Magnesium in PDB 6sd0: Structure of Beta-Galactosidase From Thermotoga Maritima.

All present enzymatic activity of Structure of Beta-Galactosidase From Thermotoga Maritima.:
3.2.1.23;

The structure of Structure of Beta-Galactosidase From Thermotoga Maritima., PDB code: 6sd0 was solved by E.Jimenez-Ortega, M.Ramirez-Escudero, J.Sanz-Aparicio, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 3.70
Space group	I 4
Cell size a, b, c (Å), α, β, γ (°)	167.852, 167.852, 519.990, 90.00, 90.00, 90.00
R / Rfree (%)	24.1 / 28.6

The binding sites of Magnesium atom in the Structure of Beta-Galactosidase From Thermotoga Maritima. (pdb code 6sd0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of Beta-Galactosidase From Thermotoga Maritima., PDB code: 6sd0:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structure of Beta-Galactosidase From Thermotoga Maritima.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Beta-Galactosidase From Thermotoga Maritima. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1101 b:39.6 occ:1.00 O A:ALA511 2.3 0.7 1.0 O A:GLY575 2.3 0.2 1.0 OE1 A:GLU584 2.4 0.6 1.0 OE1 A:GLU586 2.7 0.1 1.0 O A:GLY513 2.8 0.9 1.0 C A:GLY575 3.4 0.2 1.0 CD A:GLU584 3.4 0.3 1.0 C A:ALA511 3.5 0.4 1.0 N A:GLY513 3.6 0.2 1.0 C A:GLY513 3.8 0.9 1.0 CD A:GLU586 3.8 0.6 1.0 N A:GLY575 3.8 0.2 1.0 OE2 A:GLU584 3.9 0.9 1.0 CA A:GLY513 4.0 0.2 1.0 OD1 A:ASP542 4.0 0.2 1.0 C A:MET512 4.1 0.1 1.0 CA A:GLY575 4.1 0.6 1.0 OE2 A:GLU586 4.3 0.4 1.0 N A:MET512 4.3 0.5 1.0 CA A:MET512 4.3 0.8 1.0 CB A:ALA511 4.4 0.2 1.0 N A:VAL576 4.4 0.3 1.0 C A:ASN574 4.4 0.8 1.0 CA A:ALA511 4.5 0.5 1.0 OD2 A:ASP542 4.6 0.9 1.0 CG A:GLU584 4.6 0.7 1.0 O A:ILE573 4.7 0.0 1.0 CA A:VAL576 4.7 1.0 1.0 CG A:ASP542 4.7 0.7 1.0 O A:MET512 4.8 0.6 1.0 O A:ASN574 5.0 0.1 1.0 N A:ASN514 5.0 0.1 1.0

Magnesium binding site 2 out of 4 in the Structure of Beta-Galactosidase From Thermotoga Maritima.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Beta-Galactosidase From Thermotoga Maritima. within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1101 b:41.8 occ:1.00 O B:GLY513 1.9 0.7 1.0 OE1 B:GLU584 2.0 0.5 1.0 OE1 B:GLU586 2.4 0.6 1.0 O B:ALA511 2.7 91.5 1.0 CD B:GLU586 3.0 0.9 1.0 C B:GLY513 3.0 0.1 1.0 O B:GLY575 3.1 0.7 1.0 OE2 B:GLU586 3.1 0.7 1.0 CD B:GLU584 3.2 0.6 1.0 N B:GLY513 3.6 0.8 1.0 CA B:GLY513 3.7 0.1 1.0 OE2 B:GLU584 3.8 0.3 1.0 C B:ALA511 3.8 0.5 1.0 N B:ASN514 4.1 0.1 1.0 CE1 B:TYR883 4.2 0.7 1.0 C B:MET512 4.2 0.4 1.0 C B:GLY575 4.2 0.6 1.0 CG B:GLU584 4.3 0.2 1.0 CG B:GLU586 4.3 0.8 1.0 CB B:GLU584 4.5 0.7 1.0 CD1 B:TYR883 4.5 0.6 1.0 CA B:ASN514 4.6 0.7 1.0 O B:MET512 4.6 1.0 1.0 N B:MET512 4.7 0.8 1.0 CB B:ALA511 4.7 0.8 1.0 CA B:ALA511 4.7 0.5 1.0 N B:SER515 4.8 0.9 1.0 CA B:MET512 4.8 0.7 1.0

