Manganese in PDB 5ram: Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with XS038544D

The structure of Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with XS038544D, PDB code: 5ram 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)	88.35 / 2.05
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	57.030, 93.500, 92.920, 90.00, 108.05, 90.00
R / Rfree (%)	17.5 / 23.6

The structure of Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with XS038544D 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 XS038544D (pdb code 5ram). 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 XS038544D, PDB code: 5ram:
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 XS038544D


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 XS038544D within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1806 b:28.5 occ:1.00 N A:S3V1801 2.1 11.4 0.6 NE2 A:HIS1560 2.2 22.7 1.0 NE2 A:HIS1689 2.2 19.9 0.6 O A:HOH2073 2.3 8.1 0.6 OD2 A:ASP1562 2.4 33.5 1.0 C1 A:S3V1801 3.0 12.0 0.6 C2 A:S3V1801 3.0 11.6 0.6 CE1 A:HIS1560 3.1 24.6 1.0 CE1 A:HIS1689 3.1 19.6 0.6 CD2 A:HIS1560 3.2 23.4 1.0 CD2 A:HIS1689 3.3 19.3 0.6 CG A:ASP1562 3.4 34.9 1.0 OD1 A:ASP1562 3.8 38.6 1.0 O A:HOH1985 3.9 18.4 0.6 ND1 A:HIS1560 4.2 24.6 1.0 ND1 A:HIS1689 4.3 19.9 0.6 CG A:HIS1560 4.3 22.8 1.0 C3 A:S3V1801 4.4 12.1 0.6 C A:S3V1801 4.4 11.9 0.6 CG A:HIS1689 4.4 20.0 0.6 O A:HOH1984 4.4 18.3 0.6 O A:HOH2187 4.5 26.1 0.6 O A:HOH2125 4.5 10.3 0.6 O A:HOH2193 4.6 32.0 1.0 CB A:ASP1562 4.8 30.8 1.0 C4 A:S3V1801 4.9 12.2 0.6 OH A:TYR1541 5.0 33.3 1.0

Manganese binding site 2 out of 2 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with XS038544D


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 XS038544D within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn1803 b:30.8 occ:1.00 N B:S3V1801 2.1 28.8 0.8 OD2 B:ASP1562 2.2 28.8 1.0 NE2 B:HIS1560 2.2 30.7 1.0 NE2 B:HIS1689 2.3 26.2 1.0 C1 B:S3V1801 2.9 31.6 0.8 CE1 B:HIS1689 3.1 26.1 1.0 CE1 B:HIS1560 3.1 32.7 1.0 C2 B:S3V1801 3.1 29.8 0.8 CG B:ASP1562 3.2 28.7 1.0 CD2 B:HIS1560 3.3 27.8 1.0 CD2 B:HIS1689 3.3 24.9 1.0 OD1 B:ASP1562 3.5 34.2 1.0 ND1 B:HIS1689 4.2 23.2 1.0 ND1 B:HIS1560 4.3 30.8 1.0 C B:S3V1801 4.3 33.5 0.8 CG B:HIS1689 4.4 23.7 1.0 CG B:HIS1560 4.4 27.6 1.0 C3 B:S3V1801 4.4 31.2 0.8 CB B:ASP1562 4.6 28.7 1.0 O B:HOH2165 4.7 32.6 0.8 OH B:TYR1541 4.8 39.4 1.0 C4 B:S3V1801 4.9 32.1 0.8

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.