Calcium in PDB 7v0i: Crystal Structure of A Celr Catalytic Domain Active Site Mutant with Bound Cellohexaose Substrate

The structure of Crystal Structure of A Celr Catalytic Domain Active Site Mutant with Bound Cellohexaose Substrate, PDB code: 7v0i was solved by C.A.Bingman, N.Kuch, M.E.Kutsche, A.Parker, R.W.Smith, B.G.Fox, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.87 / 1.90
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	93.302, 162.419, 210.522, 90, 90, 90
R / Rfree (%)	18.5 / 23.2

The binding sites of Calcium atom in the Crystal Structure of A Celr Catalytic Domain Active Site Mutant with Bound Cellohexaose Substrate (pdb code 7v0i). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of A Celr Catalytic Domain Active Site Mutant with Bound Cellohexaose Substrate, PDB code: 7v0i:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of A Celr Catalytic Domain Active Site Mutant with Bound Cellohexaose Substrate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of A Celr Catalytic Domain Active Site Mutant with Bound Cellohexaose Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca500 b:56.4 occ:1.00 O A:HOH612 2.0 43.0 1.0 O A:HOH613 2.1 57.0 1.0 O A:GLY228 2.2 63.9 1.0 OE1 A:GLU232 2.2 44.0 1.0 OD1 A:ASP231 2.5 48.2 1.0 OG A:SER227 2.9 63.2 1.0 CD A:GLU232 3.0 42.6 1.0 HG A:SER227 3.1 75.8 1.0 OE2 A:GLU232 3.2 37.3 1.0 CG A:ASP231 3.2 50.7 1.0 OD2 A:ASP231 3.2 52.5 1.0 O A:ASP278 3.3 41.3 1.0 C A:GLY228 3.4 59.0 1.0 O A:HOH749 3.5 48.4 1.0 HA A:TRP229 3.8 48.0 1.0 HG23 A:THR169 3.9 40.1 1.0 HA A:ASP279 3.9 49.3 1.0 H A:GLU232 3.9 51.8 1.0 HG A:SER225 3.9 70.0 1.0 N A:GLY228 3.9 67.8 1.0 C A:SER227 4.0 61.1 1.0 HG22 A:VAL280 4.0 42.4 1.0 H A:GLY228 4.1 81.4 1.0 H A:VAL280 4.1 43.7 1.0 O A:SER227 4.2 58.8 1.0 CB A:SER227 4.2 64.9 1.0 CA A:GLY228 4.2 60.5 1.0 C A:ASP278 4.3 41.7 1.0 N A:TRP229 4.3 40.2 1.0 H A:ASP231 4.4 48.5 1.0 H A:SER227 4.4 84.4 1.0 HG21 A:THR169 4.4 40.1 1.0 CA A:TRP229 4.5 40.0 1.0 HB2 A:GLU232 4.5 47.8 1.0 CG A:GLU232 4.5 37.1 1.0 OG A:SER225 4.5 58.4 1.0 N A:GLU232 4.5 43.2 1.0 CA A:SER227 4.6 64.1 1.0 CG2 A:THR169 4.6 33.4 1.0 HB3 A:SER227 4.7 77.8 1.0 CB A:ASP231 4.7 47.2 1.0 CA A:ASP279 4.7 41.1 1.0 HB2 A:SER227 4.8 77.8 1.0 HA3 A:GLY228 4.8 72.5 1.0 HA A:ASP278 4.8 57.5 1.0 N A:ASP279 4.9 38.9 1.0 N A:SER227 4.9 70.3 1.0 HA2 A:GLY228 4.9 72.5 1.0 CB A:GLU232 4.9 39.9 1.0 N A:VAL280 4.9 36.4 1.0 HG2 A:GLU232 5.0 44.5 1.0 C A:TRP229 5.0 42.1 1.0 CG2 A:VAL280 5.0 35.4 1.0 N A:ASP231 5.0 40.5 1.0 HG3 A:GLU232 5.0 44.5 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of A Celr Catalytic Domain Active Site Mutant with Bound Cellohexaose Substrate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of A Celr Catalytic Domain Active Site Mutant with Bound Cellohexaose Substrate within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca500 b:52.7 occ:1.00 O B:HOH601 2.1 42.3 1.0 O B:HOH676 2.2 47.4 1.0 O B:GLY228 2.2 50.6 1.0 OE1 B:GLU232 2.3 35.8 1.0 HG B:SER227 2.4 60.3 1.0 OD1 B:ASP231 2.6 46.3 1.0 OG B:SER227 2.7 50.3 1.0 O B:ASP278 2.9 