Sodium in PDB 8qzb: D-2-Hydroxyacid Dehydrogenase (D2HDH) From Haloferax Mediterranei in Complex with 2-Ketohexanoic Acid, Nad+ and Chloride (1.16 A Resolution)
Protein crystallography data
The structure of D-2-Hydroxyacid Dehydrogenase (D2HDH) From Haloferax Mediterranei in Complex with 2-Ketohexanoic Acid, Nad+ and Chloride (1.16 A Resolution), PDB code: 8qzb
was solved by
P.J.Baker,
J.R.Barrett,
A.A.A.B.Dakhil,
J.Domenech,
C.Bisson,
N.Pramanpol,
J.Ferrer,
D.W.Rice,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
46.63 /
1.16
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
66.182,
74.777,
78.172,
109.07,
107.88,
95.56
|
R / Rfree (%)
|
13.5 /
16.5
|
Other elements in 8qzb:
The structure of D-2-Hydroxyacid Dehydrogenase (D2HDH) From Haloferax Mediterranei in Complex with 2-Ketohexanoic Acid, Nad+ and Chloride (1.16 A Resolution) also contains other interesting chemical elements:
Sodium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
12;
Binding sites:
The binding sites of Sodium atom in the D-2-Hydroxyacid Dehydrogenase (D2HDH) From Haloferax Mediterranei in Complex with 2-Ketohexanoic Acid, Nad+ and Chloride (1.16 A Resolution)
(pdb code 8qzb). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 12 binding sites of Sodium where determined in the
D-2-Hydroxyacid Dehydrogenase (D2HDH) From Haloferax Mediterranei in Complex with 2-Ketohexanoic Acid, Nad+ and Chloride (1.16 A Resolution), PDB code: 8qzb:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Sodium binding site 1 out
of 12 in 8qzb
Go back to
Sodium Binding Sites List in 8qzb
Sodium binding site 1 out
of 12 in the D-2-Hydroxyacid Dehydrogenase (D2HDH) From Haloferax Mediterranei in Complex with 2-Ketohexanoic Acid, Nad+ and Chloride (1.16 A Resolution)
 Mono view
 Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of D-2-Hydroxyacid Dehydrogenase (D2HDH) From Haloferax Mediterranei in Complex with 2-Ketohexanoic Acid, Nad+ and Chloride (1.16 A Resolution) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na409
b:11.2
occ:1.00
|
O
|
A:MET215
|
2.2
|
10.5
|
1.0
|
O
|
A:PHE212
|
2.3
|
10.8
|
1.0
|
O
|
A:HOH761
|
2.3
|
20.9
|
1.0
|
O
|
A:ASP243
|
2.4
|
10.7
|
1.0
|
O
|
A:GLU213
|
2.7
|
11.3
|
1.0
|
C
|
A:GLU213
|
3.3
|
10.9
|
1.0
|
C
|
A:MET215
|
3.3
|
10.3
|
1.0
|
C
|
A:ASP243
|
3.4
|
9.9
|
1.0
|
C
|
A:PHE212
