Magnesium in PDB 2d0o: Strcuture of Diol Dehydratase-Reactivating Factor Complexed with Adp and MG2+

The structure of Strcuture of Diol Dehydratase-Reactivating Factor Complexed with Adp and MG2+, PDB code: 2d0o was solved by N.Shibata, K.Mori, N.Hieda, Y.Higuchi, M.Yamanishi, T.Toraya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.48 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	83.261, 84.599, 280.090, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 23.2

The binding sites of Magnesium atom in the Strcuture of Diol Dehydratase-Reactivating Factor Complexed with Adp and MG2+ (pdb code 2d0o). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Strcuture of Diol Dehydratase-Reactivating Factor Complexed with Adp and MG2+, PDB code: 2d0o:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Strcuture of Diol Dehydratase-Reactivating Factor Complexed with Adp and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Strcuture of Diol Dehydratase-Reactivating Factor Complexed with Adp and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1003 b:27.7 occ:1.00 O A:HOH1119 2.0 30.5 1.0 O A:HOH1118 2.0 21.8 1.0 O A:HOH1117 2.1 31.4 1.0 O3B A:ADP1001 2.1 22.8 1.0 O A:HOH1081 2.1 25.4 1.0 O A:HOH1116 2.2 25.8 1.0 PB A:ADP1001 3.4 26.0 1.0 O2B A:ADP1001 3.7 28.3 1.0 O A:HOH1021 3.8 28.7 1.0 O1A A:ADP1001 4.1 24.2 1.0 O A:HOH1106 4.1 36.8 1.0 OE1 A:GLU391 4.1 35.0 1.0 O3A A:ADP1001 4.2 27.5 1.0 OD2 A:ASP8 4.2 29.8 1.0 OD1 A:ASP413 4.2 41.4 1.0 O A:HOH1212 4.2 33.3 1.0 OD2 A:ASP413 4.3 47.5 1.0 OD1 A:ASP8 4.4 33.9 1.0 O A:HOH1080 4.5 29.4 1.0 O A:HOH1016 4.5 31.7 1.0 O1B A:ADP1001 4.6 22.3 1.0 CG A:ASP413 4.6 45.2 1.0 CA A:GLY10 4.7 22.5 1.0 CG A:ASP8 4.7 29.8 1.0 PA A:ADP1001 4.7 27.4 1.0 CG2 A:VAL594 4.9 27.3 1.0 CD A:GLU391 4.9 37.7 1.0

Magnesium binding site 2 out of 4 in the Strcuture of Diol Dehydratase-Reactivating Factor Complexed with Adp and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Strcuture of Diol Dehydratase-Reactivating Factor Complexed with Adp and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1005 b:26.9 occ:1.00 OD2 A:ASP166 2.0 31.1 1.0 OG1 A:THR105 2.0 28.9 1.0 OE1 B:GLU31 2.1 28.0 1.0 O A:THR105 2.2 27.1 1.0 OD1 A:ASP183 2.2 25.9 1.0 O A:HOH1184 2.3 24.9 1.0 CB A:THR105 3.0 27.1 1.0 C A:THR105 3.0 24.6 1.0 CD B:GLU31 3.2 29.5 1.0 CG A:ASP183 3.2 28.0 1.0 CG A:ASP166 3.2 28.1 1.0 CA A:THR105 3.5 25.9 1.0 OD2 A:ASP183 3.6 24.5 1.0 CG B:GLU31 3.6 31.4 1.0 OD1 A:ASP166 3.9 27.1 1.0 N A:GLY168 4.0 25.9 1.0 N A:THR105 4.0 25.3 1.0 O A:HOH1076 4.0 45.1 1.0 OE2 A:GLU184 4.1 36.9 1.0 C A:ASP166 4.2 25.6 1.0 N A:PRO106 4.2 22.9 1.0 CA A:ASP166 4.2 26.9 1.0 OE2 B:GLU31 4.3 25.6 1.0 CB A:ASP166 4.3 25.1 1.0 O A:ASP166 4.3 24.7 1.0 CG2 A:THR105 4.4 28.6 1.0 CA A:GLY168 4.4 21.2 1.0 N A:VAL169 4.5 17.7 1.0 N A:ASP167 4.5 28.4 1.0 CB A:ASP183 4.6 25.6 1.0 CA A:PRO106 4.6 20.2 1.0 CG A:GLU184 4.8 30.5 1.0 CD A:GLU184 4.8 36.7 1.0 CG2 A:VAL169 4.9 26.6 1.0 C A:ASP167 5.0 25.5 1.0

