Sodium in PDB 4q92: 1.90 Angstrom Resolution Crystal Structure of Apo Betaine Aldehyde Dehydrogenase (Betb) G234S Mutant From Staphylococcus Aureus (IDP00699) with Bme-Modified CYS289
Enzymatic activity of 1.90 Angstrom Resolution Crystal Structure of Apo Betaine Aldehyde Dehydrogenase (Betb) G234S Mutant From Staphylococcus Aureus (IDP00699) with Bme-Modified CYS289
All present enzymatic activity of 1.90 Angstrom Resolution Crystal Structure of Apo Betaine Aldehyde Dehydrogenase (Betb) G234S Mutant From Staphylococcus Aureus (IDP00699) with Bme-Modified CYS289:
1.2.1.8;
Protein crystallography data
The structure of 1.90 Angstrom Resolution Crystal Structure of Apo Betaine Aldehyde Dehydrogenase (Betb) G234S Mutant From Staphylococcus Aureus (IDP00699) with Bme-Modified CYS289, PDB code: 4q92
was solved by
A.S.Halavaty,
G.Minasov,
C.Chen,
J.C.Joo,
A.F.Yakunin,
W.F.Anderson,
Centerfor Structural Genomics Of Infectious Diseases (Csgid),
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
29.50 /
1.90
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
157.363,
156.438,
88.417,
90.00,
110.01,
90.00
|
R / Rfree (%)
|
19.4 /
22.3
|
Sodium Binding Sites:
The binding sites of Sodium atom in the 1.90 Angstrom Resolution Crystal Structure of Apo Betaine Aldehyde Dehydrogenase (Betb) G234S Mutant From Staphylococcus Aureus (IDP00699) with Bme-Modified CYS289
(pdb code 4q92). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the
1.90 Angstrom Resolution Crystal Structure of Apo Betaine Aldehyde Dehydrogenase (Betb) G234S Mutant From Staphylococcus Aureus (IDP00699) with Bme-Modified CYS289, PDB code: 4q92:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
6;
Sodium binding site 1 out
of 6 in 4q92
Go back to
Sodium Binding Sites List in 4q92
Sodium binding site 1 out
of 6 in the 1.90 Angstrom Resolution Crystal Structure of Apo Betaine Aldehyde Dehydrogenase (Betb) G234S Mutant From Staphylococcus Aureus (IDP00699) with Bme-Modified CYS289
![](/pictures/NA/pdb/q9/4q92-NA-sphere_01.jpg) Mono view
