Magnesium in PDB 5gl3: Crystal Structure of TON_0340 in Complex with Mg

The structure of Crystal Structure of TON_0340 in Complex with Mg, PDB code: 5gl3 was solved by S.G.Lee, Y.S.Sohn, B.H.Oh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.40
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	106.982, 106.982, 363.688, 90.00, 90.00, 90.00
R / Rfree (%)	19.9 / 24.3

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>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of TON_0340 in Complex with Mg (pdb code 5gl3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the Crystal Structure of TON_0340 in Complex with Mg, PDB code: 5gl3:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in the Crystal Structure of TON_0340 in Complex with Mg


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 TON_0340 in Complex with Mg within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:48.3 occ:1.00 OD1 A:ASP61 2.4 33.1 1.0 O A:HOH404 2.4 61.3 1.0 OD2 A:ASP157 2.5 33.1 1.0 OD2 A:ASP246 2.7 37.0 1.0 O A:HOH402 2.7 35.1 1.0 OD1 A:ASP246 2.8 37.8 1.0 OD1 A:ASP157 3.0 30.8 1.0 CG A:ASP246 3.1 36.7 1.0 CG A:ASP157 3.1 31.6 1.0 CG A:ASP61 3.4 30.0 1.0 MG A:MG302 3.6 55.5 1.0 OE2 A:GLU115 3.6 37.1 1.0 CB A:ASP61 3.8 28.0 1.0 CD A:GLU115 3.9 34.6 1.0 O A:HOH431 3.9 30.1 1.0 OE1 A:GLU59 4.0 46.3 1.0 OE1 A:GLU115 4.4 34.4 1.0 CG A:GLU115 4.4 32.9 1.0 OE2 A:GLU59 4.5 43.6 1.0 OD2 A:ASP61 4.5 27.9 1.0 CB A:ASP246 4.6 35.9 1.0 CB A:ASP157 4.6 30.0 1.0 CD A:GLU59 4.7 43.4 1.0 OG A:SER196 4.7 32.1 1.0 N A:SER196 4.8 26.4 1.0

Magnesium binding site 2 out of 12 in the Crystal Structure of TON_0340 in Complex with Mg


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 TON_0340 in Complex with Mg within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:55.5 occ:1.00 OD1 A:ASP157 2.5 30.8 1.0 OE2 A:GLU115 2.5 37.1 1.0 OE2 A:GLU161 2.5 32.9 1.0 O A:HOH404 2.9 61.3 1.0 CD A:GLU115 3.5 34.6 1.0 MG A:MG301 3.6 48.3 1.0 CD A:GLU161 3.6 31.6 1.0 CG A:ASP157 3.7 31.6 1.0 OD1 A:ASN160 3.7 34.2 1.0 OE1 A:GLU115 3.8 34.4 1.0 N A:GLY158 3.8 32.2 1.0 CA A:GLY158 3.9 33.3 1.0 C A:ASP157 4.1 31.5 1.0 CG A:MET128 4.1 56.5 1.0 OD2 A:ASP157 4.3 33.1 1.0 O A:HOH402 4.3 35.1 1.0 CG A:GLU161 4.3 33.6 1.0 OE1 A:GLU161 4.4 31.4 1.0 O A:ASP157 4.5 33.3 1.0 N A:ASP157 4.6 28.7 1.0 SD A:MET128 4.6 60.6 1.0 CG A:ASN160 4.7 34.3 1.0 CA A:ASP157 4.7 30.7 1.0 CB A:ASP157 4.8 30.0 1.0 CG A:GLU115 4.8 32.9 1.0 ND2 A:ASN160 4.9 33.8 1.0

Magnesium binding site 3 out of 12 in the Crystal Structure of TON_0340 in Complex with Mg