Magnesium binding site 3 out of 4 in the Strcuture of Diol Dehydratase-Reactivating Factor Complexed with Adp and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Strcuture of Diol Dehydratase-Reactivating Factor Complexed with Adp and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1004 b:25.3 occ:1.00 O C:HOH1040 1.9 26.0 1.0 O3B C:ADP1002 1.9 22.9 1.0 O C:HOH1136 2.0 27.6 1.0 O C:HOH1202 2.1 27.9 1.0 O C:HOH1203 2.1 26.9 1.0 O C:HOH1204 2.1 27.3 1.0 PB C:ADP1002 3.3 23.9 1.0 O C:HOH1015 3.7 24.7 1.0 O2B C:ADP1002 3.7 27.2 1.0 O1A C:ADP1002 4.0 22.0 1.0 O C:HOH1126 4.0 35.2 1.0 O3A C:ADP1002 4.1 26.3 1.0 OD2 C:ASP8 4.1 30.0 1.0 OE1 C:GLU391 4.2 39.9 1.0 OD1 C:ASP413 4.2 43.1 1.0 O C:HOH1233 4.3 33.4 1.0 OD2 C:ASP413 4.3 44.0 1.0 O1B C:ADP1002 4.4 22.1 1.0 OD1 C:ASP8 4.5 31.3 1.0 O C:HOH1058 4.6 31.1 1.0 O C:HOH1013 4.6 31.5 1.0 PA C:ADP1002 4.6 24.9 1.0 CG C:ASP413 4.7 40.0 1.0 CA C:GLY10 4.7 23.8 1.0 CG C:ASP8 4.8 34.7 1.0 CD C:GLU391 5.0 40.0 1.0 OE2 C:GLU15 5.0 30.4 1.0 CG2 C:VAL594 5.0 28.4 1.0

Magnesium binding site 4 out of 4 in the Strcuture of Diol Dehydratase-Reactivating Factor Complexed with Adp and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Strcuture of Diol Dehydratase-Reactivating Factor Complexed with Adp and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1006 b:25.1 occ:1.00 OG1 C:THR105 2.0 27.0 1.0 OD2 C:ASP166 2.1 23.1 1.0 O C:HOH1211 2.1 22.1 1.0 O C:THR105 2.1 28.3 1.0 OE1 D:GLU31 2.1 29.6 1.0 OD1 C:ASP183 2.3 34.3 1.0 C C:THR105 3.0 30.2 1.0 CB C:THR105 3.0 28.7 1.0 CD D:GLU31 3.2 33.1 1.0 CG C:ASP183 3.3 33.0 1.0 CG C:ASP166 3.3 31.0 1.0 CA C:THR105 3.4 29.8 1.0 OD2 C:ASP183 3.6 27.4 1.0 CG D:GLU31 3.7 30.0 1.0 N C:THR105 3.9 30.1 1.0 OD1 C:ASP166 4.0 34.3 1.0 N C:PRO106 4.2 30.6 1.0 O C:HOH1142 4.2 36.6 1.0 N C:GLY168 4.2 25.3 1.0 C C:ASP166 4.2 30.7 1.0 OE2 D:GLU31 4.3 28.8 1.0 CA C:ASP166 4.3 31.4 1.0 CG2 C:THR105 4.3 27.6 1.0 OE2 C:GLU184 4.4 36.6 1.0 CB C:ASP166 4.4 28.2 1.0 O C:ASP166 4.4 29.5 1.0 N C:VAL169 4.6 23.3 1.0 N C:ASP167 4.6 30.9 1.0 CA C:PRO106 4.6 26.8 1.0 CB C:ASP183 4.6 29.6 1.0 CA C:GLY168 4.7 21.9 1.0 CG2 C:VAL169 4.7 23.1 1.0 CG C:GLU184 4.7 31.7 1.0 CD C:GLU184 4.7 30.9 1.0

N.Shibata, K.Mori, N.Hieda, Y.Higuchi, M.Yamanishi, T.Toraya. Release of A Damaged Cofactor From A Coenzyme B12-Dependent Enzyme: X-Ray Structures of Diol Dehydratase-Reactivating Factor Structure V. 13 1745 2005.
ISSN: ISSN 0969-2126
PubMed: 16338403
DOI: 10.1016/J.STR.2005.08.011