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Magnesium in PDB 5hmq: Xylose Isomerase-Like Tim Barrel/4-Hydroxyphenylpyruvate Dioxygenase Fusion Protein

Enzymatic activity of Xylose Isomerase-Like Tim Barrel/4-Hydroxyphenylpyruvate Dioxygenase Fusion Protein

All present enzymatic activity of Xylose Isomerase-Like Tim Barrel/4-Hydroxyphenylpyruvate Dioxygenase Fusion Protein:
4.2.1.118;

Protein crystallography data

The structure of Xylose Isomerase-Like Tim Barrel/4-Hydroxyphenylpyruvate Dioxygenase Fusion Protein, PDB code: 5hmq was solved by J.Peek, D.Christendat, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.44 / 2.37
Space group P 63
Cell size a, b, c (Å), α, β, γ (°) 262.503, 262.503, 139.644, 90.00, 90.00, 120.00
R / Rfree (%) 20.4 / 22.9

Magnesium Binding Sites:

Pages:

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

Binding sites:

The binding sites of Magnesium atom in the Xylose Isomerase-Like Tim Barrel/4-Hydroxyphenylpyruvate Dioxygenase Fusion Protein (pdb code 5hmq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the Xylose Isomerase-Like Tim Barrel/4-Hydroxyphenylpyruvate Dioxygenase Fusion Protein, PDB code: 5hmq:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in 5hmq

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Magnesium binding site 1 out of 12 in the Xylose Isomerase-Like Tim Barrel/4-Hydroxyphenylpyruvate Dioxygenase Fusion Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Xylose Isomerase-Like Tim Barrel/4-Hydroxyphenylpyruvate Dioxygenase Fusion Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg701

b:45.2
occ:1.00
 OE2 A:GLU134 2.0 44.0 1.0
OE1 A:GLU239 2.1 44.5 1.0
OD2 A:ASP165 2.1 47.1 1.0
OE1 A:GLN191 2.2 42.9 1.0
O A:HOH832 2.4 42.3 1.0
O A:HOH837 2.6 44.8 1.0
CD A:GLN191 3.0 42.5 1.0
CD A:GLU239 3.1 41.3 1.0
CD A:GLU134 3.1 45.1 1.0
CG A:ASP165 3.2 46.8 1.0
OE2 A:GLU239 3.5 42.0 1.0
NE2 A:GLN191 3.5 42.6 1.0
OE1 A:GLU134 3.6 46.0 1.0
CB A:ASP165 3.6 44.7 1.0
CD2 A:HIS168 4.1 45.2 1.0
NE2 A:HIS168 4.1 45.4 1.0
NH1 A:ARG210 4.2 43.1 1.0
CG A:GLN191 4.2 42.1 1.0
OD1 A:ASP165 4.3 44.5 1.0
CB A:GLN191 4.4 40.5 1.0
NH2 A:ARG210 4.4 45.6 1.0
CG A:GLU134 4.4 46.0 1.0
CG A:GLU239 4.4 39.2 1.0
CD1 A:LEU97 4.6 42.1 1.0
O A:HOH928 4.7 49.5 1.0
CB A:GLU239 4.7 40.6 1.0
CZ A:ARG210 4.8 45.0 1.0
CA A:ASP165 4.9 42.2 1.0

Magnesium binding site 2 out of 12 in 5hmq

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Magnesium binding site 2 out of 12 in the Xylose Isomerase-Like Tim Barrel/4-Hydroxyphenylpyruvate Dioxygenase Fusion Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Xylose Isomerase-Like Tim Barrel/4-Hydroxyphenylpyruvate Dioxygenase Fusion Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg702

