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Magnesium in PDB 5nh4: Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with One MG2+ Ions and Glycerol

Enzymatic activity of Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with One MG2+ Ions and Glycerol

All present enzymatic activity of Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with One MG2+ Ions and Glycerol:
5.3.1.5;

Protein crystallography data

The structure of Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with One MG2+ Ions and Glycerol, PDB code: 5nh4 was solved by H.J.Rozeboom, D.B.Janssen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.46 / 1.80
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 78.606, 79.365, 92.096, 115.50, 90.15, 116.92
R / Rfree (%) 19.4 / 22.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with One MG2+ Ions and Glycerol (pdb code 5nh4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with One MG2+ Ions and Glycerol, PDB code: 5nh4:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5nh4

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Magnesium binding site 1 out of 4 in the Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with One MG2+ Ions and Glycerol


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 Piromyces E2 in Complex with One MG2+ Ions and Glycerol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:20.9
occ:1.00
 OD2 A:ASP340 2.0 13.3 1.0
OD2 A:ASP297 2.0 14.7 1.0
OE1 A:GLU269 2.1 17.9 1.0
OE2 A:GLU233 2.1 16.9 1.0
O3 A:GOL503 2.1 26.0 1.0
O2 A:GOL503 2.2 17.9 1.0
CD A:GLU233 3.0 13.9 1.0
C2 A:GOL503 3.1 21.0 1.0
CG A:ASP340 3.1 13.0 1.0
C3 A:GOL503 3.1 23.6 1.0
CG A:ASP297 3.2 14.5 1.0
OE1 A:GLU233 3.2 15.3 1.0
CD A:GLU269 3.3 15.7 1.0
CB A:ASP340 3.7 12.7 1.0
CB A:ASP297 3.8 13.6 1.0
O A:HOH841 4.0 24.2 1.0
OD1 A:ASP340 4.1 13.8 1.0
OE2 A:GLU269 4.1 18.5 1.0
OD1 A:ASP297 4.2 14.7 1.0
NE2 A:HIS272 4.3 19.4 1.0
CG A:GLU269 4.3 14.3 1.0
CB A:GLU269 4.3 12.6 1.0
CG A:GLU233 4.4 12.7 1.0
C1 A:GOL503 4.4 18.5 1.0
CE1 A:HIS272 4.7 18.1 1.0
ND2 A:ASN267 4.8 16.8 1.0
CZ2 A:TRP50 4.9 13.4 1.0

Magnesium binding site 2 out of 4 in 5nh4

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Magnesium binding site 2 out of 4 in the Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with One MG2+ Ions and Glycerol


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 Piromyces E2 in Complex with One MG2+ Ions and Glycerol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg501

b:17.0
occ:1.00
 OD2 B:ASP297 1.9 12.5 1.0
OD2 B:ASP340 2.0 16.6 1.0
OE1 B:GLU269 2.0 15.0 1.0
OE2 B:GLU233 2.1 14.9 1.0
O2 B:GOL503 2.2 17.8 1.0
O1 B:GOL503 2.3 20.2 1.0
CD B:GLU233 3.0 14.4 1.0
C2 B:GOL503 3.0 21.0 1.0
CG B:ASP297 3.1 11.9 1.0
C1 B:GOL503 3.1 21.5 1.0
CG B:ASP340 3.1 15.1 1.0
OE1 B:GLU233 3.2 15.2 1.0
CD B:GLU269 3.3 13.9 1.0
CB B:ASP340 3.7 13.1 1.0
CB B:ASP297 3.7 11.2 1.0
O B:HOH644 4.0 28.5 1.0
OD1 B:ASP297 4.1 12.4 1.0
OE2 B:GLU269 4.1 15.1 1.0
OD1 B:ASP340 4.1 16.6 1.0
CB B:GLU269 4.2 12.7 1.0
CG B:GLU269 4.2 12.7 1.0
C3 B:GOL503 4.3 21.7 1.0
CE1 B:HIS272 4.3 13.1 1.0
CG B:GLU233 4.3 13.4 1.0
O B:HOH613 4.6 39.4 1.0
ND2 B:ASN267 4.7 15.4 1.0
NE2 B:HIS272 4.8 14.1 1.0
CZ2 B:TRP50 4.9 12.1 1.0
ND1 B:HIS272 5.0 13.8 1.0

