Calcium in PDB 5gl2: Crystal Structure of TON_0340 in Complex with Ca

The structure of Crystal Structure of TON_0340 in Complex with Ca, PDB code: 5gl2 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 / 2.03
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	106.840, 106.840, 364.019, 90.00, 90.00, 90.00
R / Rfree (%)	21.9 / 25

The binding sites of Calcium atom in the Crystal Structure of TON_0340 in Complex with Ca (pdb code 5gl2). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of TON_0340 in Complex with Ca, PDB code: 5gl2:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Crystal Structure of TON_0340 in Complex with Ca


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of TON_0340 in Complex with Ca within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:33.0 occ:1.00 OD1 A:ASP61 2.5 29.7 1.0 OD2 A:ASP246 2.5 25.8 1.0 OE2 A:GLU115 2.5 27.9 1.0 O A:HOH401 2.6 34.9 1.0 OD2 A:ASP157 2.6 24.7 1.0 OD1 A:ASP157 2.7 27.0 1.0 O A:HOH468 2.7 30.6 1.0 CG A:ASP157 3.0 25.9 1.0 CG A:ASP246 3.3 31.0 1.0 OD1 A:ASP246 3.3 27.7 1.0 CG A:ASP61 3.5 26.4 1.0 CD A:GLU115 3.7 30.0 1.0 O A:HOH452 3.8 43.1 1.0 CB A:ASP61 3.9 24.5 1.0 O A:HOH410 4.2 26.7 1.0 OG A:SER196 4.3 24.0 1.0 N A:SER196 4.4 21.2 1.0 OE1 A:GLU59 4.4 31.6 1.0 OE1 A:GLU115 4.5 30.8 1.0 CB A:ASP157 4.5 26.9 1.0 CG A:GLU115 4.6 26.3 1.0 OD2 A:ASP61 4.6 26.6 1.0 CB A:ASP246 4.7 29.6 1.0 CB A:SER196 4.8 22.1 1.0 OE2 A:GLU161 4.8 29.9 1.0 OE2 A:GLU59 4.8 30.5 1.0 CA A:VAL195 5.0 21.2 1.0

Calcium binding site 2 out of 6 in the Crystal Structure of TON_0340 in Complex with Ca


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of TON_0340 in Complex with Ca within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:33.4 occ:1.00 OE2 B:GLU115 2.5 34.3 1.0 OD2 B:ASP246 2.5 35.4 1.0 OD1 B:ASP61 2.6 25.9 1.0 O B:HOH405 2.7 31.2 1.0 OD1 B:ASP157 2.7 31.9 1.0 OD2 B:ASP157 2.8 35.1 1.0 CG B:ASP157 3.1 31.7 1.0 OD1 B:ASP246 3.2 34.8 1.0 CG B:ASP246 3.2 35.0 1.0 CG B:ASP61 3.6 26.0 1.0 CD B:GLU115 3.7 32.3 1.0 CB B:ASP61 3.9 26.0 1.0 O B:HOH402 4.3 36.7 1.0 O B:HOH451 4.4 36.2 1.0 OE1 B:GLU59 4.5 31.5 1.0 OE1 B:GLU115 4.5 34.6 1.0 OG B:SER196 4.5 25.3 1.0 O B:HOH458 4.5 31.2 1.0 N B:SER196 4.5 21.4 1.0 CB B:ASP157 4.6 28.9 1.0 CG B:GLU115 4.7 28.0 1.0 OE2 B:GLU59 4.7 29.1 1.0 CB B:ASP246 4.7 31.6 1.0 OD2 B:ASP61 4.7 25.7 1.0 CB B:SER196 4.8 24.2 1.0 OE2 B:GLU161 5.0 34.2 1.0

Calcium binding site 3 out of 6 in the Crystal Structure of TON_0340 in Complex with Ca


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of TON_0340 in Complex with Ca within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca301 b:40.0 occ:1.00 OE2 C:GLU115 2.5 34.3 1.0 OD2 C:ASP246 2.6 39.2 1.0 OD1 C:ASP61 2.6 31.4 1.0 O C:HOH446 2.6 35.8 1.0 OD2 C:ASP157 2.7 36.4 1.0 O C:HOH405 2.7 28.9 1.0 OD1 C:ASP157 2.7 36.6 1.0 CG C:ASP157 3.1 36.2 1.0 CG C:ASP246 3.4 39.6 1.0 OD1 C:ASP246 3.4 41.3 1.0 CG C:ASP61 3.6 28.9 1.0 CD C:GLU115 3.6 34.7 1.0 CB C:ASP61 3.9 30.1 1.0 O C:HOH403 4.2 39.8 1.0 OE1 C:GLU115 4.3 33.5 1.0 OG C:SER196 4.3 27.9 1.0 OE1 C:GLU59 4.3 35.1 1.0 N C:SER196 4.4 23.6 1.0 CG C:GLU115 4.5 32.4 1.0 CB C:ASP157 4.6 33.4 1.0 OD2 C:ASP61 4.7 28.2 1.0 CB C:SER196 4.7 26.2 1.0 OE2 C:GLU59 4.8 35.2 1.0 CB C:ASP246 4.8 37.0 1.0 OE2 C:GLU161 4.8 29.8 1.0 CD C:GLU59 5.0 35.2 1.0

