Calcium in PDB 6wnu: Crystal Structure of the Three-Domain Cyclomaltodextrin Glucanotransferase Clda in the Monomeric Form

All present enzymatic activity of Crystal Structure of the Three-Domain Cyclomaltodextrin Glucanotransferase Clda in the Monomeric Form:
2.4.1.19;

The structure of Crystal Structure of the Three-Domain Cyclomaltodextrin Glucanotransferase Clda in the Monomeric Form, PDB code: 6wnu was solved by E.Magana-Cuevas, S.Centeno-Leija, H.Serrano-Posada, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.08 / 1.88
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	67.77, 67.77, 105.1, 90, 90, 120
R / Rfree (%)	18.6 / 22.7

The binding sites of Calcium atom in the Crystal Structure of the Three-Domain Cyclomaltodextrin Glucanotransferase Clda in the Monomeric Form (pdb code 6wnu). 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 the Three-Domain Cyclomaltodextrin Glucanotransferase Clda in the Monomeric Form, PDB code: 6wnu:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of the Three-Domain Cyclomaltodextrin Glucanotransferase Clda in the Monomeric Form


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 the Three-Domain Cyclomaltodextrin Glucanotransferase Clda in the Monomeric Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca601 b:26.7 occ:1.00 O A:HOH835 2.4 28.4 1.0 O A:HIS254 2.4 24.8 1.0 O A:HOH754 2.4 30.8 1.0 O A:HOH767 2.5 21.1 1.0 OD1 A:ASN159 2.5 21.7 1.0 O A:GLN211 2.5 30.9 1.0 OD2 A:ASP220 2.5 28.3 1.0 OD1 A:ASP220 2.8 25.5 1.0 CG A:ASP220 3.0 25.8 1.0 C A:GLN211 3.6 34.0 1.0 CG A:ASN159 3.6 18.1 1.0 C A:HIS254 3.6 24.9 1.0 CA A:GLN211 4.1 36.3 1.0 ND2 A:ASN159 4.1 19.0 1.0 O A:ASN159 4.3 19.0 1.0 O A:LEU221 4.3 22.0 1.0 CA A:MET255 4.4 22.1 1.0 N A:MET255 4.4 26.9 1.0 CG A:MET255 4.4 24.9 1.0 CB A:HIS254 4.4 21.8 1.0 CB A:ASP220 4.5 26.7 1.0 NE2 A:GLN223 4.6 24.0 1.0 CA A:HIS254 4.6 24.2 1.0 OE1 A:GLN223 4.6 24.6 1.0 O A:LEU210 4.6 29.8 1.0 O A:HOH792 4.6 36.7 1.0 O A:LYS213 4.6 24.8 1.0 ND1 A:HIS196 4.6 31.6 1.0 N A:ASP212 4.6 29.9 1.0 CE1 A:HIS196 4.8 29.4 1.0 CB A:ASN159 4.8 19.6 1.0 CB A:GLN211 5.0 33.2 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of the Three-Domain Cyclomaltodextrin Glucanotransferase Clda in the Monomeric Form


