Manganese 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
Calcium	(Ca)	2 atoms

The binding sites of Manganese 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 Manganese atom.
In total only one binding site of Manganese was determined in the Crystal Structure of the Catalytic Domain of A Multi-Domain Alginate Lyase DP0100 From Thermophilic Bacterium Defluviitalea Phaphyphila, PDB code: 6jpn:

Manganese binding site 1 out of 1 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 Manganese with other atoms in the Mn 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:Mn801 b:61.9 occ:1.00 O A:HOH901 2.1 67.2 1.0 OD1 A:ASP425 2.1 58.3 1.0 NE2 A:HIS448 2.2 58.3 1.0 O A:HOH910 2.2 43.7 1.0 ND1 A:HIS407 2.2 59.2 1.0 O A:HOH906 2.4 38.3 1.0 CE1 A:HIS448 3.1 59.6 1.0 CE1 A:HIS407 3.1 59.2 1.0 CD2 A:HIS448 3.2 59.1 1.0 CG A:ASP425 3.2 62.8 1.0 CG A:HIS407 3.2 60.4 1.0 CB A:HIS407 3.6 61.5 1.0 OD2 A:ASP425 3.7 63.5 1.0 O A:TYR442 3.8 61.5 1.0 O A:GLY427 4.0 61.4 1.0 N A:GLY427 4.0 60.9 1.0 ND1 A:HIS448 4.2 58.4 1.0 CG A:HIS448 4.3 59.0 1.0 NE2 A:HIS407 4.3 59.0 1.0 CD2 A:HIS407 4.3 59.2 1.0 O A:GLU287 4.4 54.6 1.0 N A:GLU287 4.4 57.1 1.0 O A:ASN285 4.4 56.9 1.0 C A:GLY427 4.4 60.8 1.0 CB A:ASP425 4.5 64.2 1.0 N A:SER426 4.5 63.4 1.0 CA A:GLY427 4.5 60.4 1.0 CA A:GLU287 4.9 56.5 1.0 C A:TYR442 4.9 60.3 1.0 C A:ASP425 4.9 63.4 1.0 C A:GLU287 5.0 55.6 1.0 OD2 A:ASP409 5.0 55.1 1.0 CA A:ASP425 5.0 63.7 1.0 C A:SER426 5.0 62.4 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