Magnesium binding site 3 out of 4 in the Structure of Beta-Galactosidase From Thermotoga Maritima.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Beta-Galactosidase From Thermotoga Maritima. within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1101 b:41.0 occ:1.00 OE1 C:GLU584 1.8 0.8 1.0 O C:GLY513 2.4 0.1 1.0 OE1 C:GLU586 2.6 0.9 1.0 O C:GLY575 2.7 0.5 1.0 O C:ALA511 2.8 0.7 1.0 CD C:GLU584 3.0 0.5 1.0 CD C:GLU586 3.3 0.8 1.0 C C:GLY513 3.4 0.9 1.0 OE2 C:GLU586 3.6 0.3 1.0 N C:GLY513 3.7 0.0 1.0 OE2 C:GLU584 3.7 0.9 1.0 CA C:GLY513 3.8 0.5 1.0 C C:GLY575 3.8 0.8 1.0 CG C:GLU584 4.0 0.9 1.0 C C:ALA511 4.1 0.8 1.0 CE1 C:TYR883 4.2 0.7 1.0 CB C:GLU584 4.3 0.8 1.0 C C:MET512 4.4 0.2 1.0 CD1 C:TYR883 4.4 0.9 1.0 N C:GLY575 4.5 0.0 1.0 N C:ASN514 4.5 0.1 1.0 CG C:GLU586 4.6 0.7 1.0 CA C:GLY575 4.7 0.5 1.0 N C:VAL576 4.7 0.9 1.0 CA C:VAL576 4.7 0.7 1.0 OD1 C:ASP542 4.8 0.0 1.0 OD2 C:ASP542 4.8 0.5 1.0 CB C:ALA511 4.8 0.5 1.0 N C:MET512 4.9 0.5 1.0 CA C:MET512 4.9 0.6 1.0 CA C:ALA511 5.0 0.0 1.0

Magnesium binding site 4 out of 4 in the Structure of Beta-Galactosidase From Thermotoga Maritima.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Beta-Galactosidase From Thermotoga Maritima. within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg1101 b:41.2 occ:1.00 O D:ALA511 2.4 0.0 1.0 O D:GLY513 2.4 0.7 1.0 OE1 D:GLU584 2.5 0.3 1.0 O D:GLY575 2.8 0.3 1.0 N D:GLY513 2.9 1.0 1.0 OE1 D:GLU586 3.1 0.4 1.0 C D:GLY513 3.2 0.7 1.0 CA D:GLY513 3.3 0.8 1.0 C D:ALA511 3.5 0.6 1.0 CD D:GLU584 3.5 0.3 1.0 C D:MET512 3.7 1.0 1.0 OE2 D:GLU584 3.9 0.1 1.0 C D:GLY575 3.9 0.8 1.0 CD D:GLU586 4.0 0.9 1.0 CA D:MET512 4.1 0.8 1.0 OE2 D:GLU586 4.1 0.5 1.0 N D:MET512 4.2 0.4 1.0 N D:GLY575 4.2 0.9 1.0 OD1 D:ASP542 4.4 0.4 1.0 N D:ASN514 4.5 0.1 1.0 O D:MET512 4.6 0.9 1.0 CE1 D:TYR883 4.6 0.7 1.0 CA D:ALA511 4.6 0.8 1.0 C D:ASN574 4.6 0.6 1.0 CA D:GLY575 4.7 0.3 1.0 CB D:ALA511 4.7 0.1 1.0 CD1 D:TYR883 4.7 0.9 1.0 CG D:GLU584 4.9 0.2 1.0 O D:ILE573 4.9 0.2 1.0 N D:VAL576 5.0 0.5 1.0

S.Miguez Amil, E.Jimenez-Ortega, M.Ramirez-Escudero, D.Talens-Perales, J.Marin-Navarro, J.Polaina, J.Sanz-Aparicio, R.Fernandez-Leiro. The Cryo-Em Structure Ofthermotoga Maritimabeta-Galactosidase: Quaternary Structure Guides Protein Engineering. Acs Chem.Biol. 2019.
ISSN: ESSN 1554-8937
PubMed: 31874027
DOI: 10.1021/ACSCHEMBIO.9B00752