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Manganese 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 (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 1s5n). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 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: 1s5n:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 1s5n

Go back to Manganese Binding Sites List in 1s5n
Manganese binding site 1 out of 4 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:6.6
occ:0.95
HO2 A:XYL1001 1.7 11.2 1.0
HO4 A:XYL1001 1.7 10.3 1.0
OE1 A:GLU216 2.1 10.9 1.0
OD2 A:ASP244 2.1 8.5 1.0
OE2 A:GLU180 2.1 7.3 1.0
OD2 A:ASP286 2.1 10.0 1.0
O2 A:XYL1001 2.2 7.5 1.0
O4 A:XYL1001 2.3 6.8 1.0
CD A:GLU180 3.0 6.5 1.0
HO A:OH2006 3.2 21.6 1.0
CG A:ASP286 3.2 6.8 1.0
CG A:ASP244 3.3 6.7 1.0
CD A:GLU216 3.3 7.3 1.0
OE1 A:GLU180 3.3 7.4 1.0
C2 A:XYL1001 3.3 7.4 1.0
C4 A:XYL1001 3.3 6.7 1.0
HB2 A:GLU216 3.4 6.7 1.0
HB3 A:ASP286 3.4 7.6 1.0
HO3 A:XYL1001 3.5 11.4 1.0
C3 A:XYL1001 3.5 7.2 1.0
H2 A:XYL1001 3.6 8.9 1.0
HE1 A:HIS219 3.6 15.7 1.0
HB3 A:ASP244 3.6 7.5 1.0
HB2 A:ASP286 3.7 7.6 1.0
CB A:ASP286 3.7 6.3 1.0
H4 A:XYL1001 3.7 8.0 1.0
O3 A:XYL1001 3.7 7.6 1.0
MN A:MN2002 3.8 6.3 0.1
HB2 A:ASP244 3.8 7.5 1.0
CB A:ASP244 3.8 6.2 1.0
O A:HOH2078 3.9 8.6 1.0
O A:OH2006 3.9 14.4 1.0
CE1 A:HIS219 4.1 13.1 1.0
CB A:GLU216 4.1 5.6 1.0
CG A:GLU216 4.1 6.2 1.0
OE2 A:GLU216 4.2 9.8 1.0
OD1 A:ASP244 4.3 8.0 1.0
OD1 A:ASP286 4.3 7.9 1.0
HG3 A:GLU216 4.4 7.4 1.0
HD21 A:ASN214 4.4 9.0 1.0
NE2 A:HIS219 4.4 13.0 1.0
CG A:GLU180 4.4 6.4 1.0
HB3 A:GLU216 4.4 6.7 1.0
H3 A:XYL1001 4.5 8.6 1.0
C1 A:XYL1001 4.6 8.5 1.0
C5 A:XYL1001 4.6 7.5 1.0
HD22 A:ASN214 4.6 9.0 1.0
HO1 A:XYL1001 4.6 15.8 1.0
HZ2 A:TRP15 4.6 8.9 1.0
HG3 A:GLU180 4.7 7.7 1.0
H51 A:XYL1001 4.7 9.0 1.0
HG2 A:GLU180 4.7 7.7 1.0
H11 A:XYL1001 4.7 10.2 1.0
ND2 A:ASN214 4.8 7.5 1.0
H52 A:XYL1001 4.8 9.0 1.0
MN A:MN2002 4.8 6.2 0.3
MN A:MN2002 4.9 6.0 0.3
ND1 A:HIS219 4.9 8.9 1.0

