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Manganese in PDB 9xia: X-Ray Analysis of D-Xylose Isomerase at 1.9 Angstroms: Native Enzyme in Complex with Substrate and with A Mechanism-Designed Inactivator

Enzymatic activity of X-Ray Analysis of D-Xylose Isomerase at 1.9 Angstroms: Native Enzyme in Complex with Substrate and with A Mechanism-Designed Inactivator

All present enzymatic activity of X-Ray Analysis of D-Xylose Isomerase at 1.9 Angstroms: Native Enzyme in Complex with Substrate and with A Mechanism-Designed Inactivator:
5.3.1.5;

Protein crystallography data

The structure of X-Ray Analysis of D-Xylose Isomerase at 1.9 Angstroms: Native Enzyme in Complex with Substrate and with A Mechanism-Designed Inactivator, PDB code: 9xia was solved by H.L.Carrell, J.P.Glusker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 1.90
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 93.800, 100.000, 103.000, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Manganese Binding Sites:

The binding sites of Manganese atom in the X-Ray Analysis of D-Xylose Isomerase at 1.9 Angstroms: Native Enzyme in Complex with Substrate and with A Mechanism-Designed Inactivator (pdb code 9xia). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the X-Ray Analysis of D-Xylose Isomerase at 1.9 Angstroms: Native Enzyme in Complex with Substrate and with A Mechanism-Designed Inactivator, PDB code: 9xia:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 9xia

Go back to Manganese Binding Sites List in 9xia
Manganese binding site 1 out of 2 in the X-Ray Analysis of D-Xylose Isomerase at 1.9 Angstroms: Native Enzyme in Complex with Substrate and with A Mechanism-Designed Inactivator


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of X-Ray Analysis of D-Xylose Isomerase at 1.9 Angstroms: Native Enzyme in Complex with Substrate and with A Mechanism-Designed Inactivator within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn390

b:8.8
occ:1.00
 OE1 A:GLU217 2.2 8.2 1.0
OD1 A:ASP255 2.3 7.9 1.0
OD2 A:ASP257 2.3 5.2 1.0
NE2 A:HIS220 2.4 8.1 1.0
O A:HOH408 2.4 11.2 1.0
OD2 A:ASP255 2.4 5.0 1.0
CG A:ASP255 2.8 5.9 1.0
CD2 A:HIS220 3.0 5.0 1.0
CD A:GLU217 3.1 6.8 1.0
CG A:ASP257 3.2 8.2 1.0
OD1 A:ASP257 3.3 12.6 1.0
CE1 A:HIS220 3.4 7.9 1.0
OE2 A:GLU217 3.4 8.5 1.0
O A:HOH562 3.8 9.8 1.0
ND2 A:ASN247 4.0 5.0 1.0
O A:HOH411 4.1 8.8 1.0
CG A:HIS220 4.2 5.7 1.0
CB A:ASP255 4.3 5.0 1.0
ND1 A:HIS220 4.4 7.4 1.0
CG A:GLU217 4.4 5.0 1.0
CB A:ASP257 4.5 5.0 1.0
O5 A:DFR389 4.7 7.4 1.0
O A:HOH610 4.7 23.1 1.0
OD2 A:ASP287 4.8 5.0 1.0
NZ A:LYS183 4.8 5.0 1.0
CE A:LYS183 4.8 5.0 1.0
CA A:ASP257 5.0 5.0 1.0

Manganese binding site 2 out of 2 in 9xia

Go back to Manganese Binding Sites List in 9xia
Manganese binding site 2 out of 2 in the X-Ray Analysis of D-Xylose Isomerase at 1.9 Angstroms: Native Enzyme in Complex with Substrate and with A Mechanism-Designed Inactivator


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of X-Ray Analysis of D-Xylose Isomerase at 1.9 Angstroms: Native Enzyme in Complex with Substrate and with A Mechanism-Designed Inactivator within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn391

b:13.1
occ:1.00
 OD2 A:ASP287 2.3 5.0 1.0
OE2 A:GLU181 2.3 12.1 1.0
OD1 A:ASP245 2.3 5.6 1.0
OE2 A:GLU217 2.3 8.5 1.0
O5 A:DFR389 2.5 7.4 1.0
O1 A:DFR389 2.6 14.2 1.0
CD A:GLU181 3.1 12.3 1.0
C4 A:DFR389 3.1 11.7 1.0
OE1 A:GLU181 3.2 14.6 1.0
CG A:ASP287 3.3 6.3 1.0
CG A:ASP245 3.4 5.0 1.0
C5 A:DFR389 3.4 10.7 1.0
CD A:GLU217 3.5 6.8 1.0
C1 A:DFR389 3.6 14.8 1.0
O4 A:DFR389 3.6 10.4 1.0
CB A:ASP287 3.6 5.3 1.0
O6 A:DFR389 3.9 15.9 1.0
CB A:ASP245 3.9 5.0 1.0
O A:HOH408 4.1 11.2 1.0
CG A:GLU217 4.2 5.0 1.0
OE1 A:GLU217 4.2 8.2 1.0
OD1 A:ASP287 4.3 7.1 1.0
OD2 A:ASP245 4.4 5.4 1.0
C6 A:DFR389 4.4 16.4 1.0
CB A:GLU217 4.4 5.0 1.0
CG A:GLU181 4.4 8.6 1.0
CE1 A:HIS220 4.4 7.9 1.0
C3 A:DFR389 4.5 12.2 1.0
C2 A:DFR389 4.8 13.2 1.0
ND2 A:ASN215 4.8 7.0 1.0

Reference:

H.L.Carrell, J.P.Glusker, V.Burger, F.Manfre, D.Tritsch, J.F.Biellmann. X-Ray Analysis of D-Xylose Isomerase at 1.9 A: Native Enzyme in Complex with Substrate and with A Mechanism-Designed Inactivator. Proc.Natl.Acad.Sci.Usa V. 86 4440 1989.
ISSN: ISSN 0027-8424
PubMed: 2734296
DOI: 10.1073/PNAS.86.12.4440
Page generated: Sun Oct 6 14:16:37 2024

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