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Magnesium in PDB 8yud: Crystal Structure of Xylose Isomerase From Streptomyces Avermitilis

Enzymatic activity of Crystal Structure of Xylose Isomerase From Streptomyces Avermitilis

All present enzymatic activity of Crystal Structure of Xylose Isomerase From Streptomyces Avermitilis:
5.3.1.5;

Protein crystallography data

The structure of Crystal Structure of Xylose Isomerase From Streptomyces Avermitilis, PDB code: 8yud was solved by K.H.Nam, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.21 / 2.81
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 129.135, 129.135, 233.058, 90, 90, 120
R / Rfree (%) 18.7 / 24.3

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of Xylose Isomerase From Streptomyces Avermitilis (pdb code 8yud). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the Crystal Structure of Xylose Isomerase From Streptomyces Avermitilis, PDB code: 8yud:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in 8yud

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Magnesium binding site 1 out of 12 in the Crystal Structure of Xylose Isomerase From Streptomyces Avermitilis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Xylose Isomerase From Streptomyces Avermitilis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:38.5
occ:1.00
 OD2 A:ASP287 1.8 50.3 1.0
OE2 A:GLU181 1.9 42.3 1.0
OE1 A:GLU217 2.5 37.3 1.0
OD2 A:ASP245 2.6 40.8 1.0
CD A:GLU181 2.8 36.5 1.0
CG A:ASP287 3.0 41.5 1.0
OE1 A:GLU181 3.2 41.2 1.0
CD A:GLU217 3.7 41.2 1.0
CB A:ASP287 3.7 31.1 1.0
CG A:ASP245 3.8 38.5 1.0
OD1 A:ASP287 4.0 41.0 1.0
CG A:GLU181 4.1 28.2 1.0
CB A:ASP245 4.4 31.9 1.0
CE1 A:HIS220 4.4 42.7 1.0
OE2 A:GLU217 4.5 35.9 1.0
MG A:MG402 4.6 40.0 1.0
CB A:GLU217 4.7 28.8 1.0
CG A:GLU217 4.7 30.4 1.0
ND2 A:ASN215 4.7 32.4 1.0
OD1 A:ASP245 4.8 33.9 1.0
NE2 A:HIS220 4.9 36.6 1.0

Magnesium binding site 2 out of 12 in 8yud

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Magnesium binding site 2 out of 12 in the Crystal Structure of Xylose Isomerase From Streptomyces Avermitilis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Xylose Isomerase From Streptomyces Avermitilis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:40.0
occ:1.00
 OD2 A:ASP255 1.9 39.3 1.0
OE2 A:GLU217 1.9 35.9 1.0
OD1 A:ASP257 2.6 50.2 1.0
CD A:GLU217 2.8 41.2 1.0
NE2 A:HIS220 2.8 36.6 1.0
CG A:ASP255 2.8 44.8 1.0
OE1 A:GLU217 3.1 37.3 1.0
OD1 A:ASP255 3.2 47.0 1.0
OD2 A:ASP257 3.3 46.1 1.0
CG A:ASP257 3.3 40.7 1.0
CD2 A:HIS220 3.5 33.2 1.0
CE1 A:HIS220 3.8 42.7 1.0
ND2 A:ASN247 3.9 47.6 1.0
CG A:GLU217 4.1 30.4 1.0
CB A:ASP255 4.2 34.2 1.0
OD2 A:ASP287 4.5 50.3 1.0
MG A:MG401 4.6 38.5 1.0
CE A:LYS183 4.6 36.3 1.0
CG A:HIS220 4.6 30.2 1.0
NZ A:LYS183 4.6 39.0 1.0
ND1 A:HIS220 4.7 32.4 1.0
CB A:ASP257 4.8 34.5 1.0
O A:ASP287 4.8 43.6 1.0
CG A:ASP287 4.9 41.5 1.0
OE2 A:GLU181 5.0 42.3 1.0

