Calcium in PDB 7dmk: PL6 Alginate Lyase BCALYPL6

The structure of PL6 Alginate Lyase BCALYPL6, PDB code: 7dmk was solved by S.Dong, B.Wang, X.Q.Ma, F.L.Li, Y.G.Feng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.42 / 2.21
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	83.688, 97.693, 103.561, 76.56, 86.45, 88.69
R / Rfree (%)	16.7 / 21.5

The binding sites of Calcium atom in the PL6 Alginate Lyase BCALYPL6 (pdb code 7dmk). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the PL6 Alginate Lyase BCALYPL6, PDB code: 7dmk:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the PL6 Alginate Lyase BCALYPL6


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of PL6 Alginate Lyase BCALYPL6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca801 b:37.1 occ:1.00 OD1 A:ASN188 2.5 26.9 1.0 O A:HOH1147 2.5 27.2 1.0 OE1 A:GLU220 2.5 29.2 1.0 OE1 A:GLU222 2.5 37.9 1.0 O A:HOH938 2.5 28.3 1.0 OE2 A:GLU191 2.7 32.6 1.0 OE2 A:GLU220 2.8 27.5 1.0 CD A:GLU220 3.0 25.6 1.0 CD A:GLU191 3.4 31.5 1.0 CG A:ASN188 3.5 28.0 1.0 CD A:GLU222 3.5 35.3 1.0 CG A:GLU191 3.8 29.5 1.0 ND2 A:ASN188 3.8 28.0 1.0 O A:HOH1010 3.9 29.1 1.0 O A:HOH1004 4.0 28.1 1.0 CG A:GLU222 4.0 30.7 1.0 OG A:SER625 4.2 27.7 1.0 CB A:GLU222 4.2 24.2 1.0 OE1 A:GLU191 4.4 31.1 1.0 OE2 A:GLU222 4.4 35.7 1.0 CG A:GLU220 4.5 24.0 1.0 N A:GLY189 4.5 25.5 1.0 CB A:SER625 4.6 24.1 1.0 CB A:ASN188 4.8 27.1 1.0 O A:HOH1073 4.8 39.8 1.0

Calcium binding site 2 out of 4 in the PL6 Alginate Lyase BCALYPL6


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of PL6 Alginate Lyase BCALYPL6 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca801 b:40.0 occ:1.00 OE1 B:GLU222 2.5 39.0 1.0 OE2 B:GLU191 2.5 33.9 1.0 OE2 B:GLU220 2.5 29.7 1.0 O B:HOH1023 2.6 28.4 1.0 OD1 B:ASN188 2.6 29.8 1.0 OE1 B:GLU220 2.6 23.6 1.0 O B:HOH1214 2.7 32.5 1.0 CD B:GLU220 2.9 26.1 1.0 CD B:GLU191 3.3 32.0 1.0 CD B:GLU222 3.6 36.7 1.0 CG B:ASN188 3.6 30.9 1.0 CG B:GLU191 3.7 30.7 1.0 O B:HOH1006 3.7 29.5 1.0 ND2 B:ASN188 4.0 33.9 1.0 O B:HOH1163 4.1 33.3 1.0 CG B:GLU222 4.2 33.3 1.0 CB B:GLU222 4.2 28.5 1.0 O B:HOH1084 4.2 29.1 1.0 OG B:SER625 4.3 34.0 1.0 OE1 B:GLU191 4.3 32.5 1.0 CG B:GLU220 4.4 22.7 1.0 N B:GLY189 4.4 27.6 1.0 O B:HOH1096 4.5 32.4 1.0 OE2 B:GLU222 4.5 38.9 1.0 CB B:SER625 4.6 28.9 1.0 CB B:ASN188 5.0 24.6 1.0

Calcium binding site 3 out of 4 in the PL6 Alginate Lyase BCALYPL6


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of PL6 Alginate Lyase BCALYPL6 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca801 b:39.7 occ:1.00 OD1 C:ASN188 2.4 31.5 1.0 OE2 C:GLU222 2.4 37.0 1.0 O C:HOH1182 2.4 28.2 1.0 OE1 C:GLU220 2.4 28.9 1.0 OE2 C:GLU191 2.5 35.2 1.0 O C:HOH940 2.5 28.8 1.0 OE2 C:GLU220 2.9 31.9 1.0 CD C:GLU220 3.0 31.3 1.0 CD C:GLU222 3.1 35.1 1.0 CG C:GLU222 3.3 31.7 1.0 CD C:GLU191 3.4 31.6 1.0 CG C:ASN188 3.5 35.1 1.0 O C:HOH973 3.7 33.8 1.0 ND2 C:ASN188 3.9 35.0 1.0 CG C:GLU191 3.9 28.5 1.0 O C:HOH1031 4.0 32.3 1.0 OG C:SER625 4.2 33.4 1.0 OE1 C:GLU222 4.2 34.7 1.0 N C:GLY189 4.3 27.9 1.0 OE1 C:GLU191 4.4 33.6 1.0 CG C:GLU220 4.5 20.0 1.0 CB C:SER625 4.6 23.8 1.0 CB C:ASN188 4.8 29.3 1.0 CB C:GLU222 4.8 28.5 1.0 CA C:ASN188 5.0 29.3 1.0

Calcium binding site 4 out of 4 in the PL6 Alginate Lyase BCALYPL6


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of PL6 Alginate Lyase BCALYPL6 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca801 b:46.5 occ:1.00 O D:HOH992 2.4 29.0 1.0 OD1 D:ASN188 2.5 41.1 1.0 O D:HOH1166 2.5 38.5 1.0 OE1 D:GLU222 2.5 37.5 1.0 OE1 D:GLU220 2.6 26.9 1.0 OE2 D:GLU191 2.6 31.9 1.0 OE2 D:GLU220 2.8 31.2 1.0 CD D:GLU220 3.0 26.4 1.0 CD D:GLU191 3.5 32.1 1.0 CG D:ASN188 3.5 36.8 1.0 CD D:GLU222 3.6 31.6 1.0 O D:HOH975 3.6 29.9 1.0 CG D:GLU191 3.8 32.9 1.0 ND2 D:ASN188 4.0 37.7 1.0 O D:HOH1032 4.0 28.0 1.0 CG D:GLU222 4.1 27.1 1.0 OG D:SER625 4.3 33.0 1.0 CB D:GLU222 4.3 24.0 1.0 CB D:SER625 4.4 27.8 1.0 N D:GLY189 4.5 31.0 1.0 OE2 D:GLU222 4.5 32.1 1.0 OE1 D:GLU191 4.5 31.8 1.0 CG D:GLU220 4.6 24.7 1.0 O D:HOH1172 4.7 41.0 1.0 O6 D:MLI802 4.8 45.8 1.0 CB D:ASN188 4.8 29.9 1.0

B.Wang, S.Dong, F.L.Li, X.Q.Ma. Structural Basis For the Exolytic Activity of Polysaccharide Lyase Family 6 Alginate Lyase BCALYPL6 From Human Gut Microbe Bacteroides Clarus. Biochem.Biophys.Res.Commun. V. 547 111 2021.
ISSN: ESSN 1090-2104
PubMed: 33610038
DOI: 10.1016/J.BBRC.2021.02.040