Manganese in PDB 5rak: Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with XS040486B

The structure of Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with XS040486B, PDB code: 5rak was solved by M.Snee, R.Nowak, C.Johansson, N.A.Burgess-Brown, C.H.Arrowsmith, C.Bountra, A.M.Edwards, U.Oppermann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	64.76 / 1.69
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	57.590, 93.460, 94.182, 90.00, 107.94, 90.00
R / Rfree (%)	18.2 / 21.3

The structure of Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with XS040486B also contains other interesting chemical elements:

Chlorine

(Cl)

5 atoms

The binding sites of Manganese atom in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with XS040486B (pdb code 5rak). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with XS040486B, PDB code: 5rak:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with XS040486B


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with XS040486B within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1806 b:17.7 occ:1.00 NE2 A:HIS1560 2.1 17.9 1.0 OD2 A:ASP1562 2.1 23.4 1.0 NE2 A:HIS1689 2.1 16.1 1.0 CE1 A:HIS1560 3.0 17.3 1.0 CE1 A:HIS1689 3.0 18.3 1.0 CD2 A:HIS1560 3.1 20.0 1.0 CD2 A:HIS1689 3.2 16.2 1.0 CG A:ASP1562 3.4 31.3 1.0 O A:HOH1939 3.8 23.0 1.0 OD1 A:ASP1562 3.8 42.0 1.0 ND1 A:HIS1560 4.1 17.9 1.0 ND1 A:HIS1689 4.2 16.8 1.0 CG A:HIS1560 4.2 17.1 1.0 CG A:HIS1689 4.3 17.1 1.0 O A:HOH2168 4.4 35.0 1.0 OH A:TYR1541 4.5 27.0 1.0 CB A:ASP1562 4.8 27.1 1.0

Manganese binding site 2 out of 2 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with XS040486B


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with XS040486B within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn1802 b:19.1 occ:1.00 OD2 B:ASP1562 2.1 22.3 1.0 NE2 B:HIS1689 2.1 20.0 1.0 NE2 B:HIS1560 2.1 24.2 1.0 CE1 B:HIS1689 3.0 20.9 1.0 CE1 B:HIS1560 3.1 25.8 1.0 CG B:ASP1562 3.1 22.8 1.0 CD2 B:HIS1689 3.2 22.1 1.0 CD2 B:HIS1560 3.2 26.2 1.0 OD1 B:ASP1562 3.5 24.1 1.0 O B:HOH2078 4.0 23.4 1.0 ND1 B:HIS1689 4.2 21.6 1.0 ND1 B:HIS1560 4.2 22.5 1.0 CG B:HIS1689 4.3 20.6 1.0 CG B:HIS1560 4.3 25.4 1.0 O B:HOH2156 4.4 32.1 1.0 OH B:TYR1541 4.4 24.4 1.0 CB B:ASP1562 4.5 22.3 1.0

M.Snee, R.Nowak, C.Johansson, N.A.Burgess-Brown, C.H.Arrowsmith, C.Bountra, A.M.Edwards, U.Oppermann. Pandda Analysis Group Deposition of Human JMJD1B Screened Against the Dspl Fragment Library To Be Published.