Calcium in PDB 6iot: The Ligand Binding Domain of MLP24 with Arginine

The structure of The Ligand Binding Domain of MLP24 with Arginine, PDB code: 6iot was solved by Y.Takahashi, K.Sumita, S.Nishiyama, I.Kawagishi, K.Imada, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.48 / 2.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	64.530, 102.750, 93.410, 90.00, 94.51, 90.00
R / Rfree (%)	21.7 / 25.4

The binding sites of Calcium atom in the The Ligand Binding Domain of MLP24 with Arginine (pdb code 6iot). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the The Ligand Binding Domain of MLP24 with Arginine, PDB code: 6iot:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the The Ligand Binding Domain of MLP24 with Arginine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Ligand Binding Domain of MLP24 with Arginine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:49.2 occ:1.00 O A:HOH602 2.5 43.5 1.0 O A:ASP111 2.7 36.7 1.0 OE2 A:GLU109 2.7 50.2 1.0 CD A:GLU109 2.8 47.6 1.0 OE1 A:GLU109 2.9 57.2 1.0 O A:HOH605 3.4 27.8 1.0 C A:ASP111 3.6 33.1 1.0 O A:TRP114 3.7 53.5 1.0 CG A:GLU109 3.7 38.6 1.0 N A:ASP111 4.0 26.3 1.0 O A:HOH601 4.0 16.7 1.0 O A:GLU109 4.3 33.6 1.0 CA A:ASP111 4.4 31.7 1.0 N A:ASP112 4.4 33.3 1.0 CB A:GLU109 4.4 32.6 1.0 C A:GLU109 4.5 32.0 1.0 OE2 A:GLU115 4.5 44.1 1.0 CA A:ASP112 4.5 31.8 1.0 C A:ASN110 4.6 24.5 1.0 C A:TRP114 4.7 44.5 1.0 N A:ASN110 4.8 24.0 1.0 CA A:ASN110 4.8 21.6 1.0 C A:ASP112 4.9 33.8 1.0 O A:ASP112 4.9 34.1 1.0

Calcium binding site 2 out of 4 in the The Ligand Binding Domain of MLP24 with Arginine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Ligand Binding Domain of MLP24 with Arginine within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca502 b:41.3 occ:1.00 O B:ASP111 2.3 25.6 1.0 OE2 B:GLU109 2.4 44.4 1.0 O B:TRP114 2.8 37.9 1.0 O B:HOH605 2.8 41.1 1.0 CD B:GLU109 2.8 46.8 1.0 C B:ASP111 3.1 21.1 1.0 N B:ASP111 3.3 25.0 1.0 CG B:GLU109 3.4 36.2 1.0 OE1 B:GLU109 3.5 60.0 1.0 O B:HOH606 3.6 25.3 1.0 O B:GLU109 3.6 32.3 1.0 CA B:ASP111 3.7 26.1 1.0 C B:TRP114 3.9 32.2 1.0 C B:GLU109 4.1 29.8 1.0 C B:ASN110 4.1 26.9 1.0 N B:ASP112 4.1 23.8 1.0 CB B:ASP111 4.2 25.6 1.0 N B:ASN110 4.4 25.4 1.0 CA B:ASN110 4.5 25.8 1.0 CA B:ASP112 4.5 27.1 1.0 N B:TRP114 4.5 27.5 1.0 CA B:TRP114 4.6 28.5 1.0 CB B:GLU109 4.7 33.0 1.0 OE1 B:GLU115 4.8 58.1 1.0 O B:HOH601 4.8 36.9 1.0 CB B:TRP114 4.9 29.7 1.0 N B:GLU115 4.9 29.8 1.0 C B:ASP112 4.9 27.8 1.0 CA B:GLU109 4.9 34.5 1.0 O B:ASN110 4.9 26.9 1.0 O B:HOH604 4.9 37.6 1.0

Calcium binding site 3 out of 4 in the The Ligand Binding Domain of MLP24 with Arginine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The Ligand Binding Domain of MLP24 with Arginine within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca502 b:70.4 occ:1.00 OE2 C:GLU109 2.3 39.9 1.0 O C:HOH622 2.4 30.7 1.0 O C:ASP111 2.4 36.3 1.0 O C:HOH617 2.6 27.5 1.0 O C:TRP114 3.1 49.4 1.0 OE2 C:GLU115 3.3 41.8 1.0 CD C:GLU109 3.4 42.0 1.0 C C:ASP111 3.6 35.9 1.0 O C:HOH607 3.8 41.5 1.0 CG C:GLU115 4.0 31.6 1.0 CG C:GLU109 4.0 39.5 1.0 CD C:GLU115 4.0 39.8 1.0 CA C:ASP112 4.2 36.7 1.0 C C:TRP114 4.3 37.6 1.0 N C:ASP112 4.4 37.6 1.0 OE1 C:GLU109 4.4 56.8 1.0 C C:ASP112 4.5 36.3 1.0 N C:ASP111 4.6 26.4 1.0 CA C:ASP111 4.6 28.1 1.0 N C:TRP114 4.8 35.4 1.0 O C:ASP112 4.8 38.8 1.0 N C:GLY113 4.9 36.0 1.0

Calcium binding site 4 out of 4 in the The Ligand Binding Domain of MLP24 with Arginine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of The Ligand Binding Domain of MLP24 with Arginine within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca502 b:35.2 occ:1.00 O D:ASP111 2.4 35.4 1.0 OE2 D:GLU109 2.4 38.5 1.0 OE2 D:GLU115 2.5 35.7 1.0 O D:HOH605 2.5 36.4 1.0 O D:TRP114 2.6 32.1 1.0 O D:HOH611 2.9 27.0 1.0 CD D:GLU109 3.1 32.5 1.0 OE1 D:GLU109 3.1 26.8 1.0 CD D:GLU115 3.3 34.6 1.0 C D:ASP111 3.4 31.6 1.0 CG D:GLU115 3.7 26.8 1.0 C D:TRP114 3.7 34.4 1.0 N D:ASP112 4.2 39.4 1.0 OE1 D:GLU115 4.2 36.5 1.0 CA D:ASP112 4.2 37.7 1.0 N D:ASP111 4.2 23.3 1.0 N D:TRP114 4.3 38.1 1.0 CA D:ASP111 4.3 34.2 1.0 C D:ASP112 4.5 37.1 1.0 CA D:TRP114 4.6 36.0 1.0 CG D:GLU109 4.6 34.2 1.0 N D:GLU115 4.6 34.0 1.0 O D:HOH602 4.7 22.1 1.0 O D:GLU109 4.7 29.5 1.0 N D:GLY113 4.7 41.7 1.0 CA D:GLU115 4.8 35.2 1.0 CB D:ASP111 4.8 38.9 1.0 CB D:GLU115 4.8 31.8 1.0

Y.Takahashi, S.I.Nishiyama, K.Sumita, I.Kawagishi, K.Imada. Calcium Ions Modulate Amino Acid Sensing of the Chemoreceptor MLP24 Ofvibrio Cholerae. J. Bacteriol. V. 201 2019.
ISSN: ESSN 1098-5530
PubMed: 30745373
DOI: 10.1128/JB.00779-18