Sodium in PDB 7p9q: Crystal Structure of Indole 3-Carboxylic Acid Decarboxylase From Arthrobacter Nicotianae FI1612 in Complex with Co-Factor Prfmn.
Protein crystallography data
The structure of Crystal Structure of Indole 3-Carboxylic Acid Decarboxylase From Arthrobacter Nicotianae FI1612 in Complex with Co-Factor Prfmn., PDB code: 7p9q
was solved by
D.Gahloth,
D.Leys,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
43.42 /
2.53
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
104.2,
195.45,
105.21,
90,
116.35,
90
|
R / Rfree (%)
|
18.4 /
22.1
|
Other elements in 7p9q:
The structure of Crystal Structure of Indole 3-Carboxylic Acid Decarboxylase From Arthrobacter Nicotianae FI1612 in Complex with Co-Factor Prfmn. also contains other interesting chemical elements:
Sodium Binding Sites:
The binding sites of Sodium atom in the Crystal Structure of Indole 3-Carboxylic Acid Decarboxylase From Arthrobacter Nicotianae FI1612 in Complex with Co-Factor Prfmn.
(pdb code 7p9q). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the
Crystal Structure of Indole 3-Carboxylic Acid Decarboxylase From Arthrobacter Nicotianae FI1612 in Complex with Co-Factor Prfmn., PDB code: 7p9q:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
6;
Sodium binding site 1 out
of 6 in 7p9q
Go back to
Sodium Binding Sites List in 7p9q
Sodium binding site 1 out
of 6 in the Crystal Structure of Indole 3-Carboxylic Acid Decarboxylase From Arthrobacter Nicotianae FI1612 in Complex with Co-Factor Prfmn.
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Crystal Structure of Indole 3-Carboxylic Acid Decarboxylase From Arthrobacter Nicotianae FI1612 in Complex with Co-Factor Prfmn. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na501
b:51.8
occ:1.00
|
O
|
A:THR151
|
2.7
|
71.1
|
1.0
|
OE1
|
A:GLU217
|
2.8
|
84.4
|
1.0
|
O
|
A:ALA204
|
2.8
|
62.7
|
1.0
|
O2P
|
A:4LU503
|
2.9
|
86.0
|
1.0
|
O5'
|
A:4LU503
|
2.9
|
93.2
|
1.0
|
O
|
A:THR206
|
2.9
|
82.5
|
1.0
|
O
|
A:ALA203
|
3.2
|
60.7
|
1.0
|
O
|
A:HOH652
|
3.4
|
75.6
|
1.0
|
P
|
A:4LU503
|
3.5
|
88.7
|
1.0
|
C
|
A:ALA204
|
3.6
|
60.3
|
1.0
|
O4'
|
A:4LU503
|
3.6
|
98.9
|
1.0
|
CD
|
A:GLU217
|
3.7
|
74.0
|
1.0
|
MN
|
A:MN502
|
3.8
|
93.7
|
1.0
|
CG
|
A:GLU217
|
3.8
|
72.4
|
1.0
|
C
|
A:THR151
|
3.9
|
70.0
|
1.0
|
O3P
|
A:4LU503
|
3.9
|
71.2
|
1.0
|
C
|
A:THR206
|
4.0
|
75.1
|
1.0
|
C4'
|
A:4LU503
|
4.0
|
93.5
|
1.0
|
N
|
A:THR206
|
4.1
|
69.0
|
1.0
|
C5'
|
A:4LU503
|
4.1
|
93.7
|
1.0
|
CA
|
A:ALA204
|
4.1
|
58.0
|
1.0
|
C
|
A:ALA203
|
4.3
|
60.4
|
1.0
|
CA
|
A:THR206
|
4.5
|
74.3
|
1.0
|
N
|
A:ALA205
|
4.5
|
64.2
|
1.0
|
CA
|
A:SER152
|
4.5
|
71.2
|
1.0
|
C
|
A:ALA205
|
4.6
|
63.1
|
1.0
|
N
|
A:SER152
|
4.7
|
68.9
|
1.0
|
N
|
A:ALA204
|
4.7
|
54.1
|
1.0
|
CB
|
A:GLU217
|
4.7
|
67.5
|
1.0
|
CB
|
A:THR206
|
4.8
|
73.1
|
1.0
|
O1P
|
A:4LU503
|
4.9
|
83.4
|
1.0
|
OD1
|
A:ASN150
|
4.9
|
71.8
|
1.0
|
OE2
|
A:GLU217
|
4.9
|
79.5
|
1.0
|
CB
|
A:SER152
|
4.9
|
74.8
|
1.0
|
CA
|
A:ALA205
|
4.9
|
66.7
|
1.0
|
CA
|
A:THR151
|
5.0
|
67.1
|
1.0
|
|
Sodium binding site 2 out
of 6 in 7p9q
Go back to
Sodium Binding Sites List in 7p9q
Sodium binding site 2 out
of 6 in the Crystal Structure of Indole 3-Carboxylic Acid Decarboxylase From Arthrobacter Nicotianae FI1612 in Complex with Co-Factor Prfmn.
