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Manganese 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:

Sodium (Na) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese 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 Manganese atom.
In total 2 binding sites of Manganese 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 Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 1s5m

Go back to Manganese Binding Sites List in 1s5m
Manganese 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 Manganese with other atoms in the Mn 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:Mn2001

b:8.1
occ:0.77
 HO4 A:GLC1001 1.6 17.0 1.0
HO3 A:GLC1001 2.0 16.3 1.0
OE1 A:GLU216 2.0 9.7 1.0
OE2 A:GLU180 2.1 11.6 1.0
OD2 A:ASP286 2.1 8.8 0.7
OD2 A:ASP244 2.2 12.2 1.0
OD2 A:ASP286 2.2 12.0 0.3
O4 A:GLC1001 2.2 11.3 1.0
O3 A:GLC1001 2.4 10.9 1.0
CD A:GLU180 3.0 10.3 1.0
CG A:ASP286 3.1 9.8 0.3
C4 A:GLC1001 3.1 12.1 1.0
C3 A:GLC1001 3.1 11.4 1.0
CG A:ASP286 3.2 7.6 0.7
H3 A:GLC1001 3.2 13.7 1.0
CD A:GLU216 3.2 7.9 1.0
HB3 A:ASP286 3.3 12.1 0.3
HB2 A:GLU216 3.3 8.5 1.0
CG A:ASP244 3.3 8.9 1.0
OE1 A:GLU180 3.3 11.4 1.0
HB3 A:ASP286 3.4 9.1 0.7
H4 A:GLC1001 3.5 14.5 1.0
HE1 A:HIS219 3.5 9.1 1.0
HB2 A:ASP286 3.6 9.1 0.7
CB A:ASP286 3.6 7.6 0.7
CB A:ASP286 3.6 10.1 0.3
O A:HOH2416 3.7 11.0 1.0
HB3 A:ASP244 3.8 9.6 1.0
HB2 A:ASP286 3.8 12.1 0.3
HB2 A:ASP244 4.0 9.6 1.0
CB A:ASP244 4.0 8.0 1.0
CG A:GLU216 4.0 7.7 1.0
CE1 A:HIS219 4.0 7.6 1.0
HG3 A:GLU216 4.0 9.2 1.0
CB A:GLU216 4.0 7.1 1.0
O A:HOH2078 4.1 11.7 1.0
OD1 A:ASP286 4.1 11.7 0.3
OE2 A:GLU216 4.2 8.7 1.0
OD1 A:ASP286 4.3 8.3 0.7
OD1 A:ASP244 4.3 10.1 1.0
H62 A:GLC1001 4.3 28.4 1.0
HB3 A:GLU216 4.4 8.5 1.0
CG A:GLU180 4.4 9.5 1.0
C5 A:GLC1001 4.4 17.6 1.0
H5 A:GLC1001 4.5 21.2 1.0
NE2 A:HIS219 4.5 8.2 1.0
HG3 A:GLU180 4.6 11.3 1.0
C2 A:GLC1001 4.6 12.2 1.0
MN A:MN2002 4.6 7.2 0.9
HG2 A:GLU180 4.6 11.3 1.0
ND1 A:HIS219 4.6 7.6 1.0
HD21 A:ASN214 4.7 11.8 1.0
HZ2 A:TRP15 4.7 10.8 1.0
HD1 A:HIS219 4.8 9.1 1.0
HO2 A:GLC1001 4.8 20.1 1.0
H2 A:GLC1001 4.8 14.7 1.0
C6 A:GLC1001 4.9 23.7 1.0
HD22 A:ASN214 4.9 11.8 1.0
HG2 A:GLU216 4.9 9.2 1.0

Manganese binding site 2 out of 2 in 1s5m

Go back to Manganese Binding Sites List in 1s5m
Manganese 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 Manganese with other atoms in the Mn 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:Mn2002

b:7.2
occ:0.88
 OE2 A:GLU216 2.1 8.7 1.0
O A:HOH2416 2.2 11.0 1.0
OD1 A:ASP256 2.2 9.1 1.0
OD2 A:ASP254 2.2 10.3 1.0
OD1 A:ASP254 2.3 8.6 1.0
NE2 A:HIS219 2.3 8.2 1.0
CG A:ASP254 2.6 8.5 1.0
CD A:GLU216 2.9 7.9 1.0
OE1 A:GLU216 3.0 9.7 1.0
CD2 A:HIS219 3.1 7.3 1.0
HD2 A:HIS219 3.1 8.8 1.0
CG A:ASP256 3.1 8.6 1.0
CE1 A:HIS219 3.3 7.6 1.0
HD21 A:ASN246 3.3 9.2 1.0
OD2 A:ASP256 3.4 11.4 1.0
HE1 A:HIS219 3.6 9.1 1.0
O A:HOH2138 3.7 13.9 1.0
O A:HOH2026 4.0 8.3 1.0
HE3 A:LYS182 4.0 10.1 1.0
O3 A:GLC1001 4.0 10.9 1.0
HD22 A:ASN246 4.0 9.2 1.0
ND2 A:ASN246 4.0 7.7 1.0
CB A:ASP254 4.1 8.7 1.0
CG A:HIS219 4.2 6.9 1.0
OD2 A:ASP286 4.2 8.8 0.7
CG A:GLU216 4.3 7.7 1.0
HO3 A:GLC1001 4.3 16.3 1.0
ND1 A:HIS219 4.4 7.6 1.0
HB2 A:ASP254 4.4 10.4 1.0
HG2 A:GLU216 4.5 9.2 1.0
HB3 A:ASP254 4.5 10.4 1.0
HZ3 A:LYS182 4.5 19.2 1.0
HO2 A:GLC1001 4.5 20.1 1.0
CB A:ASP256 4.5 8.8 1.0
HA A:ASP256 4.5 9.3 1.0
MN A:MN2001 4.6 8.1 0.8
H A:ASP256 4.6 9.2 1.0
CE A:LYS182 4.8 8.4 1.0
HG3 A:GLU216 4.8 9.2 1.0
O A:HOH2306 4.9 33.0 1.0
HD2 A:LYS182 4.9 9.5 1.0
HA3 A:GLY218 4.9 8.2 1.0
HZ1 A:LYS182 4.9 19.2 1.0
CA A:ASP256 4.9 7.8 1.0
N A:ASP256 4.9 7.7 1.0
HA A:ASP254 5.0 9.2 1.0
NZ A:LYS182 5.0 12.8 1.0
CA A:ASP254 5.0 7.7 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: Sat Oct 5 12:22:56 2024

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