Calcium in PDB 1h4j: Methylobacterium Extorquens Methanol Dehydrogenase D303E Mutant

All present enzymatic activity of Methylobacterium Extorquens Methanol Dehydrogenase D303E Mutant:
1.1.2.7;

The structure of Methylobacterium Extorquens Methanol Dehydrogenase D303E Mutant, PDB code: 1h4j was solved by F.Mohammed, R.Gill, D.Thompson, J.B.Cooper, S.P.Wood, P.R.Afolabi, C.Anthony, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 3.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	101.850, 61.020, 212.680, 90.00, 92.83, 90.00
R / Rfree (%)	18.7 / 21.7

The binding sites of Calcium atom in the Methylobacterium Extorquens Methanol Dehydrogenase D303E Mutant (pdb code 1h4j). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Methylobacterium Extorquens Methanol Dehydrogenase D303E Mutant, PDB code: 1h4j:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Methylobacterium Extorquens Methanol Dehydrogenase D303E Mutant


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Methylobacterium Extorquens Methanol Dehydrogenase D303E Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca701 b:18.4 occ:1.00 N6 A:PQQ601 2.3 29.7 1.0 OE2 A:GLU177 2.4 23.8 1.0 OE2 A:GLU303 2.4 18.4 1.0 O7B A:PQQ601 2.6 29.7 1.0 O5 A:PQQ601 2.6 29.7 1.0 OE1 A:GLU177 2.7 22.8 1.0 OD1 A:ASN261 2.7 14.3 1.0 CD A:GLU177 2.9 23.4 1.0 C7X A:PQQ601 3.2 29.7 1.0 C7 A:PQQ601 3.2 29.7 1.0 C5 A:PQQ601 3.2 29.7 1.0 C6A A:PQQ601 3.2 29.7 1.0 CD A:GLU303 3.6 18.4 1.0 CG A:ASN261 3.6 14.8 1.0 ND2 A:ASN261 3.9 12.7 1.0 OE1 A:GLU303 4.3 18.4 1.0 CG A:GLU177 4.4 20.6 1.0 O7A A:PQQ601 4.5 29.7 1.0 CG A:GLU303 4.5 18.4 1.0 CB A:ALA305 4.6 14.2 1.0 C8 A:PQQ601 4.6 29.7 1.0 C9A A:PQQ601 4.7 29.7 1.0 C4 A:PQQ601 4.7 29.7 1.0 CB A:ALA176 4.7 13.5 1.0 NE1 A:TRP265 4.8 17.0 1.0 NH2 A:ARG331 4.8 11.7 1.0 CB A:ASN261 4.8 13.3 1.0 CZ2 A:TRP243 4.9 17.7 1.0 CZ2 A:TRP265 5.0 17.4 1.0 NE1 A:TRP243 5.0 12.5 1.0 N A:GLU177 5.0 17.7 1.0

Calcium binding site 2 out of 4 in the Methylobacterium Extorquens Methanol Dehydrogenase D303E Mutant


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Methylobacterium Extorquens Methanol Dehydrogenase D303E Mutant within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca701 b:18.4 occ:1.00 N6 C:PQQ601 2.3 29.7 1.0 OE2 C:GLU177 2.4 23.8 1.0 OE2 C:GLU303 2.4 18.4 1.0 O7B C:PQQ601 2.6 29.7 1.0 O5 C:PQQ601 2.6 29.7 1.0 OE1 C:GLU177 2.7 22.8 1.0 OD1 C:ASN261 2.7 14.3 1.0 CD C:GLU177 2.9 23.4 1.0 C7X C:PQQ601 3.2 29.7 1.0 C7 C:PQQ601 3.2 29.7 1.0 C5 C:PQQ601 3.2 29.7 1.0 C6A C:PQQ601 3.2 29.7 1.0 CD C:GLU303 3.6 18.4 1.0 CG C:ASN261 3.6 14.8 1.0 ND2 C:ASN261 3.9 12.7 1.0 OE1 C:GLU303 4.3 18.4 1.0 CG C:GLU177 4.4 20.6 1.0 O7A C:PQQ601 4.5 29.7 1.0 CG C:GLU303 4.5 18.4 1.0 CB C:ALA305 4.6 14.2 1.0 C8 C:PQQ601 4.6 29.7 1.0 C9A C:PQQ601 4.7 29.7 1.0 C4 C:PQQ601 4.7 29.7 1.0 CB C:ALA176 4.7 13.5 1.0 NE1 C:TRP265 4.8 17.0 1.0 NH2 C:ARG331 4.8 11.7 1.0 CB C:ASN261 4.8 13.3 1.0 CZ2 C:TRP243 4.9 17.7 1.0 CZ2 C:TRP265 5.0 17.4 1.0 NE1 C:TRP243 5.0 12.5 1.0 N C:GLU177 5.0 17.7 1.0