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 TON_0340 in Complex with Mg within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:22.8 occ:1.00 O B:HOH439 2.1 45.0 1.0 OD2 B:ASP157 2.2 35.3 1.0 OD1 B:ASP61 2.3 30.4 1.0 O B:HOH405 2.3 28.3 1.0 OD2 B:ASP246 2.3 30.2 1.0 OD1 B:ASP246 2.4 29.5 1.0 CG B:ASP246 2.7 30.0 1.0 CG B:ASP157 3.1 30.2 1.0 OD1 B:ASP157 3.4 26.5 1.0 CG B:ASP61 3.4 28.0 1.0 CB B:ASP61 3.9 28.3 1.0 MG B:MG302 4.1 54.8 1.0 OE2 B:GLU115 4.1 28.0 1.0 O B:HOH438 4.1 29.8 1.0 CB B:ASP246 4.2 29.6 1.0 CB B:ASP157 4.4 29.8 1.0 OE1 B:GLU59 4.4 35.2 1.0 OD2 B:ASP61 4.5 20.9 1.0 CD B:GLU115 4.5 26.6 1.0 N B:SER196 4.6 29.8 1.0 OE2 B:GLU59 4.6 40.8 1.0 CA B:VAL195 4.7 28.6 1.0 O B:ALA194 4.9 28.9 1.0 OE1 B:GLU115 4.9 27.0 1.0 CD B:GLU59 4.9 35.8 1.0 CA B:ASP246 4.9 29.8 1.0 CG1 B:VAL195 5.0 26.7 1.0

Magnesium binding site 4 out of 12 in the Crystal Structure of TON_0340 in Complex with Mg


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 TON_0340 in Complex with Mg within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg302 b:54.8 occ:1.00 OE2 B:GLU115 2.5 28.0 1.0 OD1 B:ASP157 2.6 26.5 1.0 OE2 B:GLU161 2.7 38.0 1.0 O B:HOH428 3.5 33.5 1.0 CD B:GLU115 3.7 26.6 1.0 CG B:ASP157 3.7 30.2 1.0 O B:HOH405 3.8 28.3 1.0 O B:HOH439 3.9 45.0 1.0 CD B:GLU161 3.9 35.9 1.0 CG B:MET128 4.1 45.0 1.0 OD1 B:ASN160 4.1 27.6 1.0 MG B:MG301 4.1 22.8 1.0 N B:GLY158 4.2 32.1 1.0 OE1 B:GLU115 4.2 27.0 1.0 OD2 B:ASP157 4.3 35.3 1.0 CA B:GLY158 4.3 31.2 1.0 C B:ASP157 4.4 31.5 1.0 CG B:GLU161 4.6 33.4 1.0 O B:ASP157 4.7 34.5 1.0 SD B:MET128 4.8 50.2 1.0 CG B:GLU115 4.8 24.4 1.0 OE1 B:GLU161 4.8 34.0 1.0 N B:ASP157 4.8 30.9 1.0 CB B:ASP157 4.9 29.8 1.0 CA B:ASP157 4.9 31.6 1.0 CG B:ASN160 5.0 28.7 1.0

Magnesium binding site 5 out of 12 in the Crystal Structure of TON_0340 in Complex with Mg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of TON_0340 in Complex with Mg within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg301 b:44.7 occ:1.00 OD2 C:ASP246 2.2 40.7 1.0 OD1 C:ASP61 2.3 38.1 1.0 O C:HOH402 2.3 37.1 1.0 OD2 C:ASP157 2.3 45.3 1.0 O C:HOH410 2.5 45.7 1.0 OD1 C:ASP246 2.6 40.9 1.0 CG C:ASP246 2.7 39.7 1.0 CG C:ASP157 3.1 44.2 1.0 OD1 C:ASP157 3.2 46.3 1.0 CG C:ASP61 3.3 36.5 1.0 CB C:ASP61 3.7 34.3 1.0 OE2 C:GLU115 4.1 35.1 1.0 CB C:ASP246 4.2 39.1 1.0 CD C:GLU115 4.4 36.1 1.0 OD2 C:ASP61 4.4 34.3 1.0 OE2 C:GLU59 4.4 45.1 1.0 CB C:ASP157 4.4 42.8 1.0 OE1 C:GLU59 4.5 46.1 1.0 N C:SER196 4.5 27.9 1.0 MG C:MG302 4.7 64.7 1.0 CA C:VAL195 4.8 29.6 1.0 CG C:GLU115 4.8 35.3 1.0 O C:ALA194 4.8 34.0 1.0 OE1 C:GLU115 4.8 36.2 1.0 CD C:GLU59 4.8 45.2 1.0