|
3.5
|
9.7
|
1.0
|
CA
|
A:GLU213
|
3.6
|
10.9
|
1.0
|
O
|
A:HOH748
|
3.8
|
34.6
|
1.0
|
CA
|
A:ASP243
|
3.9
|
10.8
|
1.0
|
N
|
A:MET215
|
3.9
|
9.8
|
1.0
|
CB
|
A:ASP243
|
4.0
|
11.7
|
1.0
|
N
|
A:GLU213
|
4.0
|
10.2
|
1.0
|
CA
|
A:MET215
|
4.1
|
10.0
|
1.0
|
C
|
A:ARG216
|
4.2
|
9.8
|
1.0
|
CG
|
A:GLU217
|
4.2
|
20.0
|
1.0
|
C
|
A:THR214
|
4.3
|
10.1
|
1.0
|
N
|
A:THR214
|
4.3
|
9.4
|
1.0
|
N
|
A:GLU217
|
4.3
|
10.9
|
1.0
|
O
|
A:ARG216
|
4.4
|
9.8
|
1.0
|
N
|
A:ARG216
|
4.4
|
9.8
|
1.0
|
CB
|
A:MET215
|
4.4
|
8.8
|
1.0
|
CG2
|
A:ILE244
|
4.4
|
11.3
|
1.0
|
N
|
A:ILE244
|
4.5
|
10.0
|
1.0
|
CA
|
A:ARG216
|
4.6
|
11.5
|
1.0
|
CA
|
A:GLU217
|
4.7
|
13.2
|
1.0
|
O
|
A:THR214
|
4.7
|
11.2
|
1.0
|
OE1
|
A:GLU213
|
4.7
|
34.9
|
1.0
|
CA
|
A:PHE212
|
4.7
|
10.1
|
1.0
|
CG
|
A:ASP243
|
4.7
|
19.0
|
1.0
|
CA
|
A:THR214
|
4.9
|
10.4
|
1.0
|
OD1
|
A:ASP243
|
5.0
|
24.8
|
1.0
|
|
Sodium binding site 2 out
of 12 in 8qzb
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Sodium Binding Sites List in 8qzb
Sodium binding site 2 out
of 12 in the D-2-Hydroxyacid Dehydrogenase (D2HDH) From Haloferax Mediterranei in Complex with 2-Ketohexanoic Acid, Nad+ and Chloride (1.16 A Resolution)
 Mono view
 Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of D-2-Hydroxyacid Dehydrogenase (D2HDH) From Haloferax Mediterranei in Complex with 2-Ketohexanoic Acid, Nad+ and Chloride (1.16 A Resolution) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na410
b:22.2
occ:1.00
|
O
|
A:HOH662
|
2.0
|
29.6
|
1.0
|
OG1
|
A:THR132
|
2.1
|
11.0
|
1.0
|
O
|
A:HOH742
|
2.1
|
32.4
|
1.0
|
O
|
A:HOH777
|
2.2
|
38.3
|
1.0
|
O
|
A:ALA134
|
2.2
|
10.5
|
1.0
|
O
|
A:THR132
|
2.6
|
8.9
|
1.0
|
O
|
A:HOH844
|
3.3
|
23.5
|
1.0
|
C
|
A:THR132
|
3.3
|
7.8
|
1.0
|
CB
|
A:THR132
|
3.4
|
9.2
|
1.0
|
C
|
A:ALA134
|
3.4
|
9.3
|
1.0
|
CA
|
A:THR132
|
3.6
|
8.1
|
1.0
|
N
|
A:THR132
|
3.7
|
7.6
|
1.0
|
O
|
A:HOH677
|
3.9
|
18.3
|
1.0
|
N
|
A:ALA134
|
4.2
|
8.1
|
1.0
|
CG
|
A:GLU136
|
4.2
|
10.8
|
1.0
|
OE2
|
A:GLU136
|
4.3
|
19.3
|
1.0
|
CA
|
A:ALA134
|
4.3
|
8.4
|
1.0
|
O
|
A:HOH855
|
4.3
|
21.5
|
1.0
|
C
|
A:LEU133
|
4.4
|
7.7
|
1.0
|
N
|
A:GLY135
|
4.4
|
10.2
|
1.0
|
N
|
A:LEU133
|
4.4
|
7.2
|
1.0
|
CG2
|
A:THR132
|
4.4
|
12.7
|
1.0
|
CA
|
A:GLY135
|
4.6
|
11.1
|
1.0
|
CB
|
A:ALA134
|
4.6
|
9.7
|
1.0
|
N
|
A:GLU136
|
4.7
|
8.9
|