Magnesium binding site 3 out of 12 in 8yud

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Magnesium binding site 3 out of 12 in the Crystal Structure of Xylose Isomerase From Streptomyces Avermitilis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Xylose Isomerase From Streptomyces Avermitilis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg401

b:38.9
occ:1.00
 OE2 B:GLU181 1.8 42.7 1.0
OD2 B:ASP287 2.1 58.3 1.0
OD2 B:ASP245 2.2 27.2 1.0
OE1 B:GLU217 2.6 42.4 1.0
CD B:GLU181 2.7 35.2 1.0
OE1 B:GLU181 3.0 46.8 1.0
CG B:ASP287 3.2 47.4 1.0
CG B:ASP245 3.4 41.3 1.0
CB B:ASP287 3.8 34.5 1.0
CD B:GLU217 3.8 40.5 1.0
CG B:GLU181 4.1 20.9 1.0
OD1 B:ASP245 4.2 41.9 1.0
OD1 B:ASP287 4.2 48.8 1.0
CB B:ASP245 4.3 35.3 1.0
CE1 B:HIS220 4.5 36.3 1.0
MG B:MG402 4.5 36.8 1.0
ND2 B:ASN215 4.6 33.0 1.0
OE2 B:GLU217 4.6 42.1 1.0
CG B:GLU217 4.8 33.7 1.0
CB B:GLU217 4.9 30.9 1.0
NE2 B:HIS220 4.9 43.4 1.0

Magnesium binding site 4 out of 12 in 8yud

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Magnesium binding site 4 out of 12 in the Crystal Structure of Xylose Isomerase From Streptomyces Avermitilis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Xylose Isomerase From Streptomyces Avermitilis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:36.8
occ:1.00
 OE2 B:GLU217 2.6 42.1 1.0
OD2 B:ASP255 2.6 39.5 1.0
OD1 B:ASP257 2.6 41.1 1.0
NE2 B:HIS220 2.8 43.4 1.0
OD2 B:ASP257 3.0 50.4 1.0
CG B:ASP257 3.2 45.6 1.0
OE1 B:GLU217 3.3 42.4 1.0
CD B:GLU217 3.3 40.5 1.0
CG B:ASP255 3.6 43.5 1.0
CE1 B:HIS220 3.7 36.3 1.0
CD2 B:HIS220 3.8 43.5 1.0
OD1 B:ASP255 4.0 54.8 1.0
OD2 B:ASP287 4.2 58.3 1.0
OD1 B:ASP287 4.2 48.8 1.0
CG B:ASP287 4.3 47.4 1.0
MG B:MG401 4.5 38.9 1.0
NZ B:LYS289 4.5 59.9 1.0
NZ B:LYS183 4.5 43.0 1.0
ND2 B:ASN247 4.6 30.3 1.0
CE B:LYS183 4.7 38.0 1.0
CB B:ASP257 4.7 34.4 1.0
CG B:GLU217 4.8 33.7 1.0
OE2 B:GLU181 4.8 42.7 1.0
ND1 B:HIS220 4.8 35.7 1.0
CG B:HIS220 4.9 32.7 1.0
CB B:ASP255 4.9 31.3 1.0
O B:ASP287 5.0 37.7 1.0

Magnesium binding site 5 out of 12 in 8yud

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Magnesium binding site 5 out of 12 in the Crystal Structure of Xylose Isomerase From Streptomyces Avermitilis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Xylose Isomerase From Streptomyces Avermitilis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg401

b:37.1
occ:1.00
 OD2 C:ASP287 1.7 47.5 1.0
OE2 C:GLU181 2.1 46.2 1.0
OE1 C:GLU217 2.3 40.4 1.0
CG C:ASP287 2.9 39.7 1.0
CD C:GLU181 3.0 44.8 1.0
OD2 C:ASP245 3.1 44.6 1.0
OE1 C:GLU181 3.1 55.3 1.0
CD C:GLU217 3.5 42.6 1.0
MG C:MG402 3.6 35.3 1.0
CB C:ASP287 3.8 43.4 1.0
OD1 C:ASP287 3.8 41.6 1.0
OE2 C:GLU217 4.2 33.3 1.0
CE1 C:HIS220 4.2 40.3 1.0
CG C:ASP245 4.2 38.7 1.0
CG C:GLU181 4.4 35.7 1.0
CG C:GLU217 4.6 28.9 1.0
NE2 C:HIS220 4.7 37.1 1.0
CB C:ASP245 4.7 31.6 1.0
CB C:GLU217 4.8 26.1 1.0