Manganese binding site 2 out of 4 in 1s5n

Go back to Manganese Binding Sites List in 1s5n
Manganese binding site 2 out of 4 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:6.0
occ:0.31
MN A:MN2002 0.0 6.0 0.3
MN A:MN2002 0.9 6.2 0.3
OD2 A:ASP254 1.5 12.8 0.4
O A:HOH2488 1.5 20.6 0.5
MN A:MN2002 1.5 6.3 0.1
OE2 A:GLU216 2.0 9.8 1.0
OD2 A:ASP254 2.2 17.1 0.4
OD1 A:ASP254 2.2 17.1 0.4
CG A:ASP254 2.2 13.4 0.4
OD1 A:ASP254 2.2 8.9 0.4
OD1 A:ASP256 2.4 13.2 0.7
O A:OH2006 2.4 14.4 1.0
OD1 A:ASP256 2.4 13.9 0.3
CG A:ASP254 2.5 10.6 0.4
O A:HOH2488 2.5 18.7 0.5
HO1 A:XYL1001 2.7 15.8 1.0
NE2 A:HIS219 2.8 13.0 1.0
HO A:OH2006 2.8 21.6 1.0
HD2 A:HIS219 3.0 11.0 1.0
HB2 A:ASP254 3.0 12.4 0.2
CD A:GLU216 3.1 7.3 1.0
CD2 A:HIS219 3.2 9.2 1.0
CG A:ASP256 3.3 13.1 0.3
HD21 A:ASN246 3.3 8.1 1.0
CG A:ASP256 3.3 10.0 0.7
OD2 A:ASP256 3.5 22.8 0.3
OD2 A:ASP256 3.5 18.9 0.7
OE1 A:GLU216 3.5 10.9 1.0
O1 A:XYL1001 3.5 10.5 1.0
CB A:ASP254 3.7 10.6 0.4
O2 A:XYL1001 3.7 7.5 1.0
OD2 A:ASP254 3.8 9.7 0.2
CB A:ASP254 3.9 10.4 0.2
HE3 A:LYS182 3.9 8.0 1.0
HD22 A:ASN246 3.9 8.1 1.0
ND2 A:ASN246 4.0 6.7 1.0
CE1 A:HIS219 4.0 13.1 1.0
HB2 A:ASP254 4.0 12.8 0.4
CB A:ASP254 4.0 10.6 0.4
O A:HOH2027 4.1 9.8 1.0
HB3 A:ASP254 4.1 12.4 0.2
HO2 A:XYL1001 4.1 11.2 1.0
HB3 A:ASP254 4.2 12.8 0.4
H11 A:XYL1001 4.2 10.2 1.0
HG2 A:GLU216 4.2 7.4 1.0
HZ3 A:LYS182 4.3 13.5 1.0
CG A:GLU216 4.3 6.2 1.0
CG A:ASP254 4.3 10.3 0.2
HB3 A:ASP254 4.4 12.8 0.4
C1 A:XYL1001 4.4 8.5 1.0
HE1 A:HIS219 4.4 15.7 1.0
HB2 A:ASP254 4.4 12.8 0.4
CG A:HIS219 4.5 7.1 1.0
HZ1 A:LYS182 4.5 13.5 1.0
HA A:ASP256 4.6 9.2 0.3
H A:ASP256 4.6 8.7 0.3
HA A:ASP256 4.7 9.1 0.7
H A:ASP256 4.7 8.3 0.7
C2 A:XYL1001 4.7 7.4 1.0
NZ A:LYS182 4.7 9.0 1.0
CB A:ASP256 4.7 9.2 0.3
CB A:ASP256 4.7 8.9 0.7
CE A:LYS182 4.7 6.7 1.0
HA A:ASP254 4.8 11.7 0.4
CA A:ASP254 4.8 9.7 0.4
ND1 A:HIS219 4.9 8.9 1.0
HA A:ASP254 4.9 10.1 0.4
HA3 A:GLY218 4.9 6.9 1.0
HG3 A:GLU216 4.9 7.4 1.0
MN A:MN2001 4.9 6.6 0.9
CA A:ASP254 4.9 8.4 0.4
HZ2 A:LYS288 5.0 45.9 1.0