b:44.8
occ:1.00
 O A:HOH819 2.0 47.2 1.0
O A:HOH916 2.1 41.5 1.0
NE2 A:HIS443 2.1 49.7 1.0
OE1 A:GLU599 2.2 48.2 1.0
O A:HOH897 2.2 40.6 1.0
NE2 A:HIS521 2.3 45.7 1.0
CE1 A:HIS443 3.0 50.1 1.0
CD A:GLU599 3.1 49.7 1.0
CE1 A:HIS521 3.1 45.9 1.0
CD2 A:HIS443 3.2 50.6 1.0
OE2 A:GLU599 3.3 46.4 1.0
CD2 A:HIS521 3.4 46.0 1.0
ND1 A:HIS443 4.1 50.9 1.0
CG A:HIS443 4.3 49.5 1.0
ND1 A:HIS521 4.3 47.1 1.0
O A:TYR610 4.4 49.8 1.0
CB A:ALA523 4.4 45.4 1.0
OH A:TYR588 4.5 47.8 1.0
CG A:HIS521 4.5 45.7 1.0
CG A:GLU599 4.5 50.3 1.0
CE1 A:TYR588 4.6 46.9 1.0
CB A:GLU599 4.8 49.5 1.0
CB A:TYR610 4.9 47.4 1.0
CD1 A:TYR610 4.9 46.0 1.0

Magnesium binding site 3 out of 12 in 5hmq

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Magnesium binding site 3 out of 12 in the Xylose Isomerase-Like Tim Barrel/4-Hydroxyphenylpyruvate Dioxygenase Fusion Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Xylose Isomerase-Like Tim Barrel/4-Hydroxyphenylpyruvate Dioxygenase Fusion Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg701

b:38.7
occ:1.00
 OE1 B:GLU239 2.0 37.1 1.0
OE1 B:GLU134 2.1 37.8 1.0
OD2 B:ASP165 2.2 37.0 1.0
O B:HOH909 2.2 39.0 1.0
O B:HOH811 2.3 34.5 1.0
OE1 B:GLN191 2.4 38.7 1.0
CD B:GLU239 2.9 38.4 1.0
CD B:GLU134 3.1 36.8 1.0
CD B:GLN191 3.2 35.4 1.0
OE2 B:GLU239 3.3 37.7 1.0
CG B:ASP165 3.3 37.7 1.0
OE2 B:GLU134 3.5 38.5 1.0
NE2 B:GLN191 3.7 37.4 1.0
CB B:ASP165 3.9 35.4 1.0
NE2 B:HIS168 4.0 37.8 1.0
CD2 B:HIS168 4.1 36.9 1.0
NH1 B:ARG210 4.1 33.9 1.0
CG B:GLU239 4.3 36.0 1.0
NH2 B:ARG210 4.4 36.8 1.0
OD1 B:ASP165 4.4 38.8 1.0
CG B:GLN191 4.4 36.5 1.0
CG B:GLU134 4.5 35.8 1.0
CB B:GLN191 4.5 36.9 1.0
CB B:GLU239 4.6 35.5 1.0
CD1 B:LEU97 4.7 33.8 1.0
CZ B:ARG210 4.7 36.0 1.0

Magnesium binding site 4 out of 12 in 5hmq

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Magnesium binding site 4 out of 12 in the Xylose Isomerase-Like Tim Barrel/4-Hydroxyphenylpyruvate Dioxygenase Fusion Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Xylose Isomerase-Like Tim Barrel/4-Hydroxyphenylpyruvate Dioxygenase Fusion Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg702

b:38.1
occ:1.00
 O B:HOH941 2.1 39.2 1.0
O B:HOH865 2.1 39.9 1.0
OE1 B:GLU599 2.1 44.1 1.0
O B:HOH880 2.2 40.1 1.0
NE2 B:HIS521 2.2 40.2 1.0
NE2 B:HIS443 2.4 39.9 1.0
CE1 B:HIS521 3.0 41.0 1.0
CD2 B:HIS521 3.2 41.8 1.0
CD B:GLU599 3.2 44.7 1.0
CE1 B:HIS443 3.3 39.2 1.0
CD2 B:HIS443 3.4 39.1 1.0
OE2 B:GLU599 3.6 42.5 1.0
ND1 B:HIS521 4.1 42.5 1.0
CG B:HIS521 4.3 41.8 1.0
OH B:TYR588 4.3 45.0 1.0
ND1 B:HIS443 4.4 41.0 1.0
CE1 B:TYR588 4.4 44.0 1.0
CB B:ALA523 4.5 37.6 1.0
CG B:HIS443 4.5 39.2 1.0
CG B:GLU599 4.5 43.2 1.0
O B:TYR610 4.6 45.5 1.0
CB B:GLU599 4.7 40.1 1.0
CZ B:TYR588 4.9 44.0 1.0
CD1 B:TYR610 5.0 46.5 1.0

