Manganese in PDB 5gl4: Crystal Structure of TON_0340 in Complex with Mn

The structure of Crystal Structure of TON_0340 in Complex with Mn, PDB code: 5gl4 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 / 2.20
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	107.041, 107.041, 360.961, 90.00, 90.00, 90.00
R / Rfree (%)	21.7 / 25.9

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>>> Page 1 <<< Page 2, Binding sites: 11 - 17;

Binding sites:

The binding sites of Manganese atom in the Crystal Structure of TON_0340 in Complex with Mn (pdb code 5gl4). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 17 binding sites of Manganese where determined in the Crystal Structure of TON_0340 in Complex with Mn, PDB code: 5gl4:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 17 in the Crystal Structure of TON_0340 in Complex with Mn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of TON_0340 in Complex with Mn within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn301 b:35.3 occ:1.00 O A:HOH403 2.1 34.3 1.0 OD2 A:ASP157 2.2 28.5 1.0 OD2 A:ASP246 2.2 34.6 1.0 OD1 A:ASP61 2.2 31.6 1.0 O A:HOH448 2.3 41.6 1.0 OD1 A:ASP246 2.5 34.2 1.0 CG A:ASP246 2.7 34.2 1.0 CG A:ASP157 3.2 26.4 1.0 CG A:ASP61 3.3 29.6 1.0 OD1 A:ASP157 3.5 25.3 1.0 O A:HOH436 3.6 43.3 1.0 CB A:ASP61 3.7 29.0 1.0 OE2 A:GLU115 3.7 33.2 1.0 MN A:MN302 4.1 35.6 1.0 O A:HOH441 4.2 37.7 1.0 CB A:ASP246 4.2 33.2 1.0 CD A:GLU115 4.2 32.1 1.0 N A:SER196 4.3 26.4 1.0 OD2 A:ASP61 4.4 30.2 1.0 CG1 A:VAL195 4.5 24.9 1.0 CB A:ASP157 4.5 23.3 1.0 OE1 A:GLU115 4.5 32.6 1.0 CA A:VAL195 4.6 24.8 1.0 OG A:SER196 4.7 25.3 1.0 OE1 A:GLU59 4.7 47.2 1.0 OE2 A:GLU59 4.8 44.8 1.0

Manganese binding site 2 out of 17 in the Crystal Structure of TON_0340 in Complex with Mn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of TON_0340 in Complex with Mn within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn302 b:35.6 occ:1.00 OD1 A:ASP157 2.1 25.3 1.0 OE1 A:GLU161 2.1 33.2 1.0 O A:HOH419 2.2 29.6 1.0 O A:HOH436 2.3 43.3 1.0 OE2 A:GLU115 2.4 33.2 1.0 OE1 A:GLU115 2.6 32.6 1.0 CD A:GLU115 2.8 32.1 1.0 CG A:ASP157 3.3 26.4 1.0 CD A:GLU161 3.4 35.3 1.0 N A:GLY158 3.8 27.7 1.0 O A:HOH403 3.8 34.3 1.0 OD2 A:ASP157 3.9 28.5 1.0 N A:ASP157 3.9 21.4 1.0 C A:ASP157 4.0 25.8 1.0 OE2 A:GLU161 4.1 35.8 1.0 MN A:MN301 4.1 35.3 1.0 CA A:GLY158 4.2 29.0 1.0 OD1 A:ASN160 4.2 24.9 1.0 O A:HOH448 4.2 41.6 1.0 CG A:GLU115 4.3 31.7 1.0 OG A:SER196 4.3 25.3 1.0 CA A:ASP157 4.4 24.3 1.0 CB A:ASP157 4.4 23.3 1.0 CG A:GLU161 4.4 32.7 1.0 O A:ASP157 4.6 27.5 1.0 CE1 A:PHE50 4.9 35.8 1.0 CB A:GLU161 4.9 31.7 1.0

Manganese binding site 3 out of 17 in the Crystal Structure of TON_0340 in Complex with Mn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of TON_0340 in Complex with Mn within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn303 b:88.8 occ:1.00 O A:GLY247 2.5 37.3 1.0 OE1 B:GLU266 3.0 42.9 1.0 O B:HOH428 3.3 44.7 1.0 OE2 B:GLU266 3.5 41.0 1.0 CD B:GLU266 3.6 41.1 1.0 C A:GLY247 3.7 35.6 1.0 CA A:ILE248 4.4 35.7 1.0 N A:ILE248 4.5 35.2 1.0 CA A:GLY247 4.7 35.8 1.0 N A:ARG249 4.8 38.2 1.0 O B:GLU266 4.9 39.4 1.0 C A:ILE248 5.0 37.5 1.0

