Sodium in PDB 1s5n: Xylose Isomerase in Substrate and Inhibitor Michaelis States: Atomic Resolution Studies of A Metal-Mediated Hydride Shift
Enzymatic activity of Xylose Isomerase in Substrate and Inhibitor Michaelis States: Atomic Resolution Studies of A Metal-Mediated Hydride Shift
All present enzymatic activity of Xylose Isomerase in Substrate and Inhibitor Michaelis States: Atomic Resolution Studies of A Metal-Mediated Hydride Shift:
5.3.1.5;
Protein crystallography data
The structure of Xylose Isomerase in Substrate and Inhibitor Michaelis States: Atomic Resolution Studies of A Metal-Mediated Hydride Shift, PDB code: 1s5n
was solved by
T.D.Fenn,
D.Ringe,
G.A.Petsko,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
50.00 /
0.95
|
Space group
|
I 2 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
86.031,
92.854,
98.312,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
10.6 /
12.8
|
Other elements in 1s5n:
The structure of Xylose Isomerase in Substrate and Inhibitor Michaelis States: Atomic Resolution Studies of A Metal-Mediated Hydride Shift also contains other interesting chemical elements:
Sodium Binding Sites:
The binding sites of Sodium atom in the Xylose Isomerase in Substrate and Inhibitor Michaelis States: Atomic Resolution Studies of A Metal-Mediated Hydride Shift
(pdb code 1s5n). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the
Xylose Isomerase in Substrate and Inhibitor Michaelis States: Atomic Resolution Studies of A Metal-Mediated Hydride Shift, PDB code: 1s5n:
Jump to Sodium binding site number:
1;
2;
Sodium binding site 1 out
of 2 in 1s5n
Go back to
Sodium Binding Sites List in 1s5n
Sodium binding site 1 out
of 2 in the Xylose Isomerase in Substrate and Inhibitor Michaelis States: Atomic Resolution Studies of A Metal-Mediated Hydride Shift
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Xylose Isomerase in Substrate and Inhibitor Michaelis States: Atomic Resolution Studies of A Metal-Mediated Hydride Shift within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na2004
b:17.4
occ:1.00
|
H
|
A:ARG207
|
2.1
|
14.5
|
0.7
|
H
|
A:ARG207
|
2.2
|
15.6
|
0.3
|
HA
|
A:ASP162
|
2.6
|
10.7
|
1.0
|
OD1
|
A:ASP162
|
2.7
|
10.8
|
1.0
|
HE1
|
A:TYR211
|
2.8
|
12.6
|
1.0
|
OH
|
A:TYR211
|
2.8
|
11.1
|
1.0
|
HB3
|
A:GLU206
|
2.8
|
16.6
|
0.5
|
O
|
A:HOH2346
|
2.8
|
16.2
|
1.0
|
H
|
A:GLU206
|
2.9
|
13.7
|
0.5
|
N
|
A:ARG207
|
2.9
|
12.1
|
0.7
|
HB3
|
A:LEU205
|
2.9
|
10.8
|
1.0
|
H
|
A:GLU206
|
2.9
|
14.2
|
0.5
|
N
|
A:ARG207
|
3.0
|
13.0
|
0.3
|
HB3
|
A:GLU206
|
3.0
|
20.3
|
0.5
|
HB2