Calcium binding site 4 out of 6 in the Crystal Structure of TON_0340 in Complex with Ca


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of TON_0340 in Complex with Ca within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca301 b:37.9 occ:1.00 OE2 D:GLU115 2.6 32.2 1.0 O D:HOH401 2.6 36.0 1.0 OD1 D:ASP61 2.7 31.9 1.0 OD2 D:ASP157 2.7 35.1 1.0 OD2 D:ASP246 2.8 42.4 1.0 OD1 D:ASP157 2.8 38.2 1.0 O D:HOH444 2.8 37.3 1.0 CG D:ASP157 3.1 36.9 1.0 OD1 D:ASP246 3.1 41.5 1.0 CG D:ASP246 3.3 41.5 1.0 CG D:ASP61 3.7 30.6 1.0 CD D:GLU115 3.7 33.6 1.0 CB D:ASP61 4.0 30.1 1.0 O D:HOH420 4.0 31.9 1.0 OE1 D:GLU59 4.3 35.0 1.0 OG D:SER196 4.5 23.1 1.0 OE1 D:GLU115 4.5 34.8 1.0 CG D:GLU115 4.6 32.8 1.0 N D:SER196 4.6 25.6 1.0 CB D:ASP246 4.6 37.5 1.0 CB D:ASP157 4.7 34.8 1.0 OE2 D:GLU59 4.7 35.9 1.0 OD2 D:ASP61 4.8 31.4 1.0 OE2 D:GLU161 4.9 28.8 1.0 CD D:GLU59 4.9 32.3 1.0 CB D:SER196 4.9 22.1 1.0

Calcium binding site 5 out of 6 in the Crystal Structure of TON_0340 in Complex with Ca


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of TON_0340 in Complex with Ca within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca301 b:45.6 occ:1.00 OD1 E:ASP61 2.5 39.1 1.0 O E:HOH407 2.5 41.1 1.0 OE2 E:GLU115 2.6 41.0 1.0 OD1 E:ASP157 2.7 42.0 1.0 OD1 E:ASP246 2.8 58.4 1.0 OD2 E:ASP246 2.8 60.6 1.0 OD2 E:ASP157 3.0 43.7 1.0 O E:HOH424 3.0 42.6 1.0 CG E:ASP246 3.1 59.1 1.0 CG E:ASP157 3.2 41.8 1.0 CG E:ASP61 3.5 38.9 1.0 CD E:GLU115 3.8 39.1 1.0 CB E:ASP61 3.9 38.9 1.0 O E:HOH413 4.0 40.8 1.0 OE2 E:GLU59 4.4 41.5 1.0 OE1 E:GLU115 4.5 40.9 1.0 OE1 E:GLU59 4.5 38.6 1.0 N E:SER196 4.5 33.5 1.0 OD2 E:ASP61 4.6 38.5 1.0 CB E:ASP246 4.6 57.8 1.0 OG E:SER196 4.6 34.4 1.0 O E:HOH414 4.7 43.1 1.0 CB E:ASP157 4.7 37.8 1.0 CB E:SER196 4.8 33.1 1.0 CG E:GLU115 4.8 38.9 1.0 CD E:GLU59 4.9 40.8 1.0

Calcium binding site 6 out of 6 in the Crystal Structure of TON_0340 in Complex with Ca


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of TON_0340 in Complex with Ca within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca301 b:31.6 occ:1.00 OD1 F:ASP61 2.5 26.2 1.0 OD2 F:ASP246 2.5 29.6 1.0 OE2 F:GLU115 2.5 34.7 1.0 O F:HOH401 2.6 25.3 1.0 O F:HOH473 2.7 33.7 1.0 OD2 F:ASP157 2.8 30.9 1.0 OD1 F:ASP157 2.8 30.3 1.0 CG F:ASP157 3.1 30.1 1.0 CG F:ASP246 3.3 32.9 1.0 OD1 F:ASP246 3.4 31.6 1.0 CG F:ASP61 3.5 25.4 1.0 CD F:GLU115 3.7 34.7 1.0 CB F:ASP61 3.8 22.8 1.0 OG F:SER196 4.2 28.4 1.0 O F:HOH410 4.2 26.0 1.0 O F:HOH438 4.3 33.2 1.0 OE1 F:GLU59 4.4 28.9 1.0 N F:SER196 4.4 21.4 1.0 OE1 F:GLU115 4.5 35.3 1.0 CG F:GLU115 4.6 30.3 1.0 O F:HOH471 4.6 33.9 1.0 OD2 F:ASP61 4.6 23.8 1.0 CB F:ASP157 4.6 32.0 1.0 OE2 F:GLU59 4.7 29.6 1.0 CB F:SER196 4.8 21.9 1.0 CB F:ASP246 4.8 28.1 1.0 OE2 F:GLU161 4.8 28.2 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