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Calcium in PDB 4yli: Cl-K1 Trimer

Protein crystallography data

The structure of Cl-K1 Trimer, PDB code: 4yli was solved by R.Wallis, U.V.Girija, A.R.Gingras, P.C.E.Moody, J.E.Marshall, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.21 / 2.45
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 72.990, 107.590, 77.820, 90.00, 91.49, 90.00
R / Rfree (%) 18.7 / 22.1

Other elements in 4yli:

The structure of Cl-K1 Trimer also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Calcium atom in the Cl-K1 Trimer (pdb code 4yli). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 18 binding sites of Calcium where determined in the Cl-K1 Trimer, PDB code: 4yli:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 18 in 4yli

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Calcium binding site 1 out of 18 in the Cl-K1 Trimer


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Cl-K1 Trimer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:62.1
occ:1.00
O A:HOH406 2.3 67.0 1.0
OE1 A:GLU211 2.3 72.5 1.0
O A:GLU240 2.4 51.1 1.0
OD2 A:ASP207 2.4 62.5 1.0
OE2 A:GLU211 2.5 63.9 1.0
OD1 A:ASP241 2.6 61.2 1.0
CD A:GLU211 2.7 71.7 1.0
OD1 A:ASN235 2.9 62.9 1.0
OD1 A:ASP207 3.0 72.8 1.0
CG A:ASP207 3.1 66.6 1.0
CG A:ASN235 3.4 57.2 1.0
C A:GLU240 3.5 53.0 1.0
CG A:ASP241 3.8 60.5 1.0
CA A:ASP241 3.9 60.4 1.0
CB A:ASN235 4.0 54.2 1.0
ND2 A:ASN235 4.0 55.4 1.0
O2 A:GOL306 4.0 49.4 1.0
CA A:CA303 4.1 0.4 1.0
N A:ASP241 4.2 49.9 1.0
CG A:GLU211 4.2 67.8 1.0
O A:HOH401 4.3 64.9 1.0
CB A:ASP241 4.4 57.0 1.0
CB A:ASP207 4.6 72.0 1.0
CZ A:PHE214 4.6 76.2 1.0
CA A:ASN235 4.6 54.9 1.0
N A:GLY212 4.7 75.6 1.0
CA A:GLU240 4.7 49.6 1.0
OD2 A:ASP241 4.8 68.5 1.0
N A:GLU240 4.8 50.5 1.0
CA A:GLU211 4.9 75.3 1.0
O A:ASP207 4.9 76.5 1.0
OD2 A:ASP253 4.9 59.5 1.0
CB A:GLU211 5.0 71.3 1.0

Calcium binding site 2 out of 18 in 4yli

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Calcium binding site 2 out of 18 in the Cl-K1 Trimer


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Cl-K1 Trimer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca302

b:72.8
occ:1.00
OD1 A:ASP253 2.4 68.4 1.0
OD1 A:ASN234 2.4 65.5 1.0
OE1 A:GLU240 2.6 57.3 1.0
O A:ASP253 2.6 60.6 1.0
O1 A:GOL305 2.6 50.2 1.0
O2 A:GOL305 2.6 52.6 1.0
OD1 A:ASN252 2.6 59.8 1.0
OE1 A:GLU232 2.8 66.6 1.0
CG A:ASP253 3.4 64.0 1.0
CD A:GLU240 3.4 57.0 1.0
CG A:ASN234 3.4 61.2 1.0
CD A:GLU232 3.5 62.9 1.0
OE2 A:GLU240 3.5 64.2 1.0
C2 A:GOL305 3.6 59.8 1.0
C1 A:GOL305 3.6 46.2 1.0
C A:ASP253 3.6 52.9 1.0
OE2 A:GLU232 3.7 66.9 1.0
CG A:ASN252 3.7 68.9 1.0
ND2 A:ASN234 3.9 61.2 1.0
N A:ASP253 4.0 59.7 1.0
OD2 A:ASP253 4.0 59.5 1.0
ND2 A:ASN252 4.1 72.1 1.0
CA A:ASP253 4.2 53.7 1.0
CB A:ASP253 4.4 51.7 1.0
N A:ASN234 4.4 62.1 1.0
CB A:ASN234 4.7 62.4 1.0
N A:ASN235 4.7 62.2 1.0
CB A:ALA236 4.7 53.3 1.0
N A:ALA236 4.7 56.0 1.0
C A:ASN252 4.7 63.6 1.0
CG A:GLU232 4.7 62.0 1.0
N A:VAL254 4.8 58.8 1.0
CG A:GLU240 4.8 54.8 1.0
C3 A:GOL305 4.9 72.6 1.0
CB A:ASN252 5.0 64.1 1.0
CA A:ASN234 5.0 66.8 1.0

