Sodium in PDB 6qap: Structure of the Human Aldehyde Dehydrogenase 9A1 in C2 Space Group
Enzymatic activity of Structure of the Human Aldehyde Dehydrogenase 9A1 in C2 Space Group
All present enzymatic activity of Structure of the Human Aldehyde Dehydrogenase 9A1 in C2 Space Group:
1.2.1.19;
1.2.1.3;
1.2.1.47;
Protein crystallography data
The structure of Structure of the Human Aldehyde Dehydrogenase 9A1 in C2 Space Group, PDB code: 6qap
was solved by
S.Morera,
A.Vigouroux,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
47.74 /
2.30
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
164.290,
160.030,
84.600,
90.00,
91.09,
90.00
|
R / Rfree (%)
|
22 /
25.1
|
Sodium Binding Sites:
The binding sites of Sodium atom in the Structure of the Human Aldehyde Dehydrogenase 9A1 in C2 Space Group
(pdb code 6qap). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the
Structure of the Human Aldehyde Dehydrogenase 9A1 in C2 Space Group, PDB code: 6qap:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Sodium binding site 1 out
of 8 in 6qap
Go back to
Sodium Binding Sites List in 6qap
Sodium binding site 1 out
of 8 in the Structure of the Human Aldehyde Dehydrogenase 9A1 in C2 Space Group
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Structure of the Human Aldehyde Dehydrogenase 9A1 in C2 Space Group within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na501
b:74.2
occ:1.00
|
O
|
C:HOH677
|
2.9
|
53.0
|
1.0
|
O
|
C:HOH678
|
3.5
|
56.1
|
1.0
|
CB
|
C:ALA155
|
4.1
|
39.3
|
1.0
|
O
|
C:HOH693
|
4.3
|
72.8
|
1.0
|
O
|
C:HOH694
|
4.4
|
59.3
|
1.0
|
OD1
|
C:ASN157
|
4.7
|
52.6
|
1.0
|
ND2
|
C:ASN157
|
4.7
|
50.2
|
1.0
|
CG
|
C:ASN157
|
4.9
|
60.4
|
1.0
|
|
Sodium binding site 2 out
of 8 in 6qap
Go back to
Sodium Binding Sites List in 6qap
Sodium binding site 2 out
of 8 in the Structure of the Human Aldehyde Dehydrogenase 9A1 in C2 Space Group
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Structure of the Human Aldehyde Dehydrogenase 9A1 in C2 Space Group within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na502
b:71.9
occ:1.00
|
NE2
|
C:GLN10
|
3.2
|
69.8
|
1.0
|
OE1
|
C:GLN10
|
3.2
|
75.8
|
1.0
|
OE2
|
C:GLU194
|
3.4
|
68.4
|
1.0
|
CD
|
C:GLN10
|
3.7
|
78.2
|
1.0
|
OE1
|
C:GLU194
|
3.9
|
65.7
|
1.0
|
CD
|
C:GLU194
|
4.0
|
75.6
|
1.0
|
O
|
C:HOH614
|
4.4
|
65.3
|
1.0
|
NE
|
C:ARG19
|
4.6
|
53.3
|
1.0
|
NH1
|
C:ARG19
|
4.8
|
56.2
|
1.0
|
CZ
|
C:ARG19
|
4.9
|
57.5
|
1.0
|
|
Sodium binding site 3 out
of 8 in 6qap
Go back to
