Calcium in PDB 6jph: 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: 6jph 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)	131.31 / 2.76
Space group	P 3 2 1
Cell size a, b, c (Å), α, β, γ (°)	261.923, 261.923, 58.292, 90.00, 90.00, 120.00
R / Rfree (%)	19.9 / 22.6

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)	1 atom
Manganese	(Mn)	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 6jph). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 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: 6jph:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 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:Ca802 b:54.5 occ:1.00 OD1 A:ASP409 2.2 51.5 1.0 O A:HIS407 2.5 53.1 1.0 OE2 A:GLU401 2.5 75.5 1.0 OE1 A:GLU287 2.6 45.1 1.0 OE2 A:GLU287 2.8 83.5 1.0 OE1 A:GLU401 2.9 65.4 1.0 CG A:ASP409 3.0 44.7 1.0 CD A:GLU401 3.1 71.9 1.0 CD A:GLU287 3.1 63.3 1.0 OD2 A:ASP409 3.2 32.8 1.0 O A:HOH946 3.3 46.8 1.0 C A:HIS407 3.7 53.1 1.0 O A:HOH971 3.7 64.3 1.0 N A:ASP409 4.2 52.9 1.0 N A:HIS407 4.2 40.3 1.0 CB A:ASP409 4.4 49.8 1.0 O A:VAL399 4.5 49.2 1.0 CA A:HIS407 4.5 45.0 1.0 ND1 A:HIS410 4.5 49.4 1.0 CG A:GLU401 4.6 59.3 1.0 NE2 A:GLN397 4.6 68.6 1.0 CG A:GLU287 4.6 55.9 1.0 CE1 A:HIS410 4.7 53.3 1.0 CA A:ASP409 4.7 50.2 1.0 N A:TYR408 4.7 51.6 1.0 CB A:HIS407 4.9 40.4 1.0 CA A:TYR408 4.9 54.5 1.0 C A:ASP409 4.9 45.8 1.0 C A:TYR408 5.0 53.4 1.0

Calcium binding site 2 out of 2 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:Ca803 b:43.6 occ:1.00 OD1 A:ASP474 2.2 53.0 1.0 OE1 A:GLN513 2.3 45.8 1.0 O A:THR475 2.5 48.1 1.0 OD1 A:ASP479 2.7 53.6 1.0 OD2 A:ASP479 2.7 56.5 1.0 CG A:ASP479 3.0 57.2 1.0 OG A:SER367 3.3 57.4 1.0 CG A:ASP474 3.4 57.8 1.0 CD A:GLN513 3.5 49.0 1.0 C A:THR475 3.6 47.8 1.0 N A:THR475 3.8 44.4 1.0 OG1 A:THR369 3.8 57.2 1.0 OD2 A:ASP474 3.9 59.4 1.0 CB A:THR369 4.3 62.5 1.0 NE2 A:GLN513 4.3 51.9 1.0 CA A:THR475 4.3 44.2 1.0 CG A:GLN513 4.5 53.2 1.0 C A:ASP474 4.5 50.5 1.0 CB A:ASP474 4.5 57.7 1.0 CB A:ASP479 4.5 60.2 1.0 CA A:ASP474 4.6 56.3 1.0 N A:ASP476 4.6 60.2 1.0 CB A:SER367 4.6 56.5 1.0 CA A:ASP476 4.9 67.5 1.0 O A:ARG381 5.0 50.8 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