Sodium in PDB 6r6u: Crystal Structure of Human Cis-Aconitate Decarboxylase
Enzymatic activity of Crystal Structure of Human Cis-Aconitate Decarboxylase
All present enzymatic activity of Crystal Structure of Human Cis-Aconitate Decarboxylase:
4.1.1.6;
Protein crystallography data
The structure of Crystal Structure of Human Cis-Aconitate Decarboxylase, PDB code: 6r6u
was solved by
P.Lukat,
F.Chen,
K.Saile,
K.Buessow,
F.Pessler,
W.Blankenfeldt,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
60.41 /
1.71
|
|
Space group
|
P 21 21 2
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
102.010,
109.980,
74.974,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
14.5 /
16.2
|
Sodium Binding Sites:
The binding sites of Sodium atom in the Crystal Structure of Human Cis-Aconitate Decarboxylase
(pdb code 6r6u). 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 Human Cis-Aconitate Decarboxylase, PDB code: 6r6u:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
6;
Sodium binding site 1 out
of 6 in 6r6u
Go back to
Sodium Binding Sites List in 6r6u
Sodium binding site 1 out
of 6 in the Crystal Structure of Human Cis-Aconitate Decarboxylase
 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 Human Cis-Aconitate Decarboxylase within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na502
b:20.8
occ:1.00
|
O
|
A:ALA195
|
2.3
|
19.2
|
1.0
|
|
O
|
B:ALA195
|
2.3
|
16.8
|
1.0
|
|
O
|
B:GLY196
|
2.3
|
22.7
|
1.0
|
|
O
|
A:GLY196
|
2.4
|
25.8
|
1.0
|
|
O
|
A:HOH785
|
2.4
|
33.0
|
1.0
|
|
O
|
B:HOH711
|
2.6
|
38.5
|
1.0
|
|
C
|
A:ALA195
|
3.2
|
20.2
|
1.0
|
|
C
|
B:ALA195
|
3.2
|
17.4
|
1.0
|
|
C
|
A:GLY196
|
3.3
|
23.2
|
1.0
|
|
C
|
B:GLY196
|
3.3
|
20.9
|
1.0
|
|
HA3
|
A:GLY196
|
3.3
|
26.1
|
1.0
|
|
HA3
|
B:GLY196
|
3.4
|
25.2
|
1.0
|
|
CA
|
A:GLY196
|
3.6
|
21.7
|
1.0
|
|
CA
|
B:GLY196
|
3.6
|
21.0
|
1.0
|
|
N
|
A:GLY196
|
3.7
|
21.6
|
1.0
|
|
N
|
B:GLY196
|
3.7
|
20.2
|
1.0
|
|
HE1
|
A:PHE245
|
3.8
|
23.1
|
1.0
|
|
HE1
|
B:PHE245
|
3.8
|
27.4
|
1.0
|
|
O
|
A:HOH729
|
4.1
|