Magnesium binding site 5 out of 12 in 5hmq

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Magnesium binding site 5 out of 12 in the Xylose Isomerase-Like Tim Barrel/4-Hydroxyphenylpyruvate Dioxygenase Fusion Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Xylose Isomerase-Like Tim Barrel/4-Hydroxyphenylpyruvate Dioxygenase Fusion Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg701

b:43.9
occ:1.00
 O C:HOH823 2.0 45.8 1.0
O C:HOH832 2.0 41.7 1.0
OE1 C:GLN191 2.0 44.9 1.0
OE1 C:GLU134 2.1 39.4 1.0
OE1 C:GLU239 2.1 45.0 1.0
OD2 C:ASP165 2.1 43.6 1.0
CD C:GLU239 3.1 45.8 1.0
CD C:GLU134 3.1 43.3 1.0
CD C:GLN191 3.1 42.1 1.0
CG C:ASP165 3.2 43.3 1.0
OE2 C:GLU239 3.4 46.9 1.0
OE2 C:GLU134 3.5 42.5 1.0
NE2 C:GLN191 3.7 40.2 1.0
CB C:ASP165 3.7 43.3 1.0
CD2 C:HIS168 4.0 45.3 1.0
NE2 C:HIS168 4.0 45.9 1.0
NH1 C:ARG210 4.1 45.3 1.0
NH2 C:ARG210 4.3 45.1 1.0
OD1 C:ASP165 4.3 46.2 1.0
CG C:GLN191 4.4 41.8 1.0
CG C:GLU239 4.4 42.6 1.0
CG C:GLU134 4.4 44.2 1.0
CB C:GLN191 4.5 40.6 1.0
CZ C:ARG210 4.6 47.0 1.0
CB C:GLU239 4.7 43.3 1.0
CD1 C:LEU97 4.7 39.7 1.0

Magnesium binding site 6 out of 12 in 5hmq

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Magnesium binding site 6 out of 12 in the Xylose Isomerase-Like Tim Barrel/4-Hydroxyphenylpyruvate Dioxygenase Fusion Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Xylose Isomerase-Like Tim Barrel/4-Hydroxyphenylpyruvate Dioxygenase Fusion Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg702

b:45.4
occ:1.00
 O C:HOH882 2.1 51.0 1.0
O C:HOH843 2.1 47.0 1.0
NE2 C:HIS443 2.2 47.8 1.0
OE1 C:GLU599 2.3 52.3 1.0
O C:HOH919 2.4 46.3 1.0
NE2 C:HIS521 2.4 45.5 1.0
CE1 C:HIS443 3.1 47.6 1.0
CE1 C:HIS521 3.2 45.4 1.0
CD2 C:HIS443 3.2 48.3 1.0
CD C:GLU599 3.3 49.1 1.0
CD2 C:HIS521 3.4 47.1 1.0
OE2 C:GLU599 3.5 48.9 1.0
ND1 C:HIS443 4.2 46.4 1.0
CG C:HIS443 4.3 46.2 1.0
ND1 C:HIS521 4.3 45.5 1.0
OH C:TYR588 4.3 52.9 1.0
CG C:HIS521 4.5 48.0 1.0
O C:TYR610 4.5 55.5 1.0
CB C:ALA523 4.5 44.0 1.0
CD1 C:TYR610 4.5 51.0 1.0
CE1 C:TYR588 4.6 50.4 1.0
CG C:GLU599 4.6 46.2 1.0
CB C:TYR610 4.7 51.9 1.0
CB C:GLU599 4.9 46.8 1.0
CZ C:TYR588 5.0 50.2 1.0

