Calcium in PDB 5gkd: Structure of PL6 Family Alginate Lyase Alygc

The structure of Structure of PL6 Family Alginate Lyase Alygc, PDB code: 5gkd was solved by Y.Z.Zhang, P.Wang, F.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.45 / 2.19
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	116.608, 142.840, 126.276, 90.00, 111.09, 90.00
R / Rfree (%)	16.5 / 19.7

The binding sites of Calcium atom in the Structure of PL6 Family Alginate Lyase Alygc (pdb code 5gkd). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Structure of PL6 Family Alginate Lyase Alygc, PDB code: 5gkd:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Structure of PL6 Family Alginate Lyase Alygc


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of PL6 Family Alginate Lyase Alygc within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca801 b:22.2 occ:1.00 OE1 A:GLU215 2.4 20.1 1.0 OE2 A:GLU213 2.5 19.2 1.0 O2 A:PO4804 2.5 20.2 1.0 ND2 A:ASN181 2.5 15.5 1.0 O A:HOH933 2.5 20.5 1.0 OE2 A:GLU184 2.6 22.8 1.0 OE1 A:GLU213 2.8 21.2 1.0 CD A:GLU213 3.0 19.7 1.0 CD A:GLU184 3.4 21.6 1.0 CG A:ASN181 3.5 22.3 1.0 CD A:GLU215 3.5 19.2 1.0 P A:PO4804 3.6 22.3 1.0 O1 A:PO4804 3.6 23.8 1.0 O A:HOH1029 3.7 22.6 1.0 OD1 A:ASN181 3.8 22.5 1.0 CG A:GLU184 3.9 18.7 1.0 CG A:GLU215 4.0 18.6 1.0 O3 A:PO4804 4.2 27.4 1.0 OG A:SER633 4.2 20.0 1.0 CB A:GLU215 4.2 17.8 1.0 O A:HOH1048 4.2 17.6 1.0 OE1 A:GLU184 4.4 23.6 1.0 N A:GLY182 4.4 18.7 1.0 CB A:SER633 4.5 18.9 1.0 CG A:GLU213 4.5 18.1 1.0 O1 A:CO3806 4.6 23.0 1.0 OE2 A:GLU215 4.6 17.6 1.0 O3 A:CO3806 4.6 39.0 1.0 O4 A:PO4804 4.8 17.4 1.0 CB A:ASN181 4.9 19.4 1.0

Calcium binding site 2 out of 4 in the Structure of PL6 Family Alginate Lyase Alygc


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of PL6 Family Alginate Lyase Alygc within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca801 b:19.7 occ:1.00 ND2 B:ASN181 2.4 16.4 1.0 OE2 B:GLU184 2.4 19.7 1.0 O3 B:PO4804 2.4 20.8 1.0 O B:HOH972 2.5 19.6 1.0 OE1 B:GLU215 2.5 17.1 1.0 OE2 B:GLU213 2.5 21.4 1.0 OE1 B:GLU213 2.8 19.7 1.0 CD B:GLU213 3.0 19.1 1.0 CD B:GLU184 3.4 21.6 1.0 CG B:ASN181 3.5 21.6 1.0 P B:PO4804 3.6 21.0 1.0 CD B:GLU215 3.6 17.8 1.0 O2 B:PO4804 3.7 22.9 1.0 O B:HOH1059 3.7 27.5 1.0 OD1 B:ASN181 3.7 23.2 1.0 CG B:GLU184 3.9 18.2 1.0 CG B:GLU215 4.1 17.5 1.0 O1 B:PO4804 4.1 32.0 1.0 OG B:SER633 4.2 18.0 1.0 O B:HOH1053 4.2 15.5 1.0 CB B:GLU215 4.2 17.8 1.0 OE1 B:GLU184 4.4 21.7 1.0 N B:GLY182 4.4 23.3 1.0 CB B:SER633 4.5 17.3 1.0 CG B:GLU213 4.5 16.1 1.0 O2 B:CO3806 4.5 22.3 1.0 O3 B:CO3806 4.6 37.1 1.0 OE2 B:GLU215 4.7 18.1 1.0 O4 B:PO4804 4.7 24.9 1.0 CB B:ASN181 4.8 20.0 1.0