48.5
|
1.0
|
|
HZ
|
B:PHE245
|
4.3
|
27.6
|
1.0
|
|
HZ
|
A:PHE245
|
4.3
|
22.8
|
1.0
|
|
H
|
A:GLY196
|
4.4
|
26.0
|
1.0
|
|
CA
|
A:ALA195
|
4.4
|
20.2
|
1.0
|
|
H
|
B:GLY196
|
4.4
|
24.3
|
1.0
|
|
CA
|
B:ALA195
|
4.4
|
17.8
|
1.0
|
|
N
|
A:ALA197
|
4.5
|
18.5
|
1.0
|
|
N
|
B:ALA197
|
4.5
|
16.8
|
1.0
|
|
N
|
A:ALA195
|
4.5
|
21.3
|
1.0
|
|
N
|
B:ALA195
|
4.5
|
19.1
|
1.0
|
|
HA2
|
A:GLY196
|
4.5
|
26.1
|
1.0
|
|
O
|
B:HIS194
|
4.5
|
24.9
|
1.0
|
|
CE1
|
A:PHE245
|
4.5
|
19.2
|
1.0
|
|
CE1
|
B:PHE245
|
4.6
|
22.8
|
1.0
|
|
HA2
|
B:GLY196
|
4.6
|
25.2
|
1.0
|
|
HA
|
A:ALA197
|
4.6
|
19.9
|
1.0
|
|
HA
|
B:ALA197
|
4.6
|
19.4
|
1.0
|
|
O
|
A:HIS194
|
4.6
|
27.1
|
1.0
|
|
C
|
B:HIS194
|
4.7
|
21.7
|
1.0
|
|
C
|
A:HIS194
|
4.7
|
23.5
|
1.0
|
|
H
|
A:ALA195
|
4.7
|
25.5
|
1.0
|
|
H
|
B:ALA195
|
4.8
|
22.9
|
1.0
|
|
CZ
|
A:PHE245
|
4.8
|
18.9
|
1.0
|
|
CZ
|
B:PHE245
|
4.8
|
23.0
|
1.0
|
|
HA
|
A:ALA195
|
4.8
|
24.3
|
1.0
|
|
HA
|
B:ALA195
|
4.9
|
21.4
|
1.0
|
|
HE1
|
A:PHE158
|
4.9
|
25.8
|
1.0
|
|
Sodium binding site 2 out
of 6 in 6r6u
Go back to
Sodium Binding Sites List in 6r6u
Sodium binding site 2 out
of 6 in the Crystal Structure of Human Cis-Aconitate Decarboxylase
 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 Human Cis-Aconitate Decarboxylase within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na503
b:27.6
occ:0.92
|
O
|
A:ARG401
|
2.3
|
22.6
|
1.0
|
|
OD1
|
A:ASP400
|
2.3
|
21.4
|
1.0
|
|
O
|
A:HOH800
|
2.4
|
25.9
|
1.0
|
|
O
|
A:HOH647
|
2.5
|
25.2
|
1.0
|
|
HG
|
A:SER289
|
2.9
|
37.0
|
1.0
|
|
H
|
A:ARG401
|
3.0
|
26.2
|
1.0
|
|
C
|
A:ARG401
|
3.5
|
21.9
|
1.0
|
|
HB2
|
A:SER289
|
3.5
|
33.3
|
1.0
|
|
CG
|
A:ASP400
|
3.5
|
23.1
|
1.0
|
|
OG
|
A:SER289
|
3.6
|
30.8
|
1.0
|
|
O
|
A:HOH679
|
3.7
|
26.3
|
1.0
|
|
HB3
|
A:SER289
|
3.8
|
33.3
|
1.0
|
|
N
|
A:ARG401
|
3.8
|
21.8
|
1.0
|
|
CB
|
A:SER289
|
3.9
|
27.7
|
1.0
|
|
HA
|
A:SER402
|
4.0
|
24.4
|
1.0
|
|
HA
|
A:ALA286
|
4.0
|
24.5
|
1.0
|
|
OD2
|
A:ASP400
|
4.2
|
23.9
|
1.0
|
|
CA
|
A:ARG401
|
4.3
|
21.5
|
1.0