|
A:ARG207
|
3.0
|
17.7
|
0.7
|
HB2
|
A:ARG207
|
3.1
|
17.7
|
0.3
|
N
|
A:GLU206
|
3.3
|
11.4
|
0.5
|
N
|
A:GLU206
|
3.3
|
11.8
|
0.5
|
CE1
|
A:TYR211
|
3.4
|
10.5
|
1.0
|
HH
|
A:TYR211
|
3.4
|
16.6
|
1.0
|
CZ
|
A:TYR211
|
3.5
|
9.7
|
1.0
|
HG3
|
A:ARG207
|
3.5
|
18.8
|
0.7
|
CA
|
A:ASP162
|
3.6
|
8.9
|
1.0
|
CG
|
A:ASP162
|
3.6
|
9.8
|
1.0
|
CB
|
A:GLU206
|
3.6
|
13.8
|
0.5
|
CB
|
A:ARG207
|
3.7
|
14.8
|
0.7
|
C
|
A:GLU206
|
3.7
|
14.7
|
0.5
|
CA
|
A:GLU206
|
3.7
|
12.4
|
0.5
|
CA
|
A:ARG207
|
3.7
|
13.1
|
0.7
|
CA
|
A:GLU206
|
3.8
|
13.3
|
0.5
|
C
|
A:GLU206
|
3.8
|
12.6
|
0.5
|
HG3
|
A:ARG207
|
3.8
|
19.5
|
0.3
|
CB
|
A:ARG207
|
3.8
|
14.8
|
0.3
|
CB
|
A:GLU206
|
3.8
|
16.9
|
0.5
|
CA
|
A:ARG207
|
3.8
|
13.4
|
0.3
|
CB
|
A:LEU205
|
3.9
|
9.0
|
1.0
|
HA3
|
A:GLY165
|
3.9
|
12.6
|
1.0
|
HD2
|
A:ARG207
|
4.0
|
20.0
|
0.3
|
CB
|
A:ASP162
|
4.0
|
9.6
|
1.0
|
CG
|
A:ARG207
|
4.1
|
15.6
|
0.7
|
C
|
A:LEU205
|
4.1
|
11.4
|
1.0
|
O
|
A:ARG207
|
4.2
|
10.8
|
0.7
|
C
|
A:ARG207
|
4.2
|
12.3
|
0.7
|
HB3
|
A:ASP162
|
4.2
|
11.5
|
1.0
|
CG
|
A:ARG207
|
4.2
|
16.2
|
0.3
|
HB2
|
A:LEU205
|
4.2
|
10.8
|
1.0
|
O
|
A:ARG207
|
4.2
|
14.8
|
0.3
|
C
|
A:ARG207
|
4.2
|
12.5
|
0.3
|
HB2
|
A:GLU206
|
4.3
|
16.6
|
0.5
|
O
|
A:PHE161
|
4.3
|
8.7
|
1.0
|
HB2
|
A:GLU206
|
4.3
|
20.3
|
0.5
|
N
|
A:ASP162
|
4.3
|
8.4
|
1.0
|
HD13
|
A:LEU205
|
4.4
|
14.0
|
1.0
|
HG2
|
A:GLU206
|
4.4
|
33.0
|
0.5
|
O
|
A:ASP162
|
4.4
|
10.5
|
1.0
|
HD2
|
A:ARG207
|
4.4
|
21.6
|
0.7
|
HD22
|
A:LEU205
|
4.4
|
14.3
|
1.0
|
HH11
|
A:ARG207
|
4.5
|
32.6
|
0.7
|
CA
|
A:LEU205
|
4.5
|
9.6
|
1.0
|
C
|
A:ASP162
|
4.5
|
9.2
|
1.0
|
HB3
|
A:ARG207
|
4.5
|
17.7
|
0.7
|
HA
|
A:LEU205
|
4.5
|
11.5
|
1.0
|
CG
|
A:GLU206
|
4.6
|
27.5
|
0.5
|
CD1
|
A:TYR211
|
4.6
|
10.3
|
1.0
|
C
|
A:PHE161
|
4.6
|
8.3
|
1.0
|
HD13
|
A:LEU210
|
4.6
|
23.6
|
1.0
|
CD
|
A:ARG207
|
4.6
|
16.6
|
0.3
|
HB3
|
A:ARG207
|
4.6
|
17.7
|
0.3
|
HA
|
A:ARG207
|
4.6
|
15.8
|
0.7
|
HA
|
A:GLU206
|
4.7
|
14.9
|
0.5
|
HA
|
A:ARG207
|
4.7
|
16.0
|
0.3
|
CE2
|
A:TYR211
|
4.7
|
9.5
|
1.0
|
HA
|
A:GLU206
|
4.7
|
16.0
|
0.5
|
OD2
|
A:ASP162
|
4.7
|
11.2
|
1.0
|
H
|
A:GLY165
|
4.8
|
11.6
|
1.0
|
CG
|
A:GLU206
|
4.8
|
20.0
|
0.5
|
O
|
A:GLU206
|
4.9
|
17.8
|
0.5
|
HG3
|
A:GLU206
|
4.9
|
24.1
|
0.5
|
CA
|
A:GLY165
|
4.9
|
10.5
|
1.0
|
CD
|
A:ARG207
|
4.9
|
18.0
|
0.7
|
H
|
A:ASP162
|
4.9
|
10.1
|
1.0
|
CG
|
A:LEU205
|
4.9
|
8.4
|
1.0
|
HG2
|
A:GLU206
|
4.9
|
24.1
|
0.5
|
HG2
|
A:ARG207
|
4.9
|
18.8
|
0.7
|
HD1
|
A:TYR211
|
4.9
|
12.3
|
1.0
|
O
|
A:GLU206
|
4.9
|
14.9
|
0.5
|
HB2
|
A:ASP162
|
5.0
|
11.5
|
1.0
|
O
|
A:LEU205
