Calcium in PDB 1wpc: Crystal Structure of Maltohexaose-Producing Amylase Complexed with Pseudo-Maltononaose

All present enzymatic activity of Crystal Structure of Maltohexaose-Producing Amylase Complexed with Pseudo-Maltononaose:
3.2.1.98;

The structure of Crystal Structure of Maltohexaose-Producing Amylase Complexed with Pseudo-Maltononaose, PDB code: 1wpc was solved by R.Kanai, K.Haga, T.Akiba, K.Yamane, K.Harata, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	6.00 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	47.410, 82.490, 126.880, 90.00, 90.00, 90.00
R / Rfree (%)	17.2 / 20.7

The structure of Crystal Structure of Maltohexaose-Producing Amylase Complexed with Pseudo-Maltononaose also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Calcium atom in the Crystal Structure of Maltohexaose-Producing Amylase Complexed with Pseudo-Maltononaose (pdb code 1wpc). 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 Maltohexaose-Producing Amylase Complexed with Pseudo-Maltononaose, PDB code: 1wpc:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of Maltohexaose-Producing Amylase Complexed with Pseudo-Maltononaose


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 Maltohexaose-Producing Amylase Complexed with Pseudo-Maltononaose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:19.9 occ:1.00 OD1 A:ASP207 2.3 20.6 1.0 O A:ALA186 2.3 18.6 1.0 OD1 A:ASP188 2.3 22.9 1.0 OD2 A:ASP209 2.4 23.2 1.0 OD1 A:ASP163 2.5 16.6 1.0 OD2 A:ASP163 2.5 18.2 1.0 O A:HOH711 2.5 18.9 1.0 CG A:ASP163 2.8 18.8 1.0 CG A:ASP207 3.1 18.7 1.0 CG A:ASP209 3.3 23.9 1.0 CG A:ASP188 3.4 20.6 1.0 C A:ALA186 3.6 20.5 1.0 OD2 A:ASP207 3.7 19.2 1.0 CB A:ASP209 3.7 22.8 1.0 N A:ASP188 3.9 19.4 1.0 C A:TRP187 4.0 20.8 1.0 OD2 A:ASP188 4.0 19.5 1.0 N A:ALA186 4.1 21.9 1.0 CB A:ASP207 4.1 19.7 1.0 CA A:ASP188 4.2 20.4 1.0 CB A:ASP163 4.3 16.5 1.0 CA A:ASP207 4.3 18.7 1.0 N A:ASP209 4.3 21.1 1.0 OD1 A:ASP209 4.4 23.3 1.0 CB A:ASP188 4.4 19.3 1.0 O A:TRP187 4.4 19.6 1.0 CA A:TRP187 4.4 19.3 1.0 NA A:NA504 4.5 21.2 1.0 N A:TRP187 4.5 19.4 1.0 CA A:ALA186 4.5 20.7 1.0 O A:HOH833 4.6 29.9 1.0 N A:MET208 4.7 19.5 1.0 CA A:ASP209 4.7 21.5 1.0 O A:HOH860 4.7 32.0 1.0 C A:ASP207 4.7 19.7 1.0 OD2 A:ASP199 4.9 20.8 1.0 O A:GLY184 5.0 22.6 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of Maltohexaose-Producing Amylase Complexed with Pseudo-Maltononaose


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 Maltohexaose-Producing Amylase Complexed with Pseudo-Maltononaose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:18.7 occ:1.00 O A:HIS240 2.3 17.6 1.0 O A:ASP199 2.3 15.7 1.0 OD1 A:ASP205 2.3 16.3 1.0 OD1 A:ASN106 2.3 15.9 1.0 O A:HOH719 2.4 18.6 1.0 OD1 A:ASP199 2.4 18.8 1.0 CG A:ASP205 3.1 17.1 1.0 OD2 A:ASP205 3.2 20.9 1.0 C A:ASP199 3.3 16.9 1.0 CG A:ASN106 3.5 19.0 1.0 CG A:ASP199 3.5 18.1 1.0 C A:HIS240 3.5 16.4 1.0 CA A:ASP199 3.8 17.9 1.0 O A:HOH720 3.9 19.8 1.0 CB A:HIS240 4.0 15.4 1.0 NA A:NA504 4.0 21.2 1.0 O A:ASN106 4.1 16.3 1.0 ND2 A:ASN106 4.1 17.1 1.0 CB A:ASP199 4.2 18.1 1.0 CA A:HIS240 4.3 15.8 1.0 OD2 A:ASP199 4.3 20.8 1.0 O A:HOH713 4.3 17.7 1.0 N A:TYR200 4.4 17.1 1.0 N A:ILE241 4.5 16.8 1.0 CB A:ASP205 4.6 17.2 1.0 CB A:ASN106 4.6 16.4 1.0 CA A:ILE241 4.6 16.5 1.0 O A:ILE206 4.6 17.8 1.0 CA A:TYR200 4.7 16.3 1.0 CA A:ASN106 4.8 16.5 1.0 C A:ASN106 4.8 17.6 1.0 CG1 A:ILE241 4.8 15.8 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of Maltohexaose-Producing Amylase Complexed with Pseudo-Maltononaose


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 Maltohexaose-Producing Amylase Complexed with Pseudo-Maltononaose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:23.7 occ:1.00 O A:TYR307 2.3 22.4 1.0 O A:GLY305 2.3 20.5 1.0 O A:HIS408 2.4 19.2 1.0 OD1 A:ASN409 2.4 23.2 1.0 OD1 A:ASP432 2.5 20.6 1.0 O A:HOH731 2.5 23.1 1.0 OD2 A:ASP432 2.6 21.9 1.0 CG A:ASP432 2.9 22.4 1.0 C A:GLY305 3.4 21.7 1.0 C A:HIS408 3.4 19.9 1.0 C A:TYR307 3.5 22.4 1.0 CG A:ASN409 3.6 21.8 1.0 CA A:ASN409 3.7 20.2 1.0 N A:TYR307 3.7 21.6 1.0 N A:ASN409 4.0 20.6 1.0 C A:ASN306 4.0 22.4 1.0 N A:ASN306 4.2 22.1 1.0 CB A:ASN409 4.2 22.4 1.0 CG A:MET309 4.2 20.1 1.0 CA A:ASN306 4.2 22.6 1.0 CA A:GLY305 4.2 20.4 1.0 CA A:TYR307 4.3 22.8 1.0 N A:MET309 4.4 18.3 1.0 CB A:ASP432 4.4 19.5 1.0 N A:ASP308 4.5 21.8 1.0 O A:HOH813 4.5 23.8 1.0 CA A:HIS408 4.6 22.2 1.0 O A:HOH775 4.6 27.0 1.0 CA A:ASP308 4.6 20.4 1.0 ND1 A:HIS408 4.6 27.0 1.0 CB A:HIS408 4.6 22.6 1.0 O A:ASN306 4.7 22.3 1.0 ND2 A:ASN409 4.7 22.4 1.0 O A:HOH737 4.8 17.5 1.0 CB A:TYR307 4.8 23.0 1.0 O A:HOH925 4.8 31.2 1.0 C A:ASN409 5.0 21.2 1.0

R.Kanai, K.Haga, T.Akiba, K.Yamane, K.Harata. Biochemical and Crystallographic Analyses of Maltohexaose-Producing Amylase From Alkalophilic Bacillus Sp. 707 Biochemistry V. 43 14047 2004.
ISSN: ISSN 0006-2960
PubMed: 15518553
DOI: 10.1021/BI048489M