Europium in PDB 6fkw: Europium-Containing Methanol Dehydrogenase

All present enzymatic activity of Europium-Containing Methanol Dehydrogenase:
1.1.2.7; 1.1.2.8;

The structure of Europium-Containing Methanol Dehydrogenase, PDB code: 6fkw was solved by T.Barends, A.Dietl, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	96.27 / 1.40
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	55.080, 101.180, 107.790, 115.21, 97.53, 91.78
R / Rfree (%)	16.9 / 18.5

The binding sites of Europium atom in the Europium-Containing Methanol Dehydrogenase (pdb code 6fkw). This binding sites where shown within 5.0 Angstroms radius around Europium atom.
In total 4 binding sites of Europium where determined in the Europium-Containing Methanol Dehydrogenase, PDB code: 6fkw:
Jump to Europium binding site number: 1; 2; 3; 4;

Europium binding site 1 out of 4 in the Europium-Containing Methanol Dehydrogenase


Mono view


Stereo pair view

A full contact list of Europium with other atoms in the Eu binding site number 1 of Europium-Containing Methanol Dehydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Eu601 b:24.1 occ:0.60 OD2 A:ASP301 2.5 24.4 1.0 O7A A:PQQ602 2.6 21.2 1.0 O5 A:PQQ602 2.6 25.2 1.0 OE1 A:GLU172 2.8 24.1 1.0 OD1 A:ASN256 2.8 21.9 1.0 N6 A:PQQ602 2.8 23.8 1.0 OD1 A:ASP301 2.8 23.2 1.0 OD1 A:ASP299 3.0 22.4 1.0 CG A:ASP301 3.0 21.4 1.0 OE2 A:GLU172 3.1 26.4 1.0 CD A:GLU172 3.3 23.8 1.0 C5 A:PQQ602 3.5 23.1 1.0 C7X A:PQQ602 3.5 22.0 1.0 C6A A:PQQ602 3.7 23.4 1.0 CG A:ASN256 3.7 20.3 1.0 C7 A:PQQ602 3.7 22.1 1.0 CG A:ASP299 3.9 20.1 1.0 OD2 A:ASP299 4.0 22.4 1.0 ND2 A:ASN256 4.4 21.1 1.0 CB A:ASP301 4.5 18.6 1.0 NH2 A:ARG326 4.5 18.9 1.0 CB A:ASN256 4.5 19.4 1.0 CB A:SER255 4.5 16.0 1.0 O7B A:PQQ602 4.7 22.4 1.0 NE1 A:TRP238 4.7 18.4 1.0 CG A:GLU172 4.8 22.6 1.0 CA A:GLY171 4.8 19.2 1.0 N A:ASN256 4.8 16.6 1.0 C4 A:PQQ602 4.9 22.8 1.0 C A:GLY171 4.9 19.7 1.0 CZ2 A:TRP238 4.9 17.5 1.0 OG A:SER255 4.9 17.2 1.0

Europium binding site 2 out of 4 in the Europium-Containing Methanol Dehydrogenase


Mono view


Stereo pair view

A full contact list of Europium with other atoms in the Eu binding site number 2 of Europium-Containing Methanol Dehydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ B:Eu601 b:23.0 occ:0.60 O7A B:PQQ602 2.6 20.9 1.0 O5 B:PQQ602 2.6 23.3 1.0 OD2 B:ASP301 2.6 27.4 1.0 OD1 B:ASN256 2.8 24.2 1.0 OE1 B:GLU172 2.8 25.5 1.0 N6 B:PQQ602 2.8 21.2 1.0 OD1 B:ASP301 2.9 25.6 1.0 OE2 B:GLU172 2.9 28.3 1.0 OD1 B:ASP299 3.0 24.3 1.0 CG B:ASP301 3.1 23.1 1.0 CD B:GLU172 3.2 24.9 1.0 C5 B:PQQ602 3.5 22.1 1.0 C7X B:PQQ602 3.5 20.7 1.0 C6A B:PQQ602 3.6 22.0 1.0 CG B:ASN256 3.6 21.6 1.0 C7 B:PQQ602 3.7 20.9 1.0 CG B:ASP299 3.9 21.8 1.0 OD2 B:ASP299 4.0 23.1 1.0 ND2 B:ASN256 4.4 22.1 1.0 NH2 B:ARG326 4.5 21.1 1.0 CB B:ASN256 4.5 20.2 1.0 CB B:ASP301 4.5 19.9 1.0 CB B:SER255 4.6 17.1 1.0 O7B B:PQQ602 4.7 20.9 1.0 CG B:GLU172 4.7 24.0 1.0 NE1 B:TRP238 4.8 19.9 1.0 N B:ASN256 4.8 17.5 1.0 CA B:GLY171 4.9 20.4 1.0 C4 B:PQQ602 4.9 22.3 1.0 C B:GLY171 4.9 20.9 1.0 CZ2 B:TRP238 5.0 19.2 1.0