![](/pictures/NA/pdb/q9/4q92-NA-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of 1.90 Angstrom Resolution Crystal Structure of Apo Betaine Aldehyde Dehydrogenase (Betb) G234S Mutant From Staphylococcus Aureus (IDP00699) with Bme-Modified CYS289 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na501
b:23.0
occ:1.00
|
O
|
A:HOH956
|
2.3
|
29.6
|
1.0
|
O
|
A:HOH785
|
2.4
|
27.7
|
1.0
|
O
|
A:GLY286
|
2.5
|
16.0
|
1.0
|
O
|
A:HOH644
|
2.6
|
18.5
|
1.0
|
O
|
A:GLY393
|
2.6
|
15.9
|
1.0
|
N
|
A:GLY393
|
3.3
|
19.0
|
1.0
|
C
|
A:GLY286
|
3.4
|
17.2
|
1.0
|
CA
|
A:GLY286
|
3.6
|
16.5
|
1.0
|
C
|
A:GLY393
|
3.6
|
16.7
|
1.0
|
OE2
|
A:GLU390
|
3.6
|
19.5
|
0.5
|
CB
|
A:ALA291
|
3.7
|
23.8
|
1.0
|
C
|
A:PHE392
|
3.8
|
20.1
|
0.5
|
C
|
A:PHE392
|
3.8
|
20.2
|
0.5
|
CA
|
A:PHE392
|
3.8
|
20.7
|
0.5
|
CA
|
A:PHE392
|
3.9
|
20.9
|
0.5
|
CA
|
A:GLY393
|
4.0
|
18.1
|
1.0
|
N
|
A:PHE392
|
4.2
|
20.7
|
0.5
|
N
|
A:PHE392
|
4.2
|
20.6
|
0.5
|
O
|
A:HOH784
|
4.2
|
34.4
|
1.0
|
O
|
A:VAL395
|
4.2
|
16.6
|
1.0
|
CB
|
A:SER293
|
4.2
|
17.5
|
1.0
|
O
|
A:GLY281
|
4.5
|
15.7
|
1.0
|
N
|
A:GLN287
|
4.6
|
16.6
|
1.0
|
CD
|
A:GLU390
|
4.6
|
20.3
|
0.5
|
O
|
A:PHE392
|
4.7
|
19.9
|
0.5
|
O
|
A:PHE392
|
4.7
|
19.9
|
0.5
|
N
|
A:VAL395
|
4.8
|
17.5
|
1.0
|
O
|
A:HOH649
|
4.8
|
30.9
|
1.0
|
N
|
A:PRO394
|
4.8
|
16.2
|
1.0
|
CA
|
A:SER293
|
5.0
|
16.2
|
1.0
|
N
|
A:GLY286
|
5.0
|
17.3
|
1.0
|
|
Sodium binding site 2 out
of 6 in 4q92
Go back to
Sodium Binding Sites List in 4q92
Sodium binding site 2 out
of 6 in the 1.90 Angstrom Resolution Crystal Structure of Apo Betaine Aldehyde Dehydrogenase (Betb) G234S Mutant From Staphylococcus Aureus (IDP00699) with Bme-Modified CYS289
![](/pictures/NA/pdb/q9/4q92-NA-sphere_02.jpg) Mono view
![](/pictures/NA/pdb/q9/4q92-NA-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of 1.90 Angstrom Resolution Crystal Structure of Apo Betaine Aldehyde Dehydrogenase (Betb) G234S Mutant From Staphylococcus Aureus (IDP00699) with Bme-Modified CYS289 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na502
b:17.6
occ:1.00
|
O
|
B:HOH912
|
2.1
|
17.2
|
1.0
|
O
|
A:LYS460
|
2.3
|
17.2
|
1.0
|
O
|
B:VAL249
|
2.3
|
17.1
|
1.0
|
O
|
A:HOH690
|
2.4
|
17.4
|
1.0
|
O
|
A:GLY463
|
2.4
|
16.1
|
1.0
|
C
|
A:LYS460
|
3.3
|
17.1
|
1.0
|
C
|
B:VAL249
|
3.5
|
18.2
|
1.0
|
C
|
A:GLY463
|
