Calcium in PDB 6qi4: Ncs-1 Bound to A Ligand

Protein crystallography data

The structure of Ncs-1 Bound to A Ligand, PDB code: 6qi4 was solved by M.J.Sanchez-Barrena, P.Blanco-Gabella, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.35 / 1.78
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 53.729, 55.603, 77.725, 90.00, 94.97, 90.00
R / Rfree (%) 21.4 / 23.2

Other elements in 6qi4:

The structure of Ncs-1 Bound to A Ligand also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Ncs-1 Bound to A Ligand (pdb code 6qi4). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Ncs-1 Bound to A Ligand, PDB code: 6qi4:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 6qi4

Go back to Calcium Binding Sites List in 6qi4
Calcium binding site 1 out of 6 in the Ncs-1 Bound to A Ligand


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Ncs-1 Bound to A Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca201

b:36.3
occ:1.00
OD1 B:ASN75 2.0 33.2 1.0
O B:ARG79 2.0 39.4 1.0
OD1 B:ASP77 2.4 43.0 1.0
OE1 B:GLU84 2.4 31.2 1.0
OD1 B:ASP73 2.5 40.7 1.0
O B:HOH334 2.5 37.2 1.0
OE2 B:GLU84 2.6 38.6 1.0
CD B:GLU84 2.9 35.8 1.0
CG B:ASN75 3.1 51.8 1.0
CG B:ASP77 3.2 59.4 1.0
C B:ARG79 3.3 40.2 1.0
HD21 B:ASN75 3.3 75.7 1.0
H B:ARG79 3.4 49.0 1.0
CG B:ASP73 3.5 41.8 1.0
H B:ASP77 3.5 60.2 1.0
HA B:ILE80 3.5 38.0 1.0
OD2 B:ASP77 3.6 58.1 1.0
HA B:ASP73 3.6 43.1 1.0
ND2 B:ASN75 3.6 63.1 1.0
H B:ASN75 3.7 53.8 1.0
H B:GLU81 3.8 36.9 1.0
HG2 B:GLU81 4.0 40.8 1.0
N B:ARG79 4.0 40.8 1.0
OD2 B:ASP73 4.2 37.5 1.0
CA B:ARG79 4.2 38.0 1.0
N B:ILE80 4.2 31.1 1.0
HB2 B:ARG79 4.2 54.3 1.0
CA B:ASP73 4.3 35.9 1.0
CA B:ILE80 4.3 31.7 1.0
N B:ASP77 4.3 50.2 1.0
CB B:ASP73 4.3 30.9 1.0
H B:LYS76 4.3 74.2 1.0
CG B:GLU84 4.4 32.6 1.0
CB B:ASP77 4.4 53.2 1.0
HD22 B:ASN75 4.5 75.7 1.0
N B:GLU81 4.5 30.8 1.0
N B:ASN75 4.5 44.8 1.0
H B:GLY78 4.5 66.3 1.0
CB B:ASN75 4.5 44.4 1.0
H B:GLU74 4.5 43.6 1.0
HB2 B:ASP73 4.5 37.1 1.0
HB3 B:ASP77 4.5 63.9 1.0
C B:ASP73 4.6 39.9 1.0
N B:LYS76 4.6 61.8 1.0
CB B:ARG79 4.7 45.2 1.0
HG3 B:GLU84 4.7 39.2 1.0
N B:GLU74 4.7 36.4 1.0
N B:GLY78 4.8 55.2 1.0
CA B:ASN75 4.8 54.1 1.0
CA B:ASP77 4.8 51.0 1.0
HB3 B:GLU81 4.9 48.4 1.0
HB3 B:ASN75 4.9 53.2 1.0
HG2 B:GLU84 4.9 39.2 1.0
C B:ASN75 4.9 60.3 1.0
C B:ILE80 4.9 35.5 1.0
CG B:GLU81 4.9 34.0 1.0
OE1 B:GLU81 4.9 53.0 1.0
HB2 B:GLU84 5.0 31.6 1.0
HB3 B:ARG79 5.0 54.3 1.0

Calcium binding site 2 out of 6 in 6qi4

Go back to Calcium Binding Sites List in 6qi4
Calcium binding site 2 out of 6 in the Ncs-1 Bound to A Ligand


