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: Thu Jul 11 23:53:56 2024
|