3.6
|
15.9
|
1.0
|
N
|
A:LYS460
|
3.7
|
15.8
|
1.0
|
CA
|
A:LYS460
|
3.8
|
17.6
|
1.0
|
CG1
|
A:ILE464
|
4.1
|
15.0
|
1.0
|
CG1
|
B:VAL249
|
4.2
|
18.1
|
1.0
|
CB
|
B:VAL249
|
4.2
|
18.5
|
1.0
|
C
|
A:TYR459
|
4.2
|
14.4
|
1.0
|
CA
|
B:THR250
|
4.3
|
18.7
|
1.0
|
N
|
B:THR250
|
4.4
|
18.4
|
1.0
|
OD1
|
B:ASN251
|
4.4
|
16.6
|
1.0
|
N
|
A:GLY463
|
4.4
|
16.0
|
1.0
|
O
|
B:HOH644
|
4.4
|
19.2
|
1.0
|
N
|
B:ASN251
|
4.5
|
17.1
|
1.0
|
CA
|
B:VAL249
|
4.5
|
19.1
|
1.0
|
N
|
A:GLN461
|
4.5
|
16.8
|
1.0
|
O
|
A:GLY458
|
4.5
|
14.1
|
1.0
|
CA
|
A:GLY463
|
4.6
|
16.7
|
1.0
|
N
|
A:ILE464
|
4.6
|
15.5
|
1.0
|
O
|
B:HOH663
|
4.6
|
21.1
|
1.0
|
O
|
B:ASN248
|
4.6
|
21.1
|
1.0
|
O
|
A:TYR459
|
4.7
|
13.3
|
1.0
|
CA
|
A:ILE464
|
4.7
|
15.0
|
1.0
|
C
|
B:THR250
|
4.7
|
17.9
|
1.0
|
CG
|
B:ASN251
|
4.8
|
15.9
|
1.0
|
O
|
B:HOH623
|
4.9
|
18.8
|
1.0
|
CA
|
A:GLN461
|
4.9
|
16.4
|
1.0
|
CA
|
A:TYR459
|
5.0
|
13.9
|
1.0
|
|
Sodium binding site 3 out
of 6 in 4q92
Go back to
Sodium Binding Sites List in 4q92
Sodium binding site 3 out
of 6 in the 1.90 Angstrom Resolution Crystal Structure of Apo Betaine Aldehyde Dehydrogenase (Betb) G234S Mutant From Staphylococcus Aureus (IDP00699) with Bme-Modified CYS289
![](/pictures/NA/pdb/q9/4q92-NA-sphere_03.jpg) Mono view
![](/pictures/NA/pdb/q9/4q92-NA-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of 1.90 Angstrom Resolution Crystal Structure of Apo Betaine Aldehyde Dehydrogenase (Betb) G234S Mutant From Staphylococcus Aureus (IDP00699) with Bme-Modified CYS289 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na501
b:24.4
occ:1.00
|
O
|
A:HOH978
|
2.2
|
18.8
|
1.0
|
O
|
B:LYS460
|
2.3
|
22.5
|
1.0
|
O
|
A:VAL249
|
2.3
|
18.7
|
1.0
|
O
|
B:GLY463
|
2.5
|
18.8
|
1.0
|
O
|
B:HOH699
|
2.5
|
18.4
|
1.0
|
C
|
B:LYS460
|
3.3
|
21.2
|
1.0
|
C
|
A:VAL249
|
3.5
|
18.7
|
1.0
|
C
|
B:GLY463
|
3.7
|
19.1
|
1.0
|
N
|
B:LYS460
|
3.7
|
20.1
|
1.0
|
CA
|
B:LYS460
|
3.8
|
21.7
|
1.0
|
O
|
A:HOH638
|
4.0
|
16.7
|
1.0
|
CG1
|
B:ILE464
|
4.1
|
18.4
|
1.0
|
CG1
|
A:VAL249
|
4.2
|
20.0
|
1.0
|
CB
|
A:VAL249
|
4.2
|
20.0
|
1.0
|
C
|
B:TYR459
|
4.3
|
20.0
|
1.0
|
CA
|
A:THR250
|
4.3
|
17.5
|
1.0
|
O
|
B:HOH626
|
4.3
|
21.9
|
1.0
