Magnesium in PDB 6jp4: Crystal Structure of the Catalytic Domain of A Multi-Domain Alginate Lyase DP0100 From Thermophilic Bacterium Defluviitalea Phaphyphila

The structure of Crystal Structure of the Catalytic Domain of A Multi-Domain Alginate Lyase DP0100 From Thermophilic Bacterium Defluviitalea Phaphyphila, PDB code: 6jp4 was solved by S.Q.Ji, S.R.Dix, A.Aziz, S.E.Sedelnikova, F.L.Li, D.W.Rice, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	98.90 / 2.07
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	261.324, 394.812, 112.187, 90.00, 90.00, 90.00
R / Rfree (%)	22.2 / 24

The structure of Crystal Structure of the Catalytic Domain of A Multi-Domain Alginate Lyase DP0100 From Thermophilic Bacterium Defluviitalea Phaphyphila also contains other interesting chemical elements:

Manganese	(Mn)	3 atoms
Arsenic	(As)	1 atom
Calcium	(Ca)	6 atoms

The binding sites of Magnesium atom in the Crystal Structure of the Catalytic Domain of A Multi-Domain Alginate Lyase DP0100 From Thermophilic Bacterium Defluviitalea Phaphyphila (pdb code 6jp4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of the Catalytic Domain of A Multi-Domain Alginate Lyase DP0100 From Thermophilic Bacterium Defluviitalea Phaphyphila, PDB code: 6jp4:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of the Catalytic Domain of A Multi-Domain Alginate Lyase DP0100 From Thermophilic Bacterium Defluviitalea Phaphyphila


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Catalytic Domain of A Multi-Domain Alginate Lyase DP0100 From Thermophilic Bacterium Defluviitalea Phaphyphila within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg802 b:50.9 occ:1.00 O A:TRP180 2.0 30.8 1.0 O A:HOH1016 2.1 37.8 1.0 OE2 A:GLU133 2.2 32.0 1.0 O A:HOH1245 2.2 35.1 1.0 O A:HOH920 2.3 42.6 1.0 O A:HOH1292 2.3 36.8 1.0 CD A:GLU133 3.1 27.3 1.0 C A:TRP180 3.2 27.0 1.0 OE1 A:GLU133 3.5 33.0 1.0 ND1 A:HIS187 3.9 30.7 1.0 CA A:TRP180 3.9 28.2 1.0 O A:HOH1183 4.1 43.8 1.0 N A:GLY181 4.3 28.3 1.0 CB A:HIS187 4.4 25.0 1.0 O A:HOH976 4.4 49.3 1.0 CB A:TRP180 4.4 27.8 1.0 CG A:GLU133 4.4 27.8 1.0 O A:PRO124 4.5 33.4 1.0 CG A:HIS187 4.5 27.4 1.0 O A:HOH1246 4.6 35.0 1.0 OD2 A:ASP132 4.6 42.3 1.0 CA A:GLY181 4.6 28.0 1.0 OD1 A:ASP132 4.7 56.2 1.0 CD A:PRO182 4.8 32.8 1.0 CE1 A:HIS187 4.8 27.2 1.0 O A:HOH1323 4.9 56.2 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of the Catalytic Domain of A Multi-Domain Alginate Lyase DP0100 From Thermophilic Bacterium Defluviitalea Phaphyphila


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Catalytic Domain of A Multi-Domain Alginate Lyase DP0100 From Thermophilic Bacterium Defluviitalea Phaphyphila within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg802 b:56.1 occ:1.00 O B:HOH933 2.0 42.6 1.0 O B:TRP180 2.1 45.2 1.0 O B:HOH976 2.2 43.1 1.0 O B:HOH1104 2.3 35.1 1.0 OE2 B:GLU133 2.4 53.7 1.0 C B:TRP180 3.3 42.6 1.0 CD B:GLU133 3.3 47.3 1.0 OE1 B:GLU133 3.5 40.1 1.0 O B:HOH1044 3.5 52.5 1.0 CA B:TRP180 3.9 48.5 1.0 ND1 B:HIS187 4.0 39.9 1.0 O B:PRO124 4.3 61.7 1.0 N B:GLY181 4.4 41.1 1.0 CB B:TRP180 4.4 48.4 1.0 OD2 B:ASP132 4.5 52.3 1.0 O B:HOH1139 4.6 53.8 1.0 CG B:GLU133 4.6 41.0 1.0 CB B:HIS187 4.7 33.2 1.0 O B:HOH1120 4.7 47.5 1.0 CA B:GLY181 4.8 41.4 1.0 CG B:HIS187 4.8 36.4 1.0 CD B:PRO182 4.8 52.8 1.0 CA B:THR125 4.8 63.4 1.0 OD1 B:ASP132 4.8 48.6 1.0 CE1 B:HIS187 4.9 44.6 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of the Catalytic Domain of A Multi-Domain Alginate Lyase DP0100 From Thermophilic Bacterium Defluviitalea Phaphyphila


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the Catalytic Domain of A Multi-Domain Alginate Lyase DP0100 From Thermophilic Bacterium Defluviitalea Phaphyphila within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg802 b:73.0 occ:1.00 O C:TRP180 2.1 70.0 1.0 O C:HOH915 2.4 56.3 1.0 OE2 C:GLU133 2.5 86.8 1.0 OE1 C:GLU133 3.0 83.0 1.0 CD C:GLU133 3.0 77.1 1.0 C C:TRP180 3.1 83.6 1.0 CA C:TRP180 3.4 89.2 1.0 O C:PRO124 3.8 97.1 1.0 CB C:TRP180 3.9 99.8 1.0 CA C:THR125 4.2 81.8 1.0 N C:GLY181 4.3 85.3 1.0 C C:PRO124 4.4 86.8 1.0 CG C:GLU133 4.4 75.1 1.0 OD2 C:ASP132 4.5 92.2 1.0 CG2 C:THR125 4.5 80.9 1.0 N C:THR125 4.6 85.9 1.0 ND1 C:HIS187 4.6 64.9 1.0 CG C:TRP180 4.7 0.9 1.0 OD1 C:ASP132 4.8 91.0 1.0 N C:TRP180 4.8 85.7 1.0 CB C:THR125 4.8 81.9 1.0 CG C:ASP132 4.9 90.3 1.0 O C:THR179 5.0 96.1 1.0 CA C:GLY181 5.0 89.6 1.0

S.Ji, S.R.Dix, A.A.Aziz, S.E.Sedelnikova, P.J.Baker, J.B.Rafferty, P.A.Bullough, S.B.Tzokov, J.Agirre, F.L.Li, D.W.Rice. The Molecular Basis of Endolytic Activity of A Multidomain Alginate Lyase From Defluviitalea Phaphyphila, A Representative of A New Lyase Family, Plxx. J.Biol.Chem. 2019.
ISSN: ESSN 1083-351X
PubMed: 31624143
DOI: 10.1074/JBC.RA119.010716