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Magnesium in PDB 2r8q: Structure of LMJPDEB1 in Complex with Ibmx

Enzymatic activity of Structure of LMJPDEB1 in Complex with Ibmx

All present enzymatic activity of Structure of LMJPDEB1 in Complex with Ibmx:
3.1.4.17;

Protein crystallography data

The structure of Structure of LMJPDEB1 in Complex with Ibmx, PDB code: 2r8q was solved by H.Wang, Z.Yan, J.Geng, S.Kunz, T.Seebeck, H.Ke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 63.753, 78.688, 70.511, 90.00, 92.46, 90.00
R / Rfree (%) 19 / 20.8

Other elements in 2r8q:

The structure of Structure of LMJPDEB1 in Complex with Ibmx also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of LMJPDEB1 in Complex with Ibmx (pdb code 2r8q). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of LMJPDEB1 in Complex with Ibmx, PDB code: 2r8q:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 2r8q

Go back to Magnesium Binding Sites List in 2r8q
Magnesium binding site 1 out of 2 in the Structure of LMJPDEB1 in Complex with Ibmx


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of LMJPDEB1 in Complex with Ibmx within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2

b:15.9
occ:1.00
OD1 A:ASP722 2.2 14.4 1.0
O A:HOH941 2.2 17.6 1.0
O A:HOH944 2.2 15.4 1.0
O A:HOH945 2.2 14.6 1.0
O A:HOH943 2.2 14.6 1.0
O A:HOH946 2.2 15.8 1.0
CG A:ASP722 3.2 14.6 1.0
OD2 A:ASP722 3.5 12.1 1.0
ZN A:ZN1 3.8 17.0 1.0
O A:HOH949 3.9 36.5 1.0
O A:HOH942 4.0 18.7 1.0
OE2 A:GLU754 4.1 18.4 1.0
NE2 A:HIS757 4.1 14.4 1.0
OG1 A:THR795 4.2 16.8 1.0
O A:HIS721 4.2 14.1 1.0
O A:HOH947 4.3 18.3 1.0
CD2 A:HIS721 4.3 14.1 1.0
OD2 A:ASP835 4.4 21.5 1.0
CB A:ASP722 4.5 13.6 1.0
CD2 A:HIS757 4.5 14.8 1.0
NE2 A:HIS681 4.5 14.9 1.0
CD2 A:HIS725 4.5 16.2 1.0
CB A:THR795 4.7 15.8 1.0
CD2 A:HIS681 4.7 14.9 1.0
NE2 A:HIS721 4.7 15.1 1.0
CA A:ASP722 4.8 13.0 1.0
O A:THR795 4.8 16.9 1.0
NE2 A:HIS725 4.9 15.6 1.0
CD A:GLU754 5.0 18.4 1.0

Magnesium binding site 2 out of 2 in 2r8q

Go back to Magnesium Binding Sites List in 2r8q
Magnesium binding site 2 out of 2 in the Structure of LMJPDEB1 in Complex with Ibmx


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of LMJPDEB1 in Complex with Ibmx within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2

b:14.2
occ:1.00
OD1 B:ASP722 2.1 14.5 1.0
O B:HOH944 2.2 15.0 1.0
O B:HOH942 2.2 15.9 1.0
O B:HOH945 2.2 15.2 1.0
O B:HOH946 2.2 15.0 1.0
O B:HOH947 2.2 16.9 1.0
CG B:ASP722 3.2 16.0 1.0
OD2 B:ASP722 3.5 14.3 1.0
ZN B:ZN1 3.8 17.0 1.0
O B:HOH1047 3.9 30.4 1.0
O B:HOH943 4.1 18.0 1.0
OE2 B:GLU754 4.1 20.0 1.0
NE2 B:HIS757 4.1 14.6 1.0
O B:HIS721 4.2 14.8 1.0
OG1 B:THR795 4.2 15.8 1.0
CD2 B:HIS721 4.3 12.7 1.0
O B:HOH948 4.3 20.0 1.0
OD2 B:ASP835 4.4 19.9 1.0
O B:HOH995 4.4 26.7 1.0
CD2 B:HIS757 4.5 14.3 1.0
CB B:ASP722 4.5 15.2 1.0
NE2 B:HIS681 4.5 16.0 1.0
CD2 B:HIS725 4.6 15.0 1.0
NE2 B:HIS721 4.7 13.3 1.0
CD2 B:HIS681 4.7 15.8 1.0
CB B:THR795 4.7 15.5 1.0
CA B:ASP722 4.8 14.5 1.0
O B:THR795 4.9 17.6 1.0
NE2 B:HIS725 5.0 14.8 1.0

Reference:

H.Wang, Z.Yan, J.Geng, S.Kunz, T.Seebeck, H.Ke. Crystal Structure of the Leishmania Major Phosphodiesterase LMJPDEB1 and Insight Into the Design of the Parasite-Selective Inhibitors. Mol.Microbiol. V. 66 1029 2007.
ISSN: ISSN 0950-382X
PubMed: 17944832
DOI: 10.1111/J.1365-2958.2007.05976.X
Page generated: Mon Dec 14 07:38:06 2020

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