|
|
N
|
A:SER402
|
4.4
|
19.7
|
1.0
|
|
HB3
|
A:ASP400
|
4.5
|
26.5
|
1.0
|
|
HB2
|
A:SER402
|
4.5
|
27.3
|
1.0
|
|
CB
|
A:ASP400
|
4.6
|
22.0
|
1.0
|
|
CA
|
A:SER402
|
4.6
|
20.3
|
1.0
|
|
O
|
A:HOH621
|
4.7
|
33.1
|
1.0
|
|
HB3
|
A:ARG401
|
4.7
|
27.2
|
1.0
|
|
C
|
A:ASP400
|
4.9
|
22.0
|
1.0
|
|
HA
|
A:ASP400
|
5.0
|
25.9
|
1.0
|
|
CA
|
A:ALA286
|
5.0
|
20.4
|
1.0
|
|
O
|
A:ASP285
|
5.0
|
22.5
|
1.0
|
|
Sodium binding site 3 out
of 6 in 6r6u
Go back to
Sodium Binding Sites List in 6r6u
Sodium binding site 3 out
of 6 in the Crystal Structure of Human Cis-Aconitate Decarboxylase
 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 Human Cis-Aconitate Decarboxylase within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na504
b:41.0
occ:1.00
|
O
|
A:TYR246
|
2.2
|
25.9
|
1.0
|
|
O
|
A:HOH847
|
2.2
|
46.3
|
1.0
|
|
O
|
A:HOH601
|
2.3
|
34.9
|
1.0
|
|
O
|
A:GLY243
|
2.4
|
20.8
|
1.0
|
|
C
|
A:TYR246
|
3.4
|
25.7
|
1.0
|
|
H
|
A:TYR246
|
3.4
|
25.1
|
1.0
|
|
C
|
A:GLY243
|
3.5
|
20.4
|
1.0
|
|
HA
|
A:ALA244
|
3.5
|
25.7
|
1.0
|
|
HE
|
B:ARG157
|
3.7
|
54.8
|
1.0
|
|
HB2
|
A:TYR249
|
3.8
|
30.6
|
1.0
|
|
OE1
|
A:GLU239
|
3.8
|
50.1
|
1.0
|
|
HB2
|
A:TYR246
|
3.9
|
28.3
|
1.0
|
|
N
|
A:TYR246
|
4.1
|
20.9
|
1.0
|
|
HA
|
A:ALA247
|
4.1
|
41.1
|
1.0
|
|
O
|
A:ALA247
|
4.1
|
38.2
|
1.0
|
|
CA
|
A:ALA244
|
4.2
|
21.4
|
1.0
|
|
CA
|
A:TYR246
|
4.2
|
23.0
|
1.0
|
|
N
|
A:ALA244
|
4.3
|
21.0
|
1.0
|
|
C
|
A:ALA244
|
4.3
|
20.6
|
1.0
|
|
HD2
|
B:ARG157
|
4.3
|
47.2
|
1.0
|
|
O
|
A:HOH726
|
4.3
|
37.4
|
1.0
|
|
HA3
|
A:GLY243
|
4.3
|
24.4
|
1.0
|
|
C
|
A:ALA247
|
4.4
|
36.2
|
1.0
|
|
O
|
A:ALA244
|
4.4
|
21.3
|
1.0
|
|
N
|
A:ALA247
|
4.4
|
30.4
|
1.0
|
|
NE
|
B:ARG157
|
4.4
|
45.6
|
1.0
|
|
CA
|
A:GLY243
|
4.4
|
20.3
|
1.0
|
|
CB
|
A:TYR246
|
4.5
|
23.6
|
1.0
|
|
CA
|
A:ALA247
|
4.5
|
34.3
|
1.0
|
|
HA2
|
A:GLY243
|
4.5
|
24.4
|
1.0
|
|
O
|
A:GLU239
|
4.6
|
24.6
|
1.0
|
|
O
|
A:HOH663
|
4.6
|
50.4
|
1.0
|
|
H
|
A:TYR249
|
4.6
|
37.5
|
1.0
|
|
CB
|
A:TYR249
|
4.6
|
25.4
|
1.0
|
|
HB3
|
