Magnesium in PDB 3k1u: Beta-Xylosidase, Family 43 Glycosyl Hydrolase From Clostridium Acetobutylicum

The structure of Beta-Xylosidase, Family 43 Glycosyl Hydrolase From Clostridium Acetobutylicum, PDB code: 3k1u was solved by J.Osipiuk, R.Wu, R.Jedrzejczak, A.Joachimiak, Midwest Center Forstructural Genomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.20 / 1.55
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	47.450, 59.658, 112.391, 90.00, 90.00, 90.00
R / Rfree (%)	13.6 / 16.1

The structure of Beta-Xylosidase, Family 43 Glycosyl Hydrolase From Clostridium Acetobutylicum also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Magnesium atom in the Beta-Xylosidase, Family 43 Glycosyl Hydrolase From Clostridium Acetobutylicum (pdb code 3k1u). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Beta-Xylosidase, Family 43 Glycosyl Hydrolase From Clostridium Acetobutylicum, PDB code: 3k1u:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Beta-Xylosidase, Family 43 Glycosyl Hydrolase From Clostridium Acetobutylicum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Beta-Xylosidase, Family 43 Glycosyl Hydrolase From Clostridium Acetobutylicum within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg409 b:9.6 occ:1.00 O A:HOH512 2.1 5.0 1.0 OE2 A:GLU75 2.1 5.6 1.0 O A:HOH560 2.1 3.4 1.0 O A:HOH424 2.1 5.6 1.0 O A:HOH369 2.1 6.1 1.0 NE2 A:HIS260 2.3 7.1 1.0 CD A:GLU75 3.1 7.4 1.0 CD2 A:HIS260 3.2 7.8 1.0 CE1 A:HIS260 3.3 8.9 1.0 CG A:GLU75 3.6 5.9 1.0 O A:PRO198 3.9 4.8 1.0 O A:HOH352 3.9 6.9 1.0 O A:HOH427 4.0 10.5 1.0 O A:HOH372 4.1 8.9 1.0 OE1 A:GLU75 4.2 7.1 1.0 O A:ASP135 4.4 5.3 1.0 CG A:HIS260 4.4 6.2 1.0 ND1 A:HIS260 4.4 7.1 1.0 O A:HOH358 4.5 6.7 1.0 O A:ASN261 4.6 5.8 1.0 O A:ALA136 4.7 4.7 1.0 C A:ASP135 4.8 3.0 1.0 O A:ALA73 4.9 5.5 1.0 CA A:GLY197 4.9 4.5 1.0 C A:GLY197 4.9 5.1 1.0 CB A:THR137 4.9 4.5 1.0 CB A:ASP135 5.0 4.9 1.0 CA A:ASP135 5.0 4.3 1.0

Magnesium binding site 2 out of 3 in the Beta-Xylosidase, Family 43 Glycosyl Hydrolase From Clostridium Acetobutylicum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Beta-Xylosidase, Family 43 Glycosyl Hydrolase From Clostridium Acetobutylicum within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg410 b:29.4 occ:1.00 O A:HOH504 1.9 22.4 1.0 O A:HOH576 2.0 27.7 1.0 O A:HOH441 2.1 17.8 1.0 O A:HOH470 2.1 20.4 1.0 O A:HOH665 2.2 27.3 1.0 O A:HOH450 2.2 16.7 1.0 OD2 A:ASP98 3.8 15.0 1.0 O A:HOH591 4.0 28.6 1.0 OD1 A:ASP98 4.1 11.0 1.0 CG A:ASP98 4.2 11.7 1.0 OD1 A:ASP97 4.3 12.1 1.0 CA A:ASP97 4.4 8.1 1.0 O A:HOH627 4.5 28.8 1.0 O A:HOH642 4.5 34.0 1.0 O A:ASP97 4.6 9.5 1.0 C A:ASP97 4.6 8.3 1.0 CB A:ASP97 4.7 7.6 1.0 CG A:ASP97 5.0 8.7 1.0

Magnesium binding site 3 out of 3 in the Beta-Xylosidase, Family 43 Glycosyl Hydrolase From Clostridium Acetobutylicum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Beta-Xylosidase, Family 43 Glycosyl Hydrolase From Clostridium Acetobutylicum within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg411 b:25.2 occ:0.70 O A:HOH650 2.0 28.3 1.0 O A:HOH648 2.0 30.2 1.0 O A:HOH646 2.0 27.1 1.0 O A:HOH561 2.1 23.3 1.0 O A:HOH604 2.1 27.1 1.0 O A:HOH649 2.1 27.0 1.0 O A:HOH647 4.0 36.5 1.0 O A:HOH595 4.1 28.2 1.0 OH A:TYR20 4.1 15.3 1.0 OD1 A:ASN23 4.4 13.2 0.5 O A:PHE78 4.4 8.9 1.0 O A:HOH536 4.5 17.3 1.0 CE1 A:TYR20 4.7 17.8 1.0 CZ A:TYR20 4.9 15.1 1.0

J.Osipiuk, R.Wu, R.Jedrzejczak, A.Joachimiak. X-Ray Crystal Structure of Beta-Xylosidase, Family 43 Glycosyl Hydrolase From Clostridium Acetobutylicum at 1.55 A Resolution To Be Published.