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Calcium in PDB 1v3l: Crystal Structure of F283L Mutant Cyclodextrin Glycosyltransferase Complexed with A Pseudo-Tetraose Derived From Acarbose

Enzymatic activity of Crystal Structure of F283L Mutant Cyclodextrin Glycosyltransferase Complexed with A Pseudo-Tetraose Derived From Acarbose

All present enzymatic activity of Crystal Structure of F283L Mutant Cyclodextrin Glycosyltransferase Complexed with A Pseudo-Tetraose Derived From Acarbose:
2.4.1.19;

Protein crystallography data

The structure of Crystal Structure of F283L Mutant Cyclodextrin Glycosyltransferase Complexed with A Pseudo-Tetraose Derived From Acarbose, PDB code: 1v3l 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 / 2.10
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 64.970, 73.710, 80.080, 85.47, 105.53, 101.43
R / Rfree (%) 16.9 / 23.2

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of F283L Mutant Cyclodextrin Glycosyltransferase Complexed with A Pseudo-Tetraose Derived From Acarbose (pdb code 1v3l). 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 F283L Mutant Cyclodextrin Glycosyltransferase Complexed with A Pseudo-Tetraose Derived From Acarbose, PDB code: 1v3l:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 1v3l

Go back to Calcium Binding Sites List in 1v3l
Calcium binding site 1 out of 4 in the Crystal Structure of F283L 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 F283L 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:9.9
occ:1.00
 OD1 A:ASN33 2.1 13.9 1.0
O A:HOH1281 2.1 5.8 1.0
OD1 A:ASN32 2.2 16.5 1.0
O A:GLY51 2.3 9.3 1.0
OD2 A:ASP53 2.5 13.7 1.0
O A:ASN29 2.5 14.3 1.0
OD2 A:ASP27 2.6 14.9 1.0
CG A:ASN33 3.4 15.3 1.0
CG A:ASN32 3.4 14.7 1.0
C A:GLY51 3.4 3.8 1.0
CG A:ASP27 3.5 13.3 1.0
CG A:ASP53 3.5 14.2 1.0
C A:ASN29 3.7 12.7 1.0
OD1 A:ASP27 4.0 9.8 1.0
CA A:GLY51 4.0 3.4 1.0
CB A:ASP53 4.0 11.5 1.0
N A:ASN33 4.1 13.6 1.0
O A:ALA111 4.2 13.4 1.0
ND2 A:ASN32 4.2 11.7 1.0
ND2 A:ASN33 4.2 10.3 1.0
CA A:ASN33 4.3 13.5 1.0
CA A:PRO30 4.3 11.6 1.0
C A:ASN32 4.3 16.0 1.0
N A:PRO30 4.4 11.9 1.0
CB A:ASN33 4.4 12.5 1.0
CB A:ASP27 4.4 10.6 1.0
N A:GLY52 4.5 5.1 1.0
CA A:ASP27 4.5 9.4 1.0
N A:ASN29 4.5 12.9 1.0
OD1 A:ASP53 4.5 11.9 1.0
C A:GLY52 4.6 10.4 1.0
CB A:ASN32 4.6 14.1 1.0
O A:HOH1156 4.6 12.4 1.0
CA A:ASN29 4.7 13.2 1.0
O A:ASN32 4.7 14.0 1.0
O A:PRO30 4.7 16.1 1.0
C A:PRO30 4.8 13.5 1.0
N A:ASP53 4.8 13.0 1.0
CA A:ASN32 4.8 14.8 1.0
N A:ASN32 4.8 16.8 1.0
O A:GLY52 4.8 10.2 1.0
CA A:GLY52 4.8 10.8 1.0

Calcium binding site 2 out of 4 in 1v3l

Go back to Calcium Binding Sites List in 1v3l
Calcium binding site 2 out of 4 in the Crystal Structure of F283L 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 F283L 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:21.1
occ:1.00
 O A:HOH1421 2.2 13.1 1.0
O A:ILE190 2.2 9.9 1.0
O A:HOH1295 2.3 20.6 1.0
O A:HIS233 2.4 17.6 1.0
O A:HOH1358 2.5 4.1 1.0
OD1 A:ASP199 2.6 16.8 1.0
ND2 A:ASN139 2.7 9.6 1.0
OD2 A:ASP199 2.8 19.2 1.0
CG A:ASP199 3.0 18.4 1.0
C A:ILE190 3.4 10.9 1.0
C A:HIS233 3.7 13.6 1.0
CG A:ASN139 3.9 11.3 1.0
CA A:ILE190 4.1 9.6 1.0
OD1 A:ASN139 4.3 15.3 1.0
O A:LYS192 4.3 16.5 1.0
N A:TYR191 4.5 9.8 1.0
O A:GLY189 4.5 14.2 1.0
ND1 A:HIS176 4.5 17.4 1.0
CB A:HIS233 4.5 16.4 1.0
CB A:ASP199 4.5 11.1 1.0
CE1 A:HIS176 4.5 17.4 1.0
N A:MET234 4.5 13.7 1.0
O A:ASN139 4.6 11.5 1.0
CA A:MET234 4.6 13.2 1.0
CA A:HIS233 4.6 14.6 1.0
CG2 A:ILE190 4.6 7.7 1.0
CA A:TYR191 4.8 10.7 1.0
O A:LEU200 4.8 14.4 1.0
CD2 A:LEU194 4.8 32.9 1.0
O A:HOH1422 4.8 24.6 1.0
CG A:MET234 4.9 12.7 1.0