Magnesium binding site 6 out of 12 in 8yud

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Magnesium binding site 6 out of 12 in the Crystal Structure of Xylose Isomerase From Streptomyces Avermitilis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Xylose Isomerase From Streptomyces Avermitilis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg402

b:35.3
occ:1.00
 OE2 C:GLU217 2.4 33.3 1.0
OD2 C:ASP255 2.5 34.6 1.0
OD1 C:ASP257 2.8 50.0 1.0
OD2 C:ASP257 2.8 47.4 1.0
OE1 C:GLU217 3.0 40.4 1.0
CD C:GLU217 3.1 42.6 1.0
CG C:ASP257 3.2 42.3 1.0
NE2 C:HIS220 3.5 37.1 1.0
MG C:MG401 3.6 37.1 1.0
CG C:ASP255 3.7 37.5 1.0
OD2 C:ASP287 3.8 47.5 1.0
CG C:ASP287 3.9 39.7 1.0
OD1 C:ASP287 3.9 41.6 1.0
CE1 C:HIS220 4.1 40.3 1.0
OD1 C:ASP255 4.2 50.9 1.0
O C:ASP287 4.2 45.2 1.0
CD2 C:HIS220 4.4 34.2 1.0
NZ C:LYS183 4.5 39.2 1.0
ND2 C:ASN247 4.6 43.3 1.0
CG C:GLU217 4.6 28.9 1.0
CB C:ASP287 4.7 43.4 1.0
CB C:ASP257 4.7 31.9 1.0
OE2 C:GLU181 4.8 46.2 1.0
CB C:ASP255 4.8 34.1 1.0

Magnesium binding site 7 out of 12 in 8yud

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Magnesium binding site 7 out of 12 in the Crystal Structure of Xylose Isomerase From Streptomyces Avermitilis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Xylose Isomerase From Streptomyces Avermitilis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg401

b:35.7
occ:1.00
 OD2 D:ASP287 1.8 49.5 1.0
OE2 D:GLU181 1.9 48.3 1.0
OE1 D:GLU217 2.3 35.5 1.0
OD2 D:ASP245 2.7 44.5 1.0
CD D:GLU181 2.8 40.4 1.0
CG D:ASP287 3.0 44.8 1.0
OE1 D:GLU181 3.0 51.4 1.0
CD D:GLU217 3.6 40.5 1.0
CG D:ASP245 3.7 47.0 1.0
CB D:ASP287 3.7 40.6 1.0
OD1 D:ASP287 4.0 43.5 1.0
CG D:GLU181 4.2 30.2 1.0
CB D:ASP245 4.4 36.2 1.0
OE2 D:GLU217 4.4 38.5 1.0
OD1 D:ASP245 4.5 48.2 1.0
CG D:GLU217 4.5 30.6 1.0
MG D:MG402 4.5 33.0 1.0
CE1 D:HIS220 4.6 34.4 1.0
CB D:GLU217 4.8 25.9 1.0
NE2 D:HIS220 5.0 34.4 1.0

Magnesium binding site 8 out of 12 in 8yud

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Magnesium binding site 8 out of 12 in the Crystal Structure of Xylose Isomerase From Streptomyces Avermitilis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Xylose Isomerase From Streptomyces Avermitilis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg402

