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Calcium in PDB 1ukt: Crystal Structure of Y100L Mutant Cyclodextrin Glucanotransferase Compexed with An Acarbose

Enzymatic activity of Crystal Structure of Y100L Mutant Cyclodextrin Glucanotransferase Compexed with An Acarbose

All present enzymatic activity of Crystal Structure of Y100L Mutant Cyclodextrin Glucanotransferase Compexed with An Acarbose:
2.4.1.19;

Protein crystallography data

The structure of Crystal Structure of Y100L Mutant Cyclodextrin Glucanotransferase Compexed with An Acarbose, PDB code: 1ukt was solved by K.Haga, R.Kanai, O.Sakamoto, K.Harata, K.Yamane, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 2.20
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 65.680, 74.470, 80.100, 85.29, 105.59, 100.81
R / Rfree (%) 17.3 / 27.6

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Y100L Mutant Cyclodextrin Glucanotransferase Compexed with An Acarbose (pdb code 1ukt). 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 Y100L Mutant Cyclodextrin Glucanotransferase Compexed with An Acarbose, PDB code: 1ukt:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 1ukt

Go back to Calcium Binding Sites List in 1ukt
Calcium binding site 1 out of 4 in the Crystal Structure of Y100L Mutant Cyclodextrin Glucanotransferase Compexed with An 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 Y100L Mutant Cyclodextrin Glucanotransferase Compexed with An Acarbose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca687

b:24.7
occ:1.00
 OD1 A:ASN33 2.0 25.4 1.0
O A:ASN29 2.2 29.8 1.0
OD1 A:ASN32 2.2 15.0 1.0
OD2 A:ASP53 2.4 20.3 1.0
O A:GLY51 2.5 16.5 1.0
O A:HOH1001 2.6 15.4 1.0
OD2 A:ASP27 2.6 13.0 1.0
CG A:ASN33 3.3 25.7 1.0
CG A:ASN32 3.3 13.7 1.0
C A:ASN29 3.4 27.1 1.0
CG A:ASP53 3.5 17.7 1.0
CG A:ASP27 3.6 11.1 1.0
C A:GLY51 3.6 15.2 1.0
CB A:ASP53 3.8 15.4 1.0
ND2 A:ASN32 3.9 9.1 1.0
N A:ASN33 3.9 22.4 1.0
O A:ALA111 4.1 15.5 1.0
ND2 A:ASN33 4.1 26.0 1.0
OD1 A:ASP27 4.1 10.2 1.0
CA A:ASN33 4.1 24.3 1.0
CA A:GLY51 4.2 14.0 1.0
C A:ASN32 4.3 21.5 1.0
CB A:ASN33 4.3 22.9 1.0
N A:PRO30 4.3 28.8 1.0
CA A:ASN29 4.4 20.4 1.0
CA A:PRO30 4.4 29.2 1.0
N A:ASN29 4.4 17.1 1.0
O A:GLY52 4.4 25.7 1.0
C A:GLY52 4.5 16.4 1.0
OD1 A:ASP53 4.6 17.2 1.0
CB A:ASN32 4.6 18.4 1.0
N A:ASP53 4.6 18.4 1.0
CB A:ASP27 4.6 11.7 1.0
O A:ASN32 4.7 19.5 1.0
N A:GLY52 4.7 12.6 1.0
CB A:ASN29 4.7 14.8 1.0
CA A:ASP27 4.7 12.6 1.0
CA A:ASN32 4.8 21.3 1.0
CA A:ASP53 4.8 14.2 1.0
C A:PRO30 4.8 28.8 1.0
N A:ASN32 4.8 24.6 1.0
O A:PRO30 4.9 31.3 1.0
CA A:GLY52 5.0 10.5 1.0

Calcium binding site 2 out of 4 in 1ukt

Go back to Calcium Binding Sites List in 1ukt
Calcium binding site 2 out of 4 in the Crystal Structure of Y100L Mutant Cyclodextrin Glucanotransferase Compexed with An 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 Y100L Mutant Cyclodextrin Glucanotransferase Compexed with An Acarbose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca688

b:21.6
occ:1.00
 O A:HOH1003 2.1 15.7 1.0
O A:HOH1005 2.2 20.9 1.0
O A:ILE190 2.3 11.2 1.0
O A:HIS233 2.3 14.5 1.0
OD1 A:ASP199 2.4 14.0 1.0
OD1 A:ASN139 2.4 12.6 1.0
O A:HOH1004 2.5 28.8 1.0
CG A:ASP199 3.3 19.1 1.0
C A:ILE190 3.5 11.3 1.0
C A:HIS233 3.6 11.0 1.0
OD2 A:ASP199 3.6 21.8 1.0
CG A:ASN139 3.6 12.0 1.0
CA A:ILE190 4.2 9.3 1.0
ND2 A:ASN139 4.3 9.5 1.0
CA A:MET234 4.3 7.6 1.0
O A:ASN139 4.3 17.7 1.0
N A:MET234 4.4 7.3 1.0
CB A:HIS233 4.5 8.9 1.0
CG A:MET234 4.5 5.2 1.0
N A:TYR191 4.5 13.9 1.0
CG2 A:ILE190 4.6 4.5 1.0
CA A:HIS233 4.6 11.2 1.0
O A:LYS192 4.6 18.6 1.0
CB A:ASP199 4.7 13.5 1.0
O A:HOH1009 4.7 14.1 1.0
O A:GLY189 4.7 21.8 1.0
CB A:ASN139 4.8 12.3 1.0
CD2 A:HIS176 4.8 13.1 1.0
CA A:TYR191 4.8 15.7 1.0
O A:LEU200 4.9 13.0 1.0