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Crystal Structure of Indole 3-Carboxylic Acid Decarboxylase From Arthrobacter Nicotianae FI1612 in Complex with Co-Factor Prfmn. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na501
b:52.6
occ:1.00
|
O
|
B:THR151
|
2.7
|
71.8
|
1.0
|
O
|
B:THR206
|
2.8
|
74.8
|
1.0
|
OE1
|
B:GLU217
|
2.8
|
90.5
|
1.0
|
O
|
B:ALA204
|
2.9
|
76.2
|
1.0
|
O2P
|
B:4LU503
|
3.0
|
87.5
|
1.0
|
O5'
|
B:4LU503
|
3.1
|
100.1
|
1.0
|
O
|
B:ALA203
|
3.3
|
59.8
|
1.0
|
O
|
B:HOH633
|
3.4
|
90.8
|
1.0
|
P
|
B:4LU503
|
3.5
|
89.8
|
1.0
|
C
|
B:ALA204
|
3.6
|
66.3
|
1.0
|
O4'
|
B:4LU503
|
3.7
|
105.3
|
1.0
|
O3P
|
B:4LU503
|
3.7
|
69.6
|
1.0
|
CD
|
B:GLU217
|
3.7
|
84.9
|
1.0
|
CG
|
B:GLU217
|
3.8
|
81.7
|
1.0
|
C
|
B:THR206
|
3.9
|
74.7
|
1.0
|
MN
|
B:MN502
|
3.9
|
92.5
|
1.0
|
C4'
|
B:4LU503
|
4.0
|
99.0
|
1.0
|
C
|
B:THR151
|
4.0
|
71.9
|
1.0
|
N
|
B:THR206
|
4.0
|
73.7
|
1.0
|
C5'
|
B:4LU503
|
4.2
|
98.8
|
1.0
|
CA
|
B:ALA204
|
4.2
|
62.0
|
1.0
|
C
|
B:ALA203
|
4.4
|
62.2
|
1.0
|
CA
|
B:THR206
|
4.4
|
77.1
|
1.0
|
N
|
B:ALA205
|
4.5
|
67.2
|
1.0
|
CA
|
B:SER152
|
4.6
|
75.7
|
1.0
|
C
|
B:ALA205
|
4.6
|
71.2
|
1.0
|
CB
|
B:GLU217
|
4.7
|
76.2
|
1.0
|
CB
|
B:THR206
|
4.7
|
77.2
|
1.0
|
N
|
B:SER152
|
4.7
|
70.5
|
1.0
|
N
|
B:ALA204
|
4.8
|
60.7
|
1.0
|
OD1
|
B:ASN150
|
4.9
|
67.5
|
1.0
|
OE2
|
B:GLU217
|
4.9
|
102.9
|
1.0
|
O1P
|
B:4LU503
|
4.9
|
89.6
|
1.0
|
CA
|
B:ALA205
|
4.9
|
71.3
|
1.0
|
CB
|
B:SER152
|
5.0
|
75.4
|
1.0
|
|
Sodium binding site 3 out
of 6 in 7p9q
Go back to
Sodium Binding Sites List in 7p9q
Sodium binding site 3 out
of 6 in the Crystal Structure of Indole 3-Carboxylic Acid Decarboxylase From Arthrobacter Nicotianae FI1612 in Complex with Co-Factor Prfmn.