1.0
|
O
|
A:LEU133
|
4.7
|
8.2
|
1.0
|
C
|
A:GLY135
|
4.8
|
11.3
|
1.0
|
CD
|
A:GLU136
|
4.8
|
13.7
|
1.0
|
CA
|
A:LEU133
|
4.9
|
7.4
|
1.0
|
|
Sodium binding site 3 out
of 12 in 8qzb
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Sodium Binding Sites List in 8qzb
Sodium binding site 3 out
of 12 in the D-2-Hydroxyacid Dehydrogenase (D2HDH) From Haloferax Mediterranei in Complex with 2-Ketohexanoic Acid, Nad+ and Chloride (1.16 A Resolution)
 Mono view
 Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of D-2-Hydroxyacid Dehydrogenase (D2HDH) From Haloferax Mediterranei in Complex with 2-Ketohexanoic Acid, Nad+ and Chloride (1.16 A Resolution) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na411
b:31.3
occ:1.00
|
OG1
|
A:THR88
|
2.4
|
17.8
|
0.5
|
O
|
A:HOH833
|
2.4
|
40.2
|
1.0
|
O2A
|
A:NAD401
|
2.5
|
15.8
|
1.0
|
OG1
|
A:THR145
|
2.5
|
16.2
|
1.0
|
CB
|
A:THR145
|
3.6
|
11.7
|
1.0
|
CB
|
A:THR88
|
3.7
|
15.5
|
0.5
|
PA
|
A:NAD401
|
3.7
|
15.4
|
1.0
|
CB
|
A:THR88
|
3.7
|
17.1
|
0.5
|
N
|
A:GLY89
|
3.8
|
11.0
|
1.0
|
CG2
|
A:THR88
|
3.9
|
15.7
|
0.5
|
N
|
A:THR145
|
3.9
|
10.1
|
1.0
|
OG1
|
A:THR88
|
4.0
|
20.9
|
0.5
|
O1A
|
A:NAD401
|
4.1
|
16.7
|
1.0
|
CA
|
A:GLY89
|
4.1
|
11.9
|
1.0
|
O
|
A:HOH643
|
4.1
|
38.2
|
1.0
|
C
|
A:THR88
|
4.2
|
12.7
|
1.0
|
O1N
|
A:NAD401
|
4.2
|
13.7
|
1.0
|
O3
|
A:NAD401
|
4.3
|
14.6
|
1.0
|
CA
|
A:THR145
|
4.3
|
10.5
|
1.0
|
O
|
A:HOH815
|
4.5
|
35.2
|
1.0
|
CA
|
A:THR88
|
4.5
|
13.7
|
0.5
|
CA
|
A:THR88
|
4.5
|
14.0
|
0.5
|
O
|
A:HOH544
|
4.7
|
32.9
|
1.0
|
CG2
|
A:THR88
|
4.7
|
16.2
|
0.5
|
PN
|
A:NAD401
|
4.7
|
12.1
|
1.0
|
CG2
|
A:THR145
|
4.8
|
11.7
|
1.0
|
O
|
A:THR88
|
4.8
|
15.1
|
1.0
|
C
|
A:GLY144
|
4.9
|
10.7
|
1.0
|
O5B
|
A:NAD401
|
4.9
|
15.5
|
1.0
|
|
Sodium binding site 4 out
of 12 in 8qzb
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Sodium Binding Sites List in 8qzb
Sodium binding site 4 out
of 12 in the D-2-Hydroxyacid Dehydrogenase (D2HDH) From Haloferax Mediterranei in Complex with 2-Ketohexanoic Acid, Nad+ and Chloride (1.16 A Resolution)
 Mono view
 Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of D-2-Hydroxyacid Dehydrogenase (D2HDH) From Haloferax Mediterranei in Complex with 2-Ketohexanoic Acid, Nad+ and Chloride (1.16 A Resolution) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na410
b:11.6