Calcium binding site 3 out of 4 in 1ukt

Go back to Calcium Binding Sites List in 1ukt
Calcium binding site 3 out of 4 in the Crystal Structure of Y100L Mutant Cyclodextrin Glucanotransferase Compexed with An 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 Y100L Mutant Cyclodextrin Glucanotransferase Compexed with An Acarbose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca689

b:28.9
occ:1.00
 O B:HOH1002 2.0 16.4 1.0
OD1 B:ASN33 2.1 17.5 1.0
O B:ASN29 2.2 34.1 1.0
OD1 B:ASP53 2.4 24.3 1.0
OD2 B:ASP27 2.4 16.4 1.0
OD1 B:ASN32 2.5 16.7 1.0
O B:GLY51 2.6 23.1 1.0
O B:ASP27 3.2 33.1 1.0
CG B:ASN33 3.3 17.6 1.0
C B:ASN29 3.3 26.1 1.0
CG B:ASP53 3.4 24.0 1.0
C B:GLY51 3.6 22.4 1.0
CG B:ASP27 3.7 18.9 1.0
CG B:ASN32 3.7 18.1 1.0
CA B:PRO30 4.0 30.7 1.0
CB B:ASP53 4.0 22.8 1.0
ND2 B:ASN33 4.0 13.5 1.0
N B:ASN33 4.1 20.1 1.0
C B:ASP27 4.1 28.5 1.0
N B:PRO30 4.1 27.3 1.0
CA B:GLY51 4.1 21.0 1.0
O B:ALA111 4.2 19.6 1.0
OD2 B:ASP53 4.3 27.0 1.0
CA B:ASN33 4.3 21.4 1.0
CA B:ASN29 4.3 23.8 1.0
N B:ASN29 4.4 25.8 1.0
ND2 B:ASN32 4.4 15.3 1.0
CB B:ASN33 4.4 18.5 1.0
O B:HOH1118 4.4 31.1 1.0
CA B:ASP27 4.4 24.6 1.0
OD1 B:ASP27 4.4 17.7 1.0
C B:PRO30 4.5 30.8 1.0
C B:ASN32 4.5 22.1 1.0
O B:PRO30 4.5 35.9 1.0
CB B:ASP27 4.7 20.4 1.0
CB B:ASN29 4.7 21.1 1.0
C B:GLY52 4.7 18.6 1.0
N B:GLY52 4.8 17.0 1.0
N B:ASN32 4.8 25.2 1.0
O B:GLY52 4.8 22.1 1.0
N B:ASP53 4.8 20.3 1.0
CB B:ASN32 4.9 17.9 1.0
CA B:ASN32 4.9 22.3 1.0

Calcium binding site 4 out of 4 in 1ukt

Go back to Calcium Binding Sites List in 1ukt
Calcium binding site 4 out of 4 in the Crystal Structure of Y100L Mutant Cyclodextrin Glucanotransferase Compexed with An 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 Y100L Mutant Cyclodextrin Glucanotransferase Compexed with An Acarbose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca690

b:24.9
occ:1.00
 O B:HOH1006 2.1 21.7 1.0
O B:HOH1007 2.2 33.2 1.0
OD1 B:ASN139 2.3 19.3 1.0
O B:HIS233 2.4 14.2 1.0
OD2 B:ASP199 2.5 11.1 1.0
O B:ILE190 2.6 27.9 1.0
OD1 B:ASP199 2.9 14.3 1.0
CG B:ASP199 3.0 14.7 1.0
CG B:ASN139 3.5 19.0 1.0
C B:HIS233 3.7 15.2 1.0
C B:ILE190 3.8 23.4 1.0
ND2 B:ASN139 4.2 19.8 1.0
O B:ASN139 4.4 19.1 1.0
CB B:HIS233 4.4 12.8 1.0
CA B:ILE190 4.5 21.1 1.0
O B:GLY189 4.5 16.1 1.0
O B:HOH1079 4.5 21.4 1.0
CB B:ASP199 4.5 14.6 1.0
N B:MET234 4.6 16.7 1.0
CA B:HIS233 4.6 13.7 1.0
CA B:MET234 4.7 17.1 1.0
CB B:ASN139 4.7 19.4 1.0
O B:LYS192 4.7 21.7 1.0
CG B:MET234 4.8 16.9 1.0
N B:TYR191 4.8 20.8 1.0

Reference:

K.Haga, R.Kanai, O.Sakamoto, M.Aoyagi, K.Harata, K.Yamane. Effects of Essential Carbohydrate/Aromatic Stacking Interaction with TYR100 and PHE259 on Substrate Binding of Cyclodextrin Glycosyltransferase From Alkalophilic Bacillus Sp. 1011 J.Biochem.(Tokyo) V. 134 881 2003.
ISSN: ISSN 0021-924X
PubMed: 14769878
DOI: 10.1093/JB/MVG215
Page generated: Sat Dec 12 03:23:04 2020

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