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Ncs-1 Bound to A Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca202

b:22.9
occ:1.00
O B:HOH380 2.3 26.6 1.0
OD1 B:ASP113 2.3 37.2 1.0
OD1 B:ASP109 2.3 35.4 1.0
OD1 B:ASP111 2.3 35.3 1.0
O B:TYR115 2.4 30.1 1.0
OE1 B:GLU120 2.4 28.6 1.0
OE2 B:GLU120 2.6 33.9 1.0
CD B:GLU120 2.8 37.4 1.0
CG B:ASP113 3.3 44.2 1.0
CG B:ASP111 3.3 46.3 1.0
H B:ASP113 3.3 44.2 1.0
H B:ASP111 3.4 39.3 1.0
CG B:ASP109 3.4 35.0 1.0
H B:TYR115 3.4 35.7 1.0
C B:TYR115 3.6 30.6 1.0
HA B:ASP109 3.6 29.2 1.0
OD2 B:ASP111 3.8 52.5 1.0
HA B:ILE116 3.8 27.6 1.0
HG23 B:THR117 3.8 38.5 1.0
OD2 B:ASP113 3.9 38.3 1.0
H B:THR117 4.0 30.5 1.0
HB2 B:TYR115 4.0 39.2 1.0
H B:ASN112 4.1 59.1 1.0
N B:ASP113 4.1 36.9 1.0
OD2 B:ASP109 4.2 34.6 1.0
N B:TYR115 4.2 29.7 1.0
N B:ASP111 4.2 32.8 1.0
CA B:ASP109 4.3 24.4 1.0
HB3 B:ASP113 4.3 53.6 1.0
CB B:ASP113 4.3 44.7 1.0
H B:LEU110 4.4 33.6 1.0
CA B:TYR115 4.4 31.2 1.0
CG B:GLU120 4.4 30.9 1.0
CB B:ASP109 4.4 29.0 1.0
CB B:ASP111 4.4 43.1 1.0
C B:ASP109 4.4 35.1 1.0
N B:ILE116 4.5 26.1 1.0
N B:ASN112 4.5 49.3 1.0
CA B:ILE116 4.5 23.0 1.0
N B:LEU110 4.5 28.0 1.0
H B:GLY114 4.6 36.9 1.0
HB3 B:ASP111 4.7 51.8 1.0
CA B:ASP113 4.7 40.0 1.0
CB B:TYR115 4.7 32.7 1.0
CA B:ASP111 4.7 40.3 1.0
N B:THR117 4.7 25.4 1.0
HB2 B:ASP109 4.7 34.8 1.0
HG3 B:GLU120 4.7 37.1 1.0
O B:HOH394 4.7 55.6 1.0
CG2 B:THR117 4.7 32.1 1.0
C B:ASP111 4.8 42.3 1.0
HG2 B:GLU120 4.8 37.1 1.0
N B:GLY114 4.8 30.8 1.0
O B:ASP109 4.9 30.7 1.0
O B:HOH342 4.9 32.6 1.0
C B:ASP113 5.0 37.6 1.0
HG22 B:THR117 5.0 38.5 1.0

Calcium binding site 3 out of 6 in 6qi4

Go back to Calcium Binding Sites List in 6qi4
Calcium binding site 3 out of 6 in the Ncs-1 Bound to A Ligand


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Ncs-1 Bound to A Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca203

