Calcium in PDB 1v3k: Crystal Structure of F283Y Mutant Cyclodextrin Glycosyltransferase
Enzymatic activity of Crystal Structure of F283Y Mutant Cyclodextrin Glycosyltransferase
All present enzymatic activity of Crystal Structure of F283Y Mutant Cyclodextrin Glycosyltransferase:
2.4.1.19;
Protein crystallography data
The structure of Crystal Structure of F283Y Mutant Cyclodextrin Glycosyltransferase, PDB code: 1v3k
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 (°)
|
64.880,
74.430,
79.010,
85.15,
105.05,
101.02
|
R / Rfree (%)
|
15.5 /
20
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Crystal Structure of F283Y Mutant Cyclodextrin Glycosyltransferase
(pdb code 1v3k). 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, PDB code: 1v3k:
Jump to Calcium binding site number:
1;
2;
3;
4;
Calcium binding site 1 out
of 4 in 1v3k
Go back to
Calcium Binding Sites List in 1v3k
Calcium binding site 1 out
of 4 in the Crystal Structure of F283Y Mutant Cyclodextrin Glycosyltransferase
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 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca687
b:7.2
occ:1.00
|
OD1
|
A:ASN33
|
2.1
|
11.9
|
1.0
|
OD1
|
A:ASN32
|
2.2
|
10.4
|
1.0
|
O
|
A:HOH1746
|
2.3
|
7.5
|
1.0
|
O
|
A:ASN29
|
2.3
|
11.6
|
1.0
|
O
|
A:GLY51
|
2.3
|
13.5
|
1.0
|
OD2
|
A:ASP53
|
2.4
|
11.2
|
1.0
|
OD2
|
A:ASP27
|
2.4
|
9.0
|
1.0
|
CG
|
A:ASP27
|
3.3
|
10.3
|
1.0
|
CG
|
A:ASN33
|
3.4
|
10.4
|
1.0
|
C
|
A:ASN29
|
3.4
|
11.5
|
1.0
|
CG
|
A:ASN32
|
3.4
|
9.6
|
1.0
|
CG
|
A:ASP53
|
3.5
|
10.4
|
1.0
|
C
|
A:GLY51
|
3.5
|
10.9
|
1.0
|
OD1
|
A:ASP27
|
3.9
|
9.3
|
1.0
|
CB
|
A:ASP53
|
4.0
|
8.6
|
1.0
|
CA
|
A:GLY51
|
4.1
|
8.0
|
1.0
|
N
|
A:PRO30
|
4.1
|
13.8
|
1.0
|
N
|
A:ASN33
|
4.1
|
9.7
|
1.0
|
ND2
|
A:ASN32
|
4.1
|
6.9
|
1.0
|
ND2
|
A:ASN33
|
4.2
|
9.0
|
1.0
|
CA
|
A:PRO30
|
4.2
|
15.5
|
1.0
|
N
|
A:ASN29
|
4.3
|
10.1
|
1.0
|
O
|
A:ALA111
|
4.3
|
10.6
|
1.0
|
CA
|
A:ASN33
|
4.3
|
9.8
|
1.0
|
CB
|
A:ASP27
|
4.3
|
7.0
|
1.0
|
CA
|
A:ASN29
|
4.4
|
11.7
|
1.0
|
C
|
A:ASN32
|
4.4
|
9.6
|
1.0
|
CB
|
A:ASN33
|
4.4
|
10.3
|
1.0
|
OD1
|
A:ASP53
|
4.4
|
8.2
|
1.0
|
CA
|
A:ASP27
|
4.5
|
8.9
|
1.0
|
N
|
A:GLY52
|
4.6
|
9.6
|
1.0
|
CB
|
A:ASN32
|
4.7
|
10.3
|
1.0
|
C
|
A:PRO30
|
4.7
|
14.2
|
1.0
|
N
|
A:ASN32
|
4.7
|
12.1
|
1.0
|
C
|
A:GLY52
|
4.7
|
8.2
|
1.0
|
O
|
A:PRO30
|
4.8
|
16.9
|
1.0
|
CB
|
A:ASN29
|
4.8
|
11.3
|
1.0
|
O
|
A:ASN32
|
4.8
|
9.2
|
1.0
|
CA
|
A:ASN32
|
4.8