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Crystal Structure of Indole 3-Carboxylic Acid Decarboxylase From Arthrobacter Nicotianae FI1612 in Complex with Co-Factor Prfmn. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na501
b:82.0
occ:1.00
|
O
|
C:THR206
|
2.7
|
104.2
|
1.0
|
O
|
C:ALA204
|
2.8
|
87.3
|
1.0
|
O
|
C:THR151
|
2.9
|
104.6
|
1.0
|
OE1
|
C:GLU217
|
2.9
|
134.1
|
1.0
|
O
|
C:ALA203
|
3.0
|
99.0
|
1.0
|
O5'
|
C:4LU503
|
3.3
|
118.1
|
1.0
|
O
|
C:HOH638
|
3.3
|
80.2
|
1.0
|
O2P
|
C:4LU503
|
3.3
|
109.3
|
1.0
|
C
|
C:ALA204
|
3.5
|
93.1
|
1.0
|
O4'
|
C:4LU503
|
3.7
|
108.2
|
1.0
|
P
|
C:4LU503
|
3.7
|
124.5
|
1.0
|
O3P
|
C:4LU503
|
3.7
|
119.5
|
1.0
|
C
|
C:THR206
|
3.8
|
105.9
|
1.0
|
CG
|
C:GLU217
|
3.8
|
113.0
|
1.0
|
N
|
C:THR206
|
3.8
|
104.3
|
1.0
|
CD
|
C:GLU217
|
3.8
|
120.7
|
1.0
|
C4'
|
C:4LU503
|
4.0
|
119.8
|
1.0
|
CA
|
C:ALA204
|
4.1
|
94.2
|
1.0
|
MN
|
C:MN502
|
4.1
|
136.8
|
1.0
|
C
|
C:THR151
|
4.1
|
97.9
|
1.0
|
C
|
C:ALA203
|
4.1
|
88.7
|
1.0
|
CA
|
C:THR206
|
4.2
|
104.5
|
1.0
|
C5'
|
C:4LU503
|
4.2
|
118.9
|
1.0
|
N
|
C:ALA205
|
4.3
|
97.7
|
1.0
|
C
|
C:ALA205
|
4.4
|
98.9
|
1.0
|
CB
|
C:THR206
|
4.5
|
99.6
|
1.0
|
N
|
C:ALA204
|
4.5
|
90.5
|
1.0
|
CB
|
C:GLU217
|
4.6
|
109.2
|
1.0
|
CA
|
C:SER152
|
4.7
|
95.7
|
1.0
|
CA
|
C:ALA205
|
4.8
|
95.8
|
1.0
|
N
|
C:SER152
|
4.9
|
94.4
|
1.0
|
N
|
C:PRO207
|
4.9
|
102.3
|
1.0
|
|
Sodium binding site 4 out
of 6 in 7p9q
Go back to
Sodium Binding Sites List in 7p9q
Sodium binding site 4 out
of 6 in the Crystal Structure of Indole 3-Carboxylic Acid Decarboxylase From Arthrobacter Nicotianae FI1612 in Complex with Co-Factor Prfmn.