b:31.9
occ:1.00
O B:LYS163 2.2 30.4 1.0
OD1 B:ASN159 2.3 43.1 1.0
OD1 B:ASP157 2.4 29.2 1.0
OD1 B:ASP161 2.4 39.3 1.0
O B:HOH315 2.5 39.4 1.0
OE1 B:GLU168 2.5 31.2 1.0
OE2 B:GLU168 2.7 35.6 1.0
CD B:GLU168 3.0 38.4 1.0
CG B:ASP161 3.3 44.2 1.0
CG B:ASN159 3.4 43.6 1.0
C B:LYS163 3.4 31.6 1.0
H B:ASP161 3.5 46.8 1.0
HA B:LEU164 3.5 35.9 1.0
CG B:ASP157 3.5 35.0 1.0
H B:LYS163 3.6 33.6 1.0
H B:ASN159 3.6 54.6 1.0
OD2 B:ASP161 3.6 42.0 1.0
HA B:ASP157 3.7 34.7 1.0
HD21 B:ASN159 3.7 51.7 1.0
H B:THR165 3.9 28.6 1.0
ND2 B:ASN159 4.0 43.1 1.0
HD23 B:LEU164 4.0 31.9 1.0
HG23 B:THR165 4.1 38.2 1.0
HB2 B:LYS163 4.2 32.0 1.0
CA B:LEU164 4.3 29.9 1.0
N B:LYS163 4.3 28.0 1.0
N B:ASP161 4.3 39.0 1.0
N B:LEU164 4.3 28.0 1.0
OD2 B:ASP157 4.4 30.7 1.0
H B:LYS158 4.4 41.1 1.0
H B:ALA160 4.4 55.0 1.0
CA B:ASP157 4.4 28.9 1.0
CA B:LYS163 4.4 28.1 1.0
N B:ASN159 4.4 45.5 1.0
CB B:ASP157 4.5 35.8 1.0
CG B:GLU168 4.5 32.5 1.0
CB B:ASN159 4.6 57.3 1.0
CB B:ASP161 4.6 40.1 1.0
N B:THR165 4.6 23.9 1.0
HB2 B:ASP157 4.7 42.9 1.0
N B:ALA160 4.7 45.9 1.0
N B:LYS158 4.7 34.3 1.0
H B:GLY162 4.7 41.0 1.0
C B:ASP157 4.8 34.0 1.0
HD22 B:ASN159 4.8 51.7 1.0
CB B:LYS163 4.8 26.7 1.0
HB3 B:ASN159 4.8 68.8 1.0
HG3 B:GLU168 4.8 39.0 1.0
CD2 B:LEU164 4.9 26.6 1.0
CA B:ASN159 4.9 49.0 1.0
CA B:ASP161 4.9 35.1 1.0
HB3 B:ASP161 4.9 48.2 1.0
HG2 B:GLU168 4.9 39.0 1.0
HB2 B:GLU168 4.9 34.2 1.0
C B:LEU164 5.0 30.1 1.0
C B:ASN159 5.0 42.3 1.0
N B:GLY162 5.0 34.1 1.0

Calcium binding site 4 out of 6 in 6qi4

Go back to Calcium Binding Sites List in 6qi4
Calcium binding site 4 out of 6 in the Ncs-1 Bound to A Ligand


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Ncs-1 Bound to A Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca202

b:46.0
occ:1.00
OD1 C:ASN75 2.1 61.1 1.0
O C:ARG79 2.2 53.0 1.0
OD1 C:ASP77 2.3 71.7 1.0
OD1 C:ASP73 2.4 55.5 1.0
OE2 C:GLU84 2.4 54.0 1.0
O C:HOH306 2.5 45.8 1.0
OE1 C:GLU84 2.7 54.9 1.0
CD C:GLU84 2.9 56.9 1.0
CG C:ASN75 3.0 65.3 1.0
HD21 C:ASN75 3.0 65.6 1.0
CG C:ASP77 3.1 72.1 1.0
H C:ASP77 3.4 81.5 1.0
ND2 C:ASN75 3.4 54.6 1.0
OD2 C:ASP77 3.4 71.1 1.0
H C:ARG79 3.4 70.0 1.0
C C:ARG79 3.4 56.1 1.0
CG C:ASP73 3.5 58.1 1.0
H C:ASN75 3.6 77.6 1.0
HA C:ASP73 3.6 59.1 1.0
HA C:ILE80 3.9 69.3 1.0
H C:GLU81 3.9 65.8 1.0
N C:ARG79 4.1 58.4 1.0
OD2 C:ASP73 4.2 54.3 1.0
N C:ASP77 4.2 67.9 1.0
CB C:ASP77 4.2 73.3 1.0
HD22 C:ASN75 4.2 65.6 1.0
HB2 C:ARG79 4.3 86.2 1.0
CA C:ARG79 4.3 63.9 1.0
H C:LYS76 4.3 72.2 1.0
HB3 C:ASP77 4.3 88.0 1.0
CA C:ASP73 4.3 49.2 1.0
H C:GLU74 4.3 64.3 1.0
N C:ASN75 4.4 64.6 1.0
N C:ILE80 4.4 51.5 1.0
CB C:ASN75 4.4 62.2 1.0
CB C:ASP73 4.4 48.4 1.0
CG C:GLU84 4.4 52.1 1.0
HG2 C:GLU81 4.4 80.1 1.0
H C:GLY78 4.5 79.1 1.0
CA C:ILE80 4.6 57.7 1.0
C C:ASP73 4.6 58.8 1.0
N C:GLU81 4.6 54.8 1.0
N C:GLU74 4.6 53.6 1.0
N C:LYS76 4.6 60.2 1.0
CA C:ASP77 4.7 72.5 1.0
HB2 C:ASP73 4.7 58.0 1.0
CA C:ASN75 4.8 68.9 1.0
HG3 C:GLU84 4.8 62.5 1.0
HB3 C:ASN75 4.8 74.7 1.0
C C:ASN75 4.8 74.5 1.0
N C:GLY78 4.8 65.9 1.0
HG2 C:GLU84 4.8 62.5 1.0
CB C:ARG79 4.9 71.8 1.0
C C:ASP77 4.9 69.3 1.0

