Manganese in PDB 8xia: 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: 8xia 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 (°) 94.200, 100.200, 103.200, 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 8xia). 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: 8xia:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 8xia

Go back to Manganese Binding Sites List in 8xia
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:22.1
occ:1.00
 O A:HOH409 2.1 16.3 1.0
OE1 A:GLU217 2.3 16.3 1.0
OD2 A:ASP257 2.4 14.1 1.0
OD1 A:ASP255 2.4 18.5 1.0
OD2 A:ASP255 2.5 17.0 1.0
NE2 A:HIS220 2.5 12.7 1.0
CG A:ASP255 2.9 18.9 1.0
CD A:GLU217 3.1 15.2 1.0
CD2 A:HIS220 3.1 10.4 1.0
OE2 A:GLU217 3.2 13.3 1.0
CG A:ASP257 3.3 15.3 1.0
OD1 A:ASP257 3.4 17.0 1.0
O A:HOH563 3.6 24.1 1.0
CE1 A:HIS220 3.7 12.2 1.0
O5 A:XLS389 3.8 19.8 1.0
ND2 A:ASN247 4.0 8.7 1.0
O A:HOH412 4.1 20.5 1.0
CB A:ASP255 4.3 13.1 1.0
CG A:HIS220 4.3 11.2 1.0
CG A:GLU217 4.5 11.7 1.0
O A:HOH602 4.6 50.2 1.0
ND1 A:HIS220 4.6 13.0 1.0
CB A:ASP257 4.7 11.6 1.0
NZ A:LYS183 4.7 13.9 1.0
C5 A:XLS389 4.8 24.0 1.0
OD2 A:ASP287 4.8 14.8 1.0
CE A:LYS183 4.8 12.6 1.0
MN A:MN391 4.8 18.1 1.0

Manganese binding site 2 out of 2 in 8xia

Go back to Manganese Binding Sites List in 8xia
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:18.1
occ:1.00
 O3 A:XLS389 2.1 22.0 1.0
O5 A:XLS389 2.1 19.8 1.0
OE1 A:GLU181 2.3 14.8 1.0
OD1 A:ASP245 2.3 13.5 1.0
OD2 A:ASP287 2.3 14.8 1.0
OE2 A:GLU217 2.3 13.3 1.0
C3 A:XLS389 2.9 26.0 1.0
C5 A:XLS389 3.1 24.0 1.0
CD A:GLU181 3.1 13.5 1.0
CG A:ASP287 3.3 14.4 1.0
OE2 A:GLU181 3.4 13.0 1.0
CG A:ASP245 3.4 14.3 1.0
C4 A:XLS389 3.4 25.9 1.0
CD A:GLU217 3.4 15.2 1.0
O4 A:XLS389 3.7 26.7 1.0
CB A:ASP287 3.7 13.0 1.0
O A:HOH409 3.9 16.3 1.0
CB A:ASP245 3.9 10.6 1.0
CE1 A:HIS220 4.0 12.2 1.0
O A:HOH408 4.1 25.7 1.0
CG A:GLU217 4.1 11.7 1.0
CB A:GLU217 4.2 11.6 1.0
OE1 A:GLU217 4.3 16.3 1.0
C2 A:XLS389 4.3 29.5 1.0
OD2 A:ASP245 4.3 14.2 1.0
OD1 A:ASP287 4.4 14.1 1.0
CG A:GLU181 4.5 12.2 1.0
NE2 A:HIS220 4.5 12.7 1.0
MN A:MN390 4.8 22.1 1.0
ND1 A:HIS220 4.8 13.0 1.0
O2 A:XLS389 4.9 31.5 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: Tue Dec 15 05:14:59 2020

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