Calcium in PDB 6ior: The Ligand Binding Domain of MLP24 with Asparagine

Protein crystallography data

The structure of The Ligand Binding Domain of MLP24 with Asparagine, PDB code: 6ior 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) 68.07 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 91.880, 101.350, 128.370, 90.00, 90.00, 90.00
R / Rfree (%) 19.9 / 25.6

Calcium Binding Sites:

The binding sites of Calcium atom in the The Ligand Binding Domain of MLP24 with Asparagine (pdb code 6ior). 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 Asparagine, PDB code: 6ior:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 6ior

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


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 Asparagine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:33.8
occ:1.00
 O A:HOH616 2.3 26.7 1.0
O A:ASP111 2.3 26.3 1.0
O A:TRP114 2.4 34.2 1.0
OE1 A:GLU109 2.4 34.2 1.0
O A:HOH607 2.5 31.7 1.0
OE2 A:GLU109 2.6 35.0 1.0
OE2 A:GLU115 2.8 36.8 1.0
CD A:GLU109 2.9 26.1 1.0
CD A:GLU115 3.4 36.3 1.0
OE1 A:GLU115 3.5 34.6 1.0
C A:ASP111 3.5 27.1 1.0
C A:TRP114 3.6 31.6 1.0
O A:HOH601 3.6 22.5 1.0
N A:ASP111 4.1 24.1 1.0
CA A:ASP111 4.2 23.9 1.0
CG A:GLU109 4.4 27.3 1.0
CB A:ASP111 4.4 29.3 1.0
CA A:GLU115 4.4 34.1 1.0
N A:TRP114 4.4 29.2 1.0
N A:GLU115 4.4 33.8 1.0
O A:GLU109 4.5 30.1 1.0
N A:ASP112 4.5 26.0 1.0
CA A:TRP114 4.5 28.6 1.0
O A:ASP112 4.6 31.9 1.0
CG A:GLU115 4.6 38.6 1.0
C A:ASP112 4.7 29.1 1.0
CA A:ASP112 4.7 25.1 1.0
CB A:GLU115 4.8 33.4 1.0
C A:GLU109 4.9 27.2 1.0
C A:ASN110 4.9 23.4 1.0
O A:HOH605 5.0 32.6 1.0

Calcium binding site 2 out of 4 in 6ior

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


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 Asparagine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca502

b:46.8
occ:1.00
 O B:TRP114 2.4 54.9 1.0
O B:ASP111 2.4 49.8 1.0
OE1 B:GLU109 2.6 45.8 1.0
O B:HOH605 2.7 37.3 1.0
O B:HOH620 2.8 47.0 1.0
OE2 B:GLU109 2.8 42.3 1.0
OE1 B:GLU115 2.9 55.8 1.0
CD B:GLU109 3.0 41.8 1.0
C B:ASP111 3.6 43.0 1.0
CD B:GLU115 3.6 58.1 1.0
C B:TRP114 3.6 49.3 1.0
OE2 B:GLU115 3.9 58.2 1.0
N B:ASP111 4.2 43.0 1.0
CA B:ASP111 4.3 41.3 1.0
N B:TRP114 4.4 47.2 1.0
CA B:GLU115 4.4 50.0 1.0
N B:GLU115 4.4 49.4 1.0
CB B:ASP111 4.4 47.7 1.0
O B:GLU109 4.5 42.4 1.0
CG B:GLU109 4.5 36.7 1.0
CB B:GLU115 4.6 52.1 1.0
N B:ASP112 4.6 39.4 1.0
CA B:TRP114 4.6 47.1 1.0
O B:HOH602 4.6 40.1 1.0
CG B:GLU115 4.7 56.8 1.0
CA B:ASP112 4.8 48.1 1.0
N B:GLY113 4.9 50.4 1.0

Calcium binding site 3 out of 4 in 6ior

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


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 Asparagine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca502

b:46.3
occ:1.00
 OE2 C:GLU109 2.1 50.1 1.0
O C:TRP114 2.3 41.8 1.0
O C:HOH604 2.4 43.2 1.0
O C:HOH602 2.5 38.5 1.0
OE1 C:GLU115 2.6 51.1 1.0
O C:ASP111 2.6 39.3 1.0
CD C:GLU109 2.7 44.6 1.0
OE1 C:GLU109 2.7 44.5 1.0
C C:TRP114 3.3 43.1 1.0
C C:ASP111 3.6 40.5 1.0
CD C:GLU115 3.7 55.0 1.0
CG C:GLU109 4.1 44.3 1.0
N C:TRP114 4.1 44.1 1.0
N C:GLU115 4.1 45.5 1.0
CA C:TRP114 4.3 42.2 1.0
N C:ASP111 4.3 36.1 1.0
CA C:GLU115 4.3 44.8 1.0
N C:ASP112 4.4 39.9 1.0
OE2 C:GLU115 4.4 49.2 1.0
CA C:ASP111 4.4 38.8 1.0
CB C:GLU115 4.4 45.0 1.0
CA C:ASP112 4.5 38.7 1.0
C C:ASP112 4.5 44.2 1.0
O C:ASP112 4.5 43.0 1.0
O C:GLU109 4.5 40.6 1.0
O C:HOH601 4.6 50.2 1.0
CG C:GLU115 4.7 45.2 1.0
CB C:ASP111 4.8 37.6 1.0
N C:GLY113 5.0 37.7 1.0

Calcium binding site 4 out of 4 in 6ior

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


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 Asparagine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca502

b:46.7
occ:1.00
 OE2 D:GLU109 2.2 42.8 1.0
O D:ASP111 2.3 42.1 1.0
O D:TRP114 2.4 32.9 1.0
O D:HOH612 2.6 40.6 1.0
OE2 D:GLU115 2.6 49.6 1.0
O D:HOH605 2.7 37.4 1.0
CD D:GLU109 3.4 41.5 1.0
CD D:GLU115 3.4 40.8 1.0
C D:ASP111 3.5 35.2 1.0
C D:TRP114 3.6 35.1 1.0
N D:ASP111 4.1 35.1 1.0
O D:HOH606 4.1 36.2 1.0
CG D:GLU115 4.1 33.5 1.0
OE1 D:GLU115 4.2 48.5 1.0
CA D:ASP111 4.2 32.6 1.0
OE1 D:GLU109 4.2 50.1 1.0
N D:TRP114 4.3 35.9 1.0
CG D:GLU109 4.3 43.0 1.0
N D:ASP112 4.4 33.7 1.0
N D:GLU115 4.4 36.4 1.0
O D:GLU109 4.4 37.8 1.0
CA D:TRP114 4.5 40.0 1.0
CB D:ASP111 4.5 35.2 1.0
CA D:ASP112 4.5 36.8 1.0
CA D:GLU115 4.6 39.7 1.0
C D:ASP112 4.7 38.7 1.0
C D:ASN110 4.9 32.1 1.0
CB D:GLU115 5.0 37.3 1.0

Reference:

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
Page generated: Sat Dec 12 06:11:34 2020

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