD5 in Complex with Mn(II) and Succinate.

All present enzymatic activity of Human JMJD5 in Complex with Mn(II) and Succinate.:
1.14.11.47;

The structure of Human JMJD5 in Complex with Mn(II) and Succinate., PDB code: 6f4o was solved by R.Chowdhury, M.S.Islam, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.56 / 1.28
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.434, 64.411, 77.491, 90.00, 90.00, 90.00
R / Rfree (%)	14.6 / 17.4

The binding sites of Manganese atom in the Human JMJD5 in Complex with Mn(II) and Succinate. (pdb code 6f4o). 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 JMJD5 in Complex with Mn(II) and Succinate., PDB code: 6f4o:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Human JMJD5 in Complex with Mn(II) and Succinate.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Human JMJD5 in Complex with Mn(II) and Succinate. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:15.1 occ:0.65 MN A:MN501 0.0 15.1 0.7 MN A:MN501 0.5 13.1 0.3 OD2 A:ASP323 2.1 14.8 0.7 NE2 A:HIS321 2.1 15.0 1.0 O3 A:SIN502 2.1 13.8 0.3 O A:HOH684 2.1 16.4 0.4 O A:HOH684 2.2 15.1 0.6 O4 A:SIN502 2.3 16.9 0.7 O3 A:SIN502 2.3 17.8 0.7 NE2 A:HIS400 2.3 15.4 1.0 OD1 A:ASP323 2.5 12.3 0.3 C4 A:SIN502 2.6 18.5 0.7 OD2 A:ASP323 2.7 12.5 0.3 O A:HOH611 2.8 23.8 0.3 CG A:ASP323 2.9 11.4 0.3 CE1 A:HIS321 3.0 16.5 1.0 CG A:ASP323 3.0 13.8 0.7 HE1 A:HIS321 3.1 19.8 1.0 CD2 A:HIS321 3.1 14.8 1.0 C4 A:SIN502 3.1 17.0 0.3 CE1 A:HIS400 3.2 13.2 1.0 CD2 A:HIS400 3.3 14.3 1.0 HE1 A:HIS400 3.3 15.8 1.0 OD1 A:ASP323 3.3 20.4 0.7 HD2 A:HIS321 3.4 17.7 1.0 HD2 A:HIS400 3.5 17.2 1.0 O4 A:SIN502 3.5 15.3 0.3 HZ2 A:TRP414 3.7 25.9 0.7 HZ2 A:TRP414 4.0 24.6 0.3 O A:HOH712 4.0 19.8 0.7 ND1 A:HIS321 4.1 15.4 1.0 HD22 A:ASN327 4.1 16.6 0.3 C3 A:SIN502 4.1 15.4 0.7 CG A:HIS321 4.2 14.7 1.0 O A:HOH731 4.3 32.4 1.0 ND1 A:HIS400 4.3 12.5 1.0 HE1 A:TRP414 4.3 16.0 0.3 O A:HOH608 4.4 31.2 1.0 CG A:HIS400 4.4 12.7 1.0 HD21 A:ASN327 4.4 16.6 0.3 CB A:ASP323 4.4 14.8 0.7 CZ2 A:TRP414 4.4 21.6 0.7 O A:HOH611 4.4 22.1 0.7 HH2 A:TRP310 4.5 21.2 1.0 CB A:ASP323 4.5 11.5 0.3 H21 A:SIN502 4.5 15.7 0.3 C3 A:SIN502 4.5 11.7 0.3 H22 A:SIN502 4.5 15.7 0.3 HB2 A:ASP323 4.5 17.8 0.7 O A:HOH702 4.5 43.6 0.5 H31 A:SIN502 4.6 18.5 0.7 ND2 A:ASN327 4.6 13.8 0.3 HD22 A:ASN327 4.7 20.0 0.7 H22 A:SIN502 4.8 20.2 0.7 C2 A:SIN502 4.8 13.1 0.3 HB2 A:ASP323 4.8 13.8 0.3 HE1 A:TRP414 4.8 26.8 0.7 HD1 A:HIS321 4.8 18.4 1.0 H32 A:SIN502 4.8 18.5 0.7 CZ2 A:TRP414 4.8 20.5 0.3 H31 A:SIN502 4.9 14.0 0.3 H21 A:SIN502 4.9 20.2 0.7 O A:HOH706 4.9 31.3 0.4 HB3 A:ASP323 4.9 13.8 0.3 C2 A:SIN502 4.9 16.9 0.7 HZ2 A:TRP310 4.9 24.1 1.0 CH2 A:TRP310 4.9 17.7 1.0 HB3 A:ASP323 5.0 17.8 0.7