Manganese binding site 3 out of 4 in 1s5n

Go back to Manganese Binding Sites List in 1s5n
Manganese binding site 3 out of 4 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 3 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:6.2
occ:0.30
MN A:MN2002 0.0 6.2 0.3
MN A:MN2002 0.9 6.0 0.3
O A:HOH2488 1.7 20.6 0.5
OD1 A:ASP256 1.7 13.2 0.7
OD1 A:ASP256 1.8 13.9 0.3
MN A:MN2002 1.9 6.3 0.1
O A:OH2006 1.9 14.4 1.0
OD2 A:ASP254 2.0 12.8 0.4
OE2 A:GLU216 2.0 9.8 1.0
HO A:OH2006 2.3 21.6 1.0
OD1 A:ASP254 2.5 17.1 0.4
CG A:ASP256 2.6 13.1 0.3
CG A:ASP256 2.6 10.0 0.7
OD2 A:ASP254 2.7 17.1 0.4
CG A:ASP254 2.7 13.4 0.4
OD2 A:ASP256 2.8 22.8 0.3
OD1 A:ASP254 2.8 8.9 0.4
O A:HOH2488 2.9 18.7 0.5
OD2 A:ASP256 2.9 18.9 0.7
HD21 A:ASN246 3.0 8.1 1.0
CG A:ASP254 3.0 10.6 0.4
CD A:GLU216 3.0 7.3 1.0
HO1 A:XYL1001 3.2 15.8 1.0
HD22 A:ASN246 3.3 8.1 1.0
OE1 A:GLU216 3.4 10.9 1.0
HB2 A:ASP254 3.5 12.4 0.2
NE2 A:HIS219 3.5 13.0 1.0
ND2 A:ASN246 3.5 6.7 1.0
HD2 A:HIS219 3.7 11.0 1.0
O2 A:XYL1001 3.8 7.5 1.0
O1 A:XYL1001 3.9 10.5 1.0
CD2 A:HIS219 4.0 9.2 1.0
CB A:ASP256 4.0 9.2 0.3
CB A:ASP256 4.0 8.9 0.7
HO2 A:XYL1001 4.0 11.2 1.0
HA A:ASP256 4.1 9.2 0.3
HA A:ASP256 4.1 9.1 0.7
O A:HOH2027 4.1 9.8 1.0
H11 A:XYL1001 4.2 10.2 1.0
CB A:ASP254 4.2 10.6 0.4
OD2 A:ASP254 4.3 9.7 0.2
O A:ASP286 4.3 7.7 1.0
CG A:GLU216 4.3 6.2 1.0
HG2 A:GLU216 4.4 7.4 1.0
H A:ASP256 4.4 8.7 0.3
CB A:ASP254 4.4 10.4 0.2
HB3 A:ASP256 4.4 10.7 0.7
H A:ASP256 4.5 8.3 0.7
HZ2 A:LYS288 4.5 45.9 1.0
CA A:ASP256 4.5 7.6 0.3
CB A:ASP254 4.5 10.6 0.4
CA A:ASP256 4.5 7.6 0.7
C1 A:XYL1001 4.5 8.5 1.0
HB3 A:ASP256 4.5 11.0 0.3
HB2 A:ASP256 4.6 11.0 0.3
CE1 A:HIS219 4.6 13.1 1.0
HB3 A:ASP254 4.6 12.8 0.4
HB2 A:ASP254 4.6 12.8 0.4
HB2 A:ASP256 4.7 10.7 0.7
N A:ASP256 4.7 7.2 0.3
N A:ASP256 4.7 7.0 0.7
OD2 A:ASP286 4.7 10.0 1.0
CG A:ASP286 4.7 6.8 1.0
HB3 A:ASP254 4.7 12.8 0.4
HE3 A:LYS182 4.7 8.0 1.0
CG A:ASN246 4.8 5.7 1.0
HB3 A:ASP254 4.8 12.4 0.2
HO3 A:XYL1001 4.8 11.4 1.0
C2 A:XYL1001 4.8 7.4 1.0
CG A:ASP254 4.8 10.3 0.2
HG3 A:GLU216 4.8 7.4 1.0
MN A:MN2001 4.8 6.6 0.9
HB3 A:ASP286 4.8 7.6 1.0
OD1 A:ASP286 4.9 7.9 1.0
HZ3 A:LYS182 4.9 13.5 1.0
HE1 A:HIS219 4.9 15.7 1.0