A:TYR249
|
4.7
|
30.6
|
1.0
|
|
HH11
|
B:ARG157
|
4.8
|
62.7
|
1.0
|
|
HB3
|
A:GLU239
|
4.8
|
34.4
|
1.0
|
|
N
|
A:PHE245
|
4.9
|
19.5
|
1.0
|
|
HB3
|
A:TYR246
|
4.9
|
28.3
|
1.0
|
|
CD
|
B:ARG157
|
4.9
|
39.3
|
1.0
|
|
HA
|
A:GLU239
|
5.0
|
30.1
|
1.0
|
|
Sodium binding site 4 out
of 6 in 6r6u
Go back to
Sodium Binding Sites List in 6r6u
Sodium binding site 4 out
of 6 in the Crystal Structure of Human Cis-Aconitate Decarboxylase
 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 Human Cis-Aconitate Decarboxylase within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na504
b:49.0
occ:1.00
|
O
|
B:TYR246
|
2.3
|
27.3
|
1.0
|
|
O
|
B:GLY243
|
2.4
|
20.9
|
1.0
|
|
O
|
A:HOH849
|
2.4
|
51.1
|
1.0
|
|
O
|
B:HOH672
|
2.9
|
40.3
|
1.0
|
|
H
|
B:TYR246
|
3.4
|
24.9
|
1.0
|
|
C
|
B:GLY243
|
3.5
|
21.3
|
1.0
|
|
C
|
B:TYR246
|
3.5
|
25.9
|
1.0
|
|
HE
|
A:ARG157
|
3.5
|
58.0
|
1.0
|
|
HA
|
B:ALA244
|
3.6
|
25.0
|
1.0
|
|
HB2
|
B:TYR249
|
3.6
|
29.2
|
1.0
|
|
OE1
|
B:GLU239
|
3.8
|
51.2
|
1.0
|
|
HB2
|
B:TYR246
|
3.8
|
25.7
|
1.0
|
|
N
|
B:TYR246
|
4.1
|
20.7
|
1.0
|
|
HD2
|
A:ARG157
|
4.1
|
49.6
|
1.0
|
|
CA
|
B:ALA244
|
4.2
|
20.8
|
1.0
|
|
NE
|
A:ARG157
|
4.2
|
48.3
|
1.0
|
|
HA
|
B:ALA247
|
4.2
|
36.4
|
1.0
|
|
CA
|
B:TYR246
|
4.2
|
22.2
|
1.0
|
|
N
|
B:ALA244
|
4.2
|
19.9
|
1.0
|
|
HA3
|
B:GLY243
|
4.3
|
25.4
|
1.0
|
|
O
|
B:GLU239
|
4.3
|
25.2
|
1.0
|
|
O
|
B:ALA247
|
4.3
|
34.6
|
1.0
|
|
C
|
B:ALA244
|
4.3
|
19.4
|
1.0
|
|
CA
|
B:GLY243
|
4.4
|
21.1
|
1.0
|
|
C
|
B:ALA247
|
4.4
|
31.9
|
1.0
|
|
O
|
B:ALA244
|
4.5
|
20.6
|
1.0
|
|
N
|
B:ALA247
|
4.5
|
28.6
|
1.0
|
|
CB
|
B:TYR249
|
4.5
|
24.3
|
1.0
|
|
CB
|
B:TYR246
|
4.5
|
21.4
|
1.0
|
|
HB3
|
B:GLU239
|
4.5
|
40.5
|
1.0
|
|
HA2
|
B:GLY243
|
4.5
|
25.4
|
1.0
|
|
HB3
|
B:TYR249
|
4.5
|
29.2
|
1.0
|
|
HH11
|
A:ARG157
|
4.6
|
65.7
|
1.0
|
|
CA
|
B:ALA247
|
4.6
|
30.3
|
1.0
|
|
H
|
B:TYR249
|
4.7
|
36.6
|
1.0
|
|
HA
|
B:GLU239
|
4.7
|
32.5
|
1.0
|
|
CD
|
A:ARG157
|
4.7
|
41.3
|
1.0
|
|
HB3
|
B:TYR246
|
4.9
|
25.7
|
1.0
|
|
N
|
