Calcium in PDB 2d0v: Crystal Structure of Methanol Dehydrogenase From Hyphomicrobium Denitrificans

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

The structure of Crystal Structure of Methanol Dehydrogenase From Hyphomicrobium Denitrificans, PDB code: 2d0v was solved by M.Nojiri, D.Hira, K.Yamaguchi, S.Suzuki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.60 / 2.49
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	291.320, 63.999, 109.941, 90.00, 105.74, 90.00
R / Rfree (%)	14.9 / 24.7

The binding sites of Calcium atom in the Crystal Structure of Methanol Dehydrogenase From Hyphomicrobium Denitrificans (pdb code 2d0v). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of Methanol Dehydrogenase From Hyphomicrobium Denitrificans, PDB code: 2d0v:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of Methanol Dehydrogenase From Hyphomicrobium 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 Hyphomicrobium Denitrificans within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca775 b:55.5 occ:0.70 OE1 A:GLU177 2.4 28.0 1.0 OE2 A:GLU177 2.5 30.6 1.0 OD1 A:ASN261 2.5 22.9 1.0 O5 A:PQQ601 2.7 68.2 1.0 CD A:GLU177 2.8 29.1 1.0 O7A A:PQQ601 3.0 63.9 1.0 N6 A:PQQ601 3.1 69.8 1.0 OD2 A:ASP303 3.2 36.5 1.0 CG A:ASN261 3.3 20.2 1.0 ND2 A:ASN261 3.5 19.6 1.0 C5 A:PQQ601 3.6 69.0 1.0 C7X A:PQQ601 3.8 68.3 1.0 C6A A:PQQ601 3.8 69.3 1.0 CB A:ALA305 3.9 21.8 1.0 C7 A:PQQ601 4.0 69.3 1.0 OD1 A:ASP303 4.0 30.4 1.0 CG A:ASP303 4.0 30.2 1.0 CB A:ALA176 4.1 23.6 1.0 CG A:GLU177 4.3 25.9 1.0 N A:GLU177 4.5 25.4 1.0 CB A:ASN261 4.5 18.7 1.0 O A:HOH810 4.6 20.8 1.0 NE1 A:TRP243 4.7 19.2 1.0 NH1 A:ARG331 4.7 19.2 1.0 CZ2 A:TRP243 4.8 20.1 1.0 NE1 A:TRP265 4.8 25.1 1.0 O7B A:PQQ601 4.9 67.6 1.0 CA A:ALA176 4.9 24.8 1.0 C A:ALA176 5.0 26.3 1.0 CZ2 A:TRP265 5.0 26.1 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of Methanol Dehydrogenase From Hyphomicrobium 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 Hyphomicrobium Denitrificans within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca775 b:49.4 occ:0.70 N6 D:PQQ601 2.2 78.0 1.0 OE2 D:GLU177 2.3 40.3 1.0 O5 D:PQQ601 2.5 77.4 1.0 O7A D:PQQ601 2.7 76.1 1.0 OE1 D:GLU177 2.9 33.3 1.0 CD D:GLU177 2.9 35.6 1.0 OD1 D:ASN261 3.0 38.0 1.0 C6A D:PQQ601 3.0 78.3 1.0 C5 D:PQQ601 3.1 78.1 1.0 C7 D:PQQ601 3.2 77.8 1.0 C7X D:PQQ601 3.3 77.3 1.0 OD2 D:ASP303 3.6 34.5 1.0 CG D:ASN261 3.8 28.5 1.0 ND2 D:ASN261 4.2 29.3 1.0 CB D:ALA305 4.2 27.6 1.0 OD1 D:ASP303 4.2 45.6 1.0 CB D:ALA176 4.3 28.5 1.0 CG D:GLU177 4.4 31.2 1.0 CG D:ASP303 4.4 37.2 1.0 O7B D:PQQ601 4.4 75.2 1.0 NE1 D:TRP243 4.4 23.1 1.0 CZ2 D:TRP243 4.4 31.3 1.0 C9A D:PQQ601 4.5 78.0 1.0 C8 D:PQQ601 4.5 77.0 1.0 C4 D:PQQ601 4.6 78.0 1.0 O D:HOH788 4.7 23.0 1.0 CE2 D:TRP243 4.7 26.5 1.0 NH1 D:ARG331 4.8 21.5 1.0 N D:GLU177 4.9 28.7 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of Methanol Dehydrogenase From Hyphomicrobium Denitrificans


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Methanol Dehydrogenase From Hyphomicrobium Denitrificans within 5.0Å range: probe atom residue distance (Å) B Occ I:Ca775 b:49.1 occ:0.70 N6 I:PQQ601 2.4 75.3 1.0 O7A I:PQQ601 2.4 76.8 1.0 OE2 I:GLU177 2.5 42.3 1.0 O5 I:PQQ601 2.7 74.7 1.0 OE1 I:GLU177 2.8 39.9 1.0 CD I:GLU177 3.0 42.1 1.0 C7X I:PQQ601 3.2 75.2 1.0 C6A I:PQQ601 3.2 75.1 1.0 C5 I:PQQ601 3.3 75.3 1.0 C7 I:PQQ601 3.3 75.6 1.0 CB I:ASN261 3.6 35.0 1.0 OD2 I:ASP303 3.8 40.7 1.0 CG I:ASN261 3.8 39.3 1.0 CB I:ALA176 3.9 26.6 1.0 CB I:ALA305 4.1 34.2 1.0 NE1 I:TRP243 4.1 27.9 1.0 OD1 I:ASN261 4.2 49.9 1.0 O I:HOH926 4.2 34.0 1.0 ND2 I:ASN261 4.3 45.6 1.0 O7B I:PQQ601 4.4 75.2 1.0 CZ2 I:TRP243 4.5 27.4 1.0 CG I:GLU177 4.6 36.9 1.0 CE2 I:TRP243 4.6 24.6 1.0 C8 I:PQQ601 4.6 74.4 1.0 C9A I:PQQ601 4.7 75.1 1.0 N I:GLU177 4.7 32.1 1.0 C4 I:PQQ601 4.7 75.3 1.0 N I:ALA176 4.7 27.4 1.0 CA I:ALA176 4.8 28.6 1.0 CG I:ASP303 4.8 41.3 1.0 C I:ALA176 4.9 30.8 1.0 OD1 I:ASP303 4.9 47.7 1.0

M.Nojiri, D.Hira, K.Yamaguchi, T.Okajima, K.Tanizawa, S.Suzuki. Crystal Structures of Cytochrome C(L) and Methanol Dehydrogenase From Hyphomicrobium Denitrificans: Structural and Mechanistic Insights Into Interactions Between the Two Proteins Biochemistry V. 45 3481 2006.
ISSN: ISSN 0006-2960
PubMed: 16533029
DOI: 10.1021/BI051877J