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of Crystal Structure of Indole 3-Carboxylic Acid Decarboxylase From Arthrobacter Nicotianae FI1612 in Complex with Co-Factor Prfmn. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Na501
b:78.7
occ:1.00
|
O
|
D:THR206
|
2.7
|
111.1
|
1.0
|
O
|
D:ALA204
|
2.8
|
90.9
|
1.0
|
O
|
D:THR151
|
2.9
|
96.1
|
1.0
|
O
|
D:ALA203
|
2.9
|
86.6
|
1.0
|
OE1
|
D:GLU217
|
3.0
|
129.7
|
1.0
|
O5'
|
D:4LU503
|
3.0
|
116.1
|
1.0
|
O
|
D:HOH646
|
3.3
|
131.3
|
1.0
|
C
|
D:ALA204
|
3.4
|
95.7
|
1.0
|
O2P
|
D:4LU503
|
3.5
|
115.2
|
1.0
|
O4'
|
D:4LU503
|
3.7
|
115.3
|
1.0
|
N
|
D:THR206
|
3.7
|
108.8
|
1.0
|
P
|
D:4LU503
|
3.7
|
121.7
|
1.0
|
C
|
D:THR206
|
3.7
|
112.1
|
1.0
|
CG
|
D:GLU217
|
3.7
|
115.0
|
1.0
|
CD
|
D:GLU217
|
3.8
|
121.8
|
1.0
|
O3P
|
D:4LU503
|
3.9
|
121.7
|
1.0
|
C4'
|
D:4LU503
|
4.0
|
123.9
|
1.0
|
CA
|
D:ALA204
|
4.0
|
92.2
|
1.0
|
C
|
D:ALA203
|
4.0
|
85.8
|
1.0
|
C5'
|
D:4LU503
|
4.1
|
121.3
|
1.0
|
CA
|
D:THR206
|
4.1
|
109.4
|
1.0
|
MN
|
D:MN502
|
4.1
|
137.2
|
1.0
|
C
|
D:THR151
|
4.1
|
99.8
|
1.0
|
N
|
D:ALA205
|
4.2
|
98.6
|
1.0
|
C
|
D:ALA205
|
4.3
|
105.3
|
1.0
|
CB
|
D:THR206
|
4.4
|
109.0
|
1.0
|
N
|
D:ALA204
|
4.5
|
89.3
|
1.0
|
CB
|
D:GLU217
|
4.6
|
108.9
|
1.0
|
CA
|
D:ALA205
|
4.7
|
92.8
|
1.0
|
CA
|
D:SER152
|
4.8
|
98.2
|
1.0
|
N
|
D:SER152
|
4.9
|
94.3
|
1.0
|
N
|
D:PRO207
|
4.9
|
108.1
|
1.0
|
|
Sodium binding site 5 out
of 6 in 7p9q
Go back to
Sodium Binding Sites List in 7p9q
Sodium binding site 5 out
of 6 in the Crystal Structure of Indole 3-Carboxylic Acid Decarboxylase From Arthrobacter Nicotianae FI1612 in Complex with Co-Factor Prfmn.
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 5 of Crystal Structure of Indole 3-Carboxylic Acid Decarboxylase From Arthrobacter Nicotianae FI1612 in Complex with Co-Factor Prfmn. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Na501
b:84.8
occ:1.00
|
O
|
E:ALA204
|
2.7
|
98.1
|
1.0
|
O
|
E:THR206
|
2.8
|
109.8
|
1.0
|
O
|
E:THR151
|
2.8
|
128.2
|
1.0
|
OE1
|
E:GLU217
|
2.9
|
129.8
|
1.0
|
O
|
E:ALA203
|
3.0
|
90.9
|
1.0
|
O5'
|
E:4LU503
|
3.1
|
119.8
|
1.0
|
C
|
E:ALA204
|
3.4
|
99.5
|
1.0
|
O2P
|
E:4LU503
|
3.4
|
129.6
|
1.0
|
P
|
E:4LU503
|
3.7
|
125.5
|
1.0
|
O4'
|
E:4LU503
|
3.7
|
128.5
|
1.0
|
CG
|
E:GLU217
|
3.8
|
118.5
|
1.0
|
N
|
E:THR206
|
3.8
|
102.4
|
1.0
|
CD
|
E:GLU217
|
3.8
|
124.9
|
1.0
|
C
|
E:THR206
|
3.8
|
107.6
|
1.0
|
MN
|
E:MN502
|
3.8
|
135.3
|
1.0
|
O3P
|
E:4LU503
|
3.8
|
138.1
|
1.0
|
C4'
|
E:4LU503
|
4.0
|
124.7
|
1.0
|
CA
|
E:ALA204
|
4.0
|
104.2
|
1.0
|
C
|
E:THR151
|
4.0
|
121.4
|
1.0
|
C
|
E:ALA203
|
4.1
|
96.8
|
1.0
|
C5'
|
E:4LU503
|
4.1
|
123.2
|
1.0
|
CA
|
E:THR206
|
4.2
|
106.2
|
1.0
|
N
|
E:ALA205
|
4.3
|
97.2
|
1.0
|
C
|
E:ALA205
|
4.4
|
103.5
|
1.0
|
CB
|
E:THR206
|
4.5
|
107.0
|
1.0
|
N
|
E:ALA204
|
4.5
|
99.6
|
1.0
|
CB
|
E:GLU217
|
4.6
|
116.5
|
1.0
|
CA
|
E:SER152
|
4.6
|
111.0
|
1.0
|
CA
|
E:ALA205
|
4.7
|
102.7
|
1.0
|
N
|
E:SER152
|
4.8
|
117.4
|
1.0
|
N
|
E:PRO207
|
5.0
|
110.0
|
1.0
|
|
Sodium binding site 6 out
of 6 in 7p9q
Go back to
Sodium Binding Sites List in 7p9q
Sodium binding site 6 out
of 6 in the Crystal Structure of Indole 3-Carboxylic Acid Decarboxylase From Arthrobacter Nicotianae FI1612 in Complex with Co-Factor Prfmn.
