Calcium in PDB 8ah3: DG04279 Glycoside Hydrolase Family 172

The structure of DG04279 Glycoside Hydrolase Family 172, PDB code: 8ah3 was solved by O.Al-Jourani, E.C.Lowe, A.Basle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	68.11 / 1.40
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	89.15, 89.15, 289.32, 90, 90, 120
R / Rfree (%)	16.2 / 18.4

The binding sites of Calcium atom in the DG04279 Glycoside Hydrolase Family 172 (pdb code 8ah3). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the DG04279 Glycoside Hydrolase Family 172, PDB code: 8ah3:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the DG04279 Glycoside Hydrolase Family 172


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of DG04279 Glycoside Hydrolase Family 172 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:23.9 occ:1.00 OD2 A:ASP59 2.4 22.0 1.0 CG A:ASP59 3.4 24.1 1.0 HB2 A:ASP59 3.8 24.9 1.0 CA A:CA502 3.9 24.9 1.0 CB A:ASP59 4.1 25.3 1.0 HB3 A:ASP59 4.3 24.9 1.0 O A:HOH676 4.3 35.4 1.0 OD1 A:ASP59 4.4 26.9 1.0 HA A:VAL57 4.4 28.3 1.0

Calcium binding site 2 out of 4 in the DG04279 Glycoside Hydrolase Family 172


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of DG04279 Glycoside Hydrolase Family 172 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:24.9 occ:1.00 O A:HOH731 2.4 23.5 1.0 O A:GLY56 2.4 26.5 1.0 OD1 A:ASP59 2.5 26.9 1.0 O A:HOH708 2.5 26.8 1.0 OD2 A:ASP59 2.6 22.0 1.0 CG A:ASP59 2.9 24.1 1.0 HB3 A:ASP52 3.5 28.1 1.0 C A:GLY56 3.6 29.0 1.0 H A:ASP52 3.9 25.5 1.0 CA A:CA501 3.9 23.9 1.0 HA A:VAL57 4.0 28.3 1.0 OD1 A:ASN51 4.1 30.4 1.0 O A:GLY55 4.2 27.8 1.0 C A:GLY55 4.3 24.0 1.0 N A:GLY56 4.4 26.2 1.0 CB A:ASP59 4.4 25.3 1.0 CB A:ASP52 4.4 26.6 1.0 HB2 A:ASP52 4.4 28.1 1.0 CA A:GLY56 4.5 27.2 1.0 N A:VAL57 4.6 28.2 1.0 H A:GLY56 4.7 25.9 1.0 CA A:VAL57 4.7 29.0 1.0 N A:ASP52 4.7 24.8 1.0 HB3 A:ASP59 4.7 24.9 1.0 HA2 A:GLY55 4.7 26.6 1.0 HB2 A:ASP59 4.8 24.9 1.0 HA2 A:GLY56 4.9 27.4 1.0 O A:ASP52 4.9 24.9 1.0 CG A:ASN51 5.0 27.0 1.0

Calcium binding site 3 out of 4 in the DG04279 Glycoside Hydrolase Family 172


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of DG04279 Glycoside Hydrolase Family 172 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:32.7 occ:0.33 OE2 A:GLU35 2.3 40.6 1.0 OE1 A:GLU35 2.7 54.2 1.0 CD A:GLU35 2.9 54.0 1.0 CG A:GLU35 4.4 36.8 1.0 HA A:THR32 4.4 22.6 1.0 O A:PRO30 4.6 33.1 1.0 OG1 A:THR32 4.6 29.3 1.0 HG3 A:GLU35 4.8 37.8 1.0 HG2 A:GLU35 4.8 37.9 1.0 C A:GLY31 5.0 27.2 1.0 O A:HOH673 5.0 28.5 1.0

Calcium binding site 4 out of 4 in the DG04279 Glycoside Hydrolase Family 172


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of DG04279 Glycoside Hydrolase Family 172 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:48.1 occ:1.00 O A:ARG226 2.3 27.0 1.0 NE2 A:HIS333 2.4 25.3 1.0 O A:HOH703 2.4 32.4 1.0 O A:HOH603 2.5 37.0 1.0 HB3 A:ARG226 2.9 32.5 1.0 C A:ARG226 3.3 29.0 1.0 CD2 A:HIS333 3.4 27.2 1.0 HH22 A:ARG226 3.4 43.5 1.0 CE1 A:HIS333 3.4 27.1 1.0 HD2 A:HIS333 3.5 26.0 1.0 HE1 A:HIS333 3.5 26.1 1.0 HA A:ARG226 3.7 29.4 1.0 CB A:ARG226 3.8 32.1 1.0 CA A:ARG226 3.8 28.6 1.0 H A:GLU203 3.9 28.3 1.0 HB3 A:ASN337 3.9 26.8 1.0 HB2 A:GLU203 4.1 30.3 1.0 HB A:THR202 4.1 25.1 1.0 NH2 A:ARG226 4.2 41.2 1.0 HB2 A:ARG226 4.3 32.6 1.0 OE2 A:GLU200 4.4 43.8 1.0 N A:ASN227 4.5 24.0 1.0 O A:ASN227 4.5 27.2 1.0 HG2 A:ARG226 4.5 38.1 1.0 CG A:HIS333 4.5 24.2 1.0 ND1 A:HIS333 4.5 25.0 1.0 C A:ASN227 4.5 25.4 1.0 HA A:ASN227 4.7 24.5 1.0 OE1 A:GLU200 4.7 34.9 1.0 CG A:ARG226 4.7 38.2 1.0 N A:GLU203 4.7 27.6 1.0 CB A:ASN337 4.7 26.7 1.0 OE1 A:GLU203 4.7 56.6 1.0 OD1 A:ASN337 4.7 24.9 1.0 CZ A:ARG226 4.8 49.0 1.0 CA A:ASN227 4.8 24.6 1.0 CG A:ASN337 4.8 29.4 1.0 HG23 A:THR202 4.8 25.2 1.0 NE A:ARG226 4.8 47.6 1.0 HH21 A:ARG226 4.9 43.5 1.0 HE A:ARG226 4.9 47.3 1.0 CD A:GLU200 4.9 37.0 1.0 HA A:THR202 4.9 25.1 1.0 O A:GLU203 4.9 30.0 1.0

O.Al-Jourani, S.Benedict, J.Ross, A.Layton, P.Van Der Peet, N.P.Bailey, T.Heunis, V.Marando, J.Manion, F.Mensitieri, J.Abellon-Ruiz, S.L.Oram, L.Parsons, A.Cartmel, G.S.A.Wright, A.Basle, M.Trost, L.L.Kiessling, B.Henrissat, J.Munoz-Munoz, A.Lovering, R.P.Hirt, S.J.Williams, E.C.Lowe, P.J.Moynihan. Mining the Human Gut Microbiome Identifies Mycobacterial D-Arabinan Degrading Enzymes To Be Published.