Manganese in PDB 8hb2: Crystal Structure of Caenorhabditis Elegans Nmad-1 in Complex with Ligand II

All present enzymatic activity of Crystal Structure of Caenorhabditis Elegans Nmad-1 in Complex with Ligand II:
1.14.11.51;

The structure of Crystal Structure of Caenorhabditis Elegans Nmad-1 in Complex with Ligand II, PDB code: 8hb2 was solved by G.Shang, Z.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.19 / 3.06
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	180.237, 75.386, 117.215, 90, 112.53, 90
R / Rfree (%)	27.5 / 29.6

The binding sites of Manganese atom in the Crystal Structure of Caenorhabditis Elegans Nmad-1 in Complex with Ligand II (pdb code 8hb2). 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 Caenorhabditis Elegans Nmad-1 in Complex with Ligand II, PDB code: 8hb2:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Crystal Structure of Caenorhabditis Elegans Nmad-1 in Complex with Ligand II


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 Caenorhabditis Elegans Nmad-1 in Complex with Ligand II within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn301 b:50.6 occ:1.00 NE2 A:HIS239 0.8 58.2 1.0 CE1 A:HIS239 1.4 58.2 1.0 CD2 A:HIS239 2.2 58.2 1.0 OD2 A:ASP186 2.4 64.7 1.0 ND1 A:HIS239 2.6 58.2 1.0 CG A:HIS239 2.9 58.2 1.0 NE2 A:HIS184 2.9 60.0 1.0 CE1 A:HIS184 3.3 60.0 1.0 CG A:ASP186 3.5 64.7 1.0 CD2 A:HIS184 3.9 60.0 1.0 NH2 A:ARG256 4.1 55.6 1.0 CB A:ASP186 4.1 64.7 1.0 ND1 A:HIS184 4.3 60.0 1.0 CB A:HIS239 4.4 58.2 1.0 CD1 A:LEU195 4.5 56.9 1.0 OD1 A:ASP186 4.5 64.7 1.0 CG A:HIS184 4.6 60.0 1.0 N A:ASP186 4.6 64.7 1.0 O A:HIS184 4.8 60.0 1.0 CA A:ASP186 4.8 64.7 1.0 O A:HIS239 4.9 58.2 1.0 CE A:MET229 5.0 60.9 1.0

Manganese binding site 2 out of 4 in the Crystal Structure of Caenorhabditis Elegans Nmad-1 in Complex with Ligand II


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 Caenorhabditis Elegans Nmad-1 in Complex with Ligand II within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn400 b:40.7 occ:1.00 NE2 B:HIS239 1.7 41.7 1.0 O2 B:AKG401 1.7 43.5 1.0 C1 B:AKG401 1.9 43.5 1.0 NE2 B:HIS184 1.9 44.1 1.0 O1 B:AKG401 2.2 43.5 1.0 OD1 B:ASP186 2.4 47.7 1.0 OD2 B:ASP186 2.5 47.7 1.0 CE1 B:HIS239 2.5 41.7 1.0 CG B:ASP186 2.7 47.7 1.0 CE1 B:HIS184 2.7 44.1 1.0 CD2 B:HIS239 2.9 41.7 1.0 C2 B:AKG401 3.0 43.5 1.0 CD2 B:HIS184 3.0 44.1 1.0 O5 B:AKG401 3.1 43.5 1.0 ND1 B:HIS239 3.7 41.7 1.0 ND1 B:HIS184 3.8 44.1 1.0 CG B:HIS239 3.9 41.7 1.0 CG B:HIS184 4.0 44.1 1.0 CB B:ASP186 4.1 47.7 1.0 C3 B:AKG401 4.4 43.5 1.0 N B:ASP186 4.5 47.7 1.0 CA B:ASP186 4.6 47.7 1.0 NH2 B:ARG256 4.8 45.4 1.0 CD1 B:LEU195 4.9 40.3 1.0 CD1 B:ILE181 4.9 45.2 1.0 O B:HIS239 4.9 41.7 1.0