b:33.0
occ:1.00
 OE2 D:GLU217 2.0 38.5 1.0
OD2 D:ASP255 2.1 40.3 1.0
NE2 D:HIS220 2.6 34.4 1.0
OD1 D:ASP257 2.7 38.1 1.0
CD D:GLU217 2.8 40.5 1.0
CG D:ASP255 3.0 44.8 1.0
OE1 D:GLU217 3.1 35.5 1.0
OD1 D:ASP255 3.2 50.2 1.0
CD2 D:HIS220 3.4 36.5 1.0
CG D:ASP257 3.4 38.0 1.0
OD2 D:ASP257 3.4 43.7 1.0
CE1 D:HIS220 3.5 34.4 1.0
CG D:GLU217 4.2 30.6 1.0
CB D:ASP255 4.4 34.9 1.0
ND2 D:ASN247 4.5 34.2 1.0
CG D:HIS220 4.5 34.4 1.0
MG D:MG401 4.5 35.7 1.0
ND1 D:HIS220 4.5 31.8 1.0
OD2 D:ASP287 4.6 49.5 1.0
NZ D:LYS183 4.6 43.4 1.0
CE D:LYS183 4.6 34.5 1.0
CB D:ASP257 4.9 35.5 1.0
CG D:ASP287 4.9 44.8 1.0
OE2 D:GLU181 5.0 48.3 1.0

Magnesium binding site 9 out of 12 in 8yud

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Magnesium binding site 9 out of 12 in the Crystal Structure of Xylose Isomerase From Streptomyces Avermitilis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of Xylose Isomerase From Streptomyces Avermitilis within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg401

b:32.4
occ:1.00
 OE1 E:GLU217 1.7 38.0 1.0
OE2 E:GLU181 1.8 48.3 1.0
OD2 E:ASP287 2.2 50.3 1.0
OD2 E:ASP245 2.8 38.4 1.0
CD E:GLU181 2.8 45.7 1.0
CD E:GLU217 2.9 45.7 1.0
OE1 E:GLU181 3.3 54.9 1.0
CG E:ASP287 3.3 42.1 1.0
OE2 E:GLU217 3.6 45.0 1.0
MG E:MG402 3.8 44.2 1.0
CB E:ASP287 3.8 36.1 1.0
CG E:ASP245 3.9 46.3 1.0
CG E:GLU217 4.0 33.1 1.0
CG E:GLU181 4.1 34.4 1.0
CE1 E:HIS220 4.2 36.6 1.0
OD1 E:ASP287 4.3 39.1 1.0
CB E:GLU217 4.5 31.5 1.0
CB E:ASP245 4.5 36.3 1.0
NE2 E:HIS220 4.6 36.9 1.0
OD1 E:ASP245 5.0 44.6 1.0

Magnesium binding site 10 out of 12 in 8yud

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Magnesium binding site 10 out of 12 in the Crystal Structure of Xylose Isomerase From Streptomyces Avermitilis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of Xylose Isomerase From Streptomyces Avermitilis within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg402

b:44.2
occ:1.00
 OE2 E:GLU217 2.3 45.0 1.0
OD2 E:ASP255 2.5 31.3 1.0
NE2 E:HIS220 2.6 36.9 1.0
CD E:GLU217 3.2 45.7 1.0
OD2 E:ASP257 3.2 37.4 1.0
OD1 E:ASP257 3.3 42.8 1.0
CE1 E:HIS220 3.3 36.6 1.0
OE1 E:GLU217 3.3 38.0 1.0
CG E:ASP257 3.6 38.3 1.0
CG E:ASP255 3.7 35.1 1.0
CD2 E:HIS220 3.7 37.9 1.0
MG E:MG401 3.8 32.4 1.0
NZ E:LYS183 4.1 35.1 1.0
OD1 E:ASP255 4.2 43.3 1.0
OD2 E:ASP287 4.2 50.3 1.0
ND1 E:HIS220 4.5 31.9 1.0
CG E:GLU217 4.5 33.1 1.0
ND2 E:ASN247 4.7 35.0 1.0
CE E:LYS183 4.7 37.0 1.0
OE2 E:GLU181 4.7 48.3 1.0
CG E:HIS220 4.7 28.9 1.0
CG E:ASP287 4.7 42.1 1.0
CD E:LYS183 4.9 37.7 1.0
CB E:ASP255 4.9 31.0 1.0
NZ E:LYS289 5.0 44.9 1.0

Reference:

K.H.Nam, K.H.Nam. N/A N/A.
Page generated: Fri Aug 15 21:38:16 2025

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