Manganese in PDB 5zmd: Crystal Structure of Fto in Complex with M6DA Modified Ssdna

The structure of Crystal Structure of Fto in Complex with M6DA Modified Ssdna, PDB code: 5zmd was solved by X.Zhang, L.H.Wei, J.Luo, Y.Xiao, J.Liu, W.Zhang, L.Zhang, G.F.Jia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.17 / 3.30
Space group	I 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	122.736, 160.033, 276.756, 90.00, 90.00, 90.00
R / Rfree (%)	27.1 / 29.2

The binding sites of Manganese atom in the Crystal Structure of Fto in Complex with M6DA Modified Ssdna (pdb code 5zmd). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of Fto in Complex with M6DA Modified Ssdna, PDB code: 5zmd:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Crystal Structure of Fto in Complex with M6DA Modified Ssdna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Fto in Complex with M6DA Modified Ssdna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1001 b:12.0 occ:1.00 O2' A:OGA1002 2.0 8.7 1.0 O1 A:OGA1002 2.2 17.7 1.0 NE2 A:HIS307 2.3 15.2 1.0 OD2 A:ASP233 2.5 25.5 1.0 OD1 A:ASP233 2.5 13.0 1.0 NE2 A:HIS231 2.5 16.4 1.0 CG A:ASP233 2.8 15.0 1.0 C2 A:OGA1002 2.8 15.9 1.0 C1 A:OGA1002 2.9 16.0 1.0 CE1 A:HIS307 3.0 17.7 1.0 CE1 A:HIS231 3.2 14.3 1.0 CD2 A:HIS307 3.4 15.4 1.0 CD2 A:HIS231 3.6 18.5 1.0 O2 A:OGA1002 4.1 16.9 1.0 ND1 A:HIS307 4.2 18.3 1.0 CB A:ASP233 4.2 14.1 1.0 N1 A:OGA1002 4.2 21.6 1.0 ND1 A:HIS231 4.3 15.7 1.0 CG A:HIS307 4.4 16.9 1.0 NH1 A:ARG322 4.4 14.7 1.0 CG A:HIS231 4.6 17.3 1.0 CA A:ASP233 4.6 15.8 1.0 N A:ASP233 4.7 24.4 1.0 C4 A:OGA1002 4.7 16.1 1.0 NH2 A:ARG322 4.8 18.4 1.0

Manganese binding site 2 out of 4 in the Crystal Structure of Fto in Complex with M6DA Modified Ssdna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Fto in Complex with M6DA Modified Ssdna within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn1001 b:17.4 occ:1.00 OD1 C:ASP233 1.8 23.1 1.0 NE2 C:HIS231 2.1 21.4 1.0 NE2 C:HIS307 2.1 20.5 1.0 O2 C:OGA1002 2.2 13.6 1.0 CE1 C:HIS307 2.7 25.6 1.0 CG C:ASP233 2.8 20.7 1.0 CE1 C:HIS231 2.8 21.4 1.0 O2' C:OGA1002 2.9 19.4 1.0 CD2 C:HIS231 3.1 20.7 1.0 C1 C:OGA1002 3.2 18.3 1.0 OD2 C:ASP233 3.2 27.6 1.0 CD2 C:HIS307 3.4 23.9 1.0 C2 C:OGA1002 3.5 18.3 1.0 ND1 C:HIS307 3.9 23.4 1.0 ND1 C:HIS231 4.0 16.0 1.0 CB C:ASP233 4.1 15.5 1.0 CG C:HIS231 4.1 14.7 1.0 CA C:ASP233 4.3 15.9 1.0 CG C:HIS307 4.3 22.3 1.0 O1 C:OGA1002 4.3 26.4 1.0 N C:ASP233 4.3 19.9 1.0 C C:HIS232 4.6 18.6 1.0 O C:HIS232 4.8 24.4 1.0 N1 C:OGA1002 5.0 12.2 1.0

Manganese binding site 3 out of 4 in the Crystal Structure of Fto in Complex with M6DA Modified Ssdna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of Fto in Complex with M6DA Modified Ssdna within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn1001 b:20.1 occ:1.00 OD1 E:ASP233 2.0 24.3 1.0 O2' E:OGA1002 2.1 17.1 1.0 NE2 E:HIS307 2.2 23.1 1.0 NE2 E:HIS231 2.4 23.2 1.0 O2 E:OGA1002 2.4 23.9 1.0 CE1 E:HIS307 2.8 23.6 1.0 CG E:ASP233 2.9 23.5 1.0 C2 E:OGA1002 2.9 18.4 1.0 C1 E:OGA1002 3.0 24.3 1.0 OD2 E:ASP233 3.1 25.8 1.0 CE1 E:HIS231 3.1 21.2 1.0 CD2 E:HIS307 3.4 20.2 1.0 CD2 E:HIS231 3.5 21.1 1.0 ND1 E:HIS307 4.0 17.3 1.0 CB E:ASP233 4.2 19.3 1.0 O1 E:OGA1002 4.2 29.6 1.0 ND1 E:HIS231 4.3 22.2 1.0 N1 E:OGA1002 4.3 20.7 1.0 CG E:HIS307 4.3 16.1 1.0 CG E:HIS231 4.5 17.7 1.0 CA E:ASP233 4.5 19.6 1.0 N E:ASP233 4.6 22.6 1.0 NH2 E:ARG322 4.7 16.1 1.0 C4 E:OGA1002 4.7 23.9 1.0

Manganese binding site 4 out of 4 in the Crystal Structure of Fto in Complex with M6DA Modified Ssdna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of Fto in Complex with M6DA Modified Ssdna within 5.0Å range: probe atom residue distance (Å) B Occ G:Mn1001 b:13.8 occ:1.00 OD1 G:ASP233 1.7 23.8 1.0 NE2 G:HIS231 2.3 15.8 1.0 O1 G:OGA1002 2.4 11.8 1.0 NE2 G:HIS307 2.5 19.8 1.0 CG G:ASP233 2.7 24.5 1.0 CE1 G:HIS307 2.9 19.8 1.0 OD2 G:ASP233 3.0 82.6 1.0 CE1 G:HIS231 3.1 13.0 1.0 O2' G:OGA1002 3.2 10.2 1.0 CD2 G:HIS231 3.3 16.8 1.0 C1 G:OGA1002 3.4 17.5 1.0 CD2 G:HIS307 3.7 14.8 1.0 C2 G:OGA1002 3.7 11.5 1.0 CB G:ASP233 4.0 22.5 1.0 NH2 G:ARG322 4.0 22.5 1.0 ND1 G:HIS307 4.1 13.4 1.0 ND1 G:HIS231 4.2 12.4 1.0 CA G:ASP233 4.3 14.4 1.0 CG G:HIS231 4.3 13.1 1.0 N G:ASP233 4.4 9.8 1.0 O2 G:OGA1002 4.5 20.7 1.0 CG G:HIS307 4.5 13.3 1.0 C G:HIS232 4.7 13.1 1.0 O G:HIS232 4.9 17.1 1.0

X.Zhang, L.H.Wei, Y.Wang, Y.Xiao, J.Liu, W.Zhang, N.Yan, G.Amu, X.Tang, L.Zhang, G.Jia. Structural Insights Into Fto'S Catalytic Mechanism For the Demethylation of Multiple Rna Substrates. Proc. Natl. Acad. Sci. V. 116 2919 2019U.S.A..
ISSN: ESSN 1091-6490
PubMed: 30718435
DOI: 10.1073/PNAS.1820574116