Calcium binding site 3 out of 4 in 1v3l

Go back to Calcium Binding Sites List in 1v3l
Calcium binding site 3 out of 4 in the Crystal Structure of F283L 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 F283L 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:13.1
occ:1.00
 OD1 B:ASN33 2.1 15.0 1.0
OD1 B:ASN32 2.2 15.2 1.0
O B:GLY51 2.2 15.6 1.0
OD2 B:ASP27 2.4 17.0 1.0
O B:ASN29 2.4 15.3 1.0
OD2 B:ASP53 2.4 15.7 1.0
CG B:ASP53 3.3 15.9 1.0
CG B:ASN33 3.3 14.8 1.0
CG B:ASN32 3.4 16.4 1.0
C B:GLY51 3.4 13.3 1.0
CG B:ASP27 3.5 18.1 1.0
C B:ASN29 3.5 10.8 1.0
CB B:ASP53 3.8 15.3 1.0
ND2 B:ASN32 4.1 14.1 1.0
CA B:GLY51 4.1 11.8 1.0
ND2 B:ASN33 4.1 16.8 1.0
N B:ASN33 4.1 17.4 1.0
OD1 B:ASP27 4.1 21.2 1.0
O B:ALA111 4.2 12.9 1.0
OD1 B:ASP53 4.3 16.0 1.0
CA B:ASN33 4.3 15.9 1.0
N B:ASN29 4.3 11.5 1.0
N B:PRO30 4.3 13.0 1.0
C B:ASN32 4.4 15.7 1.0
CA B:PRO30 4.4 15.8 1.0
CB B:ASN33 4.4 14.4 1.0
CA B:ASN29 4.4 12.5 1.0
CB B:ASP27 4.5 17.7 1.0
N B:GLY52 4.5 12.3 1.0
C B:GLY52 4.6 14.7 1.0
CB B:ASN32 4.6 15.1 1.0
CA B:ASP27 4.6 16.6 1.0
O B:HOH1208 4.6 18.3 1.0
O B:PRO30 4.7 19.1 1.0
N B:ASP53 4.7 14.6 1.0
C B:PRO30 4.7 17.0 1.0
N B:ASN32 4.8 15.5 1.0
O B:ASN32 4.8 16.1 1.0
CB B:ASN29 4.8 16.2 1.0
O B:GLY52 4.8 14.1 1.0
CA B:ASN32 4.8 17.6 1.0
CA B:GLY52 4.9 13.2 1.0
CA B:ASP53 4.9 14.6 1.0

Calcium binding site 4 out of 4 in 1v3l

Go back to Calcium Binding Sites List in 1v3l
Calcium binding site 4 out of 4 in the Crystal Structure of F283L 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 F283L 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:26.8
occ:1.00
 O B:HOH1471 2.2 16.5 1.0
OD1 B:ASN139 2.2 16.4 1.0
O B:ILE190 2.3 16.0 1.0
O B:HOH1470 2.3 21.8 1.0
O B:HIS233 2.4 16.8 1.0
O B:HOH1377 2.5 21.2 1.0
OD2 B:ASP199 2.8 25.0 1.0
OD1 B:ASP199 2.8 22.0 1.0
CG B:ASP199 3.2 23.5 1.0
CG B:ASN139 3.4 16.6 1.0
C B:ILE190 3.4 15.0 1.0
C B:HIS233 3.6 16.9 1.0
ND2 B:ASN139 3.9 19.0 1.0
CA B:ILE190 4.1 14.3 1.0
CB B:HIS233 4.4 16.8 1.0
CA B:MET234 4.4 16.8 1.0
N B:MET234 4.5 15.5 1.0
O B:GLY189 4.5 16.9 1.0
O B:LYS192 4.5 17.6 1.0
O B:ASN139 4.5 13.9 1.0
CA B:HIS233 4.5 14.8 1.0
N B:TYR191 4.6 14.4 1.0
CG B:MET234 4.6 12.1 1.0
CB B:ASP199 4.7 19.4 1.0
CB B:ASN139 4.7 16.4 1.0
CG2 B:ILE190 4.8 14.2 1.0
ND1 B:HIS176 4.8 14.3 1.0
O B:LEU200 4.9 11.8 1.0
CA B:TYR191 4.9 14.1 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: Sat Dec 12 03:24:25 2020

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