Calcium binding site 3 out of 18 in 4yli

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Calcium binding site 3 out of 18 in the Cl-K1 Trimer


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Cl-K1 Trimer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:0.4
occ:1.00
O2 A:GOL306 2.3 49.4 1.0
O3 A:GOL306 2.6 80.7 1.0
OD1 A:ASP241 3.0 61.2 1.0
OE2 A:GLU211 3.1 63.9 1.0
O A:ASP238 3.1 71.0 1.0
OD1 A:ASN235 3.3 62.9 1.0
C2 A:GOL306 3.3 66.1 1.0
OD1 A:ASP238 3.4 86.9 1.0
C A:ASP238 3.5 60.2 1.0
OD2 A:ASP241 3.5 68.5 1.0
C3 A:GOL306 3.5 76.6 1.0
CG A:ASP241 3.6 60.5 1.0
ND2 A:ASN235 3.7 55.4 1.0
N A:GLU239 3.9 59.6 1.0
CG A:ASN235 3.9 57.2 1.0
CD A:GLU211 4.0 71.7 1.0
CA A:CA301 4.1 62.1 1.0
CA A:GLU239 4.1 52.3 1.0
N A:GLU240 4.1 50.5 1.0
CG A:ASP238 4.2 90.0 1.0
CA A:ASP238 4.3 64.8 1.0
C A:GLU239 4.4 50.9 1.0
O A:GLU240 4.5 51.1 1.0
OE1 A:GLU211 4.6 72.5 1.0
C1 A:GOL306 4.6 69.4 1.0
C A:GLU240 4.7 53.0 1.0
CB A:ASP238 4.9 73.9 1.0
CG A:GLU211 4.9 67.8 1.0
OD2 A:ASP238 5.0 93.5 1.0

Calcium binding site 4 out of 18 in 4yli

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Calcium binding site 4 out of 18 in the Cl-K1 Trimer


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Cl-K1 Trimer within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca301

b:57.7
occ:1.00
OD2 B:ASP207 2.4 52.9 1.0
O B:GLU240 2.4 55.5 1.0
O B:HOH405 2.4 53.6 1.0
OD1 B:ASP241 2.5 61.2 1.0
OE1 B:GLU211 2.5 63.9 1.0
OE2 B:GLU211 2.6 57.0 1.0
OD1 B:ASN235 2.8 70.8 1.0
CD B:GLU211 2.9 59.1 1.0
OD1 B:ASP207 3.1 62.8 1.0
CG B:ASP207 3.1 55.2 1.0
CG B:ASN235 3.4 68.0 1.0
C B:GLU240 3.5 48.9 1.0
CG B:ASP241 3.6 52.5 1.0
CA B:ASP241 3.8 43.4 1.0
CA B:CA303 3.9 78.3 1.0
CB B:ASN235 3.9 57.2 1.0
N B:ASP241 4.1 47.2 1.0
ND2 B:ASN235 4.1 66.6 1.0
O2 B:GOL305 4.2 43.8 1.0
CB B:ASP241 4.3 42.5 1.0
CG B:GLU211 4.4 56.5 1.0
CA B:ASN235 4.5 52.9 1.0
CB B:ASP207 4.6 56.6 1.0
CZ B:PHE214 4.6 45.2 1.0
CA B:GLU240 4.6 54.7 1.0
OD2 B:ASP241 4.6 63.0 1.0
OD2 B:ASP253 4.8 45.0 1.0
N B:GLU240 4.8 50.6 1.0
N B:GLY212 4.8 59.1 1.0
O B:ASP207 4.9 62.5 1.0
CA B:GLU211 5.0 60.9 1.0