Magnesium binding site 3 out of 4 in 5nh4

Go back to Magnesium Binding Sites List in 5nh4
Magnesium binding site 3 out of 4 in the Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with One MG2+ Ions and Glycerol


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 Piromyces E2 in Complex with One MG2+ Ions and Glycerol within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg501

b:13.9
occ:1.00
 OD2 C:ASP340 2.0 14.7 1.0
O3 C:GOL504 2.0 23.4 1.0
O2 C:GOL504 2.0 20.0 1.0
OE2 C:GLU233 2.1 16.5 1.0
OE1 C:GLU269 2.1 14.2 1.0
OD2 C:ASP297 2.2 14.4 1.0
C2 C:GOL504 2.8 21.7 1.0
C3 C:GOL504 2.8 22.4 1.0
CD C:GLU233 3.0 15.2 1.0
CG C:ASP340 3.1 14.7 1.0
OE1 C:GLU233 3.3 17.2 1.0
CD C:GLU269 3.3 13.0 1.0
CG C:ASP297 3.4 13.4 1.0
O C:HOH755 3.6 38.6 1.0
CB C:ASP340 3.9 13.1 1.0
O C:HOH828 4.0 31.6 1.0
CB C:ASP297 4.1 12.7 1.0
OE2 C:GLU269 4.1 13.9 1.0
OD1 C:ASP340 4.1 16.7 1.0
CE1 C:HIS272 4.1 14.1 1.0
C1 C:GOL504 4.2 22.0 1.0
CG C:GLU233 4.4 13.4 1.0
CG C:GLU269 4.4 12.5 1.0
OD1 C:ASP297 4.4 12.9 1.0
CB C:GLU269 4.4 12.5 1.0
NE2 C:HIS272 4.6 15.2 1.0
O C:HOH734 4.6 39.0 1.0
ND1 C:HIS272 4.9 13.7 1.0
ND2 C:ASN267 4.9 15.8 1.0
CZ2 C:TRP50 5.0 15.8 1.0

Magnesium binding site 4 out of 4 in 5nh4

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Magnesium binding site 4 out of 4 in the Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with One MG2+ Ions and Glycerol


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 Piromyces E2 in Complex with One MG2+ Ions and Glycerol within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg501

b:14.9
occ:1.00
 O1 D:GOL502 2.0 21.3 1.0
OE1 D:GLU269 2.0 15.0 1.0
OD2 D:ASP340 2.0 14.6 1.0
OE2 D:GLU233 2.0 17.4 1.0
OD2 D:ASP297 2.1 14.1 1.0
O2 D:GOL502 2.2 17.1 1.0
CD D:GLU233 2.9 13.9 1.0
C1 D:GOL502 2.9 20.6 1.0
C2 D:GOL502 3.0 19.8 1.0
CG D:ASP340 3.2 13.2 1.0
CG D:ASP297 3.2 14.8 1.0
OE1 D:GLU233 3.2 15.6 1.0
CD D:GLU269 3.3 13.1 1.0
CB D:ASP340 3.8 12.7 1.0
CB D:ASP297 3.9 13.2 1.0
O D:HOH823 3.9 17.3 1.0
OE2 D:GLU269 4.1 13.7 1.0
CE1 D:HIS272 4.1 11.1 1.0
OD1 D:ASP340 4.2 14.6 1.0
OD1 D:ASP297 4.2 16.1 1.0
CG D:GLU269 4.2 12.6 1.0
CB D:GLU269 4.2 11.5 1.0
CG D:GLU233 4.3 12.1 1.0
C3 D:GOL502 4.4 19.1 1.0
NE2 D:HIS272 4.6 10.9 1.0
ND2 D:ASN267 4.8 13.4 1.0
ND1 D:HIS272 4.9 11.7 1.0

Reference:

M.Lee, H.J.Rozeboom, P.P.De Waal, R.M.De Jong, H.M.Dudek, D.B.Janssen. Metal Dependence of the Xylose Isomerase From Piromyces Sp. E2 Explored By Activity Profiling and Protein Crystallography. Biochemistry V. 56 5991 2017.
ISSN: ISSN 1520-4995
PubMed: 29045784
DOI: 10.1021/ACS.BIOCHEM.7B00777
Page generated: Sun Sep 29 23:16:40 2024

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