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Calcium in PDB 1v3m: Crystal Structure of F283Y Mutant Cyclodextrin Glycosyltransferase Complexed with A Pseudo-Tetraose Derived From Acarbose

Enzymatic activity of Crystal Structure of F283Y Mutant Cyclodextrin Glycosyltransferase Complexed with A Pseudo-Tetraose Derived From Acarbose

All present enzymatic activity of Crystal Structure of F283Y Mutant Cyclodextrin Glycosyltransferase Complexed with A Pseudo-Tetraose Derived From Acarbose:
2.4.1.19;

Protein crystallography data

The structure of Crystal Structure of F283Y Mutant Cyclodextrin Glycosyltransferase Complexed with A Pseudo-Tetraose Derived From Acarbose, PDB code: 1v3m 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) 10.00 / 2.00
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 64.090, 73.600, 78.300, 84.93, 105.12, 101.00
R / Rfree (%) 16.3 / 21.8

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of F283Y Mutant Cyclodextrin Glycosyltransferase Complexed with A Pseudo-Tetraose Derived From Acarbose (pdb code 1v3m). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of F283Y Mutant Cyclodextrin Glycosyltransferase Complexed with A Pseudo-Tetraose Derived From Acarbose, PDB code: 1v3m:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 1v3m

Go back to Calcium Binding Sites List in 1v3m
Calcium binding site 1 out of 4 in the Crystal Structure of F283Y Mutant Cyclodextrin Glycosyltransferase Complexed with A Pseudo-Tetraose Derived From Acarbose


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 F283Y Mutant Cyclodextrin Glycosyltransferase Complexed with A Pseudo-Tetraose Derived From Acarbose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca687

b:13.2
occ:1.00
 OD1 A:ASN33 2.1 16.1 1.0
OD1 A:ASN32 2.2 14.0 1.0
O A:HOH1322 2.2 9.4 1.0
O A:GLY51 2.2 14.8 1.0
O A:ASN29 2.3 20.7 1.0
OD2 A:ASP53 2.5 15.3 1.0
OD2 A:ASP27 2.5 15.1 1.0
CG A:ASN33 3.4 14.0 1.0
C A:GLY51 3.4 10.8 1.0
CG A:ASN32 3.4 12.7 1.0
CG A:ASP53 3.5 14.7 1.0
CG A:ASP27 3.5 13.5 1.0
C A:ASN29 3.5 18.1 1.0
CB A:ASP53 3.9 11.8 1.0
CA A:GLY51 4.0 8.7 1.0
O A:ALA111 4.0 14.8 1.0
N A:ASN33 4.1 13.5 1.0
OD1 A:ASP27 4.1 13.2 1.0
ND2 A:ASN32 4.1 9.9 1.0
ND2 A:ASN33 4.2 15.0 1.0
N A:PRO30 4.2 20.1 1.0
CA A:PRO30 4.3 18.0 1.0
CA A:ASN33 4.3 14.6 1.0
C A:ASN32 4.3 14.2 1.0
N A:ASN29 4.3 17.3 1.0
CB A:ASN33 4.4 14.1 1.0
CB A:ASP27 4.4 11.0 1.0
CA A:ASN29 4.4 17.1 1.0
OD1 A:ASP53 4.5 13.4 1.0
N A:GLY52 4.5 11.4 1.0
CA A:ASP27 4.5 12.7 1.0
C A:GLY52 4.6 11.7 1.0
CB A:ASN32 4.6 15.0 1.0
O A:ASN32 4.7 13.6 1.0
N A:ASN32 4.7 17.6 1.0
C A:PRO30 4.7 16.2 1.0
O A:GLY52 4.7 13.4 1.0
O A:HOH1013 4.7 17.2 1.0
CB A:ASN29 4.8 17.4 1.0
CA A:ASN32 4.8 14.6 1.0
N A:ASP53 4.8 10.6 1.0
CA A:GLY52 4.8 11.1 1.0
O A:PRO30 4.8 16.9 1.0
CA A:ASP53 4.9 10.4 1.0
C A:ASP27 5.0 13.5 1.0

