Manganese in PDB 7yxj: Drosophila Melanogaster JMJD7 (DMJMJD7) in Complex with Mn and 2,4- Pdca

The structure of Drosophila Melanogaster JMJD7 (DMJMJD7) in Complex with Mn and 2,4- Pdca, PDB code: 7yxj was solved by R.Chowdhury, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	55.35 / 2.45
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	53.557, 65.762, 206.957, 90, 97.78, 90
R / Rfree (%)	20.6 / 23

The binding sites of Manganese atom in the Drosophila Melanogaster JMJD7 (DMJMJD7) in Complex with Mn and 2,4- Pdca (pdb code 7yxj). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Drosophila Melanogaster JMJD7 (DMJMJD7) in Complex with Mn and 2,4- Pdca, PDB code: 7yxj:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Drosophila Melanogaster JMJD7 (DMJMJD7) in Complex with Mn and 2,4- Pdca


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Drosophila Melanogaster JMJD7 (DMJMJD7) in Complex with Mn and 2,4- Pdca within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:35.9 occ:1.00 OD2 A:ASP177 2.1 39.3 1.0 O21 A:PD2507 2.1 37.9 1.0 NE2 A:HIS278 2.2 37.0 1.0 O A:HOH627 2.2 33.9 1.0 N1 A:PD2507 2.4 42.5 1.0 NE2 A:HIS175 2.5 36.7 1.0 C21 A:PD2507 2.9 42.6 1.0 CE1 A:HIS278 3.0 36.5 1.0 C2 A:PD2507 3.0 42.9 1.0 HE1 A:HIS278 3.1 43.8 1.0 CG A:ASP177 3.1 37.1 1.0 CD2 A:HIS278 3.3 35.6 1.0 CE1 A:HIS175 3.4 36.7 1.0 CD2 A:HIS175 3.4 38.7 1.0 C6 A:PD2507 3.4 40.3 1.0 HE1 A:HIS175 3.5 44.0 1.0 HZ2 A:TRP292 3.5 53.6 1.0 HD2 A:HIS278 3.6 42.7 1.0 HD2 A:HIS175 3.6 46.5 1.0 OD1 A:ASP177 3.6 40.9 1.0 H6 A:PD2507 3.6 48.4 1.0 O A:HOH631 3.9 29.7 1.0 O22 A:PD2507 4.1 43.6 1.0 ND1 A:HIS278 4.2 32.8 1.0 C3 A:PD2507 4.3 41.4 1.0 CG A:HIS278 4.3 30.8 1.0 HE1 A:TRP292 4.4 49.1 1.0 CZ2 A:TRP292 4.4 44.7 1.0 HB2 A:ASP177 4.4 45.4 1.0 ND1 A:HIS175 4.4 34.3 1.0 CB A:ASP177 4.4 37.8 1.0 CG A:HIS175 4.5 36.6 1.0 HD22 A:ASN181 4.5 46.6 1.0 HD21 A:ASN181 4.6 46.6 1.0 C5 A:PD2507 4.6 40.2 1.0 ND2 A:ASN181 4.9 38.8 1.0 HD1 A:HIS278 4.9 39.4 1.0 HB3 A:ASP177 4.9 45.4 1.0 O A:HOH679 5.0 48.9 1.0 H3 A:PD2507 5.0 49.6 1.0 NE1 A:TRP292 5.0 40.9 1.0

Manganese binding site 2 out of 4 in the Drosophila Melanogaster JMJD7 (DMJMJD7) in Complex with Mn and 2,4- Pdca