|
OD1
|
A:ASN251
|
4.3
|
22.1
|
1.0
|
N
|
A:THR250
|
4.4
|
18.1
|
1.0
|
N
|
B:GLN461
|
4.5
|
21.8
|
1.0
|
N
|
B:GLY463
|
4.5
|
20.8
|
1.0
|
N
|
A:ASN251
|
4.5
|
15.8
|
1.0
|
CA
|
A:VAL249
|
4.5
|
20.0
|
1.0
|
O
|
A:ASN248
|
4.6
|
19.5
|
1.0
|
N
|
B:ILE464
|
4.6
|
18.1
|
1.0
|
O
|
B:GLY458
|
4.6
|
19.1
|
1.0
|
CA
|
B:GLY463
|
4.6
|
20.2
|
1.0
|
O
|
B:TYR459
|
4.7
|
19.7
|
1.0
|
C
|
A:THR250
|
4.7
|
16.8
|
1.0
|
O
|
A:HOH735
|
4.7
|
22.6
|
1.0
|
CA
|
B:ILE464
|
4.8
|
17.1
|
1.0
|
CG
|
A:ASN251
|
4.8
|
18.1
|
1.0
|
CA
|
B:GLN461
|
4.8
|
21.1
|
1.0
|
CA
|
B:TYR459
|
5.0
|
19.3
|
1.0
|
|
Sodium binding site 4 out
of 6 in 4q92
Go back to
Sodium Binding Sites List in 4q92
Sodium binding site 4 out
of 6 in the 1.90 Angstrom Resolution Crystal Structure of Apo Betaine Aldehyde Dehydrogenase (Betb) G234S Mutant From Staphylococcus Aureus (IDP00699) with Bme-Modified CYS289
![](/pictures/NA/pdb/q9/4q92-NA-sphere_04.jpg) Mono view
![](/pictures/NA/pdb/q9/4q92-NA-sphere_04_stereo.jpg) Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of 1.90 Angstrom Resolution Crystal Structure of Apo Betaine Aldehyde Dehydrogenase (Betb) G234S Mutant From Staphylococcus Aureus (IDP00699) with Bme-Modified CYS289 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na501
b:14.5
occ:1.00
|
O
|
D:HOH645
|
2.3
|
14.4
|
1.0
|
O
|
C:HOH646
|
2.3
|
16.9
|
1.0
|
O
|
D:VAL249
|
2.4
|
14.6
|
1.0
|
O
|
C:GLY463
|
2.4
|
13.2
|
1.0
|
O
|
C:LYS460
|
2.4
|
15.7
|
1.0
|
C
|
C:LYS460
|
3.4
|
16.9
|
1.0
|
C
|
D:VAL249
|
3.6
|
15.0
|
1.0
|
C
|
C:GLY463
|
3.6
|
13.7
|
1.0
|
N
|
C:LYS460
|
3.8
|
17.1
|
1.0
|
CA
|
C:LYS460
|
3.9
|
17.7
|
1.0
|
CG1
|
C:ILE464
|
4.0
|
14.1
|
1.0
|
CG1
|
D:VAL249
|
4.2
|
16.0
|
1.0
|
CB
|
D:VAL249
|
4.3
|
16.3
|
1.0
|
OD1
|
D:ASN251
|
4.3
|
17.7
|
1.0
|
C
|
C:TYR459
|
4.3
|
16.9
|
1.0
|
CA
|
D:THR250
|
4.4
|
14.0
|
1.0
|
O
|
D:HOH636
|
4.4
|
17.1
|
1.0
|
N
|
C:GLY463
|
4.4
|
14.9
|
1.0
|
N
|
D:THR250
|
4.4
|
14.4
|
1.0
|
N
|
C:ILE464
|
4.5
|
13.6
|
1.0
|
O
|
D:HOH678
|
4.5
|
17.9
|
1.0
|
N
|
D:ASN251
|
4.5
|
13.5
|
1.0
|
O
|
C:GLY458
|
4.5
|
16.6
|
1.0
|
CA
|
C:GLY463
|
4.5
|
14.5
|
1.0
|
CA
|
D:VAL249
|
4.6
|
15.9
|
1.0
|
N
|
C:GLN461
|
4.6
|
17.2
|
