Calcium in PDB 6jpn: 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: 6jpn 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)	62.86 / 2.85
Space group	P 3 2 1
Cell size a, b, c (Å), α, β, γ (°)	261.380, 261.380, 58.450, 90.00, 90.00, 120.00
R / Rfree (%)	20.7 / 22.3

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 6jpn). 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: 6jpn:
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:69.3 occ:1.00 OD1 A:ASP409 2.1 58.2 1.0 OE2 A:GLU401 2.3 70.8 1.0 OE2 A:GLU287 2.5 65.7 1.0 O A:HIS407 2.7 65.5 1.0 OE1 A:GLU287 2.7 60.9 1.0 CG A:ASP409 2.9 58.2 1.0 OD2 A:ASP409 2.9 55.1 1.0 CD A:GLU287 3.0 61.3 1.0 CD A:GLU401 3.1 69.2 1.0 OE1 A:GLU401 3.3 69.0 1.0 O A:HOH909 3.5 58.4 1.0 C A:HIS407 3.9 63.9 1.0 O A:VAL399 4.2 57.5 1.0 CB A:ASP409 4.3 58.8 1.0 N A:ASP409 4.3 63.0 1.0 N A:HIS407 4.4 62.2 1.0 CG A:GLU401 4.4 66.5 1.0 CG A:GLU287 4.5 59.2 1.0 NE2 A:GLN397 4.5 58.5 1.0 ND1 A:HIS410 4.6 57.2 1.0 CE1 A:HIS410 4.6 57.1 1.0 CA A:HIS407 4.7 62.5 1.0 CA A:ASP409 4.8 60.5 1.0 N A:TYR408 4.9 63.9 1.0 CA A:GLU401 4.9 62.1 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:56.1 occ:1.00 OD1 A:ASP474 2.2 60.5 1.0 OE1 A:GLN513 2.4 59.9 1.0 O A:THR475 2.5 64.0 1.0 OD1 A:ASP479 2.6 59.8 1.0 OD2 A:ASP479 2.7 62.1 1.0 CG A:ASP479 3.0 61.2 1.0 OG A:SER367 3.3 63.5 1.0 CG A:ASP474 3.4 62.2 1.0 CD A:GLN513 3.4 62.4 1.0 OG1 A:THR369 3.5 64.4 1.0 C A:THR475 3.6 65.1 1.0 N A:THR475 3.7 60.9 1.0 OD2 A:ASP474 4.0 62.9 1.0 NE2 A:GLN513 4.1 62.9 1.0 CB A:THR369 4.1 64.7 1.0 CA A:THR475 4.3 62.9 1.0 C A:ASP474 4.5 61.0 1.0 CB A:ASP479 4.5 61.6 1.0 CG A:GLN513 4.6 64.0 1.0 CB A:ASP474 4.6 62.1 1.0 CA A:ASP474 4.6 61.9 1.0 CB A:SER367 4.7 63.8 1.0 N A:ASP476 4.7 69.5 1.0 O A:ARG381 5.0 58.5 1.0 CG2 A:THR369 5.0 64.9 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