45.6 1.0 OE2 B:GLU232 3.0 33.5 1.0 CD B:GLU232 3.0 39.6 1.0 OD2 B:ASP231 3.0 48.9 1.0 CG B:ASP231 3.2 42.4 1.0 C B:GLY228 3.4 49.6 1.0 HA B:ASP279 3.7 45.6 1.0 HA B:TRP229 3.9 45.1 1.0 H B:GLY228 3.9 67.4 1.0 N B:GLY228 3.9 56.2 1.0 C B:ASP278 4.0 42.7 1.0 HG21 B:THR169 4.0 42.9 1.0 CB B:SER227 4.0 53.7 1.0 H B:GLU232 4.0 47.0 1.0 H B:VAL280 4.1 38.6 1.0 H B:SER227 4.2 76.6 1.0 HG22 B:VAL280 4.2 42.2 1.0 C B:SER227 4.2 54.3 1.0 HG23 B:THR169 4.3 42.9 1.0 CA B:GLY228 4.3 53.8 1.0 HB3 B:SER227 4.3 64.4 1.0 N B:TRP229 4.4 45.3 1.0 CG B:GLU232 4.5 36.4 1.0 H B:ASP231 4.5 45.3 1.0 CA B:SER227 4.6 60.1 1.0 CA B:TRP229 4.6 37.6 1.0 HA B:ASP278 4.6 50.9 1.0 CA B:ASP279 4.6 38.0 1.0 HB2 B:GLU232 4.6 39.3 1.0 CG2 B:THR169 4.6 35.7 1.0 HB2 B:SER227 4.6 64.4 1.0 CB B:ASP231 4.6 38.3 1.0 OG B:SER225 4.6 47.1 1.0 N B:GLU232 4.6 39.2 1.0 N B:ASP279 4.7 36.6 1.0 HG B:SER225 4.7 56.5 1.0 N B:SER227 4.7 63.9 1.0 O B:SER227 4.8 48.2 1.0 O B:HOH774 4.8 44.9 1.0 HA3 B:GLY228 4.8 64.5 1.0 HG2 B:GLU232 4.9 43.6 1.0 CA B:ASP278 4.9 42.5 1.0 N B:VAL280 4.9 32.2 1.0 HG3 B:GLU232 4.9 43.6 1.0 HB2 B:ASP231 5.0 45.9 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of A Celr Catalytic Domain Active Site Mutant with Bound Cellohexaose Substrate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of A Celr Catalytic Domain Active Site Mutant with Bound Cellohexaose Substrate within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca500 b:55.8 occ:1.00 O C:GLY228 2.1 53.4 1.0 O C:HOH601 2.2 52.1 1.0 O C:HOH681 2.3 51.7 1.0 OE1 C:GLU232 2.5 42.7 1.0 OD1 C:ASP231 2.5 53.2 1.0 OD2 C:ASP231 2.5 54.2 1.0 HG C:SER227 2.6 68.3 1.0 OG C:SER227 2.8 57.0 1.0 CG C:ASP231 2.8 52.0 1.0 O C:ASP278 3.0 47.6 1.0 OE2 C:GLU232 3.2 39.4 1.0 CD C:GLU232 3.2 43.6 1.0 C C:GLY228 3.3 52.2 1.0 H C:GLY228 3.6 75.7 1.0 N C:GLY228 3.7 63.1 1.0 HA C:ASP279 3.7 48.6 1.0 HA C:TRP229 3.9 56.4 1.0 C C:ASP278 4.0 43.8 1.0 C C:SER227 4.1 63.7 1.0 CB C:SER227 4.1 60.1 1.0 CA C:GLY228 4.1 59.4 1.0 H C:VAL280 4.2 45.1 1.0 H C:GLU232 4.2 54.3 1.0 H C:SER227 4.2 80.2 1.0 HG23 C:THR169 4.2 50.8 1.0 HG22 C:VAL280 4.3 47.0 1.0 HG21 C:THR169 4.3 50.8 1.0 CB C:ASP231 4.4 52.1 1.0 N C:TRP229 4.4 49.7 1.0 H C:ASP231 4.5 62.6 1.0 OG C:SER225 4.5 54.7 1.0 CA C:SER227 4.5 68.8 1.0 HB2 C:SER227 4.6 72.0 1.0 CA C:TRP229 4.6 47.0 1.0 CA C:ASP279 4.6 40.6 1.0 O C:SER227 4.6 63.2 1.0 CG C:GLU232 4.7 43.2 1.0 HA3 C:GLY228 4.7 71.2 1.0 HA C:ASP278 4.7 49.9 1.0 HB3 C:SER227 4.7 72.0 1.0 HB3 C:ASP231 4.7 62.5 1.0 HG C:SER225 4.7 65.6 1.0 CG2 C:THR169 4.7 42.4 1.0 N C:GLU232 4.7 45.2 1.0 N C:ASP279 4.7 40.6 1.0 HB2 C:ASP231 4.8 62.5 1.0 N C:SER227 4.8 66.8 1.0 HB2 C:GLU232 4.8 52.2 1.0 HA2 C:GLY228 4.8 71.2 1.0 N C:VAL280 4.9 37.6 1.0 OD1 C:ASP278 5.0 58.2 1.0 CA C:ASP278 5.0 41.6 1.0

N.J.Kuch, M.E.Kutschke, A.Parker, C.A.Bingman, B.G.Fox. Contribution of Calcium Ligands in Substrate Binding and Product Release in the Acetovibrio Thermocellus Glycoside Hydrolase Family 9 Cellulase Celr. J.Biol.Chem. 04655 2023.
ISSN: ESSN 1083-351X
PubMed: 36990218
DOI: 10.1016/J.JBC.2023.104655