Calcium 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:

Magnesium	(Mg)	3 atoms
Manganese	(Mn)	3 atoms
Arsenic	(As)	1 atom

The binding sites of Calcium 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 Calcium atom.
In total 6 binding sites of Calcium 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 Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 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 Calcium with other atoms in the Ca 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:Ca803 b:26.3 occ:1.00 O A:HOH991 2.3 25.5 1.0 OD1 A:ASP409 2.4 22.1 1.0 OE2 A:GLU401 2.4 20.6 1.0 O A:HIS407 2.5 21.8 1.0 O A:HOH1120 2.5 23.9 1.0 OE2 A:GLU287 2.6 26.5 1.0 OE1 A:GLU287 2.6 30.3 1.0 OD2 A:ASP409 2.8 23.8 1.0 CG A:ASP409 2.8 26.1 1.0 CD A:GLU287 2.9 31.3 1.0 CD A:GLU401 3.4 22.3 1.0 C A:HIS407 3.6 25.7 1.0 OE1 A:GLU401 3.6 30.1 1.0 N A:HIS407 4.0 22.4 1.0 N A:ASP409 4.0 22.5 1.0 O A:HOH1103 4.1 23.4 1.0 O A:HOH1243 4.1 24.1 1.0 CB A:ASP409 4.2 30.4 1.0 CA A:HIS407 4.3 24.2 1.0 O A:HOH1214 4.4 24.1 1.0 NE2 A:GLN397 4.4 25.4 1.0 CG A:GLU287 4.4 23.6 1.0 N A:TYR408 4.6 23.9 1.0 CB A:HIS407 4.6 25.3 1.0 CA A:ASP409 4.6 23.1 1.0 CG A:GLU401 4.8 24.2 1.0 CA A:TYR408 4.8 27.1 1.0 C A:TYR408 4.8 26.9 1.0 ND1 A:HIS410 4.9 22.6 1.0

Calcium binding site 2 out of 6 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 Calcium with other atoms in the Ca 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 A:Ca804 b:29.2 occ:1.00 OE1 A:GLN513 2.1 28.9 1.0 O A:HOH1163 2.1 23.1 1.0 OD1 A:ASP474 2.3 30.0 1.0 O A:THR475 2.3 35.5 1.0 O A:HOH1049 2.5 24.9 1.0 OD1 A:ASP479 2.6 26.2 1.0 OD2 A:ASP479 2.6 24.8 1.0 CG A:ASP479 2.9 27.3 1.0 CD A:GLN513 3.4 27.9 1.0 CG A:ASP474 3.5 33.8 1.0 C A:THR475 3.5 32.4 1.0 OG A:SER367 3.8 39.2 1.0 N A:THR475 3.8 27.6 1.0 OG1 A:THR369 4.0 25.1 1.0 O A:HOH1303 4.1 44.0 1.0 OD2 A:ASP474 4.2 35.6 1.0 CG A:GLN513 4.2 26.9 1.0 O A:HOH1300 4.3 40.3 1.0 NE2 A:GLN513 4.3 24.3 1.0 CA A:THR475 4.3 31.2 1.0 CB A:THR369 4.3 26.4 1.0 CB A:ASP479 4.4 29.1 1.0 C A:ASP474 4.4 29.2 1.0 O A:HOH931 4.5 24.7 1.0 CA A:ASP474 4.5 29.6 1.0 N A:ASP476 4.5 28.0 1.0 CB A:ASP474 4.6 29.0 1.0 CA A:ASP476 4.7 32.6 1.0

Calcium binding site 3 out of 6 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 Calcium with other atoms in the Ca 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 B:Ca803 b:30.3 occ:1.00 OE2 B:GLU401 2.3 28.6 1.0 OD1 B:ASP409 2.3 26.3 1.0 O B:HIS407 2.5 27.6 1.0 O B:HOH1036 2.5 31.8 1.0 OE1 B:GLU287 2.5 25.1 1.0 OE2 B:GLU287 2.6 28.9 1.0 O B:HOH907 2.6 27.5 1.0 OD2 B:ASP409 2.8 32.2 1.0 CG B:ASP409 2.9 30.4 1.0 CD B:GLU287 2.9 29.6 1.0 CD B:GLU401 3.2 43.8 1.0 OE1 B:GLU401 3.5 28.6 1.0 C B:HIS407 3.6 33.0 1.0 N B:HIS407 4.0 28.1 1.0 O B:HOH1072 4.0 27.7 1.0 N B:ASP409 4.1 27.5 1.0 O B:HOH1060 4.1 31.4 1.0 CB B:ASP409 4.2 29.3 1.0 CA B:HIS407 4.3 28.6 1.0 NE2 B:GLN397 4.4 28.1 1.0 CG B:GLU287 4.4 32.5 1.0 O B:HOH1065 4.5 33.6 1.0 CB B:HIS407 4.6 30.0 1.0 N B:TYR408 4.6 29.6 1.0 CG B:GLU401 4.6 32.9 1.0 CA B:ASP409 4.7 27.0 1.0 CA B:TYR408 4.8 29.1 1.0 C B:TYR408 4.9 26.9 1.0 O B:HOH980 4.9 29.8 1.0 ND1 B:HIS410 4.9 32.4 1.0 C B:TYR406 5.0 27.2 1.0