Magnesium binding site 6 out of 12 in the Crystal Structure of TON_0340 in Complex with Mg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of TON_0340 in Complex with Mg within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg302 b:64.7 occ:1.00 OE2 C:GLU115 2.5 35.1 1.0 OE2 C:GLU161 3.1 42.4 1.0 O C:HOH402 3.3 37.1 1.0 OD1 C:ASP157 3.3 46.3 1.0 OD1 C:ASN160 3.4 44.0 1.0 CD C:GLU115 3.8 36.1 1.0 CG C:MET128 3.8 69.4 1.0 CD C:GLU161 3.9 40.7 1.0 SD C:MET128 4.2 73.0 1.0 CG C:ASN160 4.2 44.0 1.0 ND2 C:ASN160 4.3 44.4 1.0 CA C:GLY158 4.3 44.4 1.0 N C:GLY158 4.3 43.2 1.0 CG C:GLU161 4.3 39.4 1.0 CZ C:PHE50 4.4 43.3 1.0 OE1 C:GLU115 4.5 36.2 1.0 CE1 C:PHE50 4.5 42.6 1.0 CG C:ASP157 4.5 44.2 1.0 OE1 C:GLU161 4.7 39.3 1.0 CE2 C:PHE50 4.7 44.1 1.0 MG C:MG301 4.7 44.7 1.0 CG C:GLU115 4.8 35.3 1.0 OE1 C:GLU59 4.8 46.1 1.0

Magnesium binding site 7 out of 12 in the Crystal Structure of TON_0340 in Complex with Mg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of TON_0340 in Complex with Mg within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg301 b:37.2 occ:1.00 O D:HOH420 2.2 30.3 1.0 O D:HOH403 2.3 54.5 1.0 OD1 D:ASP61 2.4 36.6 1.0 OD2 D:ASP157 2.4 37.3 1.0 OD2 D:ASP246 2.4 45.8 1.0 OD1 D:ASP246 2.4 47.9 1.0 CG D:ASP246 2.7 49.4 1.0 CG D:ASP157 3.3 35.5 1.0 CG D:ASP61 3.3 37.4 1.0 OD1 D:ASP157 3.4 35.0 1.0 CB D:ASP61 3.6 38.7 1.0 O D:HOH418 3.8 33.8 1.0 O D:HOH413 3.9 35.5 1.0 MG D:MG302 4.1 57.1 1.0 OE2 D:GLU59 4.1 51.2 1.0 CB D:ASP246 4.2 49.4 1.0 OE1 D:GLU59 4.3 48.8 1.0 OE2 D:GLU115 4.4 41.8 1.0 OD2 D:ASP61 4.5 36.9 1.0 CD D:GLU115 4.5 40.3 1.0 CD D:GLU59 4.6 49.6 1.0 CB D:ASP157 4.7 34.5 1.0 N D:SER196 4.7 33.0 1.0 OE1 D:GLU115 4.8 41.8 1.0 CG D:GLU115 4.8 38.5 1.0 CA D:ASP246 4.9 49.2 1.0 OG D:SER196 5.0 30.8 1.0