Calcium binding site 5 out of 6 in 6qi4

Go back to Calcium Binding Sites List in 6qi4
Calcium binding site 5 out of 6 in the Ncs-1 Bound to A Ligand


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Ncs-1 Bound to A Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca203

b:46.0
occ:1.00
OD1 C:ASP113 2.0 48.4 1.0
O C:TYR115 2.3 48.0 1.0
OE2 C:GLU120 2.4 49.0 1.0
OD1 C:ASP109 2.4 45.1 1.0
OD1 C:ASP111 2.4 54.7 1.0
O C:HOH320 2.4 40.9 1.0
OE1 C:GLU120 2.5 48.5 1.0
CD C:GLU120 2.7 51.2 1.0
CG C:ASP113 3.1 64.1 1.0
CG C:ASP111 3.2 53.3 1.0
H C:ASP111 3.4 69.8 1.0
H C:ASP113 3.4 65.6 1.0
HA C:ASP109 3.5 55.1 1.0
CG C:ASP109 3.5 47.3 1.0
H C:TYR115 3.5 60.9 1.0
C C:TYR115 3.5 42.9 1.0
OD2 C:ASP111 3.6 55.9 1.0
HG23 C:THR117 3.7 57.6 1.0
OD2 C:ASP113 3.7 56.9 1.0
HA C:ILE116 3.8 48.1 1.0
H C:THR117 4.0 53.1 1.0
H C:LEU110 4.1 59.0 1.0
HB3 C:ASP113 4.1 72.7 1.0
CB C:ASP113 4.2 60.6 1.0
CA C:ASP109 4.2 45.9 1.0
HB2 C:TYR115 4.2 55.1 1.0
CG C:GLU120 4.2 49.3 1.0
N C:ASP111 4.2 58.1 1.0
N C:ASP113 4.2 54.7 1.0
N C:TYR115 4.3 50.7 1.0
OD2 C:ASP109 4.3 40.7 1.0
C C:ASP109 4.3 54.7 1.0
N C:LEU110 4.4 49.1 1.0
CB C:ASP109 4.4 42.6 1.0
CA C:TYR115 4.4 44.0 1.0
H C:ASN112 4.5 69.2 1.0
CB C:ASP111 4.5 56.1 1.0
N C:ILE116 4.5 38.0 1.0
HG3 C:GLU120 4.5 59.2 1.0
CA C:ILE116 4.5 40.1 1.0
HG2 C:GLU120 4.6 59.2 1.0
CG2 C:THR117 4.6 48.0 1.0
N C:THR117 4.6 44.2 1.0
N C:ASN112 4.7 57.6 1.0
HB2 C:ASP109 4.7 51.1 1.0
CA C:ASP113 4.7 54.6 1.0
CA C:ASP111 4.7 56.5 1.0
H C:GLY114 4.7 60.0 1.0
C C:ASP111 4.8 54.5 1.0
HB3 C:ASP111 4.8 67.3 1.0
CB C:TYR115 4.8 45.9 1.0
O C:ASP109 4.9 43.6 1.0
HG22 C:THR117 4.9 57.6 1.0
HG21 C:THR117 5.0 57.6 1.0
HB2 C:GLU120 5.0 54.0 1.0
HB2 C:ASP113 5.0 72.7 1.0
HG1 C:THR117 5.0 58.2 1.0
N C:GLY114 5.0 50.0 1.0

