Calcium in PDB 5u95: Structure of the Open Conformation of 4-Coumarate-Coa Ligase From Nicotiana Tabacum
Enzymatic activity of Structure of the Open Conformation of 4-Coumarate-Coa Ligase From Nicotiana Tabacum
All present enzymatic activity of Structure of the Open Conformation of 4-Coumarate-Coa Ligase From Nicotiana Tabacum:
6.2.1.12;
Protein crystallography data
The structure of Structure of the Open Conformation of 4-Coumarate-Coa Ligase From Nicotiana Tabacum, PDB code: 5u95
was solved by
W.P.Morioka,
C.M.Bianchetti,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
48.42 /
2.25
|
Space group
|
P 41
|
Cell size a, b, c (Å), α, β, γ (°)
|
108.259,
108.259,
183.220,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
19.3 /
26
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Structure of the Open Conformation of 4-Coumarate-Coa Ligase From Nicotiana Tabacum
(pdb code 5u95). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the
Structure of the Open Conformation of 4-Coumarate-Coa Ligase From Nicotiana Tabacum, PDB code: 5u95:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
Calcium binding site 1 out
of 5 in 5u95
Go back to
Calcium Binding Sites List in 5u95
Calcium binding site 1 out
of 5 in the Structure of the Open Conformation of 4-Coumarate-Coa Ligase From Nicotiana Tabacum
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Structure of the Open Conformation of 4-Coumarate-Coa Ligase From Nicotiana Tabacum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca601
b:42.4
occ:1.00
|
O
|
A:ILE178
|
2.4
|
28.6
|
1.0
|
O
|
B:HOH731
|
2.5
|
32.2
|
1.0
|
OE1
|
B:GLU268
|
2.5
|
37.9
|
1.0
|
OE2
|
B:GLU268
|
2.5
|
44.9
|
1.0
|
CD
|
B:GLU268
|
2.9
|
42.4
|
1.0
|
C
|
A:ILE178
|
3.6
|
24.1
|
1.0
|
O
|
A:HIS24
|
4.3
|
28.6
|
1.0
|
CG
|
B:GLU268
|
4.4
|
43.3
|
1.0
|
N
|
A:ILE178
|
4.4
|
28.9
|
1.0
|
CA
|
A:ILE178
|
4.5
|
24.3
|
1.0
|
NE2
|
B:GLN271
|
4.6
|
54.4
|
1.0
|
N
|
A:GLN179
|
4.6
|
24.5
|
1.0
|
CA
|
A:GLN179
|
4.6
|
30.0
|
1.0
|
CD
|
A:PRO26
|
4.8
|
21.7
|
1.0
|
OE1
|
A:GLN179
|
4.8
|
68.4
|
1.0
|
CG
|
A:PRO26
|
4.9
|
21.9
|
1.0
|
CE1
|
B:TYR297
|
4.9
|
40.7
|
1.0
|
OH
|
B:TYR297
|
5.0
|
45.7
|
1.0
|
CB
|
A:ILE178
|
5.0
|
30.3
|
1.0
|
O
|
A:HOH789
|
5.0
|
35.3
|
1.0
|
|
Calcium binding site 2 out
of 5 in 5u95
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Calcium Binding Sites List in 5u95
Calcium binding site 2 out
of 5 in the Structure of the Open Conformation of 4-Coumarate-Coa Ligase From Nicotiana Tabacum
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Structure of the Open Conformation of 4-Coumarate-Coa Ligase From Nicotiana Tabacum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca602
b:0.4
occ:1.00
|
OD2
|
D:ASP434
|
2.4
|
68.9
|
1.0
|
OD1
|
D:ASP434
|
2.6
|
67.5
|
1.0
|
O
|
D:LEU436
|
2.7
|
64.7
|
1.0
|
OD1
|
A:ASN169
|
2.8
|
56.0
|
1.0
|
CG
|
D:ASP434
|
2.8
|
61.5
|
1.0
|
C
|
D:LEU436
|
3.8
|
53.5
|
1.0
|
CB
|
D:LEU436
|
3.8
|
49.5
|
1.0
|
CG
|
A:ASN169
|
3.8
|
48.5
|
1.0
|
OE2
|
A:GLU170
|
4.1
|
47.5
|
1.0
|
OE2
|
D:GLU438
|
4.1
|
97.3
|
1.0
|
CB
|
D:ASP434
|
4.3
|
49.9
|
1.0
|
CA
|
D:LEU436
|
4.3
|
47.2
|
1.0
|
CB
|
A:ASN169
|
4.3
|
37.3
|
1.0
|
CG
|
D:LEU436
|
4.5
|
51.7
|
1.0
|
CA
|
A:ASN169
|
4.5
|
36.3
|
1.0
|
O
|
D:LYS437
|
4.5
|
62.5
|
1.0
|
N
|
D:LEU436
|
4.6
|
42.9
|
1.0
|
CD
|
D:GLU438
|
4.7
|
96.5
|
1.0
|
C
|
D:LYS437
|
4.7
|