Sodium Binding Sites List in 6qap
Sodium binding site 3 out
of 8 in the Structure of the Human Aldehyde Dehydrogenase 9A1 in C2 Space Group
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Structure of the Human Aldehyde Dehydrogenase 9A1 in C2 Space Group within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na503
b:60.5
occ:1.00
|
N
|
C:SER9
|
3.1
|
54.8
|
1.0
|
OG
|
C:SER9
|
3.3
|
68.8
|
1.0
|
OE1
|
C:GLN10
|
3.5
|
75.8
|
1.0
|
CA
|
C:VAL8
|
3.8
|
49.9
|
1.0
|
N
|
C:GLN10
|
3.8
|
52.7
|
1.0
|
C
|
C:VAL8
|
3.9
|
56.8
|
1.0
|
CA
|
C:SER9
|
4.0
|
55.3
|
1.0
|
CE1
|
C:PHE6
|
4.2
|
52.0
|
1.0
|
CB
|
C:SER9
|
4.2
|
58.4
|
1.0
|
CG
|
C:GLN10
|
4.2
|
60.5
|
1.0
|
C
|
C:SER9
|
4.2
|
58.5
|
1.0
|
CB
|
C:GLN10
|
4.3
|
53.3
|
1.0
|
CD
|
C:GLN10
|
4.3
|
78.2
|
1.0
|
CZ
|
C:PHE6
|
4.3
|
49.8
|
1.0
|
O
|
C:VAL7
|
4.3
|
56.8
|
1.0
|
CG1
|
C:VAL8
|
4.4
|
50.5
|
1.0
|
CB
|
C:VAL8
|
4.6
|
51.3
|
1.0
|
NH2
|
C:ARG19
|
4.7
|
40.6
|
1.0
|
CA
|
C:GLN10
|
4.7
|
52.4
|
1.0
|
N
|
C:VAL8
|
4.8
|
50.4
|
1.0
|
CG2
|
C:VAL8
|
4.9
|
50.1
|
1.0
|
|
Sodium binding site 4 out
of 8 in 6qap
Go back to
Sodium Binding Sites List in 6qap
Sodium binding site 4 out
of 8 in the Structure of the Human Aldehyde Dehydrogenase 9A1 in C2 Space Group
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of Structure of the Human Aldehyde Dehydrogenase 9A1 in C2 Space Group within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Na501
b:47.5
occ:1.00
|
O2
|
D:EDO507
|
2.5
|
53.6
|
1.0
|
OD1
|
D:ASN207
|
2.7
|
51.9
|
1.0
|
N
|
D:GLY17
|
2.9
|
42.4
|
1.0
|
N
|
D:GLY204
|
3.0
|
38.2
|
1.0
|
N
|
D:GLY16
|
3.2
|
44.8
|
1.0
|
C1
|
D:EDO507
|
3.3
|
51.9
|
1.0
|
C2
|
D:EDO507
|
3.3
|
51.7
|
1.0
|
CE1
|
D:TYR14
|
3.4
|
44.5
|
1.0
|
CA
|
D:GLY204
|
3.5
|
36.6
|
1.0
|
O
|
D:PHE206
|
3.5
|
40.0
|
1.0
|
CD1
|
D:TYR14
|
3.5
|
42.1
|
1.0
|
C
|
D:ARG15
|
3.7
|
46.1
|
1.0
|
CA
|
D:GLY17
|
3.8
|
42.7
|
1.0
|
CA
|
D:GLY16
|
3.8
|
45.2
|
1.0
|
C
|
D:GLY16
|
3.9
|
48.3
|
1.0
|
CA
|
D:ARG15
|
3.9
|
40.0
|
1.0
|
CG
|
D:ASN207
|
3.9
|
58.0
|
1.0
|
C
|
D:GLY204
|
4.0
|
39.2
|
1.0
|
C
|
D:PRO203
|
4.1
|
46.5
|
1.0
|
C
|
D:PHE206
|
4.2
|
40.4
|
1.0
|
N
|
D:ARG15
|
4.3
|
39.5
|
1.0
|
OD1
|
D:ASN57
|
4.3
|
37.0
|
1.0
|
N
|
D:LEU205
|
4.4
|
38.3
|
1.0
|
CA
|
D:PRO203
|
4.4
|
45.1
|
1.0
|
O
|
D:ARG15
|
4.5
|
46.2
|
1.0
|
O
|
D:HOH603
|
4.5
|
35.1
|
1.0
|
N
|
D:PHE206
|
4.6
|
37.8
|
1.0
|
CA
|
D:ASN207
|
4.6
|
38.9
|
1.0
|
O
|
D:GLY204
|
4.6
|
38.2
|
1.0
|
N
|
D:ASN207
|
4.6
|
37.8
|
1.0
|
CZ
|
D:TYR14
|
4.7
|
51.4
|
1.0
|
O
|
