Calcium in PDB 7osk: Ignisphaera Aggregans GH53 Catalytic Domain

All present enzymatic activity of Ignisphaera Aggregans GH53 Catalytic Domain:
3.2.1.89;

The structure of Ignisphaera Aggregans GH53 Catalytic Domain, PDB code: 7osk was solved by F.Fredslund, L.Lo Leggio, J.C.Poulsen, K.K.Rasmussen, S.Muderspach, K.B.R.M.Krogh, K.Jensen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.41 / 2.65
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	117.985, 65.304, 94.825, 90, 90, 90
R / Rfree (%)	21.2 / 26.3

The structure of Ignisphaera Aggregans GH53 Catalytic Domain also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Calcium atom in the Ignisphaera Aggregans GH53 Catalytic Domain (pdb code 7osk). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Ignisphaera Aggregans GH53 Catalytic Domain, PDB code: 7osk:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Ignisphaera Aggregans GH53 Catalytic Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Ignisphaera Aggregans GH53 Catalytic Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:28.5 occ:1.00 OE2 A:GLU373 2.3 27.0 1.0 O A:ASN370 2.3 24.7 1.0 OD1 A:ASP301 2.4 32.3 1.0 OE1 A:GLU373 2.4 24.2 1.0 O A:HIS305 2.5 23.8 1.0 OD1 A:ASN307 2.5 24.3 1.0 OD1 A:ASP303 2.5 25.8 1.0 CD A:GLU373 2.7 26.9 1.0 CG A:ASP301 3.4 28.3 1.0 HB3 A:HIS305 3.4 29.3 1.0 CG A:ASP303 3.4 24.9 1.0 CG A:ASN307 3.5 24.6 1.0 HD21 A:ASN307 3.5 34.2 1.0 C A:ASN370 3.5 23.1 1.0 H A:ASP303 3.5 32.0 1.0 C A:HIS305 3.6 25.8 1.0 H A:HIS305 3.6 32.2 1.0 H A:SER302 3.6 33.9 1.0 HA A:PRO371 3.7 28.1 1.0 OD2 A:ASP303 3.7 24.5 1.0 HB3 A:ASN370 3.7 27.6 1.0 OD2 A:ASP301 3.8 27.8 1.0 ND2 A:ASN307 3.8 28.5 1.0 N A:HIS305 4.2 26.9 1.0 CB A:HIS305 4.2 24.4 1.0 CG A:GLU373 4.2 23.4 1.0 CA A:HIS305 4.2 23.7 1.0 HD2 A:HIS305 4.2 29.3 1.0 H A:ASN370 4.3 27.9 1.0 HA A:ASP301 4.3 32.2 1.0 H A:GLU373 4.4 27.2 1.0 N A:ASP303 4.4 26.7 1.0 CA A:PRO371 4.4 23.4 1.0 N A:PRO371 4.4 23.9 1.0 CA A:ASN370 4.4 22.3 1.0 N A:SER302 4.5 28.3 1.0 CB A:ASN370 4.5 23.0 1.0 HG2 A:GLU373 4.5 28.1 1.0 HG3 A:GLU373 4.6 28.1 1.0 CB A:ASP301 4.6 27.7 1.0 H A:GLY304 4.6 30.8 1.0 HD22 A:ASN307 4.6 34.2 1.0 H A:TRP372 4.7 27.7 1.0 N A:ASN370 4.7 23.2 1.0 C A:PRO306 4.7 24.2 1.0 HA A:ASN307 4.7 30.8 1.0 N A:ASN307 4.7 26.1 1.0 HB3 A:GLU373 4.7 27.7 1.0 N A:PRO306 4.7 25.3 1.0 CB A:ASN307 4.8 24.6 1.0 CB A:ASP303 4.8 26.5 1.0 HB3 A:SER302 4.8 29.7 1.0 HB2 A:ASP301 4.8 33.2 1.0 CD2 A:HIS305 4.9 24.4 1.0 HB2 A:HIS305 4.9 29.3 1.0 H A:ASN307 4.9 31.3 1.0 CA A:ASP301 4.9 26.8 1.0 C A:PRO371 4.9 23.3 1.0 HA A:PRO306 4.9 29.4 1.0 N A:GLY304 4.9 25.7 1.0 CG A:HIS305 4.9 25.4 1.0 O A:PRO306 4.9 25.7 1.0 CA A:ASN307 5.0 25.7 1.0 CA A:ASP303 5.0 25.5 1.0