66.8
|
1.0
|
CD
|
A:GLU170
|
4.8
|
48.3
|
1.0
|
OE1
|
D:GLU438
|
4.8
|
96.8
|
1.0
|
ND2
|
A:ASN169
|
4.9
|
41.7
|
1.0
|
N
|
D:LYS437
|
4.9
|
54.4
|
1.0
|
OE1
|
A:GLU170
|
4.9
|
47.9
|
1.0
|
|
Calcium binding site 3 out
of 5 in 5u95
Go back to
Calcium Binding Sites List in 5u95
Calcium binding site 3 out
of 5 in the Structure of the Open Conformation of 4-Coumarate-Coa Ligase From Nicotiana Tabacum
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Structure of the Open Conformation of 4-Coumarate-Coa Ligase From Nicotiana Tabacum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca601
b:62.3
occ:1.00
|
OD1
|
B:ASP434
|
2.4
|
80.8
|
1.0
|
O
|
B:LEU436
|
2.4
|
66.2
|
1.0
|
OD2
|
B:ASP434
|
2.7
|
65.5
|
1.0
|
CG
|
B:ASP434
|
2.9
|
69.1
|
1.0
|
C
|
B:LEU436
|
3.6
|
61.7
|
1.0
|
CB
|
B:LEU436
|
3.9
|
67.2
|
1.0
|
CA
|
B:LEU436
|
4.2
|
63.9
|
1.0
|
CB
|
B:ASP434
|
4.4
|
59.3
|
1.0
|
N
|
B:LEU436
|
4.4
|
68.1
|
1.0
|
N
|
B:LYS437
|
4.7
|
61.1
|
1.0
|
C
|
B:LYS437
|
4.7
|
67.1
|
1.0
|
CG
|
B:LEU436
|
4.7
|
70.7
|
1.0
|
N
|
B:GLU438
|
4.9
|
73.0
|
1.0
|
O
|
B:LYS437
|
4.9
|
65.7
|
1.0
|
CA
|
B:LYS437
|
5.0
|
65.5
|
1.0
|
|
Calcium binding site 4 out
of 5 in 5u95
Go back to
Calcium Binding Sites List in 5u95
Calcium binding site 4 out
of 5 in the Structure of the Open Conformation of 4-Coumarate-Coa Ligase From Nicotiana Tabacum
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Structure of the Open Conformation of 4-Coumarate-Coa Ligase From Nicotiana Tabacum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca601
b:0.6
occ:1.00
|
OD2
|
C:ASP434
|
2.4
|
93.7
|
1.0
|
O
|
C:LEU436
|
2.5
|
80.6
|
1.0
|
OD1
|
C:ASP434
|
2.6
|
80.7
|
1.0
|
CG
|
C:ASP434
|
2.9
|
84.1
|
1.0
|
C
|
C:LEU436
|
3.6
|
76.2
|
1.0
|
CB
|
C:LEU436
|
3.7
|
72.5
|
1.0
|
CA
|
C:LEU436
|
4.1
|
75.7
|
1.0
|
O
|
C:LYS437
|
4.1
|
79.9
|
1.0
|
OD1
|
B:ASN169
|
4.4
|
60.0
|
1.0
|
N
|
C:LEU436
|
4.4
|
74.7
|
1.0
|
CB
|
C:ASP434
|
4.4
|
68.5
|
1.0
|
OE1
|
B:GLU170
|
4.5
|
68.6
|
1.0
|
O
|
B:HOH708
|
4.5
|
42.5
|
1.0
|
CG
|
C:LEU436
|
4.5
|
72.6
|
1.0
|
N
|
C:LYS437
|
4.7
|
71.7
|
1.0
|
CG
|
B:ASN169
|
4.8
|
53.6
|
1.0
|
NZ
|
B:LYS64
|
4.8
|
47.0
|
1.0
|
C
|
C:LYS437
|
4.9
|
83.6
|
1.0
|
CB
|
B:ASN169
|
4.9
|
50.0
|
1.0
|
OE2
|
B:GLU170
|
5.0
|
66.7
|
1.0
|
|
Calcium binding site 5 out
of 5 in 5u95
Go back to
Calcium Binding Sites List in 5u95
Calcium binding site 5 out
of 5 in the Structure of the Open Conformation of 4-Coumarate-Coa Ligase From Nicotiana Tabacum
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Structure of the Open Conformation of 4-Coumarate-Coa Ligase From Nicotiana Tabacum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca601
b:0.7
occ:1.00
|
O
|
D:ILE178
|
2.4
|
37.7
|
1.0
|
O
|
D:HOH815
|
2.6
|
34.0
|
1.0
|
C
|
D:ILE178
|
3.7
|
24.7
|
1.0
|
O
|
D:HIS24
|
4.2
|
45.6
|
1.0
|
N
|
D:ILE178
|
4.5
|
31.1
|
1.0
|
O
|
D:HOH778
|
4.5
|
42.6
|
1.0
|
N
|
D:GLN179
|
4.5
|
35.6
|
1.0
|
CA
|
D:ILE178
|
4.6
|
32.2
|
1.0
|
O
|
D:HOH801
|
4.6
|
34.9
|
1.0
|
CA
|
D:GLN179
|
4.7
|
35.8
|
1.0
|
OE1
|
D:GLU177
|
4.9
|
64.7
|
1.0
|
CD
|
D:PRO180
|
5.0
|
31.8
|
1.0
|
CD
|
D:PRO26
|
5.0
|
25.0
|
1.0
|
CG
|
D:PRO26
|
5.0
|
23.3
|
1.0
|
|
Reference:
W.P.Morioka,
C.M.Bianchetti.
Structure of the Open Conformation of 4-Coumarate-Coa Ligase From Nicotiana Tabacum To Be Published.
Page generated: Mon Jul 15 11:27:52 2024
|