occ:1.00
|
O
|
B:MET215
|
2.2
|
10.9
|
1.0
|
O
|
B:PHE212
|
2.3
|
12.1
|
1.0
|
O
|
B:ASP243
|
2.3
|
10.6
|
1.0
|
O
|
B:HOH810
|
2.3
|
21.9
|
1.0
|
O
|
B:HOH805
|
2.6
|
43.5
|
1.0
|
O
|
B:GLU213
|
2.8
|
12.4
|
1.0
|
C
|
B:GLU213
|
3.4
|
10.4
|
1.0
|
C
|
B:ASP243
|
3.4
|
9.7
|
1.0
|
C
|
B:MET215
|
3.4
|
10.1
|
1.0
|
C
|
B:PHE212
|
3.5
|
9.5
|
1.0
|
CA
|
B:GLU213
|
3.6
|
10.3
|
1.0
|
CA
|
B:ASP243
|
3.8
|
10.7
|
1.0
|
O
|
B:HOH765
|
3.9
|
31.6
|
1.0
|
N
|
B:MET215
|
3.9
|
9.4
|
1.0
|
CB
|
B:ASP243
|
4.0
|
13.6
|
1.0
|
N
|
B:GLU213
|
4.0
|
9.7
|
1.0
|
CA
|
B:MET215
|
4.1
|
9.7
|
1.0
|
C
|
B:ARG216
|
4.2
|
10.4
|
1.0
|
C
|
B:THR214
|
4.3
|
10.3
|
1.0
|
CG
|
B:GLU217
|
4.3
|
24.8
|
1.0
|
N
|
B:GLU217
|
4.3
|
11.4
|
1.0
|
N
|
B:THR214
|
4.3
|
9.6
|
1.0
|
CB
|
B:MET215
|
4.4
|
9.7
|
1.0
|
O
|
B:ARG216
|
4.4
|
10.1
|
1.0
|
N
|
B:ARG216
|
4.4
|
10.2
|
1.0
|
CG2
|
B:ILE244
|
4.5
|
11.2
|
1.0
|
N
|
B:ILE244
|
4.5
|
10.0
|
1.0
|
CA
|
B:GLU217
|
4.6
|
12.2
|
1.0
|
CA
|
B:ARG216
|
4.7
|
10.8
|
1.0
|
O
|
B:THR214
|
4.7
|
11.3
|
1.0
|
CA
|
B:PHE212
|
4.7
|
9.9
|
1.0
|
CG
|
B:ASP243
|
4.7
|
21.2
|
1.0
|
OE1
|
B:GLU213
|
4.8
|
38.4
|
1.0
|
CA
|
B:THR214
|
4.9
|
10.2
|
1.0
|
OD1
|
B:ASP243
|
4.9
|
26.9
|
1.0
|
CD
|
B:GLU213
|
4.9
|
28.4
|
1.0
|
|
Sodium binding site 5 out
of 12 in 8qzb
Go back to
Sodium Binding Sites List in 8qzb
Sodium binding site 5 out
of 12 in the D-2-Hydroxyacid Dehydrogenase (D2HDH) From Haloferax Mediterranei in Complex with 2-Ketohexanoic Acid, Nad+ and Chloride (1.16 A Resolution)
 Mono view
 Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 5 of D-2-Hydroxyacid Dehydrogenase (D2HDH) From Haloferax Mediterranei in Complex with 2-Ketohexanoic Acid, Nad+ and Chloride (1.16 A Resolution) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na411
b:29.1
occ:1.00
|
O
|
B:HOH570
|
1.8
|
15.5
|
1.0
|
O
|
B:HOH707
|
2.1
|
28.3
|
1.0
|
OG1
|
B:THR132
|
2.2
|
10.9
|
1.0
|
O
|
B:ALA134
|
2.3
|
10.1
|
1.0
|
O
|
B:THR132
|
2.6
|
8.8
|
1.0
|
O
|
B:HOH880
|
3.1
|
16.2
|
1.0
|
C
|
B:THR132
|
3.4
|
7.6
|
1.0
|
CB
|
B:THR132
|
3.5
|
8.8
|
1.0
|
C
|
B:ALA134
|
3.5
|
8.6
|
1.0
|
CA
|
B:THR132
|
3.7
|
7.5
|
1.0
|
N
|
B:THR132
|
3.7
|
8.1
|
1.0
|
OE2
|
B:GLU136
|
4.0
|
15.8
|
1.0
|
CG
|
B:GLU136
|
4.0
|
10.7
|
1.0
|
O
|
B:HOH711
|
4.1
|
19.9
|
1.0
|
O
|
B:HOH893
|
4.2
|
16.4
|
1.0
|
N
|
B:ALA134
|
4.3