Calcium binding site 3 out of 4 in the Structure of PL6 Family Alginate Lyase Alygc


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of PL6 Family Alginate Lyase Alygc within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca801 b:22.1 occ:1.00 O C:HOH1030 2.1 20.4 1.0 ND2 C:ASN181 2.4 23.4 1.0 O2 C:PO4804 2.4 23.4 1.0 OE2 C:GLU184 2.5 25.8 1.0 OE2 C:GLU213 2.5 21.2 1.0 OE1 C:GLU215 2.5 22.6 1.0 OE1 C:GLU213 2.9 22.6 1.0 CD C:GLU213 3.1 20.0 1.0 CG C:ASN181 3.4 25.3 1.0 CD C:GLU184 3.4 22.6 1.0 CD C:GLU215 3.6 22.1 1.0 P C:PO4804 3.6 24.4 1.0 O C:HOH998 3.6 25.9 1.0 OD1 C:ASN181 3.6 25.9 1.0 O1 C:PO4804 3.7 24.5 1.0 CG C:GLU184 3.9 19.4 1.0 CG C:GLU215 3.9 19.3 1.0 O3 C:PO4804 4.1 32.5 1.0 OG C:SER633 4.2 18.6 1.0 O C:HOH1016 4.2 21.0 1.0 CB C:GLU215 4.3 19.4 1.0 N C:GLY182 4.4 22.1 1.0 OE1 C:GLU184 4.4 21.9 1.0 CB C:SER633 4.4 21.1 1.0 O1 C:CO3806 4.5 24.1 1.0 CG C:GLU213 4.6 16.2 1.0 O3 C:CO3806 4.6 38.8 1.0 OE2 C:GLU215 4.7 22.9 1.0 CB C:ASN181 4.8 21.4 1.0 O4 C:PO4804 4.8 29.6 1.0 C C:CO3806 5.0 25.6 1.0

Calcium binding site 4 out of 4 in the Structure of PL6 Family Alginate Lyase Alygc


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of PL6 Family Alginate Lyase Alygc within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca801 b:20.7 occ:1.00 O D:HOH1103 2.2 19.0 1.0 OE2 D:GLU184 2.4 24.6 1.0 ND2 D:ASN181 2.4 20.1 1.0 OE2 D:GLU213 2.5 19.8 1.0 O3 D:PO4804 2.5 25.9 1.0 OE1 D:GLU215 2.6 22.5 1.0 OE1 D:GLU213 2.8 20.1 1.0 CD D:GLU213 3.0 23.1 1.0 CD D:GLU184 3.3 25.7 1.0 CG D:ASN181 3.5 26.6 1.0 O D:HOH956 3.6 23.7 1.0 CD D:GLU215 3.7 24.4 1.0 P D:PO4804 3.7 24.7 1.0 CG D:GLU184 3.8 22.6 1.0 O2 D:PO4804 3.8 27.4 1.0 OD1 D:ASN181 3.9 31.6 1.0 CG D:GLU215 4.1 22.4 1.0 CB D:GLU215 4.3 19.8 1.0 O4 D:PO4804 4.3 31.1 1.0 OG D:SER633 4.3 22.5 1.0 O D:HOH1224 4.3 18.4 1.0 OE1 D:GLU184 4.4 22.8 1.0 N D:GLY182 4.4 20.9 1.0 CB D:SER633 4.4 22.1 1.0 O3 D:CO3806 4.5 25.2 1.0 CG D:GLU213 4.5 20.7 1.0 O1 D:CO3806 4.7 37.2 1.0 OE2 D:GLU215 4.7 23.3 1.0 O1 D:PO4804 4.8 25.6 1.0 CB D:ASN181 4.8 22.8 1.0

F.Xu, F.Dong, P.Wang, H.Y.Cao, C.Y.Li, P.Y.Li, X.H.Pang, Y.Z.Zhang, X.L.Chen. Novel Molecular Insights Into the Catalytic Mechanism of Marine Bacterial Alginate Lyase Alygc From Polysaccharide Lyase Family 6 J. Biol. Chem. V. 292 4457 2017.
ISSN: ESSN 1083-351X
PubMed: 28154171
DOI: 10.1074/JBC.M116.766030