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Calcium in PDB 7osk: Ignisphaera Aggregans GH53 Catalytic Domain

Enzymatic activity of Ignisphaera Aggregans GH53 Catalytic Domain

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

Protein crystallography data

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

Other elements in 7osk:

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

Chlorine (Cl) 2 atoms

Calcium Binding Sites:

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 7osk

Go back to Calcium Binding Sites List in 7osk
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 7osk

Go back to Calcium Binding Sites List in 7osk
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

Reference:

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
Page generated: Fri Jul 19 02:39:58 2024

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