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Magnesium in PDB 5nh6: Crystal Structure of Xylose Isomerase From Piromyces E2 Complexed with One MG2+ Ion and Xylitol

Enzymatic activity of Crystal Structure of Xylose Isomerase From Piromyces E2 Complexed with One MG2+ Ion and Xylitol

All present enzymatic activity of Crystal Structure of Xylose Isomerase From Piromyces E2 Complexed with One MG2+ Ion and Xylitol:
5.3.1.5;

Protein crystallography data

The structure of Crystal Structure of Xylose Isomerase From Piromyces E2 Complexed with One MG2+ Ion and Xylitol, PDB code: 5nh6 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) 36.10 / 1.75
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 78.820, 79.340, 91.800, 115.42, 90.18, 116.72
R / Rfree (%) 14 / 16.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Xylose Isomerase From Piromyces E2 Complexed with One MG2+ Ion and Xylitol (pdb code 5nh6). 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 Complexed with One MG2+ Ion and Xylitol, PDB code: 5nh6:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5nh6

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Magnesium binding site 1 out of 4 in the Crystal Structure of Xylose Isomerase From Piromyces E2 Complexed with One MG2+ Ion and Xylitol


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 Complexed with One MG2+ Ion and Xylitol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:13.2
occ:1.00
 OD2 A:ASP297 2.0 16.1 1.0
OE1 A:GLU269 2.0 14.5 1.0
OE2 A:GLU233 2.0 16.2 1.0
OD2 A:ASP340 2.1 15.7 1.0
O4 A:XYL502 2.1 16.7 1.0
O2 A:XYL502 2.1 16.9 1.0
CD A:GLU233 3.0 16.2 1.0
C4 A:XYL502 3.1 18.1 1.0
CG A:ASP297 3.2 14.3 1.0
CG A:ASP340 3.2 14.4 1.0
CD A:GLU269 3.2 14.5 1.0
C2 A:XYL502 3.3 18.3 1.0
OE1 A:GLU233 3.3 16.9 1.0
C3 A:XYL502 3.5 17.7 1.0
O3 A:XYL502 3.7 18.5 1.0
CB A:ASP340 3.7 14.0 1.0
CB A:ASP297 3.7 13.1 1.0
OE2 A:GLU269 4.0 17.2 1.0
O A:HOH843 4.0 25.9 1.0
CE1 A:HIS272 4.1 13.0 1.0
OD1 A:ASP297 4.2 14.5 1.0
OD1 A:ASP340 4.2 14.8 1.0
CG A:GLU269 4.3 12.8 1.0
CB A:GLU269 4.3 12.1 1.0
CG A:GLU233 4.4 15.2 1.0
C5 A:XYL502 4.4 18.0 1.0
NE2 A:HIS272 4.4 13.1 1.0
C1 A:XYL502 4.5 19.5 1.0
ND2 A:ASN267 4.8 13.5 1.0
O1 A:XYL502 4.9 23.0 1.0

Magnesium binding site 2 out of 4 in 5nh6

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Magnesium binding site 2 out of 4 in the Crystal Structure of Xylose Isomerase From Piromyces E2 Complexed with One MG2+ Ion and Xylitol


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 Complexed with One MG2+ Ion and Xylitol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg501

b:10.7
occ:1.00
 OE1 B:GLU269 2.0 12.3 1.0
OD2 B:ASP297 2.0 13.0 1.0
OD2 B:ASP340 2.1 12.5 1.0
OE2 B:GLU233 2.1 14.4 1.0
O4 B:XYL502 2.1 14.6 1.0
O2 B:XYL502 2.1 15.5 1.0
CD B:GLU233 3.0 13.4 1.0
C4 B:XYL502 3.1 15.4 1.0
CG B:ASP340 3.2 11.7 1.0
CG B:ASP297 3.2 12.8 1.0
C2 B:XYL502 3.2 15.8 1.0
CD B:GLU269 3.2 12.0 1.0
OE1 B:GLU233 3.3 15.0 1.0
C3 B:XYL502 3.5 15.4 1.0
O3 B:XYL502 3.6 14.8 1.0
CB B:ASP340 3.7 11.2 1.0
CB B:ASP297 3.7 11.6 1.0
OE2 B:GLU269 4.0 13.0 1.0
O B:HOH835 4.0 22.9 1.0
CE1 B:HIS272 4.1 10.7 1.0
OD1 B:ASP340 4.2 12.2 1.0
OD1 B:ASP297 4.2 13.1 1.0
CG B:GLU269 4.3 11.1 1.0
CB B:GLU269 4.3 10.6 1.0
CG B:GLU233 4.4 12.4 1.0
C5 B:XYL502 4.4 15.5 1.0
NE2 B:HIS272 4.4 10.7 1.0
C1 B:XYL502 4.5 17.2 1.0
ND2 B:ASN267 4.8 11.6 1.0