|
5.0
|
13.2
|
1.0
|
|
Sodium binding site 2 out
of 2 in 1s5n
Go back to
Sodium Binding Sites List in 1s5n
Sodium binding site 2 out
of 2 in the Xylose Isomerase in Substrate and Inhibitor Michaelis States: Atomic Resolution Studies of A Metal-Mediated Hydride Shift
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Xylose Isomerase in Substrate and Inhibitor Michaelis States: Atomic Resolution Studies of A Metal-Mediated Hydride Shift within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na2005
b:23.6
occ:1.00
|
HD1
|
A:HIS70
|
2.1
|
20.8
|
1.0
|
HG2
|
A:PRO35
|
2.5
|
16.0
|
1.0
|
O
|
A:LEU57
|
2.7
|
13.3
|
1.0
|
O
|
A:HOH2089
|
2.7
|
16.7
|
1.0
|
ND1
|
A:HIS70
|
2.8
|
17.3
|
1.0
|
HD2
|
A:PRO35
|
3.1
|
14.6
|
1.0
|
O
|
A:HOH2379
|
3.2
|
29.8
|
1.0
|
HB3
|
A:HIS70
|
3.2
|
16.4
|
1.0
|
HD11
|
A:LEU57
|
3.2
|
21.5
|
1.0
|
CG
|
A:PRO35
|
3.4
|
13.3
|
1.0
|
O
|
A:HOH2387
|
3.4
|
36.5
|
1.0
|
HH11
|
A:ARG73
|
3.5
|
17.1
|
0.7
|
O
|
A:HOH2366
|
3.6
|
33.2
|
1.0
|
CD
|
A:PRO35
|
3.6
|
12.2
|
1.0
|
CG
|
A:HIS70
|
3.7
|
14.3
|
1.0
|
HA
|
A:LEU57
|
3.8
|
13.3
|
1.0
|
CE1
|
A:HIS70
|
3.8
|
17.7
|
1.0
|
C
|
A:LEU57
|
3.8
|
11.1
|
1.0
|
HH22
|
A:ARG73
|
3.8
|
30.7
|
0.3
|
CB
|
A:HIS70
|
3.8
|
13.7
|
1.0
|
HB2
|
A:PRO35
|
3.9
|
14.2
|
1.0
|
HE1
|
A:HIS70
|
3.9
|
21.2
|
1.0
|
HD3
|
A:PRO35
|
4.0
|
14.6
|
1.0
|
HH12
|
A:ARG73
|
4.1
|
17.1
|
0.7
|
HG3
|
A:PRO35
|
4.1
|
16.0
|
1.0
|
HA
|
A:HIS70
|
4.1
|
18.6
|
1.0
|
NH1
|
A:ARG73
|
4.1
|
14.2
|
0.7
|
CD1
|
A:LEU57
|
4.1
|
14.3
|
1.0
|
HD3
|
A:PRO59
|
4.1
|
17.5
|
1.0
|
CB
|
A:PRO35
|
4.2
|
11.8
|
1.0
|
HD12
|
A:LEU57
|
4.3
|
21.5
|
1.0
|
CA
|
A:LEU57
|
4.3
|
11.1
|
1.0
|
CA
|
A:HIS70
|
4.4
|
15.5
|
1.0
|
HA
|
A:ILE58
|
4.5
|
13.2
|
1.0
|
O
|
A:HIS70
|
4.5
|
14.9
|
1.0
|
NH2
|
A:ARG73
|
4.6
|
25.6
|
0.3
|
O
|
A:ASP56
|
4.7
|
11.6
|
1.0
|
HB2
|
A:HIS70
|
4.7
|
16.4
|
1.0
|
HD13
|
A:LEU57
|
4.7
|
21.5
|
1.0
|
HG
|
A:LEU57
|
4.8
|
14.6
|
1.0
|
HB3
|
A:PRO35
|
4.8
|
14.2
|
1.0
|
HH21
|
A:ARG73
|
4.8
|
30.7
|
0.3
|
NE2
|
A:HIS70
|
4.8
|
18.4
|
1.0
|
CD2
|
A:HIS70
|
4.8
|
19.9
|
1.0
|
N
|
A:ILE58
|
4.9
|
10.6
|
1.0
|
HB2
|
A:PHE74
|
4.9
|
15.3
|
1.0
|
C
|
A:HIS70
|
4.9
|
14.1
|
1.0
|
HE
|
A:ARG73
|
4.9
|
26.4
|
0.3
|
N
|
A:PRO35
|
4.9
|
11.0
|
1.0
|
CG
|
A:LEU57
|
5.0
|
12.2
|
1.0
|
|
Reference:
T.D.Fenn,
D.Ringe,
G.A.Petsko.
Xylose Isomerase in Substrate and Inhibitor Michaelis States: Atomic Resolution Studies of A Metal-Mediated Hydride Shift(,). Biochemistry V. 43 6464 2004.
ISSN: ISSN 0006-2960
PubMed: 15157080
DOI: 10.1021/BI049812O
Page generated: Sun Oct 6 22:22:41 2024
|