Calcium binding site 4 out of 6 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 Calcium with other atoms in the Ca binding site number 4 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:Ca804 b:46.6 occ:1.00 OD1 B:ASP474 2.1 38.0 1.0 OE1 B:GLN513 2.2 38.4 1.0 O B:THR475 2.3 43.2 1.0 OD1 B:ASP479 2.6 45.4 1.0 OD2 B:ASP479 2.7 37.5 1.0 CG B:ASP479 3.0 46.9 1.0 CG B:ASP474 3.4 45.7 1.0 CD B:GLN513 3.4 50.1 1.0 C B:THR475 3.5 45.5 1.0 N B:THR475 3.6 48.0 1.0 OG B:SER367 3.7 49.3 1.0 OG1 B:THR369 4.1 36.6 1.0 OD2 B:ASP474 4.1 53.7 1.0 CA B:THR475 4.2 48.9 1.0 C B:ASP474 4.3 49.5 1.0 CG B:GLN513 4.3 46.8 1.0 CB B:THR369 4.4 38.7 1.0 CA B:ASP474 4.4 46.5 1.0 NE2 B:GLN513 4.4 39.3 1.0 CB B:ASP474 4.4 47.9 1.0 CB B:ASP479 4.5 45.6 1.0 N B:ASP476 4.5 52.8 1.0 CA B:ASP476 4.8 59.8 1.0

Calcium binding site 5 out of 6 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 Calcium with other atoms in the Ca binding site number 5 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:Ca803 b:51.8 occ:1.00 OE2 C:GLU401 2.2 46.2 1.0 OD1 C:ASP409 2.3 59.7 1.0 O C:HIS407 2.5 53.4 1.0 OE1 C:GLU287 2.6 53.2 1.0 OE2 C:GLU287 2.6 53.1 1.0 OD2 C:ASP409 2.8 55.6 1.0 CG C:ASP409 2.8 49.4 1.0 CD C:GLU287 3.0 55.3 1.0 CD C:GLU401 3.2 54.3 1.0 OE1 C:GLU401 3.4 56.4 1.0 C C:HIS407 3.6 53.8 1.0 N C:HIS407 4.0 52.4 1.0 N C:ASP409 4.1 46.1 1.0 CB C:ASP409 4.2 50.9 1.0 CA C:HIS407 4.3 52.4 1.0 NE2 C:GLN397 4.4 48.8 1.0 CG C:GLU287 4.5 54.2 1.0 N C:TYR408 4.6 57.8 1.0 CG C:GLU401 4.6 54.5 1.0 CB C:HIS407 4.6 52.6 1.0 O C:HOH909 4.6 43.5 1.0 CA C:ASP409 4.7 48.2 1.0 CA C:TYR408 4.8 51.8 1.0 C C:TYR408 4.9 48.8 1.0 ND1 C:HIS410 4.9 47.7 1.0 O C:VAL399 5.0 47.0 1.0 O C:HOH903 5.0 44.7 1.0

Calcium binding site 6 out of 6 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 Calcium with other atoms in the Ca binding site number 6 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:Ca804 b:45.4 occ:1.00 OD1 C:ASP474 2.1 38.6 1.0 OE1 C:GLN513 2.2 40.9 1.0 O C:THR475 2.4 46.9 1.0 O C:HOH946 2.5 36.6 1.0 OD1 C:ASP479 2.6 47.3 1.0 OD2 C:ASP479 2.6 44.5 1.0 O C:HOH930 2.7 42.2 1.0 CG C:ASP479 2.9 43.8 1.0 CD C:GLN513 3.4 51.3 1.0 CG C:ASP474 3.4 44.6 1.0 C C:THR475 3.5 42.0 1.0 N C:THR475 3.7 43.6 1.0 OG C:SER367 3.7 50.9 1.0 OG1 C:THR369 4.0 45.6 1.0 OD2 C:ASP474 4.1 50.6 1.0 CG C:GLN513 4.3 52.7 1.0 CA C:THR475 4.3 43.0 1.0 CB C:THR369 4.3 47.2 1.0 NE2 C:GLN513 4.3 47.8 1.0 C C:ASP474 4.4 43.8 1.0 CA C:ASP474 4.4 45.7 1.0 CB C:ASP479 4.4 42.7 1.0 CB C:ASP474 4.5 42.1 1.0 O C:HOH922 4.5 41.4 1.0 N C:ASP476 4.5 46.8 1.0 O C:HOH972 4.6 55.5 1.0 CA C:ASP476 4.9 53.8 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