Magnesium binding site 3 out of 4 in 5nh6

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Magnesium binding site 3 out of 4 in the Crystal Structure of Xylose Isomerase From Piromyces E2 Complexed with One MG2+ Ion and Xylitol


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 Complexed with One MG2+ Ion and Xylitol within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg501

b:10.1
occ:1.00
 OD2 C:ASP297 2.0 13.4 1.0
OE1 C:GLU269 2.0 14.0 1.0
OE2 C:GLU233 2.0 12.0 1.0
OD2 C:ASP340 2.1 13.5 1.0
O4 C:XYL502 2.1 13.8 1.0
O2 C:XYL502 2.1 16.0 1.0
CD C:GLU233 3.0 13.0 1.0
CG C:ASP297 3.1 12.4 1.0
C4 C:XYL502 3.1 15.8 1.0
CG C:ASP340 3.2 12.1 1.0
C2 C:XYL502 3.2 16.9 1.0
OE1 C:GLU233 3.2 13.9 1.0
CD C:GLU269 3.2 13.8 1.0
C3 C:XYL502 3.5 16.3 1.0
O3 C:XYL502 3.7 16.2 1.0
CB C:ASP340 3.7 11.7 1.0
CB C:ASP297 3.7 11.5 1.0
OE2 C:GLU269 4.0 14.8 1.0
O C:HOH808 4.1 31.1 1.0
CE1 C:HIS272 4.2 12.3 1.0
OD1 C:ASP297 4.2 13.0 1.0
OD1 C:ASP340 4.2 12.6 1.0
CG C:GLU269 4.3 11.8 1.0
CB C:GLU269 4.3 11.2 1.0
CG C:GLU233 4.3 12.4 1.0
C5 C:XYL502 4.4 16.1 1.0
C1 C:XYL502 4.5 18.4 1.0
NE2 C:HIS272 4.5 12.4 1.0
ND2 C:ASN267 4.8 13.0 1.0
O1 C:XYL502 5.0 20.2 1.0

Magnesium binding site 4 out of 4 in 5nh6

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Magnesium binding site 4 out of 4 in the Crystal Structure of Xylose Isomerase From Piromyces E2 Complexed with One MG2+ Ion and Xylitol


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 Complexed with One MG2+ Ion and Xylitol within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg501

b:13.2
occ:1.00
 OE1 D:GLU269 1.9 16.6 1.0
OD2 D:ASP297 2.0 16.1 1.0
OD2 D:ASP340 2.0 14.8 1.0
OE2 D:GLU233 2.1 15.9 1.0
O4 D:XYL502 2.1 17.6 1.0
O2 D:XYL502 2.2 17.1 1.0
CD D:GLU233 3.0 15.4 1.0
CG D:ASP297 3.1 14.7 1.0
CG D:ASP340 3.1 13.8 1.0
C4 D:XYL502 3.1 18.8 1.0
CD D:GLU269 3.2 15.2 1.0
C2 D:XYL502 3.3 19.3 1.0
OE1 D:GLU233 3.3 15.9 1.0
C3 D:XYL502 3.5 18.5 1.0
O3 D:XYL502 3.6 19.3 1.0
CB D:ASP340 3.7 13.0 1.0
CB D:ASP297 3.7 13.6 1.0
OE2 D:GLU269 3.9 15.6 1.0
O D:HOH835 4.0 32.1 1.0
CE1 D:HIS272 4.2 14.1 1.0
OD1 D:ASP297 4.2 14.0 1.0
OD1 D:ASP340 4.2 15.1 1.0
CG D:GLU269 4.2 13.7 1.0
CB D:GLU269 4.3 12.9 1.0
CG D:GLU233 4.4 14.7 1.0
NE2 D:HIS272 4.4 14.2 1.0
C5 D:XYL502 4.5 18.0 1.0
C1 D:XYL502 4.5 20.5 1.0
ND2 D:ASN267 4.8 13.3 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 23:17:27 2024

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