1.0
|
CA
|
C:ILE464
|
4.6
|
13.5
|
1.0
|
O
|
C:TYR459
|
4.7
|
16.7
|
1.0
|
O
|
D:ASN248
|
4.7
|
19.7
|
1.0
|
C
|
D:THR250
|
4.8
|
13.4
|
1.0
|
CG
|
D:ASN251
|
4.8
|
13.5
|
1.0
|
ND2
|
D:ASN251
|
4.9
|
12.9
|
1.0
|
CA
|
C:GLN461
|
4.9
|
17.1
|
1.0
|
O
|
D:HOH621
|
4.9
|
14.1
|
1.0
|
|
Sodium binding site 5 out
of 6 in 4q92
Go back to
Sodium Binding Sites List in 4q92
Sodium binding site 5 out
of 6 in the 1.90 Angstrom Resolution Crystal Structure of Apo Betaine Aldehyde Dehydrogenase (Betb) G234S Mutant From Staphylococcus Aureus (IDP00699) with Bme-Modified CYS289
![](/pictures/NA/pdb/q9/4q92-NA-sphere_05.jpg) Mono view
![](/pictures/NA/pdb/q9/4q92-NA-sphere_05_stereo.jpg) Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 5 of 1.90 Angstrom Resolution Crystal Structure of Apo Betaine Aldehyde Dehydrogenase (Betb) G234S Mutant From Staphylococcus Aureus (IDP00699) with Bme-Modified CYS289 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na502
b:23.6
occ:1.00
|
O
|
C:HOH1001
|
2.1
|
20.2
|
1.0
|
O
|
C:HOH1030
|
2.3
|
23.9
|
1.0
|
O
|
C:HOH651
|
2.3
|
19.6
|
1.0
|
O
|
C:GLY393
|
2.4
|
25.1
|
1.0
|
O
|
C:GLY286
|
2.5
|
23.4
|
1.0
|
OG
|
C:SER293
|
3.0
|
21.3
|
0.5
|
C
|
C:GLY286
|
3.3
|
22.8
|
1.0
|
N
|
C:GLY393
|
3.3
|
25.3
|
1.0
|
CA
|
C:GLY286
|
3.4
|
23.9
|
1.0
|
C
|
C:GLY393
|
3.5
|
25.9
|
1.0
|
CB
|
C:ALA291
|
3.7
|
22.3
|
1.0
|
C
|
C:PHE392
|
3.9
|
25.1
|
1.0
|
CA
|
C:GLY393
|
4.0
|
26.0
|
1.0
|
CA
|
C:PHE392
|
4.0
|
24.6
|
1.0
|
OE2
|
C:GLU390
|
4.0
|
25.0
|
1.0
|
O
|
C:VAL395
|
4.1
|
23.7
|
1.0
|
O
|
C:GLY281
|
4.2
|
21.4
|
1.0
|
CB
|
C:SER293
|
4.2
|
20.4
|
0.5
|
CB
|
C:SER293
|
4.3
|
21.1
|
0.5
|
N
|
C:PHE392
|
4.4
|
24.2
|
1.0
|
N
|
C:GLN287
|
4.6
|
22.9
|
1.0
|
N
|
C:VAL395
|
4.6
|
25.3
|
1.0
|
N
|
C:PRO394
|
4.6
|
26.6
|
1.0
|
O
|
C:PHE392
|
4.8
|
26.4
|
1.0
|
N
|
C:GLY286
|
4.8
|
23.9
|
1.0
|
CA
|
C:SER293
|
4.9
|
20.8
|
0.5
|
CA
|
C:SER293
|
4.9
|
21.3
|
0.5
|
CA
|
C:PRO394
|
4.9
|
26.6
|
1.0
|
O
|
C:HOH695
|
5.0
|
22.8
|
1.0
|
CD
|
C:GLU390
|
5.0
|
23.8
|
1.0
|
|
Sodium binding site 6 out
of 6 in 4q92
Go back to
Sodium Binding Sites List in 4q92
Sodium binding site 6 out
