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Sodium in PDB 1s5m: 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: 1s5m 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 / 0.98
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 85.865, 92.968, 98.298, 90.00, 90.00, 90.00
R / Rfree (%) 11.1 / 12.9

Other elements in 1s5m:

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:

Manganese (Mn) 2 atoms

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 1s5m). 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: 1s5m:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 1s5m

Go back to Sodium Binding Sites List in 1s5m
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:19.1
occ:1.00
 H A:ARG207 2.2 15.5 1.0
HG2 A:GLU206 2.5 30.5 0.4
HA A:ASP162 2.6 12.3 1.0
OD1 A:ASP162 2.7 11.8 1.0
OH A:TYR211 2.8 12.5 1.0
HG3 A:GLU206 2.8 30.5 0.4
HE1 A:TYR211 2.8 14.0 1.0
HB3 A:GLU206 2.8 16.3 0.6
O A:HOH2319 2.8 17.4 1.0
H A:GLU206 2.8 14.5 0.4
H A:GLU206 2.9 13.5 0.6
N A:ARG207 2.9 12.9 1.0
HB3 A:LEU205 2.9 12.1 1.0
HB2 A:ARG207 3.0 17.2 1.0
CG A:GLU206 3.1 25.4 0.4
N A:GLU206 3.3 11.2 0.6
N A:GLU206 3.3 12.1 0.4
HH A:TYR211 3.3 18.7 1.0
CE1 A:TYR211 3.4 11.7 1.0
CZ A:TYR211 3.5 11.1 1.0
CA A:ASP162 3.6 10.3 1.0
CB A:GLU206 3.6 13.6 0.6
HG3 A:ARG207 3.6 19.1 1.0
CG A:ASP162 3.7 11.0 1.0
CB A:ARG207 3.7 14.3 1.0
C A:GLU206 3.7 15.7 0.4
CA A:GLU206 3.7 12.4 0.6
CA A:GLU206 3.8 14.3 0.4
CA A:ARG207 3.8 13.2 1.0
C A:GLU206 3.8 12.0 0.6
CB A:GLU206 3.8 17.9 0.4
HA3 A:GLY165 3.9 13.7 1.0
CB A:LEU205 3.9 10.1 1.0
HB2 A:GLU206 4.0 16.3 0.6
CB A:ASP162 4.1 10.9 1.0
C A:LEU205 4.1 11.6 1.0
HB3 A:GLU206 4.2 21.5 0.4
CG A:ARG207 4.2 15.9 1.0
HB2 A:LEU205 4.2 12.1 1.0
C A:ARG207 4.2 12.6 1.0
O A:PHE161 4.2 9.8 1.0
O A:ARG207 4.2 12.5 1.0
HB3 A:ASP162 4.3 13.1 1.0
CD A:GLU206 4.3 33.9 0.4
N A:ASP162 4.3 9.4 1.0
HD13 A:LEU205 4.3 15.1 1.0
HD2 A:ARG207 4.3 27.2 1.0
HD22 A:LEU205 4.4 15.9 1.0
O A:ASP162 4.4 11.3 1.0
CA A:LEU205 4.5 10.4 1.0
HH11 A:ARG207 4.5 45.2 1.0
C A:PHE161 4.6 9.3 1.0
C A:ASP162 4.6 10.3 1.0
HA A:LEU205 4.6 12.5 1.0
HB3 A:ARG207 4.6 17.2 1.0
CD1 A:TYR211 4.6 11.2 1.0
HD13 A:LEU210 4.6 28.9 1.0
HA A:ARG207 4.7 15.8 1.0
HB2 A:GLU206 4.7 21.5 0.4
HA A:GLU206 4.7 14.9 0.6
HA A:GLU206 4.7 17.1 0.4
CE2 A:TYR211 4.7 10.5 1.0
OD2 A:ASP162 4.7 12.0 1.0
H A:GLY165 4.8 12.8 1.0
CG A:GLU206 4.8 18.9 0.6
OE1 A:GLU206 4.8 46.9 0.4
CA A:GLY165 4.8 11.4 1.0
HG3 A:GLU206 4.8 22.7 0.6
CD A:ARG207 4.8 22.7 1.0
H A:ASP162 4.9 11.2 1.0
O A:GLU206 4.9 19.2 0.4
HD1 A:TYR211 4.9 13.4 1.0
CG A:LEU205 4.9 9.6 1.0
O A:GLU206 5.0 13.8 0.6
HG2 A:GLU206 5.0 22.7 0.6
HG2 A:ARG207 5.0 19.1 1.0
HB2 A:ASP162 5.0 13.1 1.0

Sodium binding site 2 out of 2 in 1s5m

Go back to Sodium Binding Sites List in 1s5m
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:26.1
occ:1.00
 HD1 A:HIS70 2.1 26.2 1.0
HG2 A:PRO35 2.5 18.6 1.0
O A:LEU57 2.7 16.1 1.0
O A:HOH2089 2.7 19.9 1.0
ND1 A:HIS70 2.9 21.8 1.0
HD2 A:PRO35 3.1 17.1 1.0
HD13 A:LEU57 3.2 26.6 1.0
HB3 A:HIS70 3.3 20.8 1.0
O A:HOH2384 3.3 38.9 1.0
CG A:PRO35 3.3 15.5 1.0
HH11 A:ARG73 3.5 24.4 1.0
CD A:PRO35 3.6 14.3 1.0
HA A:LEU57 3.7 15.5 1.0
CG A:HIS70 3.7 17.9 1.0
C A:LEU57 3.7 13.4 1.0
CE1 A:HIS70 3.9 21.2 1.0
CB A:HIS70 3.9 17.4 1.0
HB2 A:PRO35 3.9 16.5 1.0
HD3 A:PRO35 3.9 17.1 1.0
HG3 A:PRO35 4.0 18.6 1.0
HE1 A:HIS70 4.1 25.4 1.0
HH12 A:ARG73 4.1 24.4 1.0
CD1 A:LEU57 4.1 17.7 1.0
HA A:HIS70 4.1 20.8 1.0
NH1 A:ARG73 4.1 20.3 1.0
HD3 A:PRO59 4.1 23.4 1.0
CB A:PRO35 4.2 13.7 1.0
CA A:LEU57 4.3 12.9 1.0
HD11 A:LEU57 4.3 26.6 1.0
CA A:HIS70 4.5 17.3 1.0
O A:ASP56 4.5 14.6 1.0
O A:HIS70 4.5 17.5 1.0
HA A:ILE58 4.6 16.2 1.0
HD12 A:LEU57 4.6 26.6 1.0
HB3 A:PRO35 4.7 16.5 1.0
HB2 A:HIS70 4.7 20.8 1.0
HG A:LEU57 4.8 18.3 1.0
C A:HIS70 4.8 16.7 1.0
N A:ILE58 4.8 13.2 1.0
HB2 A:PHE74 4.9 17.9 1.0
CD2 A:HIS70 4.9 23.8 1.0
NE2 A:HIS70 4.9 22.2 1.0
N A:PRO35 5.0 12.7 1.0
CG A:LEU57 5.0 15.2 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 22:21:54 2024

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