Magnesium binding site 7 out of 12 in 5hmq

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Magnesium binding site 7 out of 12 in the Xylose Isomerase-Like Tim Barrel/4-Hydroxyphenylpyruvate Dioxygenase Fusion Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Xylose Isomerase-Like Tim Barrel/4-Hydroxyphenylpyruvate Dioxygenase Fusion Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg701

b:33.7
occ:1.00
 OE1 D:GLN191 2.0 34.5 1.0
OE1 D:GLU239 2.1 36.9 1.0
OD2 D:ASP165 2.1 36.3 1.0
OE1 D:GLU134 2.1 34.7 1.0
O D:HOH923 2.2 38.3 1.0
O D:HOH814 2.3 31.2 1.0
CD D:GLU239 3.1 36.7 1.0
CD D:GLU134 3.1 34.3 1.0
CD D:GLN191 3.1 34.5 1.0
CG D:ASP165 3.2 33.6 1.0
OE2 D:GLU134 3.5 36.3 1.0
OE2 D:GLU239 3.5 38.9 1.0
CB D:ASP165 3.7 33.0 1.0
NE2 D:GLN191 3.7 35.1 1.0
NE2 D:HIS168 4.1 37.4 1.0
CD2 D:HIS168 4.1 36.3 1.0
NH1 D:ARG210 4.1 36.9 1.0
O D:HOH977 4.2 38.1 1.0
OD1 D:ASP165 4.3 39.6 1.0
CG D:GLN191 4.3 32.5 1.0
NH2 D:ARG210 4.3 37.6 1.0
CB D:GLN191 4.4 32.9 1.0
CG D:GLU239 4.4 37.4 1.0
CG D:GLU134 4.5 34.4 1.0
CD1 D:LEU97 4.6 30.8 1.0
CB D:GLU239 4.6 33.4 1.0
CZ D:ARG210 4.7 37.0 1.0
CA D:ASP165 5.0 32.1 1.0

Magnesium binding site 8 out of 12 in 5hmq

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Magnesium binding site 8 out of 12 in the Xylose Isomerase-Like Tim Barrel/4-Hydroxyphenylpyruvate Dioxygenase Fusion Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Xylose Isomerase-Like Tim Barrel/4-Hydroxyphenylpyruvate Dioxygenase Fusion Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg702

b:47.7
occ:1.00
 O D:HOH885 2.1 49.8 1.0
O D:HOH846 2.1 44.9 1.0
O D:HOH984 2.3 45.9 1.0
NE2 D:HIS521 2.3 46.9 1.0
OE1 D:GLU599 2.3 51.2 1.0
NE2 D:HIS443 2.4 49.2 1.0
CE1 D:HIS521 3.1 46.9 1.0
CE1 D:HIS443 3.3 51.7 1.0
CD D:GLU599 3.3 49.5 1.0
CD2 D:HIS521 3.4 45.6 1.0
CD2 D:HIS443 3.4 50.6 1.0
OE2 D:GLU599 3.5 46.6 1.0
OH D:TYR588 4.2 47.4 1.0
ND1 D:HIS521 4.2 48.5 1.0
CG D:HIS521 4.4 47.4 1.0
ND1 D:HIS443 4.4 50.7 1.0
O D:TYR610 4.4 50.3 1.0
CG D:HIS443 4.5 48.2 1.0
CE1 D:TYR588 4.5 47.8 1.0
CG D:GLU599 4.7 48.8 1.0
CB D:ALA523 4.7 44.3 1.0
CD1 D:TYR610 4.7 51.1 1.0
CB D:TYR610 4.7 47.6 1.0
CZ D:TYR588 4.9 47.4 1.0
CB D:GLU599 5.0 45.9 1.0

