Atomistry » Magnesium » PDB 5n78-5noj » 5nh4
Atomistry »
  Magnesium »
    PDB 5n78-5noj »
      5nh4 »

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

Go back to Magnesium Binding Sites List in 5nh4
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

Go back to Magnesium Binding Sites List in 5nh4
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

Go back to Magnesium Binding Sites List in 5nh4
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy