Calcium in PDB 1lrw: Crystal Structure of Methanol Dehydrogenase From P. Denitrificans

All present enzymatic activity of Crystal Structure of Methanol Dehydrogenase From P. Denitrificans:
1.1.99.8;

The structure of Crystal Structure of Methanol Dehydrogenase From P. Denitrificans, PDB code: 1lrw was solved by Z.-X.Xia, W.-W.Dai, Y.-N.He, S.A.White, F.S.Mathews, V.L.Davidson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.76 / 2.50
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	113.340, 122.280, 107.360, 90.00, 90.00, 90.00
R / Rfree (%)	17.9 / 23.8

The binding sites of Calcium atom in the Crystal Structure of Methanol Dehydrogenase From P. Denitrificans (pdb code 1lrw). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Methanol Dehydrogenase From P. Denitrificans, PDB code: 1lrw:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Methanol Dehydrogenase From P. Denitrificans


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Methanol Dehydrogenase From P. Denitrificans within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca702 b:40.8 occ:1.00 O5 A:PQQ701 2.4 27.8 1.0 OE1 A:GLU177 2.4 17.7 1.0 OE2 A:GLU177 2.5 18.8 1.0 CD A:GLU177 2.7 16.3 1.0 N6 A:PQQ701 2.9 29.6 1.0 OD1 A:ASN261 3.0 15.7 1.0 OD2 A:ASP303 3.2 14.4 1.0 O7A A:PQQ701 3.2 33.0 1.0 C5 A:PQQ701 3.3 28.2 1.0 C6A A:PQQ701 3.6 28.0 1.0 CG A:ASN261 3.7 13.1 1.0 O A:HOH726 3.7 8.1 1.0 ND2 A:ASN261 3.8 12.2 1.0 C7 A:PQQ701 3.8 31.3 1.0 C7X A:PQQ701 3.9 32.2 1.0 CG A:ASP303 4.0 15.2 1.0 OD1 A:ASP303 4.0 16.6 1.0 CG A:GLU177 4.2 15.1 1.0 NH1 A:ARG331 4.3 15.8 1.0 CB A:ALA305 4.4 9.1 1.0 CB A:ALA176 4.6 11.2 1.0 NE1 A:TRP265 4.6 10.0 1.0 C4 A:PQQ701 4.7 27.9 1.0 O A:HOH820 4.8 18.6 1.0 CZ2 A:TRP265 4.8 10.9 1.0 N A:GLU177 4.9 11.9 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Methanol Dehydrogenase From P. Denitrificans


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Methanol Dehydrogenase From P. Denitrificans within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca702 b:43.8 occ:1.00 OE1 C:GLU177 2.4 18.5 1.0 N6 C:PQQ701 2.4 36.8 1.0 O7A C:PQQ701 2.5 35.4 1.0 O5 C:PQQ701 2.5 36.4 1.0 OE2 C:GLU177 2.8 22.4 1.0 OD1 C:ASN261 2.9 15.1 1.0 CD C:GLU177 2.9 20.3 1.0 C7 C:PQQ701 3.3 36.5 1.0 C5 C:PQQ701 3.3 36.6 1.0 C7X C:PQQ701 3.3 36.0 1.0 C6A C:PQQ701 3.3 36.1 1.0 CG C:ASN261 3.8 15.9 1.0 OD2 C:ASP303 3.8 18.4 1.0 O C:HOH863 4.0 21.6 1.0 ND2 C:ASN261 4.0 15.1 1.0 CB C:ALA176 4.3 17.4 1.0 CG C:GLU177 4.4 17.9 1.0 O C:HOH771 4.5 2.6 1.0 O7B C:PQQ701 4.5 36.0 1.0 NH1 C:ARG331 4.5 17.5 1.0 C8 C:PQQ701 4.6 35.1 1.0 NE1 C:TRP243 4.6 4.9 1.0 CB C:ALA305 4.6 14.4 1.0 CG C:ASP303 4.7 20.4 1.0 C9A C:PQQ701 4.7 34.9 1.0 OD1 C:ASP303 4.7 22.9 1.0 CZ2 C:TRP243 4.7 1.1 1.0 C4 C:PQQ701 4.8 36.4 1.0 N C:GLU177 4.8 17.7 1.0 CE2 C:TRP243 5.0 4.9 1.0

Z.-X.Xia, W.-W.Dai, Y.-N.He, S.A.White, F.S.Mathews, V.L.Davidson. X-Ray Structure of Methanol Dehydrogenase From Paracoccus Denitrificans and Molecular Modeling of Its Interactions with Cytochrome C-551I J.Biol.Inorg.Chem. V. 8 843 2003.
ISSN: ISSN 0949-8257
PubMed: 14505072
DOI: 10.1007/S00775-003-0485-0