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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:

Manganese (Mn) 4 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 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: Tue Dec 15 05:35:41 2020

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