Manganese in PDB 5ran: Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with XS039080D

The structure of Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with XS039080D, PDB code: 5ran 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)	88.93 / 1.95
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	57.520, 93.750, 93.605, 90.00, 108.18, 90.00
R / Rfree (%)	18.3 / 22.5

The structure of Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with XS039080D 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 XS039080D (pdb code 5ran). 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 XS039080D, PDB code: 5ran:
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 XS039080D


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 XS039080D within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1806 b:29.7 occ:1.00 N07 A:RYP1801 1.9 20.0 0.5 O A:HOH2071 2.2 10.1 0.5 NE2 A:HIS1560 2.3 23.1 1.0 NE2 A:HIS1689 2.3 19.7 1.0 OD2 A:ASP1562 2.3 29.9 1.0 C08 A:RYP1801 2.7 21.2 0.5 C06 A:RYP1801 2.9 20.2 0.5 CE1 A:HIS1689 3.1 20.0 1.0 CE1 A:HIS1560 3.2 24.6 1.0 CD2 A:HIS1560 3.2 23.2 1.0 CD2 A:HIS1689 3.4 19.3 1.0 CG A:ASP1562 3.4 32.5 1.0 O A:HOH1951 3.7 33.5 1.0 OD1 A:ASP1562 3.9 40.4 1.0 C09 A:RYP1801 4.0 21.3 0.5 C05 A:RYP1801 4.2 21.4 0.5 ND1 A:HIS1689 4.3 19.1 1.0 ND1 A:HIS1560 4.3 23.8 1.0 CG A:HIS1560 4.4 22.7 1.0 O A:HOH2221 4.4 35.9 0.5 CG A:HIS1689 4.5 20.6 1.0 C04 A:RYP1801 4.6 21.6 0.5 OH A:TYR1541 4.7 29.7 0.5 CB A:ASP1562 4.8 30.1 1.0

Manganese binding site 2 out of 2 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with XS039080D


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 XS039080D within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn1803 b:32.0 occ:1.00 N07 B:RYP1801 2.1 17.0 0.5 OD2 B:ASP1562 2.2 26.7 1.0 NE2 B:HIS1689 2.2 26.1 1.0 NE2 B:HIS1560 2.3 29.8 1.0 C06 B:RYP1801 2.9 17.6 0.5 CE1 B:HIS1689 3.0 27.7 1.0 C08 B:RYP1801 3.1 17.2 0.5 CE1 B:HIS1560 3.1 31.2 1.0 CG B:ASP1562 3.2 29.1 1.0 CD2 B:HIS1560 3.3 28.9 1.0 CD2 B:HIS1689 3.3 27.1 1.0 OD1 B:ASP1562 3.5 33.5 1.0 ND1 B:HIS1689 4.2 25.3 1.0 C05 B:RYP1801 4.3 18.1 0.5 ND1 B:HIS1560 4.3 28.9 1.0 CG B:HIS1689 4.4 26.6 1.0 C09 B:RYP1801 4.4 18.1 0.5 CG B:HIS1560 4.4 28.5 1.0 CB B:ASP1562 4.5 28.6 1.0 O B:HOH1970 4.7 22.5 0.5 OH B:TYR1541 4.8 42.5 1.0 C04 B:RYP1801 4.9 17.7 0.5

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.