|
7.5
|
1.0
|
O
|
B:HOH933
|
4.3
|
57.8
|
1.0
|
C
|
B:LEU133
|
4.4
|
7.9
|
1.0
|
N
|
B:GLY135
|
4.4
|
8.6
|
1.0
|
CA
|
B:ALA134
|
4.4
|
8.5
|
1.0
|
CA
|
B:GLY135
|
4.5
|
10.3
|
1.0
|
CG2
|
B:THR132
|
4.5
|
11.8
|
1.0
|
N
|
B:LEU133
|
4.5
|
7.7
|
1.0
|
CD
|
B:GLU136
|
4.5
|
12.3
|
1.0
|
N
|
B:GLU136
|
4.6
|
9.0
|
1.0
|
C
|
B:GLY135
|
4.7
|
9.7
|
1.0
|
O
|
B:LEU133
|
4.7
|
8.1
|
1.0
|
CB
|
B:ALA134
|
4.8
|
10.0
|
1.0
|
O
|
B:HOH622
|
4.9
|
36.1
|
1.0
|
CA
|
B:LEU133
|
4.9
|
8.3
|
1.0
|
O
|
A:HOH626
|
4.9
|
10.7
|
1.0
|
|
Sodium binding site 6 out
of 12 in 8qzb
Go back to
Sodium Binding Sites List in 8qzb
Sodium binding site 6 out
of 12 in the D-2-Hydroxyacid Dehydrogenase (D2HDH) From Haloferax Mediterranei in Complex with 2-Ketohexanoic Acid, Nad+ and Chloride (1.16 A Resolution)
 Mono view
 Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 6 of D-2-Hydroxyacid Dehydrogenase (D2HDH) From Haloferax Mediterranei in Complex with 2-Ketohexanoic Acid, Nad+ and Chloride (1.16 A Resolution) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na412
b:21.6
occ:1.00
|
O
|
B:HOH878
|
2.3
|
43.5
|
1.0
|
OG1
|
B:THR88
|
2.4
|
11.4
|
0.5
|
OG1
|
B:THR145
|
2.5
|
12.7
|
1.0
|
O2A
|
B:NAD401
|
2.6
|
10.9
|
1.0
|
O
|
B:HOH753
|
3.0
|
37.3
|
1.0
|
O
|
B:HOH691
|
3.4
|
39.7
|
1.0
|
CB
|
B:THR145
|
3.6
|
10.5
|
1.0
|
CB
|
B:THR88
|
3.6
|
10.4
|
0.5
|
CB
|
B:THR88
|
3.6
|
10.6
|
0.5
|
CG2
|
B:THR88
|
3.7
|
10.4
|
0.5
|
PA
|
B:NAD401
|
3.8
|
10.1
|
1.0
|
N
|
B:GLY89
|
3.8
|
8.9
|
1.0
|
N
|
B:THR145
|
3.9
|
7.9
|
1.0
|
O1N
|
B:NAD401
|
4.0
|
9.1
|
1.0
|
OG1
|
B:THR88
|
4.0
|
14.6
|
0.5
|
CA
|
B:GLY89
|
4.1
|
8.4
|
1.0
|
C
|
B:THR88
|
4.2
|
9.0
|
1.0
|
O1A
|
B:NAD401
|
4.2
|
11.1
|
1.0
|
CA
|
B:THR145
|
4.3
|
8.7
|
1.0
|
O3
|
B:NAD401
|
4.4
|
10.1
|
1.0
|
CA
|
B:THR88
|
4.4
|
9.3
|
0.5
|
CA
|
B:THR88
|
4.5
|
9.5
|
0.5
|
CG2
|
B:THR88
|
4.5
|
10.8
|
0.5
|
O
|
B:HOH672
|
4.5
|
26.3
|
1.0
|
O
|
B:HOH840
|
4.5
|
34.1
|
1.0
|
PN
|
B:NAD401
|
4.6
|
8.7
|
1.0
|
O
|
B:HOH519
|
4.8
|
34.6
|
1.0
|
CG2
|
B:THR145
|
4.8
|
10.0
|
1.0
|
O
|
B:THR88
|
4.8
|
11.4
|
1.0
|
O
|
B:HOH701
|
4.9
|
9.3
|
1.0
|
C
|
B:GLY144
|
5.0
|
7.8
|
1.0
|
|
Sodium binding site 7 out
of 12 in 8qzb
Go back to
Sodium Binding Sites List in 8qzb
Sodium binding site 7 out