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Drosophila Melanogaster JMJD7 (DMJMJD7) in Complex with Mn and 2,4- Pdca within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn501 b:43.6 occ:1.00 O22 B:PD2506 2.0 50.8 1.0 OD2 B:ASP177 2.1 46.9 1.0 O B:HOH622 2.2 45.6 1.0 NE2 B:HIS175 2.3 41.2 1.0 N1 B:PD2506 2.3 51.5 1.0 NE2 B:HIS278 2.5 43.4 1.0 C21 B:PD2506 2.8 49.0 1.0 C2 B:PD2506 2.9 48.0 1.0 CE1 B:HIS175 3.1 44.0 1.0 HE1 B:HIS175 3.2 52.8 1.0 CG B:ASP177 3.2 46.1 1.0 CE1 B:HIS278 3.3 40.5 1.0 HE1 B:HIS278 3.3 48.6 1.0 HZ2 B:TRP292 3.3 64.6 1.0 CD2 B:HIS175 3.4 46.4 1.0 C6 B:PD2506 3.4 53.2 1.0 CD2 B:HIS278 3.6 40.7 1.0 HD2 B:HIS175 3.6 55.7 1.0 H6 B:PD2506 3.6 63.8 1.0 OD1 B:ASP177 3.7 51.9 1.0 HD2 B:HIS278 3.8 48.8 1.0 O B:HOH634 3.9 42.2 1.0 O21 B:PD2506 3.9 52.5 1.0 CZ2 B:TRP292 4.2 53.8 1.0 C3 B:PD2506 4.2 48.0 1.0 ND1 B:HIS175 4.3 41.0 1.0 HB2 B:ASP177 4.4 52.4 1.0 HE1 B:TRP292 4.4 67.2 1.0 CG B:HIS175 4.4 42.8 1.0 CB B:ASP177 4.5 43.6 1.0 ND1 B:HIS278 4.5 36.3 1.0 HD22 B:ASN181 4.6 62.9 1.0 C5 B:PD2506 4.6 55.1 1.0 CG B:HIS278 4.7 36.5 1.0 H3 B:PD2506 4.8 57.6 1.0 C4 B:PD2506 4.9 50.7 1.0 HB3 B:ASP177 4.9 52.4 1.0 CE2 B:TRP292 4.9 53.3 1.0 HH2 B:TRP292 5.0 68.6 1.0 NE1 B:TRP292 5.0 56.0 1.0 HG21 B:THR172 5.0 56.1 1.0 HD21 B:ASN181 5.0 62.9 1.0

Manganese binding site 3 out of 4 in the Drosophila Melanogaster JMJD7 (DMJMJD7) in Complex with Mn and 2,4- Pdca


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Drosophila Melanogaster JMJD7 (DMJMJD7) in Complex with Mn and 2,4- Pdca within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn501 b:44.6 occ:1.00 OD2 C:ASP177 2.0 53.2 1.0 O21 C:PD2503 2.2 54.5 1.0 O C:HOH604 2.2 45.8 1.0 NE2 C:HIS175 2.3 48.7 1.0 NE2 C:HIS278 2.3 48.2 1.0 N1 C:PD2503 2.6 59.7 1.0 C21 C:PD2503 3.0 58.4 1.0 CE1 C:HIS175 3.0 50.4 1.0 CE1 C:HIS278 3.1 46.3 1.0 HE1 C:HIS175 3.1 60.5 1.0 HE1 C:HIS278 3.1 55.6 1.0 C2 C:PD2503 3.2 58.5 1.0 CG C:ASP177 3.2 54.6 1.0 CD2 C:HIS175 3.3 47.4 1.0 CD2 C:HIS278 3.4 50.1 1.0 HZ2 C:TRP292 3.5 68.3 1.0 C6 C:PD2503 3.6 63.1 1.0 HD2 C:HIS175 3.6 56.9 1.0 HD2 C:HIS278 3.6 60.1 1.0 H6 C:PD2503 3.7 75.7 1.0 OD1 C:ASP177 3.8 56.7 1.0 ND1 C:HIS175 4.2 45.9 1.0 O22 C:PD2503 4.2 61.3 1.0 HB2 C:ASP177 4.2 64.0 1.0 HE1 C:TRP292 4.2 66.8 1.0 ND1 C:HIS278 4.3 48.0 1.0 CG C:HIS175 4.3 43.0 1.0 CZ2 C:TRP292 4.4 57.0 1.0 CB C:ASP177 4.4 53.4 1.0 CG C:HIS278 4.4 48.0 1.0 C3 C:PD2503 4.5 59.3 1.0 HD22 C:ASN181 4.5 72.0 1.0 HD21 C:ASN181 4.7 72.0 1.0 C5 C:PD2503 4.8 65.2 1.0 NE1 C:TRP292 4.9 55.6 1.0 HD1 C:HIS175 4.9 55.1 1.0 HB3 C:ASP177 4.9 64.0 1.0 ND2 C:ASN181 4.9 60.0 1.0 HD1 C:HIS278 5.0 57.6 1.0 CE2 C:TRP292 5.0 56.1 1.0

