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Magnesium in PDB 1dxi: Structure Determination of Glucose Isomerase From Streptomyces Murinus at 2.6 Angstroms Resolution

Enzymatic activity of Structure Determination of Glucose Isomerase From Streptomyces Murinus at 2.6 Angstroms Resolution

All present enzymatic activity of Structure Determination of Glucose Isomerase From Streptomyces Murinus at 2.6 Angstroms Resolution:
5.3.1.5;

Protein crystallography data

The structure of Structure Determination of Glucose Isomerase From Streptomyces Murinus at 2.6 Angstroms Resolution, PDB code: 1dxi was solved by H.Rasmussen, T.La Cour, J.Nyborg, M.Schulein, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 6.00 / 2.60
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 137.650, 137.650, 132.200, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure Determination of Glucose Isomerase From Streptomyces Murinus at 2.6 Angstroms Resolution (pdb code 1dxi). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure Determination of Glucose Isomerase From Streptomyces Murinus at 2.6 Angstroms Resolution, PDB code: 1dxi:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 1dxi

Go back to Magnesium Binding Sites List in 1dxi
Magnesium binding site 1 out of 4 in the Structure Determination of Glucose Isomerase From Streptomyces Murinus at 2.6 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure Determination of Glucose Isomerase From Streptomyces Murinus at 2.6 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg389

b:17.1
occ:1.00
 OE2 A:GLU181 2.1 18.6 1.0
OE2 A:GLU217 2.1 17.2 1.0
OD2 A:ASP245 2.1 17.0 1.0
OD2 A:ASP287 2.3 16.4 1.0
OE1 A:GLU181 2.6 21.3 1.0
O A:HOH391 2.6 36.0 1.0
CD A:GLU181 2.7 18.8 1.0
CD A:GLU217 3.2 17.9 1.0
CG A:ASP245 3.3 18.8 1.0
CG A:GLU217 3.4 20.2 1.0
CG A:ASP287 3.5 19.9 1.0
CB A:ASP245 3.9 16.3 1.0
CB A:ASP287 4.1 17.5 1.0
CG A:GLU181 4.2 20.5 1.0
CE1 A:HIS220 4.2 18.3 1.0
OD1 A:ASP245 4.2 21.1 1.0
OE1 A:GLU217 4.3 16.7 1.0
ND2 A:ASN215 4.6 16.6 1.0
OD1 A:ASP287 4.6 19.5 1.0
NE2 A:HIS220 4.6 16.6 1.0
O A:HOH392 4.6 21.6 1.0
CB A:GLU217 4.7 20.0 1.0
ND1 A:HIS220 4.9 18.2 1.0

Magnesium binding site 2 out of 4 in 1dxi

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Magnesium binding site 2 out of 4 in the Structure Determination of Glucose Isomerase From Streptomyces Murinus at 2.6 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure Determination of Glucose Isomerase From Streptomyces Murinus at 2.6 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg390

b:12.0
occ:1.00
 O A:HOH392 1.8 21.6 1.0
OD1 A:ASP257 2.0 25.5 1.0
OE1 A:GLU217 2.1 16.7 1.0
OD2 A:ASP255 2.1 22.6 1.0
OD1 A:ASP255 2.6 21.9 1.0
CG A:ASP255 2.7 21.9 1.0
NE2 A:HIS220 2.8 16.6 1.0
CG A:ASP257 2.9 26.9 1.0
CD A:GLU217 3.0 17.9 1.0
OD2 A:ASP257 3.0 28.7 1.0
CD2 A:HIS220 3.1 17.4 1.0
OE2 A:GLU217 3.3 17.2 1.0
ND2 A:ASN247 3.7 21.4 1.0
CE1 A:HIS220 4.0 18.3 1.0
CB A:ASP255 4.2 19.0 1.0
CB A:ASP257 4.3 24.7 1.0
CG A:GLU217 4.3 20.2 1.0
CG A:HIS220 4.4 18.2 1.0
O A:HOH391 4.6 36.0 1.0
OD2 A:ASP287 4.7 16.4 1.0
ND1 A:HIS220 4.8 18.2 1.0
CG A:ASN247 4.8 20.8 1.0
CA A:ASP257 4.8 21.7 1.0
O A:ASP287 4.9 16.8 1.0
CB A:GLU217 4.9 20.0 1.0
N A:ASP257 5.0 20.1 1.0

