Manganese in PDB 8jnk: Crystal Structure of Human ALKBH3 Bound to Ssdna Through Active Site Crosslink

All present enzymatic activity of Crystal Structure of Human ALKBH3 Bound to Ssdna Through Active Site Crosslink:
1.14.11.33; 1.14.11.54;

The structure of Crystal Structure of Human ALKBH3 Bound to Ssdna Through Active Site Crosslink, PDB code: 8jnk was solved by L.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.90 / 2.69
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	129.46, 136.151, 203.39, 90, 107.11, 90
R / Rfree (%)	21.8 / 22.9

The binding sites of Manganese atom in the Crystal Structure of Human ALKBH3 Bound to Ssdna Through Active Site Crosslink (pdb code 8jnk). 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 Human ALKBH3 Bound to Ssdna Through Active Site Crosslink, PDB code: 8jnk:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Crystal Structure of Human ALKBH3 Bound to Ssdna Through Active Site Crosslink


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 Human ALKBH3 Bound to Ssdna Through Active Site Crosslink within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1002 b:46.1 occ:1.00 NE2 A:HIS191 2.1 49.4 1.0 O2' A:OGA1001 2.2 66.1 1.0 OD1 A:ASP193 2.3 46.3 1.0 NE2 A:HIS257 2.4 41.9 1.0 O1 A:OGA1001 2.4 77.4 1.0 OD2 A:ASP193 2.7 48.1 1.0 CG A:ASP193 2.8 47.9 1.0 CE1 A:HIS191 3.0 46.7 1.0 C2 A:OGA1001 3.0 55.5 1.0 C1 A:OGA1001 3.1 73.2 1.0 CD2 A:HIS257 3.1 39.9 1.0 CD2 A:HIS191 3.2 48.1 1.0 CE1 A:HIS257 3.5 46.2 1.0 ND1 A:HIS191 4.1 45.7 1.0 CG A:HIS191 4.2 48.5 1.0 NH2 A:ARG275 4.3 42.2 1.0 N1 A:OGA1001 4.3 58.9 1.0 O2 A:OGA1001 4.3 86.9 1.0 CB A:ASP193 4.3 51.3 1.0 CG A:HIS257 4.4 45.8 1.0 ND1 A:HIS257 4.5 45.2 1.0 N A:ASP193 4.9 48.1 1.0 C4 A:OGA1001 4.9 51.2 1.0 O2 B:2YR5 5.0 55.2 1.0

Manganese binding site 2 out of 4 in the Crystal Structure of Human ALKBH3 Bound to Ssdna Through Active Site Crosslink


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 Human ALKBH3 Bound to Ssdna Through Active Site Crosslink within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn1002 b:61.7 occ:1.00 NE2 C:HIS191 2.0 62.8 1.0 O2' C:OGA1001 2.2 68.8 1.0 OD2 C:ASP193 2.2 73.5 1.0 NE2 C:HIS257 2.3 60.2 1.0 O1 C:OGA1001 2.6 77.0 1.0 CE1 C:HIS191 2.9 60.2 1.0 CG C:ASP193 2.9 73.3 1.0 C2 C:OGA1001 3.0 71.1 1.0 OD1 C:ASP193 3.0 77.0 1.0 CD2 C:HIS191 3.0 65.9 1.0 CD2 C:HIS257 3.1 57.1 1.0 C1 C:OGA1001 3.2 79.5 1.0 CE1 C:HIS257 3.3 66.4 1.0 ND1 C:HIS191 4.0 58.4 1.0 CG C:HIS191 4.1 62.0 1.0 N1 C:OGA1001 4.2 66.8 1.0 CG C:HIS257 4.3 56.8 1.0 CB C:ASP193 4.4 63.9 1.0 O2 C:OGA1001 4.4 83.6 1.0 ND1 C:HIS257 4.4 60.7 1.0 NH1 C:ARG275 4.8 72.8 1.0 N C:ASP193 4.8 63.2 1.0 C4 C:OGA1001 4.9 65.2 1.0 O2 D:2YR5 5.0 68.7 1.0 CA C:ASP193 5.0 63.8 1.0