B:PHE245
|
4.9
|
18.6
|
1.0
|
|
Sodium binding site 5 out
of 6 in 6r6u
Go back to
Sodium Binding Sites List in 6r6u
Sodium binding site 5 out
of 6 in the Crystal Structure of Human Cis-Aconitate Decarboxylase
 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 Human Cis-Aconitate Decarboxylase within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na505
b:32.2
occ:1.00
|
H
|
B:PHE158
|
2.1
|
22.5
|
1.0
|
|
H
|
B:ARG157
|
2.1
|
26.0
|
1.0
|
|
H
|
B:LYS156
|
2.8
|
27.5
|
1.0
|
|
O6
|
B:BU3503
|
2.8
|
46.1
|
1.0
|
|
N
|
B:PHE158
|
2.9
|
18.7
|
1.0
|
|
N
|
B:ARG157
|
2.9
|
21.6
|
1.0
|
|
HB2
|
B:ARG157
|
3.0
|
30.5
|
1.0
|
|
O
|
B:HOH691
|
3.0
|
29.1
|
1.0
|
|
H2
|
B:BU3503
|
3.1
|
52.3
|
1.0
|
|
O
|
B:HOH606
|
3.2
|
30.8
|
1.0
|
|
O
|
B:PHE158
|
3.2
|
20.3
|
1.0
|
|
N
|
B:LYS156
|
3.4
|
22.9
|
1.0
|
|
HO6
|
B:BU3503
|
3.5
|
55.3
|
1.0
|
|
CA
|
B:ARG157
|
3.6
|
21.5
|
1.0
|
|
HB2
|
B:PRO155
|
3.6
|
21.3
|
1.0
|
|
HB2
|
B:PHE158
|
3.6
|
23.7
|
1.0
|
|
HO5
|
B:BU3503
|
3.6
|
47.4
|
1.0
|
|
HA
|
B:PRO155
|
3.6
|
23.2
|
1.0
|
|
C
|
B:ARG157
|
3.7
|
18.7
|
1.0
|
|
CB
|
B:ARG157
|
3.7
|
25.4
|
1.0
|
|
C2
|
B:BU3503
|
3.7
|
43.5
|
1.0
|
|
C3
|
B:BU3503
|
3.8
|
46.0
|
1.0
|
|
HB3
|
B:PRO155
|
3.8
|
21.3
|
1.0
|
|
CA
|
B:PHE158
|
3.8
|
19.2
|
1.0
|
|
O5
|
B:BU3503
|
3.9
|
39.5
|
1.0
|
|
C
|
B:PHE158
|
4.0
|
19.5
|
1.0
|
|
C
|
B:LYS156
|
4.0
|
24.7
|
1.0
|
|
CB
|
B:PRO155
|
4.0
|
17.8
|
1.0
|
|
H41
|
B:BU3503
|
4.0
|
56.6
|
1.0
|
|
CA
|
B:PRO155
|
4.1
|
19.3
|
1.0
|
|
C
|
B:PRO155
|
4.2
|
22.0
|
1.0
|
|
CA
|
B:LYS156
|
4.2
|
27.1
|
1.0
|
|
OE2
|
B:GLU150
|
4.2
|
32.7
|
0.3
|
|
HD2
|
B:PHE158
|
4.2
|
24.2
|
1.0
|
|
CB
|
B:PHE158
|
4.2
|
19.7
|
1.0
|
|
HB2
|
B:LYS156
|
4.2
|
42.0
|
1.0
|
|
HB3
|
B:ARG157
|
4.3
|
30.5
|
1.0
|
|
C4
|
B:BU3503
|
4.4
|
47.2
|
1.0
|
|
HA
|
B:ARG157
|
4.5
|
25.9
|
1.0
|
|
HG2
|
B:ARG157
|
4.6
|
38.5
|
1.0
|
|
HG2
|
B:MET199
|
4.6
|
20.9
|
1.0
|
|
H3
|
B:BU3503
|
4.6
|
55.3
|
1.0
|
|
CD
|
B:GLU150
|
4.7
|
32.6
|
0.3
|
|
HA
|
B:PHE158
|
4.7
|
23.0
|
1.0
|
|
CB
|