D:TYR14
|
4.7
|
38.5
|
1.0
|
C
|
D:TYR14
|
4.7
|
40.3
|
1.0
|
O1
|
D:EDO507
|
4.7
|
48.2
|
1.0
|
ND2
|
D:ASN207
|
4.8
|
39.6
|
1.0
|
CG
|
D:TYR14
|
4.8
|
40.7
|
1.0
|
C
|
D:GLY17
|
4.8
|
46.3
|
1.0
|
CB
|
D:ASN207
|
4.9
|
43.6
|
1.0
|
N
|
D:ALA18
|
4.9
|
43.9
|
1.0
|
|
Sodium binding site 5 out
of 8 in 6qap
Go back to
Sodium Binding Sites List in 6qap
Sodium binding site 5 out
of 8 in the Structure of the Human Aldehyde Dehydrogenase 9A1 in C2 Space Group
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 5 of Structure of the Human Aldehyde Dehydrogenase 9A1 in C2 Space Group within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Na502
b:65.3
occ:1.00
|
OE1
|
D:GLU118
|
3.2
|
50.2
|
1.0
|
CB
|
D:GLU118
|
3.4
|
41.4
|
1.0
|
C2
|
D:EDO506
|
3.5
|
46.9
|
1.0
|
O
|
D:GLN115
|
3.7
|
45.9
|
1.0
|
SG
|
A:CYS74
|
3.9
|
44.5
|
1.0
|
CD
|
D:GLU118
|
4.1
|
63.0
|
1.0
|
O
|
D:HOH650
|
4.1
|
43.6
|
1.0
|
O2
|
D:EDO506
|
4.2
|
46.9
|
1.0
|
N
|
D:TYR119
|
4.2
|
36.8
|
1.0
|
CG
|
D:GLU118
|
4.3
|
45.4
|
1.0
|
CB
|
A:ALA125
|
4.3
|
47.3
|
1.0
|
C
|
D:GLU118
|
4.5
|
42.4
|
1.0
|
CA
|
D:GLU118
|
4.5
|
38.6
|
1.0
|
CA
|
D:GLN115
|
4.5
|
41.1
|
1.0
|
SD
|
A:MET71
|
4.5
|
71.1
|
1.0
|
C
|
D:GLN115
|
4.5
|
44.7
|
1.0
|
O
|
A:HOH629
|
4.6
|
44.2
|
1.0
|
C1
|
D:EDO506
|
4.7
|
48.5
|
1.0
|
CG
|
D:GLN115
|
4.9
|
50.4
|
1.0
|
CA
|
D:TYR119
|
4.9
|
35.7
|
1.0
|
CD1
|
A:LEU78
|
4.9
|
53.4
|
1.0
|
|
Sodium binding site 6 out
of 8 in 6qap
Go back to
Sodium Binding Sites List in 6qap
Sodium binding site 6 out
of 8 in the Structure of the Human Aldehyde Dehydrogenase 9A1 in C2 Space Group
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 6 of Structure of the Human Aldehyde Dehydrogenase 9A1 in C2 Space Group within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Na503
b:48.4
occ:1.00
|
O
|
D:ALA155
|
2.8
|
43.9
|
1.0
|
N
|
D:SER182
|
3.0
|
35.2
|
1.0
|
OG1
|
D:THR185
|
3.4
|
36.7
|
1.0
|
N
|
D:ALA155
|
3.6
|
35.6
|
1.0
|
CA
|
D:PRO181
|
3.6
|
30.4
|
1.0
|
C
|
D:ALA155
|
3.6
|
42.6
|
1.0
|
CB
|
D:PRO181
|
3.7
|
31.4
|
1.0
|
CB
|
D:SER182
|
3.8
|
37.1
|
1.0
|
CA
|
D:GLY154
|
3.8
|
34.7
|
1.0
|
C
|
D:PRO181
|
3.8
|
38.0
|
1.0
|
C
|
D:GLY154
|
3.8
|
36.7
|
1.0
|
O
|
D:THR185
|
3.9
|
41.6
|
1.0
|
CA
|
D:PRO159
|
3.9
|
39.6
|
1.0
|
CA
|
D:SER182
|
4.0
|
34.4
|
1.0
|
CB
|
D:PRO159
|
4.1
|
40.8
|
1.0
|
O
|
D:HOH621
|
4.2
|
34.8
|
1.0
|
CA
|
D:ALA155
|
4.2
|
36.3
|
1.0
|
O
|
D:PRO159
|
4.4
|
36.0
|
1.0
|
N
|
D:TRP156
|
4.5
|
39.2
|
1.0
|
O
|
D:SER182
|
4.6
|
37.0
|
1.0
|
CB
|