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 6 of Crystal Structure of Indole 3-Carboxylic Acid Decarboxylase From Arthrobacter Nicotianae FI1612 in Complex with Co-Factor Prfmn. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Na501
b:103.7
occ:1.00
|
OE1
|
F:GLU217
|
2.8
|
163.0
|
1.0
|
O
|
F:THR206
|
2.8
|
118.4
|
1.0
|
O
|
F:THR151
|
2.9
|
132.7
|
1.0
|
O5'
|
F:4LU503
|
3.0
|
131.0
|
1.0
|
O
|
F:ALA204
|
3.0
|
110.1
|
1.0
|
O2P
|
F:4LU503
|
3.1
|
128.6
|
1.0
|
O
|
F:ALA203
|
3.3
|
111.4
|
1.0
|
P
|
F:4LU503
|
3.3
|
140.2
|
1.0
|
O3P
|
F:4LU503
|
3.4
|
147.4
|
1.0
|
MN
|
F:MN502
|
3.6
|
140.8
|
1.0
|
CD
|
F:GLU217
|
3.6
|
161.6
|
1.0
|
O4'
|
F:4LU503
|
3.7
|
121.2
|
1.0
|
CG
|
F:GLU217
|
3.7
|
149.0
|
1.0
|
C
|
F:ALA204
|
3.7
|
111.2
|
1.0
|
C
|
F:THR206
|
3.9
|
119.0
|
1.0
|
C4'
|
F:4LU503
|
3.9
|
133.2
|
1.0
|
C5'
|
F:4LU503
|
4.0
|
124.7
|
1.0
|
N
|
F:THR206
|
4.1
|
112.0
|
1.0
|
C
|
F:THR151
|
4.1
|
139.2
|
1.0
|
CA
|
F:ALA204
|
4.3
|
117.6
|
1.0
|
CA
|
F:THR206
|
4.4
|
118.1
|
1.0
|
C
|
F:ALA203
|
4.4
|
116.7
|
1.0
|
CB
|
F:GLU217
|
4.6
|
140.2
|
1.0
|
N
|
F:ALA205
|
4.6
|
105.6
|
1.0
|
C
|
F:ALA205
|
4.6
|
106.5
|
1.0
|
CB
|
F:THR206
|
4.7
|
122.5
|
1.0
|
CA
|
F:SER152
|
4.7
|
122.8
|
1.0
|
O1P
|
F:4LU503
|
4.8
|
127.0
|
1.0
|
N
|
F:ALA204
|
4.8
|
118.0
|
1.0
|
OE2
|
F:GLU217
|
4.9
|
173.8
|
1.0
|
N
|
F:SER152
|
4.9
|
133.6
|
1.0
|
OD1
|
F:ASN150
|
4.9
|
169.4
|
1.0
|
|
Reference:
D.Gahloth,
K.Fisher,
K.A.P.Payne,
M.Cliff,
C.Levy,
D.Leys.
Structural and Biochemical Characterization of the Prenylated Flavin Mononucleotide-Dependent Indole-3-Carboxylic Acid Decarboxylase. J.Biol.Chem. V. 298 01771 2022.
ISSN: ESSN 1083-351X
PubMed: 35218772
DOI: 10.1016/J.JBC.2022.101771
Page generated: Tue Oct 8 18:28:24 2024
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