Manganese binding site 4 out of 17 in the Crystal Structure of TON_0340 in Complex with Mn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of TON_0340 in Complex with Mn within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn301 b:30.5 occ:1.00 OD1 B:ASP61 2.0 33.5 1.0 O B:HOH423 2.1 21.1 1.0 O B:HOH443 2.3 38.0 1.0 OD2 B:ASP157 2.3 29.7 1.0 OD2 B:ASP246 2.3 33.0 1.0 OD1 B:ASP246 2.4 26.4 1.0 CG B:ASP246 2.7 30.3 1.0 CG B:ASP61 3.1 28.6 1.0 CG B:ASP157 3.2 26.1 1.0 OD1 B:ASP157 3.3 23.6 1.0 CB B:ASP61 3.7 27.7 1.0 OE2 B:GLU115 4.0 23.9 1.0 OD2 B:ASP61 4.1 26.1 1.0 MN B:MN302 4.1 31.0 1.0 O B:HOH436 4.1 44.8 1.0 CB B:ASP246 4.2 29.1 1.0 N B:SER196 4.2 22.7 1.0 CD B:GLU115 4.4 25.5 1.0 CA B:VAL195 4.5 22.7 1.0 CB B:ASP157 4.6 23.4 1.0 OE2 B:GLU59 4.6 42.4 1.0 CG1 B:VAL195 4.6 22.6 1.0 O B:HOH456 4.6 38.7 1.0 OG B:SER196 4.7 26.3 1.0 OE1 B:GLU59 4.8 41.0 1.0 OE1 B:GLU115 4.9 27.3 1.0 CB B:SER196 4.9 25.8 1.0 O B:ALA194 4.9 28.7 1.0 C B:VAL195 4.9 22.6 1.0

Manganese binding site 5 out of 17 in the Crystal Structure of TON_0340 in Complex with Mn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of TON_0340 in Complex with Mn within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn302 b:31.0 occ:1.00 OE2 B:GLU115 2.1 23.9 1.0 OD1 B:ASP157 2.2 23.6 1.0 O B:HOH410 2.2 26.4 1.0 OE2 B:GLU161 2.2 34.7 1.0 CD B:GLU115 2.8 25.5 1.0 OE1 B:GLU115 2.9 27.3 1.0 CD B:GLU161 3.2 31.9 1.0 CG B:ASP157 3.4 26.1 1.0 O B:HOH423 3.7 21.1 1.0 CG B:GLU161 3.7 31.6 1.0 N B:GLY158 3.8 26.9 1.0 OD2 B:ASP157 4.0 29.7 1.0 N B:ASP157 4.0 25.6 1.0 C B:ASP157 4.1 27.0 1.0 O B:HOH443 4.1 38.0 1.0 MN B:MN301 4.1 30.5 1.0 CA B:GLY158 4.2 28.7 1.0 OD1 B:ASN160 4.2 27.1 1.0 OE1 B:GLU161 4.2 32.5 1.0 CG B:GLU115 4.3 23.1 1.0 CA B:ASP157 4.4 26.2 1.0 OG B:SER196 4.5 26.3 1.0 CB B:ASP157 4.5 23.4 1.0 O B:ASP157 4.6 28.8 1.0 CE1 B:PHE50 4.9 26.3 1.0

Manganese binding site 6 out of 17 in the Crystal Structure of TON_0340 in Complex with Mn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure of TON_0340 in Complex with Mn within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn301 b:37.8 occ:1.00 OD1 C:ASP61 2.1 40.3 1.0 O C:HOH401 2.1 27.5 1.0 OD2 C:ASP157 2.2 36.8 1.0 OD2 C:ASP246 2.4 37.8 1.0 OD1 C:ASP246 2.4 40.6 1.0 CG C:ASP246 2.7 38.6 1.0 CG C:ASP157 3.2 34.9 1.0 OE2 C:GLU115 3.2 38.8 1.0 CG C:ASP61 3.2 35.6 1.0 OD1 C:ASP157 3.5 34.5 1.0 CB C:ASP61 3.7 35.1 1.0 MN C:MN302 4.2 39.3 1.0 CB C:ASP246 4.2 37.2 1.0 CD C:GLU115 4.2 37.4 1.0 OD2 C:ASP61 4.3 36.5 1.0 CB C:ASP157 4.5 34.1 1.0 N C:SER196 4.5 27.2 1.0 OE1 C:GLU59 4.5 40.7 1.0 OE2 C:GLU59 4.6 38.3 1.0 CA C:VAL195 4.7 28.9 1.0 CG1 C:VAL195 4.7 27.2 1.0 CD C:GLU59 5.0 40.4 1.0 OE1 C:GLU115 5.0 37.4 1.0 O C:ALA194 5.0 34.6 1.0

