Magnesium in PDB 3s9f: The Structure of Tryparedoxin I From Leishmania Major

The structure of The Structure of Tryparedoxin I From Leishmania Major, PDB code: 3s9f was solved by A.Fiorillo, A.Ilari, G.Colotti, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	67.00 / 1.80
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	33.564, 134.663, 70.924, 90.00, 90.00, 90.00
R / Rfree (%)	20.1 / 24.2

The binding sites of Magnesium atom in the The Structure of Tryparedoxin I From Leishmania Major (pdb code 3s9f). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the The Structure of Tryparedoxin I From Leishmania Major, PDB code: 3s9f:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the The Structure of Tryparedoxin I From Leishmania Major


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Structure of Tryparedoxin I From Leishmania Major within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg146 b:32.1 occ:1.00 O A:LEU112 2.8 21.8 1.0 N A:LEU112 2.9 18.2 1.0 O A:THR125 3.1 23.1 1.0 N A:ARG128 3.1 21.0 1.0 O A:HOH180 3.1 21.6 1.0 N A:ALA127 3.3 21.6 1.0 CB A:ARG128 3.3 22.0 0.5 CB A:ARG128 3.4 15.7 0.5 C A:LEU112 3.5 20.6 1.0 CA A:LEU112 3.6 19.5 1.0 C A:ARG126 3.7 23.4 1.0 C A:THR125 3.7 23.4 1.0 CG2 A:THR111 3.8 20.4 1.0 CA A:ARG128 3.8 21.9 0.5 CA A:ARG126 3.8 24.6 1.0 CA A:ARG128 3.8 15.8 0.5 C A:THR111 3.9 18.2 1.0 CA A:THR111 3.9 18.5 1.0 CB A:LEU112 3.9 20.5 1.0 N A:ARG126 4.0 23.2 1.0 C A:ALA127 4.1 20.6 1.0 CA A:ALA127 4.2 21.0 1.0 O A:ARG126 4.4 24.4 1.0 CB A:THR111 4.4 18.7 1.0 O A:HOH199 4.4 22.4 1.0 CB A:ALA127 4.7 20.2 1.0 CG A:ARG128 4.7 25.4 0.5 N A:ILE113 4.8 19.4 1.0 N A:HIS129 4.8 23.4 1.0 CG A:ARG128 4.8 16.9 0.5 CA A:THR125 4.8 22.8 1.0 C A:ARG128 4.9 23.1 1.0 OG1 A:THR111 4.9 21.2 1.0

Magnesium binding site 2 out of 5 in the The Structure of Tryparedoxin I From Leishmania Major


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Structure of Tryparedoxin I From Leishmania Major within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg147 b:19.9 occ:1.00 O A:HOH159 3.0 12.0 1.0 O A:HOH158 3.1 9.9 1.0 N A:PHE91 3.2 20.4 1.0 NH2 A:ARG15 3.3 30.1 1.0 CA A:PRO90 3.7 18.6 1.0 CE2 A:PHE77 3.8 22.5 1.0 CB A:PRO90 3.9 19.8 1.0 CB A:PHE91 3.9 22.6 1.0 C A:PRO90 3.9 19.5 1.0 CD A:ARG15 3.9 33.6 1.0 CA A:PHE91 4.1 21.5 1.0 CZ A:PHE77 4.3 21.2 1.0 CZ A:ARG15 4.4 32.3 1.0 NE A:ARG15 4.6 32.4 1.0 CD2 A:PHE77 4.7 21.2 1.0 CG A:ARG15 4.9 31.4 1.0 N A:ALA92 4.9 23.2 1.0 CG A:PRO90 5.0 20.2 1.0

Magnesium binding site 3 out of 5 in the The Structure of Tryparedoxin I From Leishmania Major