Calcium binding site 6 out of 6 in 6qi4

Go back to Calcium Binding Sites List in 6qi4
Calcium binding site 6 out of 6 in the Ncs-1 Bound to A Ligand


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Ncs-1 Bound to A Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca204

b:48.3
occ:1.00
OD1 C:ASN159 2.2 67.0 1.0
OD1 C:ASP161 2.2 60.5 1.0
O C:LYS163 2.3 44.6 1.0
O C:HOH323 2.3 46.0 1.0
OD1 C:ASP157 2.5 46.5 1.0
OE2 C:GLU168 2.5 50.4 1.0
OE1 C:GLU168 2.5 53.2 1.0
CD C:GLU168 2.8 48.1 1.0
HD21 C:ASN159 3.2 86.0 1.0
CG C:ASN159 3.2 68.2 1.0
CG C:ASP161 3.2 66.5 1.0
C C:LYS163 3.5 49.4 1.0
ND2 C:ASN159 3.5 71.6 1.0
H C:ASN159 3.6 69.9 1.0
OD2 C:ASP161 3.6 62.0 1.0
CG C:ASP157 3.6 48.9 1.0
H C:LYS163 3.6 55.7 1.0
H C:ASP161 3.6 71.6 1.0
HA C:LEU164 3.7 51.4 1.0
HA C:ASP157 3.8 60.1 1.0
HB2 C:LYS163 4.0 66.2 1.0
H C:THR165 4.0 49.1 1.0
HD23 C:LEU164 4.1 65.0 1.0
H C:LYS158 4.1 69.2 1.0
OD2 C:ASP157 4.3 58.5 1.0
HG21 C:THR165 4.3 76.0 1.0
N C:LYS163 4.3 46.4 1.0
CG C:GLU168 4.3 48.8 1.0
CA C:LYS163 4.4 51.4 1.0
O C:HOH331 4.4 55.9 1.0
N C:LEU164 4.4 39.8 1.0
HD22 C:ASN159 4.4 86.0 1.0
N C:ASN159 4.4 58.2 1.0
N C:ASP161 4.4 59.7 1.0
CA C:LEU164 4.4 42.8 1.0
H C:ALA160 4.5 68.5 1.0
CB C:ASP161 4.5 58.8 1.0
CA C:ASP157 4.5 50.1 1.0
CB C:ASN159 4.5 68.5 1.0
N C:LYS158 4.6 57.7 1.0
CB C:ASP157 4.6 51.5 1.0
CB C:LYS163 4.6 55.1 1.0
HB3 C:ASP161 4.7 70.5 1.0
HG3 C:GLU168 4.7 58.6 1.0
HG2 C:GLU168 4.7 58.6 1.0
N C:ALA160 4.7 57.1 1.0
N C:THR165 4.7 40.9 1.0
C C:ASP157 4.8 57.0 1.0
CA C:ASN159 4.8 52.6 1.0
HG23 C:THR165 4.8 76.0 1.0
H C:GLY162 4.9 61.5 1.0
C C:ASN159 4.9 61.5 1.0
HB2 C:ASP157 4.9 61.9 1.0
HB3 C:LYS163 4.9 66.2 1.0
HB3 C:ASN159 4.9 82.2 1.0
HD22 C:LEU164 4.9 65.0 1.0
CA C:ASP161 5.0 51.8 1.0
HB2 C:GLU168 5.0 51.8 1.0
CD2 C:LEU164 5.0 54.1 1.0

Reference:

A.Canal-Martin, J.Sastre, M.J.Sanchez-Barrena, A.Canales, S.Baldominos, N.Pascual, L.Martinez-Gonzalez, D.Molero, M.E.Fernandez-Valle, E.Saez, P.Blanco-Gabella, E.Gomez-Rubio, S.Martin-Santamaria, A.Saiz, A.Mansilla, F.J.Canada, J.Jimenez-Barbero, A.Martinez, R.Perez-Fernandez. Insights Into Real-Time Chemical Processes in A Calcium Sensor Protein-Directed Dynamic Library. Nat Commun V. 10 2798 2019.
ISSN: ESSN 2041-1723
PubMed: 31243268
DOI: 10.1038/S41467-019-10627-W
Page generated: Sat Dec 12 07:27:30 2020

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