of 12 in the D-2-Hydroxyacid Dehydrogenase (D2HDH) From Haloferax Mediterranei in Complex with 2-Ketohexanoic Acid, Nad+ and Chloride (1.16 A Resolution)
 Mono view
 Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 7 of D-2-Hydroxyacid Dehydrogenase (D2HDH) From Haloferax Mediterranei in Complex with 2-Ketohexanoic Acid, Nad+ and Chloride (1.16 A Resolution) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na410
b:11.7
occ:1.00
|
O
|
C:MET215
|
2.2
|
11.5
|
1.0
|
O
|
C:HOH801
|
2.3
|
21.7
|
1.0
|
O
|
C:PHE212
|
2.3
|
10.8
|
1.0
|
O
|
C:ASP243
|
2.4
|
10.4
|
1.0
|
O
|
C:GLU213
|
2.7
|
12.3
|
1.0
|
C
|
C:GLU213
|
3.3
|
10.2
|
1.0
|
C
|
C:MET215
|
3.4
|
10.4
|
1.0
|
C
|
C:ASP243
|
3.4
|
10.0
|
1.0
|
C
|
C:PHE212
|
3.5
|
10.1
|
1.0
|
CA
|
C:GLU213
|
3.6
|
10.6
|
1.0
|
CA
|
C:ASP243
|
3.8
|
11.3
|
1.0
|
O
|
C:HOH751
|
3.8
|
34.4
|
1.0
|
N
|
C:MET215
|
3.9
|
9.6
|
1.0
|
CB
|
C:ASP243
|
3.9
|
12.5
|
1.0
|
N
|
C:GLU213
|
4.0
|
10.6
|
1.0
|
CA
|
C:MET215
|
4.1
|
10.1
|
1.0
|
CG
|
C:GLU217
|
4.2
|
22.2
|
1.0
|
C
|
C:ARG216
|
4.2
|
9.8
|
1.0
|
C
|
C:THR214
|
4.3
|
9.3
|
1.0
|
N
|
C:THR214
|
4.3
|
9.7
|
1.0
|
N
|
C:GLU217
|
4.4
|
11.2
|
1.0
|
O
|
C:ARG216
|
4.4
|
10.3
|
1.0
|
CB
|
C:MET215
|
4.4
|
8.9
|
1.0
|
N
|
C:ARG216
|
4.4
|
9.8
|
1.0
|
CG2
|
C:ILE244
|
4.4
|
10.6
|
1.0
|
N
|
C:ILE244
|
4.5
|
10.2
|
1.0
|
CA
|
C:ARG216
|
4.7
|
11.0
|
1.0
|
O
|
C:THR214
|
4.7
|
12.2
|
1.0
|
CA
|
C:GLU217
|
4.7
|
13.2
|
1.0
|
CG
|
C:ASP243
|
4.7
|
21.9
|
1.0
|
CA
|
C:PHE212
|
4.7
|
9.8
|
1.0
|
CA
|
C:THR214
|
4.8
|
10.7
|
1.0
|
OD1
|
C:ASP243
|
4.9
|
24.8
|
1.0
|
OE2
|
C:GLU217
|
4.9
|
44.5
|
1.0
|
OE1
|
C:GLU213
|
4.9
|
45.2
|
1.0
|
|
Sodium binding site 8 out
of 12 in 8qzb
Go back to
Sodium Binding Sites List in 8qzb
Sodium binding site 8 out
of 12 in the D-2-Hydroxyacid Dehydrogenase (D2HDH) From Haloferax Mediterranei in Complex with 2-Ketohexanoic Acid, Nad+ and Chloride (1.16 A Resolution)
 Mono view
 Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 8 of D-2-Hydroxyacid Dehydrogenase (D2HDH) From Haloferax Mediterranei in Complex with 2-Ketohexanoic Acid, Nad+ and Chloride (1.16 A Resolution) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na411
b:20.5
occ:1.00
|
O
|
C:HOH538
|
2.0
|
11.8
|
0.5
|
OG1
|
C:THR132
|
2.2
|
11.3
|
1.0
|
O
|
C:HOH748
|
2.2
|
30.2
|
1.0
|
O
|
C:ALA134
|
2.2
|
11.0
|
1.0
|
O
|
C:HOH781
|
2.3
|
35.2
|
1.0
|
O
|
C:HOH538
|
2.4
|
15.6
|