Magnesium binding site 9 out of 12 in 5hmq

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Magnesium binding site 9 out of 12 in the Xylose Isomerase-Like Tim Barrel/4-Hydroxyphenylpyruvate Dioxygenase Fusion Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Xylose Isomerase-Like Tim Barrel/4-Hydroxyphenylpyruvate Dioxygenase Fusion Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg701

b:30.9
occ:1.00
 NE2 E:GLN191 2.0 30.2 1.0
OD2 E:ASP165 2.0 32.7 1.0
OE1 E:GLU239 2.1 34.2 1.0
O E:HOH846 2.1 32.4 1.0
OE2 E:GLU134 2.1 33.5 1.0
O E:HOH889 2.3 33.6 1.0
CD E:GLU239 3.1 35.5 1.0
CD E:GLN191 3.1 34.6 1.0
CD E:GLU134 3.1 34.1 1.0
CG E:ASP165 3.2 33.5 1.0
OE1 E:GLU134 3.5 34.4 1.0
OE2 E:GLU239 3.5 33.0 1.0
OE1 E:GLN191 3.6 31.3 1.0
CB E:ASP165 3.7 31.5 1.0
NE2 E:HIS168 4.0 35.5 1.0
CD2 E:HIS168 4.1 38.9 1.0
NH1 E:ARG210 4.2 34.6 1.0
OD1 E:ASP165 4.2 34.2 1.0
O E:HOH1014 4.3 42.2 1.0
NH2 E:ARG210 4.3 35.1 1.0
CG E:GLN191 4.4 31.2 1.0
CG E:GLU239 4.4 33.3 1.0
CB E:GLN191 4.5 30.8 1.0
CG E:GLU134 4.5 34.7 1.0
CB E:GLU239 4.7 31.2 1.0
CD1 E:LEU97 4.7 32.7 1.0
CZ E:ARG210 4.7 33.6 1.0

Magnesium binding site 10 out of 12 in 5hmq

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Magnesium binding site 10 out of 12 in the Xylose Isomerase-Like Tim Barrel/4-Hydroxyphenylpyruvate Dioxygenase Fusion Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Xylose Isomerase-Like Tim Barrel/4-Hydroxyphenylpyruvate Dioxygenase Fusion Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg702

b:42.0
occ:1.00
 O E:HOH981 2.0 44.1 1.0
O E:HOH851 2.1 45.8 1.0
O E:HOH1003 2.2 42.5 1.0
OE1 E:GLU599 2.2 47.6 1.0
NE2 E:HIS521 2.3 43.2 1.0
NE2 E:HIS443 2.4 49.8 1.0
CE1 E:HIS521 3.1 45.0 1.0
CD E:GLU599 3.2 48.2 1.0
CE1 E:HIS443 3.3 50.2 1.0
CD2 E:HIS443 3.3 50.0 1.0
CD2 E:HIS521 3.3 44.0 1.0
OE2 E:GLU599 3.4 47.2 1.0
OH E:TYR588 4.2 48.3 1.0
ND1 E:HIS521 4.2 44.1 1.0
CG E:HIS521 4.4 43.1 1.0
ND1 E:HIS443 4.4 50.1 1.0
CG E:HIS443 4.5 50.5 1.0
O E:TYR610 4.5 49.9 1.0
CE1 E:TYR588 4.5 48.3 1.0
CG E:GLU599 4.5 46.0 1.0
CB E:ALA523 4.6 39.4 1.0
CB E:GLU599 4.9 46.3 1.0
CB E:TYR610 4.9 48.6 1.0
CD1 E:TYR610 4.9 48.9 1.0
CZ E:TYR588 4.9 50.3 1.0

Reference:

J.Peek, D.Christendat. Structure of A Putative Xylose Isomerase-Like Tim Barrel/4-Hydroxyphenylpyruvate Dioxygenase Fusion Protein From Pseudomonas Putida at 2.4 Angstroms Resolution. To Be Published.
Page generated: Sun Sep 29 16:01:56 2024

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