Calcium in PDB 8h97: GH86 Agarase AGA86A_WA

All present enzymatic activity of GH86 Agarase AGA86A_WA:
3.2.1.81;

The structure of GH86 Agarase AGA86A_WA, PDB code: 8h97 was solved by Y.Y.Zhang, S.Dong, Y.G.Feng, Y.G.Chang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.30 / 2.19
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	76.599, 90.672, 106.09, 90, 90, 90
R / Rfree (%)	15.4 / 20.7

The binding sites of Calcium atom in the GH86 Agarase AGA86A_WA (pdb code 8h97). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the GH86 Agarase AGA86A_WA, PDB code: 8h97:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the GH86 Agarase AGA86A_WA


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of GH86 Agarase AGA86A_WA within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca802 b:30.9 occ:1.00 OD1 A:ASP587 2.2 35.5 1.0 O A:TRP588 2.3 30.0 1.0 O A:HOH1179 2.3 26.6 1.0 O A:HOH1079 2.4 30.0 1.0 OD1 A:ASP430 2.4 27.5 1.0 O A:GLY590 2.4 34.8 1.0 OD2 A:ASP430 2.5 30.3 1.0 CG A:ASP430 2.7 29.7 1.0 C A:GLY590 3.4 31.1 1.0 CG A:ASP587 3.5 36.0 1.0 C A:TRP588 3.5 31.7 1.0 O A:HOH984 3.7 35.8 1.0 N A:GLY590 3.7 24.0 1.0 N A:TRP588 3.9 28.5 1.0 CA A:GLY590 4.1 23.3 1.0 C A:ASP587 4.1 33.4 1.0 OD2 A:ASP587 4.1 40.0 1.0 CB A:ASP430 4.2 31.8 1.0 C A:ARG589 4.2 29.1 1.0 CA A:TRP588 4.3 28.7 1.0 CA A:CA803 4.4 36.9 1.0 CA A:ASP587 4.4 33.0 1.0 N A:TYR591 4.4 29.1 1.0 OE2 A:GLU450 4.5 36.2 1.0 N A:ARG589 4.5 30.1 1.0 CD1 A:TRP588 4.5 34.1 1.0 CB A:ASP587 4.5 30.2 1.0 CA A:ARG589 4.6 30.2 1.0 O A:ASP587 4.6 42.2 1.0 CG A:GLU450 4.7 37.8 1.0 O A:HOH941 4.7 32.9 1.0 CA A:TYR591 4.7 27.2 1.0 CG A:TRP588 4.8 30.6 1.0 NE1 A:TRP588 4.8 26.8 1.0 O A:HOH1255 4.9 38.1 1.0 N A:ASP430 4.9 25.1 1.0 CA A:ASP430 4.9 33.5 1.0 O A:ARG589 5.0 28.9 1.0

Calcium binding site 2 out of 3 in the GH86 Agarase AGA86A_WA


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of GH86 Agarase AGA86A_WA within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca803 b:36.9 occ:1.00 OD2 A:ASP587 2.2 40.0 1.0 O A:HOH1074 2.3 32.6 1.0 OD2 A:ASP428 2.4 46.0 1.0 O A:HOH984 2.4 35.8 1.0 OD2 A:ASP430 2.4 30.3 1.0 OD1 A:ASP428 2.5 31.3 1.0 CG A:ASP428 2.8 36.3 1.0 CG A:ASP587 3.1 36.0 1.0 OD1 A:ASP587 3.4 35.5 1.0 CG A:ASP430 3.4 29.7 1.0 CB A:ASP430 3.8 31.8 1.0 CB A:ASP428 4.3 29.6 1.0 O A:HOH1079 4.3 30.0 1.0 OG A:SER27 4.3 55.2 1.0 CA A:CA802 4.4 30.9 1.0 OE2 A:GLU452 4.5 67.3 1.0 CB A:ASP587 4.5 30.2 1.0 OD1 A:ASP430 4.5 27.5 1.0 O A:HOH1024 4.5 34.3 1.0 N A:ASP430 4.6 25.1 1.0 O A:HOH1176 4.7 32.1 1.0 CG A:GLU450 4.8 37.8 1.0 CA A:ASP430 4.9 33.5 1.0

Calcium binding site 3 out of 3 in the GH86 Agarase AGA86A_WA


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of GH86 Agarase AGA86A_WA within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca804 b:36.9 occ:1.00 O A:THR424 2.2 38.5 1.0 O A:HOH1278 2.3 27.2 1.0 O A:HOH1252 2.3 39.3 1.0 O A:HOH1135 2.4 27.4 1.0 O A:HOH1233 2.4 27.6 1.0 O A:HOH1130 2.6 38.4 1.0 C A:THR424 3.3 35.5 1.0 OG1 A:THR424 3.9 31.2 1.0 N A:THR424 4.1 33.5 1.0 N A:LYS425 4.2 29.0 1.0 O A:HOH1193 4.2 42.8 1.0 O A:HOH968 4.2 26.9 1.0 CA A:THR424 4.2 32.6 1.0 CA A:LYS425 4.3 35.1 1.0 CE1 A:HIS39 4.4 29.9 1.0 O A:HOH1117 4.4 33.5 1.0 ND1 A:HIS39 4.5 28.5 1.0 O A:HOH1008 4.5 35.2 1.0 O A:HOH1289 4.5 40.3 1.0 O A:HOH1151 4.7 34.5 1.0 OD1 A:ASP423 4.7 39.0 1.0 CB A:THR424 4.7 30.8 1.0 O A:VAL433 4.8 37.7 1.0 CB A:LYS425 4.8 34.1 1.0 CD A:LYS425 4.9 48.6 1.0 NH2 A:ARG421 4.9 34.4 1.0

Y.Zhang, S.Dong, G.Chen, S.Cao, J.Shen, X.Mei, Q.Cui, Y.Feng, Y.Chang, Y.Wang, C.Xue. Structural Characterization on A Beta-Agarase AGA86A_WA From Wenyingzhuangia Aestuarii Reveals the Prevalent Methyl-Galactose Accommodation Capacity of GH86 Enzymes at Subsite -1. Carbohydr Polym V. 306 20594 2023.
ISSN: ESSN 1879-1344
PubMed: 36746585
DOI: 10.1016/J.CARBPOL.2023.120594