Calcium in PDB 2ad6: Crystal Structure of Methanol Dehydrogenase From M. W3A1 (Form C)

All present enzymatic activity of Crystal Structure of Methanol Dehydrogenase From M. W3A1 (Form C):
1.1.99.8;

The structure of Crystal Structure of Methanol Dehydrogenase From M. W3A1 (Form C), PDB code: 2ad6 was solved by J.Li, J.-H.Gan, Z.-X.Xia, F.S.Mathews, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.62 / 1.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	201.583, 61.947, 123.804, 90.00, 123.30, 90.00
R / Rfree (%)	15.6 / 17.7

The binding sites of Calcium atom in the Crystal Structure of Methanol Dehydrogenase From M. W3A1 (Form C) (pdb code 2ad6). 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 M. W3A1 (Form C), PDB code: 2ad6:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Methanol Dehydrogenase From M. W3A1 (Form C)


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 M. W3A1 (Form C) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca702 b:32.4 occ:1.00 OD1 A:ASN255 2.6 12.7 1.0 O5 A:PQQ701 2.7 13.3 1.0 OE2 A:GLU171 2.7 17.8 1.0 OE1 A:GLU171 2.9 18.3 1.0 OD2 A:ASP297 2.9 17.8 1.0 O7A A:PQQ701 2.9 13.6 1.0 N6 A:PQQ701 3.0 11.8 1.0 CD A:GLU171 3.2 17.8 1.0 CG A:ASN255 3.3 12.7 1.0 ND2 A:ASN255 3.5 13.0 1.0 C5 A:PQQ701 3.6 12.6 1.0 C6A A:PQQ701 3.8 11.7 1.0 C7X A:PQQ701 3.8 12.9 1.0 C7 A:PQQ701 3.9 11.5 1.0 CG A:ASP297 3.9 17.2 1.0 O A:HOH4001 3.9 31.9 1.0 CB A:ALA299 4.0 9.6 1.0 O A:HOH1501 4.0 10.7 1.0 OD1 A:ASP297 4.1 17.8 1.0 NH2 A:ARG324 4.5 10.7 1.0 CB A:ASN255 4.5 10.8 1.0 CB A:ALA170 4.5 10.0 1.0 CG A:GLU171 4.6 15.9 1.0 NE1 A:TRP259 4.6 14.5 1.0 NE1 A:TRP237 4.9 11.3 1.0 CZ2 A:TRP237 4.9 11.2 1.0 C4 A:PQQ701 5.0 11.7 1.0 CZ2 A:TRP259 5.0 12.8 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Methanol Dehydrogenase From M. W3A1 (Form C)


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 M. W3A1 (Form C) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca704 b:30.5 occ:1.00 OD1 C:ASN255 2.6 11.3 1.0 O5 C:PQQ703 2.7 12.9 1.0 OE2 C:GLU171 2.7 14.5 1.0 OD2 C:ASP297 2.9 13.8 1.0 OE1 C:GLU171 2.9 16.6 1.0 O7A C:PQQ703 2.9 11.6 1.0 N6 C:PQQ703 3.0 10.0 1.0 CD C:GLU171 3.1 14.8 1.0 CG C:ASN255 3.3 9.4 1.0 ND2 C:ASN255 3.5 9.2 1.0 C5 C:PQQ703 3.6 11.7 1.0 O C:HOH4002 3.7 31.4 1.0 C6A C:PQQ703 3.8 9.9 1.0 C7X C:PQQ703 3.8 10.6 1.0 CG C:ASP297 3.8 15.2 1.0 C7 C:PQQ703 3.9 9.4 1.0 CB C:ALA299 3.9 7.3 1.0 O C:HOH1914 4.0 8.7 1.0 OD1 C:ASP297 4.0 15.4 1.0 NH1 C:ARG324 4.4 7.5 1.0 CB C:ASN255 4.5 8.7 1.0 CB C:ALA170 4.5 11.0 1.0 CG C:GLU171 4.6 12.9 1.0 NE1 C:TRP259 4.6 10.5 1.0 CZ2 C:TRP259 4.9 9.5 1.0 NE1 C:TRP237 4.9 9.8 1.0 CZ2 C:TRP237 4.9 10.1 1.0 C4 C:PQQ703 5.0 10.8 1.0

J.Li, J.-H.Gan, F.S.Mathews, Z.-X.Xia. The Enzymatic Reaction-Induced Configuration Change of the Prosthetic Group Pqq of Methanol Dehydrogenase Biochem.Biophys.Res.Commun. V. 406 621 2011.
ISSN: ISSN 0006-291X
PubMed: 21356200
DOI: 10.1016/J.BBRC.2011.02.107