Manganese binding site 4 out of 4 in 1s5n

Go back to Manganese Binding Sites List in 1s5n
Manganese binding site 4 out of 4 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 4 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:6.3
occ:0.06
MN A:MN2002 0.0 6.3 0.1
MN A:MN2002 1.5 6.0 0.3
HO1 A:XYL1001 1.7 15.8 1.0
MN A:MN2002 1.9 6.2 0.3
O A:OH2006 2.1 14.4 1.0
NE2 A:HIS219 2.1 13.0 1.0
HO A:OH2006 2.2 21.6 1.0
OD2 A:ASP254 2.2 12.8 0.4
O2 A:XYL1001 2.3 7.5 1.0
OE2 A:GLU216 2.4 9.8 1.0
O1 A:XYL1001 2.5 10.5 1.0
OD2 A:ASP254 2.7 17.1 0.4
HO2 A:XYL1001 2.8 11.2 1.0
OE1 A:GLU216 2.9 10.9 1.0
CD A:GLU216 2.9 7.3 1.0
CE1 A:HIS219 2.9 13.1 1.0
O A:HOH2488 3.0 20.6 0.5
CD2 A:HIS219 3.1 9.2 1.0
HE1 A:HIS219 3.1 15.7 1.0
C1 A:XYL1001 3.1 8.5 1.0
H11 A:XYL1001 3.2 10.2 1.0
C2 A:XYL1001 3.2 7.4 1.0
HD2 A:HIS219 3.3 11.0 1.0
CG A:ASP254 3.3 13.4 0.4
CG A:ASP254 3.5 10.6 0.4
OD1 A:ASP254 3.6 8.9 0.4
OD1 A:ASP256 3.6 13.2 0.7
H2 A:XYL1001 3.7 8.9 1.0
OD1 A:ASP254 3.7 17.1 0.4
O A:HOH2488 3.7 18.7 0.5
OD1 A:ASP256 3.7 13.9 0.3
HZ3 A:LYS182 3.7 13.5 1.0
MN A:MN2001 3.8 6.6 0.9
HE3 A:LYS182 3.8 8.0 1.0
HO3 A:XYL1001 4.0 11.4 1.0
ND1 A:HIS219 4.1 8.9 1.0
H12 A:XYL1001 4.1 10.2 1.0
OD2 A:ASP256 4.1 22.8 0.3
CG A:HIS219 4.1 7.1 1.0
HB2 A:ASP254 4.1 12.4 0.2
OD2 A:ASP286 4.2 10.0 1.0
HD2 A:LYS182 4.2 7.5 1.0
CG A:GLU216 4.3 6.2 1.0
HD21 A:ASN246 4.3 8.1 1.0
OD2 A:ASP256 4.3 18.9 0.7
CG A:ASP256 4.3 13.1 0.3
OD2 A:ASP254 4.3 9.7 0.2
CG A:ASP256 4.4 10.0 0.7
OE2 A:GLU180 4.4 7.3 1.0
NZ A:LYS182 4.4 9.0 1.0
CE A:LYS182 4.5 6.7 1.0
C3 A:XYL1001 4.5 7.2 1.0
HZ1 A:LYS182 4.5 13.5 1.0
HG2 A:GLU216 4.5 7.4 1.0
HO4 A:XYL1001 4.6 10.3 1.0
HB3 A:GLU216 4.6 6.7 1.0
O3 A:XYL1001 4.7 7.6 1.0
CB A:ASP254 4.7 10.6 0.4
HB2 A:ASP254 4.8 12.8 0.4
CG A:ASP286 4.8 6.8 1.0
HD22 A:ASN246 4.8 8.1 1.0
HB2 A:GLU216 4.8 6.7 1.0
CD A:LYS182 4.9 6.2 1.0
HD1 A:HIS219 4.9 10.7 1.0
CB A:GLU216 4.9 5.6 1.0
ND2 A:ASN246 4.9 6.7 1.0
CB A:ASP254 4.9 10.4 0.2
CB A:ASP254 4.9 10.6 0.4
HG3 A:GLU216 4.9 7.4 1.0
HB3 A:ASP254 5.0 12.8 0.4
HB3 A:ASP254 5.0 12.4 0.2

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 03:55:28 2020

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