|
10.1
|
1.0
|
N
|
A:ASP53
|
4.8
|
9.1
|
1.0
|
O
|
A:HOH1082
|
4.9
|
14.8
|
1.0
|
C
|
A:ASP27
|
4.9
|
10.7
|
1.0
|
O
|
A:GLY52
|
5.0
|
7.6
|
1.0
|
CA
|
A:GLY52
|
5.0
|
9.9
|
1.0
|
N
|
A:GLY28
|
5.0
|
10.9
|
1.0
|
|
Calcium binding site 2 out
of 4 in 1v3k
Go back to
Calcium Binding Sites List in 1v3k
Calcium binding site 2 out
of 4 in the Crystal Structure of F283Y Mutant Cyclodextrin Glycosyltransferase
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 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca688
b:11.8
occ:1.00
|
O
|
A:HIS233
|
2.3
|
4.5
|
1.0
|
OD1
|
A:ASN139
|
2.3
|
4.5
|
1.0
|
O
|
A:HOH1024
|
2.3
|
7.9
|
1.0
|
O
|
A:HOH1759
|
2.3
|
9.4
|
1.0
|
O
|
A:ILE190
|
2.3
|
6.9
|
1.0
|
O
|
A:HOH1134
|
2.4
|
12.9
|
1.0
|
OD1
|
A:ASP199
|
2.6
|
14.3
|
1.0
|
OD2
|
A:ASP199
|
2.9
|
14.5
|
1.0
|
CG
|
A:ASP199
|
3.1
|
13.9
|
1.0
|
CG
|
A:ASN139
|
3.4
|
6.0
|
1.0
|
C
|
A:ILE190
|
3.5
|
8.7
|
1.0
|
C
|
A:HIS233
|
3.5
|
5.1
|
1.0
|
ND2
|
A:ASN139
|
3.9
|
7.5
|
1.0
|
CA
|
A:ILE190
|
4.1
|
7.2
|
1.0
|
O
|
A:ASN139
|
4.4
|
9.1
|
1.0
|
N
|
A:MET234
|
4.4
|
6.5
|
1.0
|
CA
|
A:MET234
|
4.4
|
7.2
|
1.0
|
CB
|
A:HIS233
|
4.5
|
5.0
|
1.0
|
CA
|
A:HIS233
|
4.5
|
2.8
|
1.0
|
CG
|
A:MET234
|
4.6
|
5.8
|
1.0
|
O
|
A:GLY189
|
4.6
|
7.5
|
1.0
|
O
|
A:LYS192
|
4.6
|
14.5
|
1.0
|
CB
|
A:ASP199
|
4.6
|
10.0
|
1.0
|
N
|
A:TYR191
|
4.6
|
8.1
|
1.0
|
CB
|
A:ASN139
|
4.7
|
3.8
|
1.0
|
CG2
|
A:ILE190
|
4.7
|
6.0
|
1.0
|
O
|
A:HOH1553
|
4.8
|
14.0
|
1.0
|
ND1
|
A:HIS176
|
4.8
|
10.6
|
1.0
|
O
|
A:LEU200
|
4.9
|
9.0
|
1.0
|
CE1
|
A:HIS176
|
4.9
|
12.9
|
1.0
|
CA
|
A:TYR191
|
5.0
|
8.3
|
1.0
|
|
Calcium binding site 3 out
of 4 in 1v3k
Go back to
Calcium Binding Sites List in 1v3k
Calcium binding site 3 out
of 4 in the Crystal Structure of F283Y Mutant Cyclodextrin Glycosyltransferase
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 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca689
b:13.3
occ:1.00
|
OD1
|
B:ASN33
|
2.1
|
13.8
|
1.0
|
OD1
|
B:ASN32
|
2.1
|
15.3
|
1.0
|
O
|
B:HOH1783
|
2.2
|
15.7
|
1.0
|
O
|
B:GLY51
|
2.3
|
12.4
|
1.0
|
O
|
B:ASN29
|
2.3
|
19.1
|
1.0
|
OD2
|
B:ASP53
|
2.4
|
11.3
|
1.0
|
OD2
|
B:ASP27
|
2.7
|
14.7
|
1.0
|
CG
|
B:ASN33
|
3.4
|
13.9
|
1.0
|
CG
|
B:ASN32
|
3.4
|
14.8
|
1.0
|
CG
|
B:ASP53
|
3.4
|
14.5
|
1.0
|
C
|
B:GLY51
|
3.4
|
9.8
|
1.0
|
C
|
B:ASN29
|
3.5
|
16.9
|
1.0
|
CG
|
B:ASP27
|
3.6
|
14.1
|
1.0
|
CB
|
B:ASP53
|
3.8
|
10.7
|
1.0
|
CA
|
B:GLY51
|
4.0
|