Calcium binding site 3 out of 4 in the Methylobacterium Extorquens Methanol Dehydrogenase D303E Mutant


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Methylobacterium Extorquens Methanol Dehydrogenase D303E Mutant within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca701 b:18.4 occ:1.00 N6 E:PQQ601 2.3 29.7 1.0 OE2 E:GLU177 2.4 23.8 1.0 OE2 E:GLU303 2.4 18.4 1.0 O7B E:PQQ601 2.6 29.7 1.0 O5 E:PQQ601 2.6 29.7 1.0 OE1 E:GLU177 2.7 22.8 1.0 OD1 E:ASN261 2.7 14.3 1.0 CD E:GLU177 2.9 23.4 1.0 C7X E:PQQ601 3.2 29.7 1.0 C7 E:PQQ601 3.2 29.7 1.0 C5 E:PQQ601 3.2 29.7 1.0 C6A E:PQQ601 3.2 29.7 1.0 CD E:GLU303 3.6 18.4 1.0 CG E:ASN261 3.6 14.8 1.0 ND2 E:ASN261 3.9 12.7 1.0 OE1 E:GLU303 4.3 18.4 1.0 CG E:GLU177 4.4 20.6 1.0 O7A E:PQQ601 4.5 29.7 1.0 CG E:GLU303 4.5 18.4 1.0 CB E:ALA305 4.6 14.2 1.0 C8 E:PQQ601 4.6 29.7 1.0 C9A E:PQQ601 4.7 29.7 1.0 C4 E:PQQ601 4.7 29.7 1.0 CB E:ALA176 4.7 13.5 1.0 NE1 E:TRP265 4.8 17.0 1.0 NH2 E:ARG331 4.8 11.7 1.0 CB E:ASN261 4.8 13.3 1.0 CZ2 E:TRP243 4.9 17.7 1.0 CZ2 E:TRP265 5.0 17.4 1.0 NE1 E:TRP243 5.0 12.5 1.0 N E:GLU177 5.0 17.7 1.0

Calcium binding site 4 out of 4 in the Methylobacterium Extorquens Methanol Dehydrogenase D303E Mutant


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Methylobacterium Extorquens Methanol Dehydrogenase D303E Mutant within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca701 b:18.4 occ:1.00 N6 G:PQQ601 2.3 29.7 1.0 OE2 G:GLU177 2.4 23.8 1.0 OE2 G:GLU303 2.4 18.4 1.0 O7B G:PQQ601 2.6 29.7 1.0 O5 G:PQQ601 2.6 29.7 1.0 OE1 G:GLU177 2.7 22.8 1.0 OD1 G:ASN261 2.7 14.3 1.0 CD G:GLU177 2.9 23.4 1.0 C7X G:PQQ601 3.2 29.7 1.0 C7 G:PQQ601 3.2 29.7 1.0 C5 G:PQQ601 3.2 29.7 1.0 C6A G:PQQ601 3.2 29.7 1.0 CD G:GLU303 3.6 18.4 1.0 CG G:ASN261 3.6 14.8 1.0 ND2 G:ASN261 3.9 12.7 1.0 OE1 G:GLU303 4.3 18.4 1.0 CG G:GLU177 4.4 20.6 1.0 O7A G:PQQ601 4.5 29.7 1.0 CG G:GLU303 4.5 18.4 1.0 CB G:ALA305 4.6 14.2 1.0 C8 G:PQQ601 4.6 29.7 1.0 C9A G:PQQ601 4.7 29.7 1.0 C4 G:PQQ601 4.7 29.7 1.0 CB G:ALA176 4.7 13.5 1.0 NE1 G:TRP265 4.8 17.0 1.0 NH2 G:ARG331 4.8 11.7 1.0 CB G:ASN261 4.8 13.3 1.0 CZ2 G:TRP243 4.9 17.7 1.0 CZ2 G:TRP265 5.0 17.4 1.0 NE1 G:TRP243 5.0 12.5 1.0 N G:GLU177 5.0 17.7 1.0

P.R.Afolabi, F.Mohammed, K.Amaratunga, O.Majekodunmi, S.L.Dales, R.Gill, D.Thompson, J.B.Cooper, S.P.Wood, P.M.Goodwin, C.Anthony. Site-Directed Mutagenesis and X-Ray Crystallography of the Pqq-Containing Quinoprotein Methanol Dehydrogenase and Its Electron Acceptor, Cytochrome C(L)(,) Biochemistry V. 40 9799 2001.
ISSN: ISSN 0006-2960
PubMed: 11502173
DOI: 10.1021/BI002932L