Calcium binding site 2 out of 4 in 1v3m

Go back to Calcium Binding Sites List in 1v3m
Calcium binding site 2 out of 4 in the Crystal Structure of F283Y Mutant Cyclodextrin Glycosyltransferase Complexed with A Pseudo-Tetraose Derived From Acarbose


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 F283Y Mutant Cyclodextrin Glycosyltransferase Complexed with A Pseudo-Tetraose Derived From Acarbose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca688

b:18.1
occ:1.00
 O A:HOH1649 2.2 20.4 1.0
O A:HOH1496 2.2 14.1 1.0
OD1 A:ASN139 2.3 11.6 1.0
O A:HOH1497 2.3 13.0 1.0
O A:HIS233 2.3 12.5 1.0
O A:ILE190 2.4 11.4 1.0
OD1 A:ASP199 2.6 20.4 1.0
OD2 A:ASP199 3.0 19.7 1.0
CG A:ASP199 3.2 18.1 1.0
CG A:ASN139 3.4 10.1 1.0
C A:ILE190 3.6 13.3 1.0
C A:HIS233 3.6 10.9 1.0
ND2 A:ASN139 4.0 12.7 1.0
CA A:ILE190 4.1 12.8 1.0
O A:ASN139 4.3 12.1 1.0
CA A:MET234 4.4 11.3 1.0
N A:MET234 4.4 11.3 1.0
CB A:HIS233 4.5 11.0 1.0
CG A:MET234 4.5 9.4 1.0
O A:HOH1498 4.5 21.4 1.0
CA A:HIS233 4.5 11.0 1.0
O A:LYS192 4.6 19.7 1.0
O A:GLY189 4.6 14.2 1.0
ND1 A:HIS176 4.6 15.8 1.0
CB A:ASP199 4.6 14.6 1.0
CB A:ASN139 4.7 8.8 1.0
N A:TYR191 4.7 13.8 1.0
CE1 A:HIS176 4.8 16.0 1.0
CG2 A:ILE190 4.8 10.4 1.0
O A:LEU200 4.8 14.6 1.0
CA A:TYR191 5.0 13.6 1.0
CA A:ASN139 5.0 11.5 1.0

Calcium binding site 3 out of 4 in 1v3m

Go back to Calcium Binding Sites List in 1v3m
Calcium binding site 3 out of 4 in the Crystal Structure of F283Y Mutant Cyclodextrin Glycosyltransferase Complexed with A Pseudo-Tetraose Derived From Acarbose


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 F283Y Mutant Cyclodextrin Glycosyltransferase Complexed with A Pseudo-Tetraose Derived From Acarbose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca689