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Structure of Tryparedoxin I From Leishmania Major within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg148 b:27.7 occ:1.00 CB A:ASN95 3.2 30.1 1.0 OD1 A:ASN93 3.3 28.5 1.0 CG1 A:ILE96 3.4 21.9 0.5 CA A:ASN93 3.6 23.2 1.0 O A:HOH154 3.6 34.2 1.0 CB A:ASN93 3.8 22.0 1.0 N A:ILE96 3.8 21.5 1.0 CG1 A:ILE96 3.9 20.6 0.5 C A:ASN93 3.9 23.6 1.0 CG A:ASN93 4.0 24.1 1.0 N A:ASN95 4.0 27.9 1.0 CD1 A:ILE96 4.0 20.6 0.5 CA A:ASN95 4.1 27.2 1.0 CD1 A:ILE96 4.1 18.1 0.5 OD1 A:ASN95 4.1 39.0 1.0 CG A:ASN95 4.2 35.0 1.0 O A:ASN93 4.2 22.8 1.0 C A:ASN95 4.4 23.5 1.0 CB A:ILE96 4.5 19.0 0.5 CB A:ILE96 4.5 18.7 0.5 N A:ARG94 4.5 29.6 1.0 O A:ALA92 4.6 26.7 1.0 CA A:ILE96 4.7 19.2 0.5 CA A:ILE96 4.7 19.0 0.5 N A:ASN93 4.8 23.0 1.0 O A:HOH210 4.9 30.6 1.0

Magnesium binding site 4 out of 5 in the The Structure of Tryparedoxin I From Leishmania Major


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Structure of Tryparedoxin I From Leishmania Major within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg149 b:38.2 occ:1.00 O A:HIS7 2.7 19.2 1.0 O A:HOH187 2.9 14.1 1.0 O A:HOH178 2.9 20.4 1.0 N A:ALA11 3.4 29.2 1.0 C A:HIS7 3.6 18.9 1.0 CB A:GLU10 3.6 25.4 1.0 C A:GLU10 3.8 22.8 1.0 CA A:HIS7 3.8 20.8 1.0 CB A:ALA11 3.8 29.6 1.0 CA A:ALA11 3.9 30.6 1.0 CB A:HIS7 4.2 21.1 1.0 CA A:GLU10 4.2 23.1 1.0 O A:GLU10 4.3 25.5 1.0 ND1 A:HIS7 4.5 27.5 1.0 OE1 A:GLU10 4.6 41.5 1.0 N A:GLU10 4.7 20.1 1.0 CG A:HIS7 4.8 25.5 1.0 N A:LEU8 4.8 18.4 1.0 CG A:GLU10 4.9 29.8 1.0

Magnesium binding site 5 out of 5 in the The Structure of Tryparedoxin I From Leishmania Major


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of The Structure of Tryparedoxin I From Leishmania Major within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg150 b:33.4 occ:1.00 O A:HOH171 1.9 31.1 1.0 O A:HOH170 2.0 23.5 1.0 NE2 A:HIS58 2.0 35.2 1.0 O A:HOH169 2.1 14.5 1.0 O A:HOH172 2.3 29.2 1.0 O A:HOH176 2.5 36.6 1.0 O A:HOH175 2.6 39.1 1.0 CD2 A:HIS58 3.0 30.7 1.0 CE1 A:HIS58 3.1 34.3 1.0 OD1 A:ASP59 4.0 40.9 1.0 OH A:TYR54 4.1 24.5 1.0 CG A:HIS58 4.1 29.7 1.0 ND1 A:HIS58 4.2 31.0 1.0 O A:HOH164 4.3 23.8 1.0 OD2 A:ASP59 4.7 44.4 1.0 CG A:ASP59 4.7 39.6 1.0 CZ A:TYR54 4.8 23.2 1.0 CE2 A:TYR54 4.9 23.5 1.0

A.Fiorillo, G.Colotti, A.Boffi, P.Baiocco, A.Ilari. The Crystal Structures of the Tryparedoxin-Tryparedoxin Peroxidase Couple Unveil the Structural Determinants of Leishmania Detoxification Pathway. Plos Negl Trop Dis V. 6 E1781 2012.
ISSN: ISSN 1935-2727
PubMed: 22928053
DOI: 10.1371/JOURNAL.PNTD.0001781