Europium binding site 3 out of 4 in the Europium-Containing Methanol Dehydrogenase


Mono view


Stereo pair view

A full contact list of Europium with other atoms in the Eu binding site number 3 of Europium-Containing Methanol Dehydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ C:Eu601 b:20.5 occ:0.60 O7B C:PQQ602 2.5 20.5 1.0 O5 C:PQQ602 2.5 23.2 1.0 OD2 C:ASP301 2.6 27.9 1.0 OD1 C:ASN256 2.7 23.9 1.0 N6 C:PQQ602 2.7 21.2 1.0 OE1 C:GLU172 2.8 24.0 1.0 OD1 C:ASP301 2.8 30.1 1.0 OD1 C:ASP299 2.9 23.5 1.0 OE2 C:GLU172 2.9 27.1 1.0 CG C:ASP301 3.0 24.3 1.0 CD C:GLU172 3.2 23.9 1.0 C5 C:PQQ602 3.4 22.0 1.0 C7X C:PQQ602 3.5 22.3 1.0 C6A C:PQQ602 3.6 21.9 1.0 C7 C:PQQ602 3.6 21.2 1.0 CG C:ASN256 3.7 21.7 1.0 CG C:ASP299 3.8 21.5 1.0 OD2 C:ASP299 3.9 23.3 1.0 ND2 C:ASN256 4.4 22.2 1.0 CB C:ASP301 4.5 20.8 1.0 NH2 C:ARG326 4.5 19.9 1.0 CB C:ASN256 4.6 20.1 1.0 CB C:SER255 4.6 18.0 1.0 O7A C:PQQ602 4.6 22.1 1.0 NE1 C:TRP238 4.7 19.8 1.0 CG C:GLU172 4.7 22.9 1.0 C4 C:PQQ602 4.8 21.6 1.0 N C:ASN256 4.8 17.5 1.0 CA C:GLY171 4.9 21.3 1.0 C C:GLY171 4.9 21.5 1.0 CZ2 C:TRP238 4.9 19.1 1.0 C8 C:PQQ602 5.0 20.8 1.0

Europium binding site 4 out of 4 in the Europium-Containing Methanol Dehydrogenase


Mono view


Stereo pair view

A full contact list of Europium with other atoms in the Eu binding site number 4 of Europium-Containing Methanol Dehydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ D:Eu601 b:42.2 occ:0.60 O5 D:PQQ602 2.4 44.1 1.0 OD2 D:ASP301 2.7 39.3 1.0 N6 D:PQQ602 2.7 44.0 1.0 OE1 D:GLU172 2.8 51.4 1.0 O7B D:PQQ602 2.8 48.0 1.0 OD1 D:ASP299 2.9 44.9 1.0 OE2 D:GLU172 2.9 51.0 1.0 OD1 D:ASP301 3.1 41.9 1.0 CD D:GLU172 3.2 51.1 1.0 CG D:ASP301 3.2 38.9 1.0 OD1 D:ASN256 3.3 44.1 1.0 C5 D:PQQ602 3.3 42.5 1.0 C6A D:PQQ602 3.4 42.5 1.0 OD2 D:ASP299 3.6 42.9 1.0 CG D:ASP299 3.6 42.7 1.0 C7X D:PQQ602 3.6 45.8 1.0 C7 D:PQQ602 3.6 44.0 1.0 CG D:ASN256 3.9 44.8 1.0 NH2 D:ARG326 4.3 34.6 1.0 ND2 D:ASN256 4.3 45.8 1.0 C4 D:PQQ602 4.7 40.7 1.0 CG D:GLU172 4.7 51.6 1.0 CB D:ASP301 4.7 37.4 1.0 CZ2 D:TRP260 4.7 42.9 1.0 CB D:ASN256 4.8 44.4 1.0 O7A D:PQQ602 4.8 45.7 1.0 O D:HOH818 4.9 41.9 1.0 C9A D:PQQ602 4.9 41.7 1.0 NE1 D:TRP260 4.9 44.2 1.0 C8 D:PQQ602 5.0 43.5 1.0 NH1 D:ARG326 5.0 33.5 1.0

B.Jahn, A.Pol, H.Lumpe, T.Barends, A.Dietl, C.Hogendoorn, H.Op Den Camp, L.Daumann. Similar But Not the Same: First Kinetic and Structural Analyses of A Methanol Dehydrogenase Containing A Europium Ion in the Active Site. Chembiochem 2018.
ISSN: ESSN 1439-7633
PubMed: 29524328
DOI: 10.1002/CBIC.201800130