Magnesium binding site 8 out of 12 in the Crystal Structure of TON_0340 in Complex with Mg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of TON_0340 in Complex with Mg within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg302 b:57.1 occ:1.00 OD1 D:ASP157 2.6 35.0 1.0 OE2 D:GLU161 3.2 32.6 1.0 O D:HOH420 3.2 30.3 1.0 O D:HOH403 3.3 54.5 1.0 CA D:GLY158 3.5 36.1 1.0 OE2 D:GLU115 3.6 41.8 1.0 CG D:MET128 3.6 51.5 1.0 N D:GLY158 3.7 36.3 1.0 CG D:ASP157 3.7 35.5 1.0 SD D:MET128 3.9 51.6 1.0 MG D:MG301 4.1 37.2 1.0 C D:ASP157 4.1 36.1 1.0 CD D:GLU161 4.2 33.3 1.0 OD2 D:ASP157 4.3 37.3 1.0 OD1 D:ASN160 4.3 37.7 1.0 O D:ASP157 4.4 37.5 1.0 CD D:GLU115 4.5 40.3 1.0 CE D:MET128 4.6 51.8 1.0 OE1 D:GLU115 4.6 41.8 1.0 O D:HOH413 4.7 35.5 1.0 OE1 D:GLU161 4.8 29.3 1.0 CB D:ASP157 4.8 34.5 1.0 C D:GLY158 4.8 36.1 1.0 CA D:ASP157 4.9 35.9 1.0 N D:ASP157 5.0 36.4 1.0

Magnesium binding site 9 out of 12 in the Crystal Structure of TON_0340 in Complex with Mg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of TON_0340 in Complex with Mg within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg301 b:46.9 occ:1.00 OD1 E:ASP61 2.4 51.8 1.0 OD1 E:ASP246 2.5 64.1 1.0 OD2 E:ASP157 2.7 40.2 1.0 OD2 E:ASP246 2.8 60.8 1.0 MG E:MG302 3.0 55.8 1.0 CG E:ASP246 3.0 63.1 1.0 OD1 E:ASP157 3.4 41.1 1.0 CG E:ASP61 3.4 50.8 1.0 CG E:ASP157 3.4 41.7 1.0 OE2 E:GLU115 3.4 49.8 1.0 OE1 E:GLU59 3.5 55.8 1.0 CB E:ASP61 3.7 52.6 1.0 OE2 E:GLU59 4.0 56.3 1.0 CD E:GLU115 4.2 48.3 1.0 CD E:GLU59 4.2 56.6 1.0 CB E:ASP246 4.5 63.8 1.0 OD2 E:ASP61 4.5 49.1 1.0 CG E:GLU115 4.6 45.5 1.0 CB E:ASP157 4.9 39.3 1.0 OG E:SER196 5.0 41.6 1.0

Magnesium binding site 10 out of 12 in the Crystal Structure of TON_0340 in Complex with Mg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of TON_0340 in Complex with Mg within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg302 b:55.8 occ:1.00 OD1 E:ASP157 2.6 41.1 1.0 OE2 E:GLU115 2.6 49.8 1.0 O E:HOH401 2.7 38.4 1.0 MG E:MG301 3.0 46.9 1.0 OE2 E:GLU161 3.5 35.1 1.0 CG E:ASP157 3.6 41.7 1.0 CD E:GLU115 3.8 48.3 1.0 OD2 E:ASP157 3.9 40.2 1.0 CG E:MET128 4.3 59.4 1.0 OE1 E:GLU115 4.4 47.8 1.0 OE1 E:GLU59 4.5 55.8 1.0 N E:GLY158 4.5 38.4 1.0 CA E:GLY158 4.6 35.9 1.0 CD E:GLU161 4.6 33.9 1.0 C E:ASP157 4.6 39.6 1.0 OD1 E:ASP246 4.8 64.1 1.0 OD1 E:ASN160 4.8 43.7 1.0 SD E:MET128 4.9 62.3 1.0 CB E:ASP157 4.9 39.3 1.0 O E:ASP157 4.9 41.2 1.0 CG E:GLU115 4.9 45.5 1.0 O E:HOH413 4.9 38.1 1.0 OD1 E:ASP61 5.0 51.8 1.0

Y.S.Sohn, S.G.Lee, K.H.Lee, B.Ku, H.C.Shin, S.S.Cha, Y.G.Kim, H.S.Lee, S.G.Kang, B.H.Oh. Identification of A Highly Conserved Hypothetical Protein TON_0340 As A Probable Manganese-Dependent Phosphatase. Plos One V. 11 67549 2016.
ISSN: ESSN 1932-6203
PubMed: 27907125
DOI: 10.1371/JOURNAL.PONE.0167549