Manganese in PDB 4ccl: X-Ray Structure of E. Coli Ycfd

The structure of X-Ray Structure of E. Coli Ycfd, PDB code: 4ccl was solved by M.A.Mcdonough, C.H.Ho, N.J.Kershaw, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.765 / 2.60
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	120.693, 120.693, 133.498, 90.00, 90.00, 90.00
R / Rfree (%)	19.83 / 24.9

The binding sites of Manganese atom in the X-Ray Structure of E. Coli Ycfd (pdb code 4ccl). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the X-Ray Structure of E. Coli Ycfd, PDB code: 4ccl:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the X-Ray Structure of E. Coli Ycfd


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of X-Ray Structure of E. Coli Ycfd within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1373 b:0.9 occ:0.50 OD2 A:ASP127 2.1 96.4 1.0 NE2 A:HIS125 2.2 0.8 1.0 NE2 A:HIS187 2.2 81.2 1.0 CE1 A:HIS187 3.0 83.4 1.0 CD2 A:HIS125 3.1 0.3 1.0 CE1 A:HIS125 3.1 0.8 1.0 CG A:ASP127 3.2 94.1 1.0 CD2 A:HIS187 3.4 79.9 1.0 OD1 A:ASP127 3.6 96.4 1.0 ND1 A:HIS125 4.1 0.2 1.0 CG A:HIS125 4.1 0.5 1.0 ND1 A:HIS187 4.2 82.2 1.0 CG A:HIS187 4.4 79.3 1.0 CB A:ASP127 4.5 84.2 1.0 CG1 A:VAL131 4.7 57.8 1.0

Manganese binding site 2 out of 4 in the X-Ray Structure of E. Coli Ycfd


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of X-Ray Structure of E. Coli Ycfd within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1374 b:0.9 occ:1.00 OD2 A:ASP11 3.0 73.7 1.0 ND1 A:HIS16 3.8 65.8 1.0 CA A:PHE12 4.1 60.9 1.0 N A:PHE12 4.1 61.3 1.0 CG A:ASP11 4.1 71.5 1.0 CB A:PHE12 4.3 55.5 1.0 O A:ASN8 4.3 68.3 1.0 CE1 A:HIS16 4.3 72.0 1.0 NH1 A:ARG15 4.3 73.9 1.0 O3 A:SO41377 4.4 0.3 1.0 CD1 A:LEU7 4.4 80.0 1.0 C A:ASP11 4.4 63.6 1.0 CB A:ASP11 4.4 65.0 1.0 CD2 A:LEU24 4.5 75.9 1.0 O A:ASP11 4.7 67.3 1.0 CD1 A:PHE12 4.7 55.0 1.0 CB A:ASN8 5.0 70.8 1.0

Manganese binding site 3 out of 4 in the X-Ray Structure of E. Coli Ycfd


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of X-Ray Structure of E. Coli Ycfd within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn1373 b:0.1 occ:1.00 O B:ASP58 2.5 0.3 1.0 ND1 B:HIS56 3.5 84.2 1.0 C B:ASP58 3.5 0.8 1.0 CE1 B:HIS56 3.7 78.9 1.0 CA B:ASP58 4.1 0.1 1.0 N B:ASP58 4.5 0.2 1.0 N B:GLY59 4.6 0.5 1.0 CG B:HIS56 4.6 83.0 1.0 NE2 B:HIS56 4.9 77.2 1.0 CA B:GLY59 4.9 98.4 1.0

Manganese binding site 4 out of 4 in the X-Ray Structure of E. Coli Ycfd


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of X-Ray Structure of E. Coli Ycfd within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn1374 b:0.8 occ:1.00 O B:HOH2099 3.3 67.1 1.0 ND1 B:HIS329 3.6 85.7 1.0 CB B:ASP349 4.0 0.8 1.0 CB B:HIS329 4.1 80.5 1.0 N B:ALA350 4.1 94.6 1.0 N B:ASP349 4.2 0.3 1.0 CG B:HIS329 4.3 85.5 1.0 C B:ASP349 4.4 99.7 1.0 CA B:ASP349 4.4 0.8 1.0 CE1 B:HIS329 4.6 85.3 1.0 CA B:ALA350 4.7 85.9 1.0 CA B:HIS329 4.7 81.3 1.0 CD B:PRO331 4.8 78.2 1.0 CB B:ALA350 4.8 81.8 1.0 OD2 B:ASP349 4.9 0.6 1.0 CG B:PRO331 4.9 74.7 1.0 CG B:ASP349 4.9 0.7 1.0 O B:PHE347 4.9 76.2 1.0

R.Chowdhury, R.Sekirnik, N.C.Brissett, T.Krojer, C.-H.Ho, S.S.Ng, I.J.Clifton, W.Ge, N.J.Kershaw, G.C.Fox, J.R.C.Muniz, M.Vollmar, C.Phillips, E.S.Pilka, K.L.Kavanagh, F.Von Deflt, U.Oppermann, M.A.Mcdonough, A.J.Doherty, C.J.Schofield. Ribosomal Oxygenases Are Structurally Conserved From Prokaryotes to Humans. Nature V. 510 422 2014.
ISSN: ISSN 0028-0836
PubMed: 24814345
DOI: 10.1038/NATURE13263