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 the Three-Domain Cyclomaltodextrin Glucanotransferase Clda in the Monomeric Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca602 b:20.4 occ:1.00 OD1 A:ASP52 2.3 22.9 1.0 OD2 A:ASP75 2.3 21.5 1.0 OD1 A:ASN51 2.4 19.0 1.0 O A:ASP48 2.4 23.0 1.0 O A:HOH789 2.5 16.3 1.0 O A:GLY73 2.5 19.9 1.0 OD1 A:ASN46 2.6 17.8 1.0 CG A:ASP75 3.3 22.2 1.0 CG A:ASN46 3.4 20.2 1.0 C A:ASP48 3.5 26.1 1.0 CG A:ASP52 3.5 21.7 1.0 CG A:ASN51 3.6 20.3 1.0 C A:GLY73 3.6 21.6 1.0 CB A:ASP75 3.8 21.8 1.0 ND2 A:ASN46 3.9 20.4 1.0 CA A:GLY73 4.0 20.1 1.0 N A:ASP52 4.0 24.2 1.0 N A:ASP48 4.1 21.4 1.0 C A:ASN51 4.2 31.1 1.0 CA A:ASP52 4.2 24.6 1.0 CA A:ASP48 4.2 20.7 1.0 ND2 A:ASN51 4.3 21.9 1.0 OD2 A:ASP52 4.3 24.3 1.0 O A:HIS131 4.3 23.9 1.0 N A:PRO49 4.4 22.1 1.0 OD1 A:ASP75 4.4 21.6 1.0 CB A:ASP52 4.5 23.5 1.0 CA A:PRO49 4.5 23.1 1.0 CB A:ASN46 4.5 20.3 1.0 O A:ASN51 4.5 29.6 1.0 CB A:ASP48 4.5 22.8 1.0 CA A:ASN46 4.6 19.1 1.0 N A:ASN51 4.7 25.4 1.0 CB A:ASN51 4.7 22.1 1.0 CA A:ASN51 4.7 20.7 1.0 N A:GLY74 4.8 15.6 1.0 O A:HOH744 4.8 18.2 1.0 C A:PRO49 4.8 23.4 1.0 C A:GLY74 4.8 18.9 1.0 N A:GLY47 4.9 19.2 1.0 O A:GLY74 4.9 19.1 1.0 N A:ASP75 4.9 17.5 1.0 C A:ASN46 5.0 23.6 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of the Three-Domain Cyclomaltodextrin Glucanotransferase Clda in the Monomeric Form


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 the Three-Domain Cyclomaltodextrin Glucanotransferase Clda in the Monomeric Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca603 b:21.5 occ:1.00 OD1 A:ASP101 2.3 20.8 1.0 OD1 A:ASN104 2.4 28.6 1.0 OE1 A:GLU129 2.4 19.8 1.0 O A:HOH857 2.4 24.9 1.0 O A:ASN102 2.5 24.1 1.0 OE2 A:GLU130 2.5 18.0 1.0 OE1 A:GLU130 2.6 23.1 1.0 CD A:GLU130 2.9 16.4 1.0 OE2 A:GLU129 3.0 20.6 1.0 CD A:GLU129 3.0 22.3 1.0 C A:ASN102 3.6 21.0 1.0 CG A:ASP101 3.6 21.7 1.0 CG A:ASN104 3.6 28.8 1.0 N A:ASN102 3.7 15.6 1.0 O A:HOH839 4.1 24.8 1.0 O A:ILE103 4.1 21.9 1.0 CA A:ASN102 4.2 15.4 1.0 ND2 A:ASN104 4.2 24.4 1.0 OD2 A:ASP101 4.3 21.7 1.0 C A:ILE103 4.4 26.2 1.0 CG A:GLU130 4.4 21.8 1.0 C A:ASP101 4.4 18.9 1.0 CG A:GLU129 4.5 16.2 1.0 CA A:ASP101 4.5 19.7 1.0 N A:GLU130 4.5 22.2 1.0 CD A:ARG123 4.5 22.5 1.0 OG A:SER57 4.6 28.5 1.0 CB A:ASP101 4.6 20.0 1.0 N A:ILE103 4.6 23.3 1.0 N A:ASN104 4.7 26.7 1.0 CA A:ASN104 4.7 29.4 1.0 CB A:ASN104 4.7 24.5 1.0 OH A:TYR71 4.7 18.1 1.0 CB A:SER57 4.8 24.3 1.0 CB A:ASN102 4.8 15.4 1.0 CA A:GLU129 4.8 22.2 1.0 ND1 A:HIS131 4.9 19.6 1.0 CA A:ILE103 5.0 24.7 1.0

S.Centeno-Leija, A.Lopez-Munguia, Y.Cardenas-Conejo, N.A.Mancilla-Margalli, B.Velazquez-Cruz, E.Magana-Cuevas, Y.Guerra-Borrego, R.Zatarain-Palacios, Y.Marin-Tovar, S.Gomez-Manzo, J.Marcial-Quino, B.Hernandez-Ochoa, J.A.Osuna-Castro, E.Rudino-Pinera, H.Serrano-Posada. Discovery of A Novel Group of Three-Domain Thermophilic Cyclomaltodextrin Glucanotransferases: Structural and Functional Implications. To Be Published.