Manganese binding site 4 out of 4 in the Drosophila Melanogaster JMJD7 (DMJMJD7) in Complex with Mn and 2,4- Pdca


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Drosophila Melanogaster JMJD7 (DMJMJD7) in Complex with Mn and 2,4- Pdca within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn501 b:48.8 occ:1.00 OD2 D:ASP177 2.1 74.2 1.0 O D:HOH612 2.1 61.1 1.0 O22 D:PD2506 2.1 56.2 1.0 NE2 D:HIS175 2.3 43.4 1.0 NE2 D:HIS278 2.4 52.0 1.0 N1 D:PD2506 2.4 61.1 1.0 C21 D:PD2506 2.7 60.8 1.0 C2 D:PD2506 2.9 59.3 1.0 CE1 D:HIS175 3.0 47.7 1.0 HE1 D:HIS175 3.1 57.2 1.0 CE1 D:HIS278 3.2 46.9 1.0 CG D:ASP177 3.2 64.5 1.0 HE1 D:HIS278 3.3 56.3 1.0 CD2 D:HIS175 3.4 47.8 1.0 CD2 D:HIS278 3.4 49.5 1.0 C6 D:PD2506 3.5 61.7 1.0 HZ2 D:TRP292 3.6 76.5 1.0 HD2 D:HIS175 3.6 57.4 1.0 HD2 D:HIS278 3.7 59.4 1.0 H6 D:PD2506 3.7 74.1 1.0 OD1 D:ASP177 3.7 66.4 1.0 O21 D:PD2506 3.8 65.2 1.0 O D:HOH614 4.2 53.6 1.0 ND1 D:HIS175 4.2 43.3 1.0 C3 D:PD2506 4.2 60.7 1.0 HE1 D:TRP292 4.3 77.3 1.0 ND1 D:HIS278 4.4 44.4 1.0 HD22 D:ASN181 4.4 75.1 1.0 HB2 D:ASP177 4.4 71.9 1.0 CG D:HIS175 4.4 44.6 1.0 CZ2 D:TRP292 4.4 63.7 1.0 CB D:ASP177 4.5 60.0 1.0 CG D:HIS278 4.5 45.0 1.0 HD21 D:ASN181 4.6 75.1 1.0 C5 D:PD2506 4.7 62.2 1.0 H3 D:PD2506 4.8 72.8 1.0 ND2 D:ASN181 4.8 62.5 1.0 NE1 D:TRP292 4.9 64.5 1.0 HB3 D:ASP177 4.9 71.9 1.0 C4 D:PD2506 4.9 62.6 1.0 HD1 D:HIS175 5.0 52.0 1.0

R.Chowdhury, M.I.Abboud, J.Wiley, A.Tumber, S.Markolovic, C.J.Schofield. Conservation of the Unusual Dimeric Jmjc Fold of JMJD7 From Drosophila Melanogaster to Humans. Sci Rep V. 12 6065 2022.
ISSN: ESSN 2045-2322
PubMed: 35410347
DOI: 10.1038/S41598-022-10028-Y