0.5
|
O
|
C:THR132
|
2.5
|
9.5
|
1.0
|
C
|
C:THR132
|
3.3
|
8.1
|
1.0
|
CB
|
C:THR132
|
3.4
|
9.7
|
1.0
|
C
|
C:ALA134
|
3.5
|
9.3
|
1.0
|
CA
|
C:THR132
|
3.6
|
8.8
|
1.0
|
N
|
C:THR132
|
3.7
|
8.1
|
1.0
|
O
|
C:HOH673
|
4.0
|
18.5
|
1.0
|
N
|
C:ALA134
|
4.2
|
7.9
|
1.0
|
CG
|
C:GLU136
|
4.2
|
10.6
|
1.0
|
OE2
|
C:GLU136
|
4.2
|
22.8
|
1.0
|
CA
|
C:ALA134
|
4.3
|
8.7
|
1.0
|
O
|
C:HOH504
|
4.3
|
28.6
|
1.0
|
C
|
C:LEU133
|
4.3
|
8.3
|
1.0
|
N
|
C:LEU133
|
4.4
|
8.1
|
1.0
|
O
|
C:HOH876
|
4.4
|
24.6
|
1.0
|
N
|
C:GLY135
|
4.4
|
10.1
|
1.0
|
CG2
|
C:THR132
|
4.5
|
13.4
|
1.0
|
CA
|
C:GLY135
|
4.6
|
10.7
|
1.0
|
CB
|
C:ALA134
|
4.7
|
8.9
|
1.0
|
N
|
C:GLU136
|
4.7
|
9.5
|
1.0
|
O
|
C:LEU133
|
4.7
|
8.3
|
1.0
|
CD
|
C:GLU136
|
4.8
|
13.7
|
1.0
|
C
|
C:GLY135
|
4.8
|
11.6
|
1.0
|
CA
|
C:LEU133
|
4.8
|
8.3
|
1.0
|
C
|
C:PHE131
|
5.0
|
7.0
|
1.0
|
|
Sodium binding site 9 out
of 12 in 8qzb
Go back to
Sodium Binding Sites List in 8qzb
Sodium binding site 9 out
of 12 in the D-2-Hydroxyacid Dehydrogenase (D2HDH) From Haloferax Mediterranei in Complex with 2-Ketohexanoic Acid, Nad+ and Chloride (1.16 A Resolution)
 Mono view
 Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 9 of D-2-Hydroxyacid Dehydrogenase (D2HDH) From Haloferax Mediterranei in Complex with 2-Ketohexanoic Acid, Nad+ and Chloride (1.16 A Resolution) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na412
b:23.7
occ:1.00
|
O
|
C:HOH837
|
2.3
|
55.0
|
1.0
|
OG1
|
C:THR88
|
2.5
|
11.4
|
0.5
|
O2A
|
C:NAD401
|
2.5
|
12.7
|
1.0
|
OG1
|
C:THR145
|
2.6
|
13.3
|
1.0
|
O
|
C:HOH565
|
3.0
|
48.2
|
1.0
|
O
|
C:HOH596
|
3.5
|
39.3
|
1.0
|
CB
|
C:THR145
|
3.6
|
9.9
|
1.0
|
CB
|
C:THR88
|
3.7
|
12.7
|
0.5
|
CB
|
C:THR88
|
3.7
|
10.9
|
0.5
|
PA
|
C:NAD401
|
3.7
|
12.0
|
1.0
|
CG2
|
C:THR88
|
3.8
|
12.8
|
0.5
|
N
|
C:THR145
|
3.9
|
8.6
|
1.0
|
N
|
C:GLY89
|
3.9
|
9.6
|
1.0
|
OG1
|
C:THR88
|
4.0
|
16.9
|
0.5
|
O1N
|
C:NAD401
|
4.0
|
11.4
|
1.0
|
O1A
|
C:NAD401
|
4.2
|
13.6
|
1.0
|
C
|
C:THR88
|
4.2
|
11.6
|
1.0
|
CA
|
C:GLY89
|
4.3
|
9.3
|
1.0
|
O3
|
C:NAD401
|
4.3
|
11.8
|
1.0
|
CA
|
C:THR145
|
4.3
|
8.9
|
1.0
|
O
|
C:HOH644
|
4.5
|
29.6
|
1.0
|
CA
|
C:THR88
|
4.5
|
10.2
|
0.5
|
CA
|
C:THR88
|
4.5
|
10.9
|
0.5
|
CG2
|
C:THR88
|
4.6
|
14.8
|
0.5
|
PN
|
C:NAD401
|
4.6
|
10.2
|
1.0
|
O
|
C:HOH816
|
4.6
|
39.6
|
1.0
|
CG2
|
C:THR145
|
4.8
|