Manganese binding site 2 out of 2 in the Human JMJD5 in Complex with Mn(II) and Succinate.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Human JMJD5 in Complex with Mn(II) and Succinate. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:13.1 occ:0.35 MN A:MN501 0.0 13.1 0.3 MN A:MN501 0.5 15.1 0.7 OD2 A:ASP323 1.9 14.8 0.7 O4 A:SIN502 2.0 16.9 0.7 O3 A:SIN502 2.1 13.8 0.3 O A:HOH684 2.2 16.4 0.4 NE2 A:HIS400 2.2 15.4 1.0 OD2 A:ASP323 2.3 12.5 0.3 O A:HOH611 2.4 23.8 0.3 O A:HOH684 2.4 15.1 0.6 O3 A:SIN502 2.5 17.8 0.7 OD1 A:ASP323 2.5 12.3 0.3 NE2 A:HIS321 2.5 15.0 1.0 C4 A:SIN502 2.6 18.5 0.7 CG A:ASP323 2.8 11.4 0.3 C4 A:SIN502 2.9 17.0 0.3 CG A:ASP323 3.0 13.8 0.7 CE1 A:HIS400 3.1 13.2 1.0 O4 A:SIN502 3.2 15.3 0.3 HE1 A:HIS400 3.2 15.8 1.0 CD2 A:HIS400 3.3 14.3 1.0 CE1 A:HIS321 3.4 16.5 1.0 OD1 A:ASP323 3.4 20.4 0.7 HE1 A:HIS321 3.4 19.8 1.0 HD2 A:HIS400 3.5 17.2 1.0 HZ2 A:TRP414 3.5 25.9 0.7 CD2 A:HIS321 3.5 14.8 1.0 O A:HOH712 3.6 19.8 0.7 HD22 A:ASN327 3.7 16.6 0.3 HD2 A:HIS321 3.7 17.7 1.0 HZ2 A:TRP414 3.9 24.6 0.3 HE1 A:TRP414 4.0 16.0 0.3 HD21 A:ASN327 4.0 16.6 0.3 C3 A:SIN502 4.1 15.4 0.7 O A:HOH611 4.1 22.1 0.7 ND2 A:ASN327 4.2 13.8 0.3 CZ2 A:TRP414 4.2 21.6 0.7 HD22 A:ASN327 4.2 20.0 0.7 O A:HOH702 4.3 43.6 0.5 ND1 A:HIS400 4.3 12.5 1.0 CB A:ASP323 4.3 11.5 0.3 CB A:ASP323 4.3 14.8 0.7 HB2 A:ASP323 4.3 17.8 0.7 C3 A:SIN502 4.4 11.7 0.3 CG A:HIS400 4.4 12.7 1.0 HE1 A:TRP414 4.4 26.8 0.7 H31 A:SIN502 4.5 18.5 0.7 ND1 A:HIS321 4.5 15.4 1.0 H21 A:SIN502 4.6 15.7 0.3 HH2 A:TRP310 4.6 21.2 1.0 HB2 A:ASP323 4.6 13.8 0.3 H22 A:SIN502 4.6 15.7 0.3 O A:HOH731 4.6 32.4 1.0 HD21 A:ASN327 4.6 20.0 0.7 CG A:HIS321 4.6 14.7 1.0 H31 A:SIN502 4.7 14.0 0.3 ND2 A:ASN327 4.7 16.7 0.7 HB3 A:ASP323 4.7 13.8 0.3 CZ2 A:TRP414 4.7 20.5 0.3 NE1 A:TRP414 4.7 13.3 0.3 O A:HOH608 4.7 31.2 1.0 H32 A:SIN502 4.7 18.5 0.7 C2 A:SIN502 4.8 13.1 0.3 HZ2 A:TRP310 4.8 24.1 1.0 HB3 A:ASP323 4.8 17.8 0.7 H22 A:SIN502 4.9 20.2 0.7 H32 A:SIN502 4.9 14.0 0.3 CE2 A:TRP414 4.9 18.1 0.7 NE1 A:TRP414 4.9 22.4 0.7 H21 A:SIN502 5.0 20.2 0.7 C2 A:SIN502 5.0 16.9 0.7 CH2 A:TRP310 5.0 17.7 1.0

S.E.Wilkins, S.Islam, J.M.Gannon, S.Markolovic, R.J.Hopkinson, W.Ge, C.J.Schofield, R.Chowdhury. JMJD5 Is A Human Arginyl C-3 Hydroxylase. Nat Commun V. 9 1180 2018.
ISSN: ESSN 2041-1723
PubMed: 29563586
DOI: 10.1038/S41467-018-03410-W