9.7
|
1.0
|
ND2
|
B:ASN32
|
4.1
|
15.5
|
1.0
|
O
|
B:ALA111
|
4.1
|
13.0
|
1.0
|
N
|
B:ASN33
|
4.1
|
12.9
|
1.0
|
ND2
|
B:ASN33
|
4.2
|
12.8
|
1.0
|
OD1
|
B:ASP27
|
4.3
|
13.3
|
1.0
|
CA
|
B:ASN33
|
4.3
|
14.2
|
1.0
|
N
|
B:PRO30
|
4.3
|
18.7
|
1.0
|
N
|
B:ASN29
|
4.4
|
17.1
|
1.0
|
C
|
B:ASN32
|
4.4
|
13.5
|
1.0
|
CA
|
B:PRO30
|
4.4
|
20.1
|
1.0
|
CB
|
B:ASN33
|
4.4
|
14.4
|
1.0
|
CA
|
B:ASN29
|
4.4
|
16.4
|
1.0
|
OD1
|
B:ASP53
|
4.5
|
13.8
|
1.0
|
CB
|
B:ASP27
|
4.6
|
12.3
|
1.0
|
N
|
B:GLY52
|
4.6
|
9.4
|
1.0
|
CB
|
B:ASN32
|
4.6
|
14.9
|
1.0
|
CA
|
B:ASP27
|
4.6
|
12.9
|
1.0
|
C
|
B:GLY52
|
4.7
|
10.2
|
1.0
|
O
|
B:HOH1782
|
4.7
|
18.3
|
1.0
|
N
|
B:ASN32
|
4.7
|
17.0
|
1.0
|
CB
|
B:ASN29
|
4.7
|
16.9
|
1.0
|
C
|
B:PRO30
|
4.7
|
19.5
|
1.0
|
O
|
B:ASN32
|
4.8
|
15.1
|
1.0
|
O
|
B:PRO30
|
4.8
|
21.3
|
1.0
|
CA
|
B:ASN32
|
4.8
|
15.0
|
1.0
|
N
|
B:ASP53
|
4.8
|
7.7
|
1.0
|
O
|
B:GLY52
|
4.9
|
9.4
|
1.0
|
CA
|
B:ASP53
|
5.0
|
8.2
|
1.0
|
CA
|
B:GLY52
|
5.0
|
9.7
|
1.0
|
|
Calcium binding site 4 out
of 4 in 1v3k
Go back to
Calcium Binding Sites List in 1v3k
Calcium binding site 4 out
of 4 in the Crystal Structure of F283Y Mutant Cyclodextrin Glycosyltransferase
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 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca690
b:13.1
occ:1.00
|
O
|
B:HOH1120
|
2.2
|
11.8
|
1.0
|
O
|
B:HIS233
|
2.3
|
9.9
|
1.0
|
O
|
B:HOH1052
|
2.3
|
8.9
|
1.0
|
O
|
B:ILE190
|
2.3
|
8.7
|
1.0
|
OD1
|
B:ASN139
|
2.3
|
11.1
|
1.0
|
O
|
B:HOH1563
|
2.3
|
14.7
|
1.0
|
OD2
|
B:ASP199
|
2.7
|
15.5
|
1.0
|
OD1
|
B:ASP199
|
2.7
|
14.4
|
1.0
|
CG
|
B:ASP199
|
3.0
|
15.8
|
1.0
|
C
|
B:ILE190
|
3.5
|
10.0
|
1.0
|
CG
|
B:ASN139
|
3.5
|
10.0
|
1.0
|
C
|
B:HIS233
|
3.6
|
11.0
|
1.0
|
ND2
|
B:ASN139
|
4.0
|
12.5
|
1.0
|
CA
|
B:ILE190
|
4.2
|
10.9
|
1.0
|
O
|
B:LYS192
|
4.4
|
14.5
|
1.0
|
CB
|
B:HIS233
|
4.4
|
9.8
|
1.0
|
N
|
B:MET234
|
4.4
|
9.0
|
1.0
|
O
|
B:ASN139
|
4.4
|
9.5
|
1.0
|
CA
|
B:MET234
|
4.5
|
9.3
|
1.0
|
CA
|
B:HIS233
|
4.5
|
11.3
|
1.0
|
O
|
B:GLY189
|
4.5
|
12.9
|
1.0
|
CB
|
B:ASP199
|
4.6
|
10.6
|
1.0
|
N
|
B:TYR191
|
4.6
|
10.5
|
1.0
|
CG
|
B:MET234
|
4.7
|
8.2
|
1.0
|
O
|
B:HOH1576
|
4.7
|
23.8
|
1.0
|
CB
|
B:ASN139
|
4.8
|
9.7
|
1.0
|
CG2
|
B:ILE190
|
4.8
|
11.1
|
1.0
|
ND1
|
B:HIS176
|
4.8
|
14.3
|
1.0
|
O
|
B:LEU200
|
4.9
|
11.2
|
1.0
|
CA
|
B:TYR191
|
4.9
|
12.0
|
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: Fri Jul 12 06:54:54 2024
|