10.4
|
1.0
|
O
|
C:THR88
|
4.8
|
12.7
|
1.0
|
O
|
C:HOH558
|
4.9
|
35.4
|
1.0
|
C
|
C:GLY144
|
4.9
|
7.8
|
1.0
|
O
|
C:HOH664
|
5.0
|
10.0
|
1.0
|
O5B
|
C:NAD401
|
5.0
|
12.6
|
1.0
|
|
Sodium binding site 10 out
of 12 in 8qzb
Go back to
Sodium Binding Sites List in 8qzb
Sodium binding site 10 out
of 12 in the D-2-Hydroxyacid Dehydrogenase (D2HDH) From Haloferax Mediterranei in Complex with 2-Ketohexanoic Acid, Nad+ and Chloride (1.16 A Resolution)
 Mono view
 Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 10 of D-2-Hydroxyacid Dehydrogenase (D2HDH) From Haloferax Mediterranei in Complex with 2-Ketohexanoic Acid, Nad+ and Chloride (1.16 A Resolution) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Na406
b:13.2
occ:1.00
|
O
|
D:MET215
|
2.2
|
13.1
|
1.0
|
O
|
D:PHE212
|
2.3
|
12.2
|
1.0
|
O
|
D:HOH756
|
2.3
|
21.9
|
1.0
|
O
|
D:ASP243
|
2.4
|
12.0
|
1.0
|
O
|
D:HOH745
|
2.7
|
46.9
|
1.0
|
O
|
D:GLU213
|
2.7
|
13.3
|
1.0
|
C
|
D:GLU213
|
3.3
|
11.6
|
1.0
|
C
|
D:MET215
|
3.3
|
10.9
|
1.0
|
C
|
D:ASP243
|
3.4
|
13.4
|
1.0
|
C
|
D:PHE212
|
3.5
|
12.2
|
1.0
|
CA
|
D:GLU213
|
3.7
|
13.7
|
1.0
|
O
|
D:HOH702
|
3.8
|
30.1
|
1.0
|
CA
|
D:ASP243
|
3.9
|
13.1
|
1.0
|
N
|
D:MET215
|
3.9
|
11.2
|
1.0
|
CB
|
D:ASP243
|
4.0
|
14.6
|
1.0
|
N
|
D:GLU213
|
4.0
|
12.8
|
1.0
|
CA
|
D:MET215
|
4.0
|
10.5
|
1.0
|
C
|
D:ARG216
|
4.2
|
11.1
|
1.0
|
CG
|
D:GLU217
|
4.2
|
23.6
|
1.0
|
C
|
D:THR214
|
4.3
|
11.4
|
1.0
|
N
|
D:GLU217
|
4.3
|
12.5
|
1.0
|
N
|
D:THR214
|
4.3
|
10.8
|
1.0
|
N
|
D:ARG216
|
4.4
|
12.3
|
1.0
|
O
|
D:ARG216
|
4.4
|
10.7
|
1.0
|
CB
|
D:MET215
|
4.4
|
11.7
|
1.0
|
CG2
|
D:ILE244
|
4.5
|
12.3
|
1.0
|
N
|
D:ILE244
|
4.5
|
11.2
|
1.0
|
CA
|
D:ARG216
|
4.6
|
12.0
|
1.0
|
CA
|
D:GLU217
|
4.6
|
14.3
|
1.0
|
CA
|
D:PHE212
|
4.7
|
10.9
|
1.0
|
O
|
D:THR214
|
4.7
|
12.3
|
1.0
|
CG
|
D:ASP243
|
4.7
|
18.4
|
1.0
|
CA
|
D:THR214
|
4.9
|
10.9
|
1.0
|
OD1
|
D:ASP243
|
4.9
|
24.2
|
1.0
|
CD
|
D:GLU213
|
5.0
|
29.8
|
1.0
|
|
Reference:
J.Domenech,
N.Pramanpol,
C.Bisson,
S.E.Sedelnikova,
J.R.Barrett,
A.A.A.B.Dakhil,
A.S.Abdelhameed,
S.E.Harding,
D.W.Rice,
P.J.Baker,
J.Ferrer.
Ternary Complexes of Haloferax Mediterranei D-2-Hydroxyacid Dehydrogenase Provide Insights Into Halophilicity and the Chiral Specificity of Its Reaction Mechanism. To Be Published.
Page generated: Mon Aug 18 15:19:04 2025
|