D:THR185
|
4.6
|
35.1
|
1.0
|
CE2
|
D:PHE179
|
4.6
|
35.9
|
1.0
|
CZ
|
D:PHE179
|
4.6
|
34.0
|
1.0
|
O
|
D:GLY154
|
4.6
|
36.1
|
1.0
|
C
|
D:PRO159
|
4.6
|
39.7
|
1.0
|
CG
|
D:PRO159
|
4.7
|
46.6
|
1.0
|
CA
|
D:TRP156
|
4.7
|
39.4
|
1.0
|
C
|
D:THR185
|
4.8
|
42.4
|
1.0
|
C
|
D:SER182
|
4.8
|
36.6
|
1.0
|
N
|
D:PRO159
|
5.0
|
41.5
|
1.0
|
N
|
D:PRO181
|
5.0
|
31.2
|
1.0
|
|
Sodium binding site 7 out
of 8 in 6qap
Go back to
Sodium Binding Sites List in 6qap
Sodium binding site 7 out
of 8 in the Structure of the Human Aldehyde Dehydrogenase 9A1 in C2 Space Group
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 7 of Structure of the Human Aldehyde Dehydrogenase 9A1 in C2 Space Group within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Na504
b:56.0
occ:1.00
|
N
|
D:SER9
|
3.1
|
50.7
|
1.0
|
OE1
|
D:GLN10
|
3.4
|
78.3
|
1.0
|
OG
|
D:SER9
|
3.5
|
64.6
|
1.0
|
N
|
D:GLN10
|
3.7
|
52.4
|
1.0
|
CA
|
D:VAL8
|
3.8
|
45.5
|
1.0
|
C
|
D:VAL8
|
3.9
|
52.5
|
1.0
|
CA
|
D:SER9
|
4.0
|
51.8
|
1.0
|
CB
|
D:GLN10
|
4.1
|
52.6
|
1.0
|
CG
|
D:GLN10
|
4.1
|
62.6
|
1.0
|
CD
|
D:GLN10
|
4.2
|
81.2
|
1.0
|
C
|
D:SER9
|
4.2
|
57.5
|
1.0
|
CG1
|
D:VAL8
|
4.3
|
46.7
|
1.0
|
CE1
|
D:PHE6
|
4.3
|
52.6
|
1.0
|
CZ
|
D:PHE6
|
4.3
|
51.4
|
1.0
|
CB
|
D:SER9
|
4.3
|
55.0
|
1.0
|
NH2
|
D:ARG19
|
4.4
|
45.4
|
1.0
|
O
|
D:VAL7
|
4.4
|
54.7
|
1.0
|
CB
|
D:VAL8
|
4.5
|
47.2
|
1.0
|
CA
|
D:GLN10
|
4.5
|
51.9
|
1.0
|
CG2
|
D:VAL8
|
4.8
|
45.5
|
1.0
|
N
|
D:VAL8
|
4.9
|
46.0
|
1.0
|
CZ
|
D:ARG19
|
5.0
|
63.1
|
1.0
|
|
Sodium binding site 8 out
of 8 in 6qap
Go back to
Sodium Binding Sites List in 6qap
Sodium binding site 8 out
of 8 in the Structure of the Human Aldehyde Dehydrogenase 9A1 in C2 Space Group
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 8 of Structure of the Human Aldehyde Dehydrogenase 9A1 in C2 Space Group within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Na505
b:72.2
occ:1.00
|
OE1
|
D:GLN10
|
3.5
|
78.3
|
1.0
|
OE2
|
D:GLU194
|
3.6
|
67.7
|
1.0
|
NE2
|
D:GLN10
|
3.7
|
71.3
|
1.0
|
OE1
|
D:GLU194
|
3.8
|
64.1
|
1.0
|
CD
|
D:GLU194
|
4.0
|
76.2
|
1.0
|
CD
|
D:GLN10
|
4.0
|
81.2
|
1.0
|
O
|
D:HOH633
|
4.3
|
63.3
|
1.0
|
NE
|
D:ARG19
|
4.8
|
55.6
|
1.0
|
NH1
|
D:ARG19
|
4.9
|
57.0
|
1.0
|
|
Reference:
R.Koncitikova,
A.Vigouroux,
M.Kopecna,
M.Sebela,
S.Morera,
D.Kopecny.
Kinetic and Structural Analysis of Human ALDH9A1. Biosci.Rep. V. 39 2019.
ISSN: ISSN 0144-8463
PubMed: 30914451
DOI: 10.1042/BSR20190558
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