Calcium binding site 2 out of 2 in the Ignisphaera Aggregans GH53 Catalytic Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Ignisphaera Aggregans GH53 Catalytic Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca501 b:22.8 occ:1.00 OE1 B:GLU373 2.3 23.2 1.0 OD1 B:ASP301 2.3 22.3 1.0 O B:HIS305 2.4 22.6 1.0 OD1 B:ASN307 2.4 19.3 1.0 O B:ASN370 2.4 21.6 1.0 OD1 B:ASP303 2.4 20.4 1.0 OE2 B:GLU373 2.4 21.8 1.0 CD B:GLU373 2.7 22.0 1.0 HD21 B:ASN307 3.3 23.9 1.0 CG B:ASN307 3.4 20.5 1.0 CG B:ASP301 3.4 24.9 1.0 H B:SER302 3.4 28.2 1.0 H B:ASP303 3.4 27.2 1.0 HB3 B:HIS305 3.5 25.6 1.0 H B:HIS305 3.5 26.0 1.0 C B:HIS305 3.5 22.5 1.0 CG B:ASP303 3.6 22.9 1.0 C B:ASN370 3.6 20.2 1.0 ND2 B:ASN307 3.7 19.9 1.0 HB3 B:ASN370 3.8 25.5 1.0 OD2 B:ASP301 3.8 24.9 1.0 N B:HIS305 3.9 21.7 1.0 H B:GLY304 3.9 26.1 1.0 HA B:PRO371 4.0 24.1 1.0 OD2 B:ASP303 4.1 22.3 1.0 CA B:HIS305 4.1 21.1 1.0 CG B:GLU373 4.2 19.6 1.0 N B:ASP303 4.2 22.7 1.0 CB B:HIS305 4.2 21.3 1.0 N B:SER302 4.2 23.5 1.0 HA B:ASP301 4.3 27.2 1.0 H B:ASN370 4.3 22.9 1.0 H B:GLU373 4.4 23.1 1.0 CA B:ASN370 4.5 19.1 1.0 HG2 B:GLU373 4.5 23.5 1.0 N B:GLY304 4.5 21.8 1.0 N B:ASN307 4.5 19.0 1.0 HD22 B:ASN307 4.5 23.9 1.0 CB B:ASN370 4.6 21.2 1.0 HA B:ASN307 4.6 26.3 1.0 HB3 B:GLU373 4.6 23.5 1.0 HB3 B:SER302 4.6 27.1 1.0 N B:PRO371 4.6 20.5 1.0 CB B:ASP301 4.6 20.6 1.0 N B:PRO306 4.6 21.0 1.0 C B:PRO306 4.6 20.4 1.0 CA B:PRO371 4.6 20.1 1.0 H B:ASN307 4.6 22.8 1.0 HD2 B:HIS305 4.6 25.9 1.0 HG3 B:GLU373 4.7 23.5 1.0 CB B:ASN307 4.7 22.6 1.0 N B:ASN370 4.7 19.1 1.0 CB B:ASP303 4.7 22.2 1.0 HA B:PRO306 4.8 26.3 1.0 H B:TRP372 4.8 25.2 1.0 CA B:ASP301 4.8 22.6 1.0 HB2 B:ASP301 4.8 24.7 1.0 C B:GLY304 4.8 20.8 1.0 CA B:ASN307 4.9 21.9 1.0 HB2 B:HIS305 4.9 25.6 1.0 CA B:PRO306 4.9 21.9 1.0 CA B:ASP303 4.9 22.8 1.0 O B:PRO306 5.0 19.7 1.0 CB B:GLU373 5.0 19.6 1.0

S.J.Muderspach, F.Fredslund, V.Volf, J.N.Poulsen, T.H.Blicher, M.H.Clausen, K.K.Rasmussen, K.B.R.M.Krogh, K.Jensen, L.Lo Leggio. Engineering the Substrate Binding Site of the Hyperthermostable Archaeal Endo-Beta-1,4-Galactanase From Ignisphaera Aggregans. Biotechnol Biofuels V. 14 183 2021.
ISSN: ESSN 1754-6834
PubMed: 34530892
DOI: 10.1186/S13068-021-02025-6