Calcium binding site 5 out of 18 in 4yli

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Calcium binding site 5 out of 18 in the Cl-K1 Trimer


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Cl-K1 Trimer within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca302

b:62.0
occ:1.00
OD1 B:ASP253 2.4 47.5 1.0
O2 B:GOL304 2.4 50.7 1.0
OD1 B:ASN252 2.5 60.0 1.0
O1 B:GOL304 2.5 44.9 1.0
O B:ASP253 2.5 53.9 1.0
OD1 B:ASN234 2.5 52.7 1.0
OE1 B:GLU240 2.6 52.3 1.0
OE1 B:GLU232 2.7 72.3 1.0
C2 B:GOL304 3.2 50.6 1.0
CG B:ASP253 3.3 46.8 1.0
C1 B:GOL304 3.4 45.5 1.0
CD B:GLU240 3.4 59.2 1.0
CD B:GLU232 3.5 57.4 1.0
CG B:ASN252 3.5 59.2 1.0
CG B:ASN234 3.5 55.1 1.0
C B:ASP253 3.6 45.4 1.0
OE2 B:GLU240 3.6 58.6 1.0
OE2 B:GLU232 3.7 56.0 1.0
N B:ASP253 3.8 38.3 1.0
ND2 B:ASN252 3.9 59.0 1.0
OD2 B:ASP253 3.9 45.0 1.0
ND2 B:ASN234 4.0 42.6 1.0
CA B:ASP253 4.1 42.7 1.0
CB B:ASP253 4.3 43.8 1.0
N B:ASN234 4.3 44.6 1.0
C B:ASN252 4.6 45.5 1.0
C3 B:GOL304 4.6 55.7 1.0
CB B:ASN234 4.7 54.1 1.0
N B:ASN235 4.7 48.2 1.0
CG B:GLU232 4.7 52.2 1.0
N B:VAL254 4.7 52.2 1.0
CG B:GLU240 4.8 56.4 1.0
CB B:ALA236 4.8 51.7 1.0
CB B:ASN252 4.8 50.5 1.0
N B:ALA236 4.8 63.0 1.0
CA B:ASN252 5.0 46.1 1.0
CB B:GLU240 5.0 51.2 1.0
CA B:ASN234 5.0 51.3 1.0

Calcium binding site 6 out of 18 in 4yli

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Calcium binding site 6 out of 18 in the Cl-K1 Trimer


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Cl-K1 Trimer within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca303

b:78.3
occ:1.00
O2 B:GOL305 2.2 43.8 1.0
O1 B:GOL305 2.5 63.4 1.0
OE2 B:GLU211 2.8 57.0 1.0
OD1 B:ASP241 2.9 61.2 1.0
C2 B:GOL305 3.2 66.1 1.0
C1 B:GOL305 3.2 68.0 1.0
OD2 B:ASP241 3.3 63.0 1.0
OD1 B:ASP238 3.3 67.3 1.0
OD1 B:ASN235 3.4 70.8 1.0
O B:ASP238 3.5 65.6 1.0
CG B:ASP241 3.5 52.5 1.0
CD B:GLU211 3.7 59.1 1.0
C B:ASP238 3.8 62.8 1.0
ND2 B:ASN235 3.9 66.6 1.0
CA B:CA301 3.9 57.7 1.0
CG B:ASN235 4.0 68.0 1.0
CG B:ASP238 4.2 75.0 1.0
N B:GLU239 4.3 60.8 1.0
OE1 B:GLU211 4.4 63.9 1.0
C3 B:GOL305 4.4 69.2 1.0
CA B:ASP238 4.5 66.5 1.0
N B:GLU240 4.5 50.6 1.0
CA B:GLU239 4.5 65.3 1.0
CG B:GLU211 4.6 56.5 1.0
O B:GLU240 4.7 55.5 1.0
C B:GLU239 4.8 49.7 1.0
O3 B:GOL305 4.9 63.6 1.0
C B:GLU240 4.9 48.9 1.0
OD2 B:ASP238 4.9 84.3 1.0
CB B:ASP241 4.9 42.5 1.0
CB B:ASP238 5.0 61.2 1.0