Manganese binding site 7 out of 17 in the Crystal Structure of TON_0340 in Complex with Mn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Crystal Structure of TON_0340 in Complex with Mn within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn302 b:39.3 occ:1.00 OE2 C:GLU161 2.1 35.3 1.0 OE2 C:GLU115 2.2 38.8 1.0 OD1 C:ASP157 2.3 34.5 1.0 CD C:GLU115 2.8 37.4 1.0 OE1 C:GLU115 2.8 37.4 1.0 CD C:GLU161 3.2 34.5 1.0 CG C:ASP157 3.4 34.9 1.0 O C:HOH401 3.6 27.5 1.0 CG C:GLU161 3.7 33.8 1.0 N C:GLY158 3.8 38.6 1.0 OD2 C:ASP157 3.9 36.8 1.0 O C:HOH407 4.0 34.7 1.0 OD1 C:ASN160 4.0 37.5 1.0 N C:ASP157 4.2 33.0 1.0 CA C:GLY158 4.2 38.6 1.0 CG C:GLU115 4.2 33.8 1.0 OE1 C:GLU161 4.2 31.6 1.0 MN C:MN301 4.2 37.8 1.0 C C:ASP157 4.3 37.0 1.0 CB C:ASP157 4.6 34.1 1.0 CA C:ASP157 4.6 35.3 1.0 OG C:SER196 4.9 26.7 1.0 CE1 C:PHE50 4.9 40.2 1.0

Manganese binding site 8 out of 17 in the Crystal Structure of TON_0340 in Complex with Mn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Crystal Structure of TON_0340 in Complex with Mn within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn303 b:87.0 occ:1.00 O F:GLY247 2.4 33.2 1.0 OE2 C:GLU266 2.6 42.8 1.0 CD C:GLU266 3.3 41.0 1.0 OE1 C:GLU266 3.4 41.3 1.0 C F:GLY247 3.6 32.8 1.0 CA F:ILE248 4.3 31.6 1.0 N F:ILE248 4.4 32.2 1.0 CA F:GLY247 4.6 32.2 1.0 N F:ARG249 4.6 35.4 1.0 CG C:GLU266 4.8 39.3 1.0 C F:ILE248 4.9 33.8 1.0 O C:GLU266 5.0 39.3 1.0

Manganese binding site 9 out of 17 in the Crystal Structure of TON_0340 in Complex with Mn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of Crystal Structure of TON_0340 in Complex with Mn within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn301 b:48.3 occ:1.00 OD1 D:ASP61 2.1 32.7 1.0 OD2 D:ASP246 2.2 55.8 1.0 OD2 D:ASP157 2.4 31.1 1.0 OD1 D:ASP246 2.6 55.2 1.0 CG D:ASP246 2.7 54.8 1.0 O D:HOH407 2.9 38.8 1.0 OE1 D:GLU115 3.1 43.8 1.0 CG D:ASP157 3.1 30.5 1.0 OD1 D:ASP157 3.2 26.9 1.0 CG D:ASP61 3.2 34.9 1.0 CB D:ASP61 3.7 34.8 1.0 MN D:MN302 3.9 40.8 1.0 OE2 D:GLU59 4.0 55.0 1.0 CD D:GLU115 4.0 43.0 1.0 CB D:ASP246 4.2 52.8 1.0 OD2 D:ASP61 4.3 32.1 1.0 CB D:ASP157 4.6 30.6 1.0 N D:SER196 4.6 33.2 1.0 OG D:SER196 4.7 26.1 1.0 OE2 D:GLU115 4.7 46.3 1.0 CD D:GLU59 4.7 53.7 1.0 CG D:GLU115 4.8 41.6 1.0 OE1 D:GLU59 4.8 54.1 1.0 CA D:VAL195 4.9 32.7 1.0

Manganese binding site 10 out of 17 in the Crystal Structure of TON_0340 in Complex with Mn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of Crystal Structure of TON_0340 in Complex with Mn within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn302 b:40.8 occ:1.00 OE1 D:GLU115 2.2 43.8 1.0 OE2 D:GLU161 2.3 31.2 1.0 OD1 D:ASP157 2.4 26.9 1.0 O D:HOH401 2.6 37.9 1.0 OE2 D:GLU115 2.7 46.3 1.0 CD D:GLU115 2.8 43.0 1.0 CD D:GLU161 3.2 31.9 1.0 CG D:ASP157 3.5 30.5 1.0 CG D:GLU161 3.6 31.9 1.0 N D:GLY158 3.9 32.9 1.0 MN D:MN301 3.9 48.3 1.0 OD1 D:ASN160 4.0 30.5 1.0 OD2 D:ASP157 4.1 31.1 1.0 N D:ASP157 4.2 32.6 1.0 OE1 D:GLU161 4.2 27.5 1.0 CG D:GLU115 4.3 41.6 1.0 C D:ASP157 4.3 32.8 1.0 O D:HOH407 4.3 38.8 1.0 CA D:GLY158 4.3 30.9 1.0 CA D:ASP157 4.6 32.4 1.0 OG D:SER196 4.6 26.1 1.0 CB D:ASP157 4.7 30.6 1.0 CE1 D:PHE50 4.9 42.1 1.0 O D:ASP157 4.9 33.6 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