Manganese in PDB 5rai: Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with XS040404C

The structure of Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with XS040404C, PDB code: 5rai 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)	89.01 / 1.54
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	57.520, 93.540, 93.681, 90.00, 108.17, 90.00
R / Rfree (%)	19.1 / 21.8

The structure of Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with XS040404C 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 XS040404C (pdb code 5rai). 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 XS040404C, PDB code: 5rai:
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 XS040404C


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 XS040404C within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1806 b:18.5 occ:1.00 NE2 A:HIS1560 2.0 19.6 1.0 NE2 A:HIS1689 2.1 17.5 1.0 OD2 A:ASP1562 2.2 24.9 1.0 CE1 A:HIS1560 3.0 18.0 1.0 CE1 A:HIS1689 3.1 19.2 1.0 CD2 A:HIS1560 3.1 20.7 1.0 CD2 A:HIS1689 3.2 15.7 1.0 CG A:ASP1562 3.5 35.7 1.0 O A:HOH1973 3.9 25.7 1.0 OD1 A:ASP1562 3.9 49.0 1.0 ND1 A:HIS1560 4.1 19.1 1.0 ND1 A:HIS1689 4.2 16.9 1.0 CG A:HIS1560 4.2 17.2 1.0 CG A:HIS1689 4.3 16.1 1.0 O A:HOH2182 4.3 33.9 1.0 OH A:TYR1541 4.4 25.0 1.0 CB A:ASP1562 4.9 29.1 1.0 O A:HOH2186 5.0 32.2 1.0

Manganese binding site 2 out of 2 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with XS040404C


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 XS040404C within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn1802 b:22.2 occ:1.00 OD2 B:ASP1562 2.1 22.6 1.0 NE2 B:HIS1689 2.1 21.2 1.0 NE2 B:HIS1560 2.1 23.1 1.0 CE1 B:HIS1689 3.0 21.5 1.0 CE1 B:HIS1560 3.0 27.1 1.0 CD2 B:HIS1560 3.1 24.1 1.0 CG B:ASP1562 3.1 24.3 1.0 CD2 B:HIS1689 3.2 22.3 1.0 OD1 B:ASP1562 3.5 24.8 1.0 ND1 B:HIS1689 4.1 23.3 1.0 ND1 B:HIS1560 4.2 23.2 1.0 CG B:HIS1560 4.2 25.6 1.0 CG B:HIS1689 4.3 21.7 1.0 OH B:TYR1541 4.4 22.8 1.0 CB B:ASP1562 4.5 22.9 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.