Calcium binding site 7 out of 18 in 4yli

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Calcium binding site 7 out of 18 in the Cl-K1 Trimer


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Cl-K1 Trimer within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca301

b:0.5
occ:1.00
O2 C:GOL305 2.4 95.8 1.0
OD1 C:ASP241 2.7 0.2 1.0
OD2 C:ASP241 2.7 1.0 1.0
OE1 C:GLU211 2.9 93.1 1.0
CG C:ASP241 3.0 100.0 1.0
C2 C:GOL305 3.1 0.3 1.0
O3 C:GOL305 3.2 93.7 1.0
C3 C:GOL305 3.7 97.1 1.0
OD1 C:ASP238 3.7 0.9 1.0
CD C:GLU211 4.0 94.7 1.0
O C:ASP238 4.1 0.3 1.0
OD1 C:ASN235 4.2 85.8 1.0
C1 C:GOL305 4.4 0.8 1.0
CA C:CA303 4.5 90.6 1.0
C C:ASP238 4.5 95.8 1.0
CB C:ASP241 4.5 88.9 1.0
ND2 C:ASN235 4.6 87.4 1.0
O1 C:GOL305 4.6 0.8 1.0
CG C:ASP238 4.7 0.6 1.0
OE2 C:GLU211 4.8 96.0 1.0
CG C:ASN235 4.8 81.0 1.0
CG C:GLU211 4.9 0.0 1.0
O C:GLU240 5.0 89.7 1.0
N C:GLU239 5.0 87.3 1.0
CB C:GLU211 5.0 0.9 1.0

Calcium binding site 8 out of 18 in 4yli

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Calcium binding site 8 out of 18 in the Cl-K1 Trimer


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Cl-K1 Trimer within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca302

b:65.8
occ:1.00
OD1 C:ASN234 2.4 81.8 1.0
OD1 C:ASP253 2.4 65.5 1.0
OD1 C:ASN252 2.5 78.9 1.0
O2 C:GOL304 2.5 66.9 1.0
O C:ASP253 2.6 69.2 1.0
OE1 C:GLU232 2.6 63.8 1.0
O3 C:GOL304 2.6 54.9 1.0
OE1 C:GLU240 2.6 78.5 1.0
CG C:ASN234 3.3 76.8 1.0
CG C:ASP253 3.4 65.2 1.0
CD C:GLU232 3.4 64.8 1.0
C3 C:GOL304 3.5 48.3 1.0
C2 C:GOL304 3.5 62.2 1.0
CD C:GLU240 3.5 77.9 1.0
CG C:ASN252 3.5 69.1 1.0
C C:ASP253 3.6 67.6 1.0
OE2 C:GLU240 3.7 73.3 1.0
OE2 C:GLU232 3.7 66.5 1.0
ND2 C:ASN234 3.8 64.8 1.0
N C:ASP253 3.8 62.9 1.0
ND2 C:ASN252 4.0 76.2 1.0
OD2 C:ASP253 4.0 68.4 1.0
CA C:ASP253 4.1 67.2 1.0
N C:ASN234 4.2 79.3 1.0
CB C:ASP253 4.3 71.0 1.0
CB C:ASN234 4.5 75.6 1.0
C C:ASN252 4.6 65.9 1.0
CG C:GLU232 4.6 55.8 1.0
N C:ASN235 4.6 78.8 1.0
C1 C:GOL304 4.8 68.6 1.0
N C:VAL254 4.8 75.6 1.0
CB C:ASN252 4.8 62.0 1.0
N C:ALA236 4.8 81.8 1.0
CA C:ASN234 4.8 83.4 1.0
CG C:GLU240 4.8 79.3 1.0
CB C:ALA236 4.9 71.8 1.0
CA C:ASN252 4.9 64.0 1.0