Magnesium binding site 3 out of 4 in 1dxi

Go back to Magnesium Binding Sites List in 1dxi
Magnesium binding site 3 out of 4 in the Structure Determination of Glucose Isomerase From Streptomyces Murinus at 2.6 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure Determination of Glucose Isomerase From Streptomyces Murinus at 2.6 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg389

b:14.8
occ:1.00
 OE1 B:GLU217 2.1 19.2 1.0
O B:HOH391 2.2 32.4 1.0
OE1 B:GLU181 2.3 28.4 1.0
OD2 B:ASP245 2.4 23.9 1.0
OD2 B:ASP287 2.4 20.1 1.0
OE2 B:GLU181 2.7 30.4 1.0
CD B:GLU181 2.9 27.3 1.0
CD B:GLU217 3.4 19.9 1.0
O B:HOH392 3.4 30.4 1.0
CG B:ASP245 3.6 21.9 1.0
CG B:ASP287 3.6 19.0 1.0
CB B:ASP287 4.0 16.8 1.0
CE1 B:HIS220 4.0 17.4 1.0
CB B:ASP245 4.0 20.5 1.0
OE2 B:GLU217 4.2 20.0 1.0
CG B:GLU217 4.2 16.5 1.0
CB B:GLU217 4.3 16.0 1.0
CG B:GLU181 4.3 22.1 1.0
NE2 B:HIS220 4.6 17.5 1.0
OD1 B:ASP245 4.6 18.4 1.0
OD1 B:ASP287 4.6 16.9 1.0
ND1 B:HIS220 4.7 15.4 1.0
ND2 B:ASN215 4.8 17.9 1.0
MG B:MG390 5.0 4.7 1.0

Magnesium binding site 4 out of 4 in 1dxi

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Magnesium binding site 4 out of 4 in the Structure Determination of Glucose Isomerase From Streptomyces Murinus at 2.6 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure Determination of Glucose Isomerase From Streptomyces Murinus at 2.6 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg390

b:4.7
occ:1.00
 OE2 B:GLU217 1.8 20.0 1.0
OD1 B:ASP257 1.8 18.2 1.0
O B:HOH392 1.8 30.4 1.0
OD2 B:ASP255 1.9 24.0 1.0
OD1 B:ASP255 2.6 24.6 1.0
CG B:ASP255 2.6 23.4 1.0
CD B:GLU217 2.9 19.9 1.0
CG B:ASP257 2.9 17.7 1.0
NE2 B:HIS220 3.0 17.5 1.0
OD2 B:ASP257 3.3 19.3 1.0
CD2 B:HIS220 3.5 16.8 1.0
OE1 B:GLU217 3.5 19.2 1.0
ND2 B:ASN247 3.8 17.0 1.0
CE1 B:HIS220 4.0 17.4 1.0
CB B:ASP255 4.1 20.8 1.0
CG B:GLU217 4.1 16.5 1.0
CB B:ASP257 4.2 14.1 1.0
O B:ASP287 4.6 12.4 1.0
CA B:ASP257 4.7 15.8 1.0
O B:HOH391 4.7 32.4 1.0
CG B:HIS220 4.7 17.1 1.0
OD2 B:ASP287 4.8 20.1 1.0
ND1 B:HIS220 4.9 15.4 1.0
N B:ASP257 5.0 15.9 1.0
MG B:MG389 5.0 14.8 1.0
CA B:ASP255 5.0 17.4 1.0

Reference:

H.Rasmussen, T.La Cour, J.Nyborg, M.Schulein. Structure Determination of Glucose Isomerase From Streptomyces Murinus at 2.6 A Resolution. Acta Crystallogr.,Sect.D V. 50 124 1994.
ISSN: ISSN 0907-4449
PubMed: 15299450
DOI: 10.1107/S0907444993009540
Page generated: Mon Dec 14 05:50:59 2020

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