B:LYS156
|
4.7
|
35.0
|
1.0
|
|
CG
|
B:ARG157
|
4.7
|
32.0
|
1.0
|
|
O
|
B:PHE245
|
4.8
|
20.8
|
1.0
|
|
H42
|
B:BU3503
|
4.9
|
56.6
|
1.0
|
|
CD2
|
B:PHE158
|
4.9
|
20.1
|
1.0
|
|
O
|
B:ARG157
|
4.9
|
18.9
|
1.0
|
|
HG3
|
B:MET199
|
4.9
|
20.9
|
1.0
|
|
OE1
|
B:GLU150
|
5.0
|
31.1
|
0.3
|
|
HB3
|
B:PHE158
|
5.0
|
23.7
|
1.0
|
|
Sodium binding site 6 out
of 6 in 6r6u
Go back to
Sodium Binding Sites List in 6r6u
Sodium binding site 6 out
of 6 in the Crystal Structure of Human Cis-Aconitate Decarboxylase
 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 Human Cis-Aconitate Decarboxylase within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na506
b:52.6
occ:1.00
|
O
|
B:HOH718
|
2.3
|
51.4
|
1.0
|
|
OE2
|
B:GLU372
|
2.5
|
30.3
|
1.0
|
|
HG2
|
B:GLU370
|
2.9
|
39.2
|
1.0
|
|
CD
|
B:GLU372
|
3.5
|
27.7
|
1.0
|
|
HG3
|
B:GLU372
|
3.5
|
29.6
|
1.0
|
|
HG22
|
B:VAL310
|
3.5
|
25.0
|
1.0
|
|
HG2
|
B:GLU372
|
3.6
|
29.6
|
1.0
|
|
O
|
B:HOH605
|
3.6
|
40.3
|
1.0
|
|
HG21
|
B:VAL310
|
3.6
|
25.0
|
1.0
|
|
CG
|
B:GLU372
|
3.8
|
24.6
|
1.0
|
|
CG
|
B:GLU370
|
3.8
|
32.6
|
1.0
|
|
O
|
B:HOH846
|
3.9
|
44.1
|
1.0
|
|
HG11
|
B:VAL310
|
4.0
|
23.9
|
1.0
|
|
CG2
|
B:VAL310
|
4.1
|
21.0
|
1.0
|
|
OE2
|
B:GLU370
|
4.1
|
26.8
|
1.0
|
|
CD
|
B:GLU370
|
4.2
|
28.7
|
1.0
|
|
HB3
|
B:GLU370
|
4.3
|
33.6
|
1.0
|
|
HG3
|
B:GLU370
|
4.3
|
39.2
|
1.0
|
|
O
|
B:HOH612
|
4.3
|
46.8
|
1.0
|
|
HG13
|
B:VAL310
|
4.6
|
23.9
|
1.0
|
|
OE1
|
B:GLU372
|
4.6
|
27.8
|
1.0
|
|
CB
|
B:GLU370
|
4.7
|
27.9
|
1.0
|
|
CG1
|
B:VAL310
|
4.7
|
20.0
|
1.0
|
|
HG23
|
B:VAL310
|
4.7
|
25.0
|
1.0
|
|
O
|
B:HOH887
|
4.9
|
38.0
|
1.0
|
|
Reference:
F.Chen,
P.Lukat,
A.A.Iqbal,
K.Saile,
V.Kaever,
J.Van Den Heuvel,
W.Blankenfeldt,
K.Bussow,
F.Pessler.
Crystal Structure Ofcis-Aconitate Decarboxylase Reveals the Impact of Naturally Occurring Human Mutations on Itaconate Synthesis. Proc.Natl.Acad.Sci.Usa V. 116 20644 2019.
ISSN: ESSN 1091-6490
PubMed: 31548418
DOI: 10.1073/PNAS.1908770116
Page generated: Tue Oct 8 13:04:20 2024
|
