Manganese 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
Arsenic	(As)	1 atom
Calcium	(Ca)	6 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 6jp4). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese 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 Manganese binding site number: 1; 2; 3;

Manganese 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 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:24.4 occ:1.00 O A:HOH984 2.1 20.4 1.0 NE2 A:HIS448 2.2 23.2 1.0 OD1 A:ASP425 2.2 21.1 1.0 ND1 A:HIS407 2.2 22.3 1.0 O A:HOH940 2.3 21.1 1.0 O A:HOH926 2.4 20.8 1.0 CG A:ASP425 3.1 20.5 1.0 CE1 A:HIS407 3.1 23.0 1.0 CD2 A:HIS448 3.2 21.4 1.0 CE1 A:HIS448 3.2 24.6 1.0 CG A:HIS407 3.3 20.9 1.0 OD2 A:ASP425 3.3 21.7 1.0 CB A:HIS407 3.6 25.3 1.0 O A:TYR442 3.8 27.2 1.0 O A:GLY427 4.0 22.5 1.0 O A:GLU287 4.1 23.5 1.0 N A:GLY427 4.1 21.4 1.0 NE2 A:HIS407 4.3 21.7 1.0 ND1 A:HIS448 4.3 24.0 1.0 CG A:HIS448 4.3 24.5 1.0 N A:GLU287 4.3 23.8 1.0 CD2 A:HIS407 4.4 21.8 1.0 N A:SER426 4.4 21.0 1.0 O A:ASN285 4.4 27.6 1.0 CB A:ASP425 4.5 21.7 1.0 C A:GLY427 4.5 23.6 1.0 CA A:GLY427 4.6 21.3 1.0 OD2 A:ASP409 4.7 23.8 1.0 CA A:GLU287 4.8 24.7 1.0 C A:GLU287 4.8 23.2 1.0 CA A:VAL286 4.9 22.3 1.0 C A:TYR442 4.9 23.8 1.0 C A:ASP425 5.0 22.2 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn801 b:28.7 occ:1.00 OD1 B:ASP425 2.0 22.9 1.0 ND1 B:HIS407 2.1 23.1 1.0 NE2 B:HIS448 2.2 26.2 1.0 O B:HOH923 2.4 24.9 1.0 O B:HOH915 2.4 23.0 1.0 O B:HOH920 2.4 22.4 1.0 CG B:ASP425 3.0 26.2 1.0 CE1 B:HIS407 3.0 31.9 1.0 CD2 B:HIS448 3.2 28.6 1.0 CG B:HIS407 3.2 29.2 1.0 CE1 B:HIS448 3.2 25.2 1.0 OD2 B:ASP425 3.4 23.8 1.0 CB B:HIS407 3.5 30.0 1.0 O B:TYR442 3.8 23.9 1.0 O B:GLY427 4.0 25.5 1.0 O B:GLU287 4.0 27.4 1.0 N B:GLY427 4.1 26.6 1.0 NE2 B:HIS407 4.2 24.9 1.0 CD2 B:HIS407 4.3 24.6 1.0 N B:GLU287 4.3 27.2 1.0 ND1 B:HIS448 4.3 31.9 1.0 CG B:HIS448 4.3 26.3 1.0 N B:SER426 4.4 27.6 1.0 CB B:ASP425 4.4 21.9 1.0 O B:ASN285 4.5 30.2 1.0 C B:GLY427 4.5 28.8 1.0 OD2 B:ASP409 4.6 32.2 1.0 CA B:GLY427 4.6 28.0 1.0 CA B:GLU287 4.8 26.3 1.0 C B:GLU287 4.8 27.1 1.0 CA B:VAL286 4.9 29.9 1.0 C B:TYR442 4.9 23.3 1.0 CA B:ASP425 4.9 29.5 1.0 C B:ASP425 5.0 26.6 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn801 b:51.8 occ:1.00 O C:HOH901 1.9 39.7 1.0 ND1 C:HIS407 2.1 52.8 1.0 OD1 C:ASP425 2.1 42.3 1.0 NE2 C:HIS448 2.3 53.3 1.0 O C:HOH903 2.5 44.7 1.0 O C:HOH905 2.5 48.7 1.0 CG C:ASP425 3.0 42.9 1.0 CE1 C:HIS407 3.0 51.8 1.0 CG C:HIS407 3.1 53.3 1.0 OD2 C:ASP425 3.2 39.7 1.0 CD2 C:HIS448 3.2 53.9 1.0 CE1 C:HIS448 3.2 54.6 1.0 CB C:HIS407 3.4 52.6 1.0 O C:TYR442 3.9 50.3 1.0 O C:GLU287 3.9 49.9 1.0 O C:GLY427 4.1 54.0 1.0 NE2 C:HIS407 4.2 47.5 1.0 CD2 C:HIS407 4.2 50.0 1.0 N C:GLU287 4.2 51.6 1.0 N C:GLY427 4.3 58.5 1.0 ND1 C:HIS448 4.3 57.0 1.0 CG C:HIS448 4.4 58.4 1.0 CB C:ASP425 4.5 40.8 1.0 O C:ASN285 4.5 58.2 1.0 OD2 C:ASP409 4.6 55.6 1.0 N C:SER426 4.6 51.3 1.0 C C:GLY427 4.6 58.5 1.0 CA C:GLU287 4.6 55.0 1.0 C C:GLU287 4.7 51.6 1.0 CA C:GLY427 4.8 59.8 1.0 CA C:VAL286 4.9 56.9 1.0 CA C:HIS407 4.9 52.4 1.0 C C:TYR442 4.9 49.2 1.0 C C:VAL286 5.0 52.9 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