Neodymium in PDB 7o6z: Structure of A Neodymium-Containing, XOXF1-Type Methanol Dehydrogenase

All present enzymatic activity of Structure of A Neodymium-Containing, XOXF1-Type Methanol Dehydrogenase:
1.1.2.7;

The structure of Structure of A Neodymium-Containing, XOXF1-Type Methanol Dehydrogenase, PDB code: 7o6z was solved by R.Schmitz, A.Dietl, H.Op Den Camp, T.Barends, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.60 / 2.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	89.87, 70.18, 97.23, 90, 91.39, 90
R / Rfree (%)	19.5 / 25.2

The binding sites of Neodymium atom in the Structure of A Neodymium-Containing, XOXF1-Type Methanol Dehydrogenase (pdb code 7o6z). This binding sites where shown within 5.0 Angstroms radius around Neodymium atom.
In total 2 binding sites of Neodymium where determined in the Structure of A Neodymium-Containing, XOXF1-Type Methanol Dehydrogenase, PDB code: 7o6z:
Jump to Neodymium binding site number: 1; 2;

Neodymium binding site 1 out of 2 in the Structure of A Neodymium-Containing, XOXF1-Type Methanol Dehydrogenase


Mono view


Stereo pair view

A full contact list of Neodymium with other atoms in the Nd binding site number 1 of Structure of A Neodymium-Containing, XOXF1-Type Methanol Dehydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Nd801 b:54.5 occ:0.72 OD2 A:ASP347 2.2 60.5 1.0 OE2 A:GLU204 2.3 61.6 1.0 ND2 A:ASN290 2.5 46.5 1.0 OD1 A:ASP345 2.7 48.2 1.0 CG A:ASP347 3.0 55.9 1.0 O A:MOH802 3.0 57.8 1.0 OD1 A:ASP347 3.0 57.3 1.0 O A:HOH998 3.1 56.9 1.0 CD A:GLU204 3.2 56.3 1.0 OE1 A:GLU204 3.5 59.9 1.0 CG A:ASP345 3.5 49.6 1.0 OD2 A:ASP345 3.5 51.3 1.0 CG A:ASN290 3.7 52.1 1.0 C A:MOH802 4.1 55.8 1.0 NH2 A:ARG372 4.3 57.3 1.0 OD2 A:ASP203 4.4 52.1 1.0 CB A:ASP347 4.4 53.7 1.0 OD1 A:ASN290 4.4 58.0 1.0 CB A:ASP203 4.4 53.9 1.0 NH1 A:ARG372 4.5 52.8 1.0 CZ2 A:TRP272 4.5 52.1 1.0 CB A:ASN290 4.5 47.9 1.0 O A:HOH1002 4.5 50.4 1.0 CG A:GLU204 4.6 55.5 1.0 NE1 A:TRP272 4.7 46.7 1.0 CZ A:ARG372 4.8 51.1 1.0 CG A:ASP203 4.9 49.9 1.0 CB A:ASP345 4.9 47.6 1.0 N A:ASN290 4.9 46.1 1.0 CE2 A:TRP272 5.0 46.5 1.0

Neodymium binding site 2 out of 2 in the Structure of A Neodymium-Containing, XOXF1-Type Methanol Dehydrogenase


Mono view


Stereo pair view

A full contact list of Neodymium with other atoms in the Nd binding site number 2 of Structure of A Neodymium-Containing, XOXF1-Type Methanol Dehydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ B:Nd702 b:56.8 occ:0.75 O5 B:PQQ701 2.4 60.1 0.7 OD2 B:ASP347 2.6 58.6 1.0 OE2 B:GLU204 2.7 56.1 1.0 O7B B:PQQ701 2.7 51.4 0.7 OD1 B:ASN290 2.7 57.6 1.0 O B:MOH703 2.7 56.6 1.0 OD1 B:ASP345 2.7 56.5 1.0 OD1 B:ASP347 2.8 58.0 1.0 N6 B:PQQ701 2.8 55.8 0.7 CG B:ASP347 3.0 56.6 1.0 OE1 B:GLU204 3.1 56.5 1.0 CD B:GLU204 3.2 57.7 1.0 C5 B:PQQ701 3.3 58.3 0.7 OD2 B:ASP345 3.3 53.0 1.0 CG B:ASP345 3.4 56.0 1.0 C6A B:PQQ701 3.5 54.5 0.7 C7X B:PQQ701 3.6 56.2 0.7 CG B:ASN290 3.8 57.1 1.0 C7 B:PQQ701 3.9 55.8 0.7 C B:MOH703 4.0 55.7 1.0 OD2 B:ASP203 4.5 54.4 1.0 CB B:ASP347 4.5 51.8 1.0 ND2 B:ASN290 4.5 49.1 1.0 NH2 B:ARG372 4.6 50.9 1.0 C4 B:PQQ701 4.6 58.0 0.7 CB B:ASN290 4.7 52.1 1.0 CG B:GLU204 4.7 54.4 1.0 CB B:ASP203 4.7 51.8 1.0 O7A B:PQQ701 4.8 57.2 0.7 CZ2 B:TRP272 4.8 59.0 1.0 C9A B:PQQ701 4.9 56.3 0.7 CB B:ASP345 4.9 55.6 1.0 NE1 B:TRP272 4.9 54.2 1.0 NE1 B:TRP294 5.0 50.4 1.0 O B:ASP345 5.0 54.9 1.0 O4 B:PQQ701 5.0 56.2 0.7

R.Schmitz, H.Op Den Camp. Neodymium As Metal Cofactor For Biological Methanol Oxidation: Structure and Kinetics of A XOXF1-Type Methanol Dehydrogenase To Be Published.