Manganese in PDB 7dyx: Human JMJD5 in Complex with Mn and 5-((2-Cyclopropylbenzyl)Amino) Pyridine-2,4-Dicarboxylic Acid.

The structure of Human JMJD5 in Complex with Mn and 5-((2-Cyclopropylbenzyl)Amino) Pyridine-2,4-Dicarboxylic Acid., PDB code: 7dyx was solved by Y.Nakashima, L.Brewitz, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.54 / 2.27
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	48.92, 64.75, 78.649, 90, 90, 90
R / Rfree (%)	24.2 / 28

The binding sites of Manganese atom in the Human JMJD5 in Complex with Mn and 5-((2-Cyclopropylbenzyl)Amino) Pyridine-2,4-Dicarboxylic Acid. (pdb code 7dyx). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total only one binding site of Manganese was determined in the Human JMJD5 in Complex with Mn and 5-((2-Cyclopropylbenzyl)Amino) Pyridine-2,4-Dicarboxylic Acid., PDB code: 7dyx:

Manganese binding site 1 out of 1 in the Human JMJD5 in Complex with Mn and 5-((2-Cyclopropylbenzyl)Amino) Pyridine-2,4-Dicarboxylic Acid.


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 and 5-((2-Cyclopropylbenzyl)Amino) Pyridine-2,4-Dicarboxylic Acid. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:18.1 occ:1.00 O A:HOH615 1.8 47.0 1.0 NE2 A:HIS321 2.2 38.8 1.0 NE2 A:HIS400 2.2 40.0 1.0 OD2 A:ASP323 2.2 53.5 1.0 O3 A:HRR502 2.2 37.5 1.0 N23 A:HRR502 2.3 40.6 1.0 C2 A:HRR502 3.0 32.8 1.0 C4 A:HRR502 3.0 32.5 1.0 CE1 A:HIS400 3.0 37.2 1.0 CE1 A:HIS321 3.0 41.5 1.0 HE1 A:HIS400 3.1 44.7 1.0 CG A:ASP323 3.1 46.6 1.0 HE1 A:HIS321 3.2 49.8 1.0 CD2 A:HIS321 3.2 33.9 1.0 C22 A:HRR502 3.2 42.5 1.0 CD2 A:HIS400 3.3 40.4 1.0 H221 A:HRR502 3.3 51.0 1.0 OD1 A:ASP323 3.4 40.6 1.0 HD2 A:HIS321 3.4 40.6 1.0 HZ2 A:TRP414 3.5 55.3 1.0 HD2 A:HIS400 3.5 48.5 1.0 ND1 A:HIS321 4.1 41.3 1.0 ND1 A:HIS400 4.2 41.1 1.0 O1 A:HRR502 4.2 49.1 1.0 CG A:HIS321 4.2 32.2 1.0 CZ2 A:TRP414 4.2 46.1 1.0 CG A:HIS400 4.3 31.6 1.0 HE1 A:TRP414 4.3 66.4 1.0 C5 A:HRR502 4.3 38.0 1.0 HD22 A:ASN327 4.4 52.4 1.0 CB A:ASP323 4.5 48.2 1.0 C10 A:HRR502 4.5 49.4 1.0 HB2 A:ASP323 4.5 57.9 1.0 NE1 A:TRP414 4.8 55.4 1.0 HD21 A:ASN327 4.9 52.4 1.0 HD1 A:HIS321 4.9 49.5 1.0 CE2 A:TRP414 4.9 47.2 1.0 HH2 A:TRP310 4.9 57.3 1.0 HD1 A:HIS400 4.9 49.4 1.0 ND2 A:ASN327 4.9 43.7 1.0 C6 A:HRR502 5.0 48.5 1.0 HZ2 A:TRP310 5.0 53.9 1.0

Y.Nakashima, L.Brewitz, C.J.Schofield. Human JMJD5 in Complex with Mn and 2OG. To Be Published.