Manganese binding site 3 out of 4 in the Crystal Structure of Caenorhabditis Elegans Nmad-1 in Complex with Ligand II


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 Caenorhabditis Elegans Nmad-1 in Complex with Ligand II within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn400 b:78.4 occ:1.00 O5 C:AKG401 1.6 73.2 1.0 C1 C:AKG401 1.7 73.2 1.0 C2 C:AKG401 1.7 73.2 1.0 OD2 C:ASP186 2.1 79.2 1.0 O2 C:AKG401 2.2 73.2 1.0 NE2 C:HIS184 2.2 73.5 1.0 O1 C:AKG401 2.3 73.2 1.0 OD1 C:ASP186 2.7 79.2 1.0 CG C:ASP186 2.7 79.2 1.0 CE1 C:HIS184 2.9 73.5 1.0 C3 C:AKG401 3.1 73.2 1.0 CD2 C:HIS184 3.3 73.5 1.0 ND1 C:HIS239 3.9 74.6 1.0 ND1 C:HIS184 4.0 73.5 1.0 CB C:ASP186 4.2 79.2 1.0 C4 C:AKG401 4.2 73.2 1.0 CG C:HIS184 4.3 73.5 1.0 CE1 C:HIS239 4.7 74.6 1.0 CD1 C:LEU195 4.7 73.1 1.0 CG C:HIS239 4.7 74.6 1.0 CB C:HIS239 4.8 74.6 1.0 NH1 C:ARG256 4.8 79.5 1.0 NH2 C:ARG256 4.9 79.5 1.0 CZ C:ARG256 4.9 79.5 1.0 N C:ASP186 4.9 79.2 1.0 CA C:ASP186 5.0 79.2 1.0

Manganese binding site 4 out of 4 in the Crystal Structure of Caenorhabditis Elegans Nmad-1 in Complex with Ligand II


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 Caenorhabditis Elegans Nmad-1 in Complex with Ligand II within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn301 b:76.7 occ:1.00 NE2 D:HIS184 1.7 73.5 1.0 NE2 D:HIS239 1.8 71.2 1.0 OD2 D:ASP186 1.9 81.0 1.0 CE1 D:HIS184 2.5 73.5 1.0 CD2 D:HIS184 2.7 73.5 1.0 CD2 D:HIS239 2.8 71.2 1.0 CE1 D:HIS239 2.8 71.2 1.0 CG D:ASP186 3.1 81.0 1.0 NH2 D:ARG256 3.2 83.0 1.0 ND1 D:HIS184 3.6 73.5 1.0 CG D:HIS184 3.8 73.5 1.0 ND1 D:HIS239 3.9 71.2 1.0 CG D:HIS239 3.9 71.2 1.0 OD1 D:ASP186 3.9 81.0 1.0 CB D:ASP186 4.1 81.0 1.0 CZ D:ARG256 4.4 83.0 1.0 CD2 D:LEU195 4.7 74.5 1.0 N D:ASP186 4.8 81.0 1.0 O D:HIS239 4.8 71.2 1.0 CA D:ASP186 4.8 81.0 1.0 NH1 D:ARG256 4.8 83.0 1.0 CD1 D:ILE181 4.9 70.8 1.0 O D:HIS184 4.9 73.5 1.0

G.Shang, M.Yang, M.Li, L.Ma, Y.Liu, J.Ma, Y.Chen, X.Wang, S.Fan, M.Xie, W.Wu, S.Dai, Z.Chen. Structural Basis of Nucleic Acid Recognition and 6MA Demethylation By Caenorhabditis Elegans Nmad-1A. Int J Mol Sci V. 25 2024.
ISSN: ESSN 1422-0067
PubMed: 38255759
DOI: 10.3390/IJMS25020686