of 6 in the 1.90 Angstrom Resolution Crystal Structure of Apo Betaine Aldehyde Dehydrogenase (Betb) G234S Mutant From Staphylococcus Aureus (IDP00699) with Bme-Modified CYS289
![](/pictures/NA/pdb/q9/4q92-NA-sphere_06.jpg) Mono view
![](/pictures/NA/pdb/q9/4q92-NA-sphere_06_stereo.jpg) Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 6 of 1.90 Angstrom Resolution Crystal Structure of Apo Betaine Aldehyde Dehydrogenase (Betb) G234S Mutant From Staphylococcus Aureus (IDP00699) with Bme-Modified CYS289 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Na501
b:14.3
occ:1.00
|
O
|
C:HOH662
|
2.2
|
15.4
|
1.0
|
O
|
C:VAL249
|
2.3
|
12.8
|
1.0
|
O
|
D:LYS460
|
2.4
|
15.7
|
1.0
|
O
|
D:GLY463
|
2.4
|
14.4
|
1.0
|
O
|
D:HOH608
|
2.4
|
13.3
|
1.0
|
C
|
D:LYS460
|
3.4
|
16.7
|
1.0
|
C
|
C:VAL249
|
3.5
|
13.9
|
1.0
|
C
|
D:GLY463
|
3.6
|
14.1
|
1.0
|
N
|
D:LYS460
|
3.7
|
15.8
|
1.0
|
CA
|
D:LYS460
|
3.9
|
17.7
|
1.0
|
CG1
|
D:ILE464
|
4.0
|
14.6
|
1.0
|
CG1
|
C:VAL249
|
4.2
|
14.0
|
1.0
|
CB
|
C:VAL249
|
4.3
|
14.1
|
1.0
|
CA
|
C:THR250
|
4.3
|
14.7
|
1.0
|
C
|
D:TYR459
|
4.3
|
16.1
|
1.0
|
OD1
|
C:ASN251
|
4.3
|
18.5
|
1.0
|
N
|
C:THR250
|
4.4
|
14.4
|
1.0
|
N
|
C:ASN251
|
4.4
|
14.6
|
1.0
|
N
|
D:GLY463
|
4.4
|
14.8
|
1.0
|
O
|
C:HOH631
|
4.4
|
20.1
|
1.0
|
O
|
C:HOH640
|
4.4
|
21.2
|
1.0
|
N
|
D:ILE464
|
4.5
|
13.8
|
1.0
|
CA
|
D:GLY463
|
4.5
|
14.6
|
1.0
|
CA
|
C:VAL249
|
4.5
|
14.3
|
1.0
|
O
|
D:GLY458
|
4.6
|
14.7
|
1.0
|
N
|
D:GLN461
|
4.6
|
17.0
|
1.0
|
CA
|
D:ILE464
|
4.6
|
13.8
|
1.0
|
C
|
C:THR250
|
4.7
|
14.9
|
1.0
|
CG
|
C:ASN251
|
4.7
|
14.0
|
1.0
|
O
|
C:ASN248
|
4.7
|
14.2
|
1.0
|
O
|
D:TYR459
|
4.7
|
15.3
|
1.0
|
ND2
|
C:ASN251
|
4.8
|
13.0
|
1.0
|
O
|
C:HOH626
|
4.9
|
12.4
|
1.0
|
CA
|
D:GLN461
|
4.9
|
17.2
|
1.0
|
O
|
C:HOH751
|
4.9
|
17.9
|
1.0
|
CD1
|
D:ILE464
|
5.0
|
15.3
|
1.0
|
CB
|
D:ILE464
|
5.0
|
14.1
|
1.0
|
|
Reference:
A.S.Halavaty,
G.Minasov,
C.Chen,
J.C.Joo,
A.F.Yakunin,
W.F.Anderson.
1.90 Angstrom Resolution Crystal Structure of Apo Betaine Aldehyde Dehydrogenase (Betb) G234S Mutant From Staphylococcus Aureus (IDP00699) with Bme-Modified CYS289 To Be Published.
Page generated: Tue Dec 15 07:05:10 2020
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