Calcium binding site 9 out of 18 in 4yli

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Calcium binding site 9 out of 18 in the Cl-K1 Trimer


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Cl-K1 Trimer within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca303

b:90.6
occ:1.00
O C:GLU240 2.4 89.7 1.0
OE2 C:GLU211 2.5 96.0 1.0
OD2 C:ASP207 2.6 94.7 1.0
OD1 C:ASN235 2.8 85.8 1.0
OD1 C:ASP241 2.8 0.2 1.0
OE1 C:GLU211 2.8 93.1 1.0
CD C:GLU211 3.0 94.7 1.0
OD1 C:ASP207 3.1 94.1 1.0
CG C:ASP207 3.2 92.7 1.0
CG C:ASN235 3.2 81.0 1.0
C C:GLU240 3.5 85.7 1.0
CB C:ASN235 3.8 77.0 1.0
CA C:ASP241 3.9 85.9 1.0
CG C:ASP241 3.9 100.0 1.0
ND2 C:ASN235 4.0 87.4 1.0
N C:ASP241 4.2 82.4 1.0
CZ C:PHE214 4.4 81.8 1.0
CA C:ASN235 4.4 79.6 1.0
CA C:CA301 4.5 0.5 1.0
CG C:GLU211 4.5 0.0 1.0
CB C:ASP241 4.5 88.9 1.0
OD2 C:ASP253 4.5 68.4 1.0
CA C:GLU240 4.7 85.2 1.0
CB C:ASP207 4.7 88.6 1.0
N C:GLY212 4.7 98.8 1.0
N C:GLU240 4.9 85.7 1.0
OD2 C:ASP241 5.0 1.0 1.0
CE2 C:PHE214 5.0 80.3 1.0

Calcium binding site 10 out of 18 in 4yli

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Calcium binding site 10 out of 18 in the Cl-K1 Trimer


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Cl-K1 Trimer within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca301

b:59.9
occ:1.00
OD2 D:ASP207 2.4 51.3 1.0
O D:GLU240 2.5 56.0 1.0
OD1 D:ASP241 2.5 59.0 1.0
O D:HOH404 2.5 54.3 1.0
OE1 D:GLU211 2.6 61.0 1.0
OE2 D:GLU211 2.6 53.5 1.0
OD1 D:ASN235 2.7 69.8 1.0
OD1 D:ASP207 2.9 58.0 1.0
CD D:GLU211 2.9 56.0 1.0
CG D:ASP207 3.0 53.5 1.0
CG D:ASN235 3.3 62.2 1.0
C D:GLU240 3.5 51.3 1.0
CG D:ASP241 3.7 56.8 1.0
CA D:ASP241 3.9 46.7 1.0
CB D:ASN235 3.9 50.8 1.0
CA D:CA302 4.0 66.7 1.0
ND2 D:ASN235 4.1 49.6 1.0
O D:HOH403 4.1 55.6 1.0
N D:ASP241 4.1 53.6 1.0
CB D:ASP241 4.3 54.6 1.0
CG D:GLU211 4.4 58.6 1.0
CA D:ASN235 4.5 52.3 1.0
CB D:ASP207 4.5 59.8 1.0
CA D:GLU240 4.7 53.0 1.0
OD2 D:ASP241 4.7 65.2 1.0
CZ D:PHE214 4.7 55.5 1.0
N D:GLY212 4.8 57.9 1.0
OD2 D:ASP253 4.8 47.9 1.0
O D:ASP207 4.8 67.4 1.0
N D:GLU240 4.9 52.0 1.0
CA D:GLU211 5.0 56.8 1.0

Reference:

U.V.Girija, C.M.Furze1, A.R.Gingras, T.Yoshizaki, K.Ohtani, J.E.Marshall, A.K.Wallis, W.J.Schwaeble, M.El-Mezgueldi, D.A.Mitchell, P.C.E.Moody, N.Wakamiya, R.Wallis. Molecular Basis of Sugar Recognition By Collectin-K1 and the Effects of Mutations Associated with 3MC Syndrome To Be Published.
Page generated: Sat Dec 12 05:13:39 2020

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