b:15.6
occ:1.00
 OD1 B:ASN33 2.1 16.5 1.0
O B:HOH1567 2.1 17.8 1.0
OD1 B:ASN32 2.1 17.8 1.0
O B:GLY51 2.2 17.0 1.0
O B:ASN29 2.3 26.9 1.0
OD2 B:ASP53 2.4 16.4 1.0
OD2 B:ASP27 2.5 16.2 1.0
CG B:ASN33 3.3 17.3 1.0
C B:GLY51 3.3 14.9 1.0
CG B:ASP53 3.4 18.7 1.0
CG B:ASN32 3.4 16.8 1.0
C B:ASN29 3.5 23.0 1.0
CG B:ASP27 3.5 15.5 1.0
CB B:ASP53 3.8 15.7 1.0
CA B:GLY51 3.9 16.2 1.0
O B:ALA111 4.0 17.9 1.0
N B:ASN33 4.1 16.3 1.0
ND2 B:ASN32 4.1 17.0 1.0
ND2 B:ASN33 4.1 17.3 1.0
OD1 B:ASP27 4.1 16.9 1.0
CA B:ASN33 4.2 17.4 1.0
N B:PRO30 4.3 24.5 1.0
C B:ASN32 4.3 16.7 1.0
CA B:PRO30 4.3 25.8 1.0
N B:ASN29 4.3 23.6 1.0
OD1 B:ASP53 4.4 15.9 1.0
CB B:ASN33 4.4 16.3 1.0
CA B:ASN29 4.4 22.1 1.0
CB B:ASP27 4.5 16.1 1.0
N B:GLY52 4.5 14.9 1.0
CA B:ASP27 4.6 17.1 1.0
CB B:ASN32 4.6 17.4 1.0
C B:GLY52 4.6 14.9 1.0
O B:ASN32 4.7 18.1 1.0
O B:HOH1086 4.7 18.4 1.0
N B:ASN32 4.7 19.6 1.0
O B:GLY52 4.8 14.1 1.0
CB B:ASN29 4.8 21.9 1.0
C B:PRO30 4.8 23.3 1.0
CA B:ASN32 4.8 18.3 1.0
N B:ASP53 4.8 14.5 1.0
O B:PRO30 4.9 25.2 1.0
CA B:GLY52 4.9 14.2 1.0
CA B:ASP53 5.0 13.9 1.0

Calcium binding site 4 out of 4 in 1v3m

Go back to Calcium Binding Sites List in 1v3m
Calcium binding site 4 out of 4 in the Crystal Structure of F283Y Mutant Cyclodextrin Glycosyltransferase Complexed with A Pseudo-Tetraose Derived From Acarbose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of F283Y Mutant Cyclodextrin Glycosyltransferase Complexed with A Pseudo-Tetraose Derived From Acarbose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca690

b:19.6
occ:1.00
 O B:HOH1577 2.2 20.8 1.0
O B:HOH1576 2.2 17.2 1.0
OD1 B:ASN139 2.2 15.6 1.0
O B:HIS233 2.3 16.1 1.0
O B:HOH1575 2.3 13.4 1.0
O B:ILE190 2.4 12.0 1.0
OD1 B:ASP199 2.7 18.2 1.0
OD2 B:ASP199 2.7 19.7 1.0
CG B:ASP199 3.0 17.4 1.0
CG B:ASN139 3.4 14.2 1.0
C B:HIS233 3.5 15.0 1.0
C B:ILE190 3.6 15.4 1.0
ND2 B:ASN139 4.0 15.3 1.0
CA B:ILE190 4.2 15.0 1.0
O B:ASN139 4.3 16.5 1.0
CA B:MET234 4.4 14.3 1.0
N B:MET234 4.4 13.8 1.0
CB B:HIS233 4.5 13.8 1.0
CB B:ASP199 4.5 16.6 1.0
O B:LYS192 4.5 17.7 1.0
CA B:HIS233 4.5 15.2 1.0
O B:HOH1122 4.6 21.3 1.0
CG B:MET234 4.6 11.8 1.0
O B:LEU200 4.6 16.7 1.0
O B:GLY189 4.6 15.8 1.0
ND1 B:HIS176 4.6 14.5 1.0
N B:TYR191 4.7 15.2 1.0
CB B:ASN139 4.7 13.5 1.0
CG2 B:ILE190 4.8 14.5 1.0
CE1 B:HIS176 4.9 14.5 1.0
CA B:TYR191 4.9 17.0 1.0

Reference:

R.Kanai, K.Haga, T.Akiba, K.Yamane, K.Harata. Role of PHE283 in Enzymatic Reaction of Cyclodextrin Glycosyltransferase From Alkalophilic Bacillus Sp.1011: Substrate Binding and Arrangement of the Catalytic Site Protein Sci. V. 13 457 2004.
ISSN: ISSN 0961-8368
PubMed: 14739329
DOI: 10.1110/PS.03408504
Page generated: Tue Jul 8 02:51:59 2025

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