Manganese binding site 3 out of 4 in the Crystal Structure of Human ALKBH3 Bound to Ssdna Through Active Site Crosslink


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 Human ALKBH3 Bound to Ssdna Through Active Site Crosslink within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn1002 b:44.9 occ:1.00 OD1 E:ASP193 1.8 48.0 1.0 NE2 E:HIS191 2.1 56.5 1.0 NE2 E:HIS257 2.2 34.6 1.0 O2 E:OGA1001 2.4 58.5 1.0 O2' E:OGA1001 2.5 56.8 1.0 CG E:ASP193 2.7 51.4 1.0 CE1 E:HIS191 3.0 50.1 1.0 OD2 E:ASP193 3.0 55.1 1.0 CD2 E:HIS191 3.0 53.0 1.0 CD2 E:HIS257 3.1 40.6 1.0 C1 E:OGA1001 3.1 58.6 1.0 C2 E:OGA1001 3.2 51.7 1.0 CE1 E:HIS257 3.2 46.4 1.0 NH2 E:ARG275 3.7 55.1 1.0 ND1 E:HIS191 4.0 47.3 1.0 CG E:HIS191 4.1 53.8 1.0 CB E:ASP193 4.2 53.1 1.0 CG E:HIS257 4.3 46.9 1.0 ND1 E:HIS257 4.3 46.6 1.0 O1 E:OGA1001 4.3 69.3 1.0 N1 E:OGA1001 4.5 51.5 1.0 N E:ASP193 4.7 53.5 1.0 O F:HOH101 4.7 42.6 1.0 CA E:ASP193 4.9 55.4 1.0 CZ E:ARG275 5.0 49.4 1.0

Manganese binding site 4 out of 4 in the Crystal Structure of Human ALKBH3 Bound to Ssdna Through Active Site Crosslink


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 Human ALKBH3 Bound to Ssdna Through Active Site Crosslink within 5.0Å range: probe atom residue distance (Å) B Occ G:Mn1002 b:68.6 occ:1.00 NE2 G:HIS191 2.1 76.1 1.0 NE2 G:HIS257 2.1 64.6 1.0 OD2 G:ASP193 2.2 75.1 1.0 O2' G:OGA1001 2.3 70.3 1.0 O2 G:OGA1001 2.7 77.5 1.0 CG G:ASP193 2.9 73.8 1.0 CE1 G:HIS191 2.9 74.6 1.0 OD1 G:ASP193 3.0 72.0 1.0 CD2 G:HIS191 3.0 77.0 1.0 CD2 G:HIS257 3.0 62.5 1.0 C2 G:OGA1001 3.1 72.4 1.0 CE1 G:HIS257 3.2 67.8 1.0 C1 G:OGA1001 3.3 79.1 1.0 ND1 G:HIS191 4.0 72.1 1.0 CG G:HIS191 4.1 76.6 1.0 CG G:HIS257 4.2 64.9 1.0 ND1 G:HIS257 4.2 68.3 1.0 CB G:ASP193 4.3 79.4 1.0 N1 G:OGA1001 4.4 67.6 1.0 NH2 G:ARG275 4.5 71.5 1.0 O1 G:OGA1001 4.6 86.6 1.0 N G:ASP193 4.8 77.2 1.0 N3 H:2YR5 4.9 82.9 1.0 CA G:ASP193 4.9 74.1 1.0 O2 H:2YR5 4.9 80.5 1.0 C4 G:OGA1001 5.0 68.7 1.0

L.Zhang, H.C.Duan, M.Paduch, J.Hu, C.Zhang, Y.Mu, H.Lin, C.He, A.A.Kossiakoff, G.Jia, L.Zhang. The Molecular Basis of Human ALKBH3 Mediated Rna N 1 -Methyladenosine (M 1 A) Demethylation. Angew.Chem.Int.Ed.Engl. 13900 2023.
ISSN: ESSN 1521-3773
PubMed: 38158383
DOI: 10.1002/ANIE.202313900