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Calcium in PDB 4rus: Carp Fishelectin, Holo Form

Protein crystallography data

The structure of Carp Fishelectin, Holo Form, PDB code: 4rus was solved by S.Capaldi, B.Faggion, M.E.Carrizo, L.Destefanis, M.C.Gonzalez, M.Perduca, M.Bovi, M.Galliano, H.L.Monaco, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.67 / 1.70
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 204.410, 120.810, 69.270, 90.00, 91.42, 90.00
R / Rfree (%) 19.5 / 21.4

Other elements in 4rus:

The structure of Carp Fishelectin, Holo Form also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Carp Fishelectin, Holo Form (pdb code 4rus). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Carp Fishelectin, Holo Form, PDB code: 4rus:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 4rus

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Calcium binding site 1 out of 6 in the Carp Fishelectin, Holo Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Carp Fishelectin, Holo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:8.8
occ:1.00
 O A:HOH401 2.3 7.9 1.0
O A:HOH402 2.4 8.2 1.0
OE2 A:GLU170 2.4 9.2 1.0
OD1 A:ASP82 2.4 8.8 1.0
O A:HOH403 2.4 10.9 1.0
OD1 A:ASP14 2.5 8.5 1.0
OD2 A:ASP14 2.6 8.7 1.0
CG A:ASP14 2.9 8.6 1.0
CD A:GLU170 3.4 9.1 1.0
CG A:ASP82 3.4 8.6 1.0
OD2 A:ASP82 3.8 8.5 1.0
OE1 A:GLU170 3.9 9.3 1.0
OG A:SER127 4.1 9.2 1.0
O A:HOH427 4.1 11.9 1.0
OG A:SER48 4.2 9.4 1.0
O A:HOH421 4.3 12.0 1.0
OG A:SER216 4.4 8.7 1.0
CB A:ASP14 4.4 8.5 1.0
O A:ALA15 4.4 7.9 1.0
O A:VAL171 4.5 8.6 1.0
CG A:GLU170 4.5 8.9 1.0
O A:VAL49 4.5 8.8 1.0
N A:GLY84 4.6 8.1 1.0
CA A:GLY84 4.7 8.1 1.0
CB A:GLU170 4.8 8.8 1.0
CB A:ASP82 4.8 8.7 1.0
O A:HOH503 4.8 12.1 1.0

Calcium binding site 2 out of 6 in 4rus

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Calcium binding site 2 out of 6 in the Carp Fishelectin, Holo Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Carp Fishelectin, Holo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca303

b:11.2
occ:1.00
 O B:HOH401 2.3 10.0 1.0
OD1 B:ASP82 2.4 10.1 1.0
O B:HOH403 2.4 8.9 1.0
O B:HOH402 2.4 10.9 1.0
OE1 B:GLU170 2.4 11.9 1.0
OD2 B:ASP14 2.5 11.2 1.0
OD1 B:ASP14 2.6 11.4 1.0
CG B:ASP14 2.9 11.4 1.0
CG B:ASP82 3.4 9.9 1.0
CD B:GLU170 3.4 11.9 1.0
OD2 B:ASP82 3.7 10.0 1.0
OE2 B:GLU170 3.9 12.4 1.0
OG B:SER48 4.0 9.8 1.0
O B:HOH427 4.0 14.3 1.0
OG B:SER127 4.1 11.8 1.0
O B:HOH410 4.2 13.4 1.0
CB B:ASP14 4.4 11.4 1.0
OG B:SER216 4.4 11.3 1.0
O B:ALA15 4.5 10.4 1.0
CG B:GLU170 4.5 11.9 1.0
O B:VAL171 4.5 10.1 1.0
O B:VAL49 4.6 8.8 1.0
N B:GLY84 4.6 9.4 1.0
CA B:GLY84 4.6 9.4 1.0
CB B:ASP82 4.7 10.0 1.0
CB B:GLU170 4.8 11.6 1.0
O B:HOH438 4.9 13.8 1.0

Calcium binding site 3 out of 6 in 4rus

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Calcium binding site 3 out of 6 in the Carp Fishelectin, Holo Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Carp Fishelectin, Holo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca303

b:15.1
occ:1.00
 O C:HOH402 2.3 16.4 1.0
OD1 C:ASP82 2.4 14.0 1.0
O C:HOH401 2.4 14.3 1.0
OE2 C:GLU170 2.4 15.2 1.0
OD1 C:ASP14 2.4 14.1 1.0
O C:HOH403 2.5 13.3 1.0
OD2 C:ASP14 2.6 13.4 1.0
CG C:ASP14 2.9 13.7 1.0
CD C:GLU170 3.3 15.4 1.0
CG C:ASP82 3.4 14.3 1.0
OD2 C:ASP82 3.8 14.4 1.0
OE1 C:GLU170 3.8 15.3 1.0
OG C:SER127 4.1 16.4 1.0
O C:HOH468 4.1 16.4 1.0
OG C:SER48 4.1 13.8 1.0
OG C:SER216 4.3 14.8 1.0
O C:HOH467 4.3 18.0 1.0
CB C:ASP14 4.4 13.5 1.0
O C:ALA15 4.4 14.2 1.0
CG C:GLU170 4.5 15.9 1.0
O C:VAL171 4.5 16.9 1.0
N C:GLY84 4.6 13.9 1.0
O C:VAL49 4.6 12.7 1.0
CA C:GLY84 4.7 14.6 1.0
CB C:GLU170 4.7 16.3 1.0
CB C:ASP82 4.8 14.1 1.0
O C:HOH465 4.8 15.7 1.0
O C:HOH417 5.0 15.9 1.0

Calcium binding site 4 out of 6 in 4rus

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Calcium binding site 4 out of 6 in the Carp Fishelectin, Holo Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Carp Fishelectin, Holo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca303

b:12.9
occ:1.00
 O D:HOH401 2.3 13.3 1.0
OE1 D:GLU170 2.4 14.5 1.0
O D:HOH402 2.4 11.2 1.0
OD1 D:ASP82 2.4 12.5 1.0
OD2 D:ASP14 2.5 12.1 1.0
O D:HOH403 2.5 11.0 1.0
OD1 D:ASP14 2.6 12.3 1.0
CG D:ASP14 2.9 11.9 1.0
CD D:GLU170 3.4 13.7 1.0
CG D:ASP82 3.4 12.7 1.0
OD2 D:ASP82 3.7 13.1 1.0
OE2 D:GLU170 3.9 13.8 1.0
OG D:SER127 4.1 14.4 1.0
OG D:SER48 4.1 11.5 1.0
O D:HOH421 4.1 14.7 1.0
O D:HOH469 4.3 15.7 1.0
CB D:ASP14 4.4 11.2 1.0
OG D:SER216 4.4 12.3 1.0
O D:ALA15 4.5 12.1 1.0
O D:VAL171 4.5 14.8 1.0
CG D:GLU170 4.5 13.7 1.0
N D:GLY84 4.5 13.5 1.0
O D:VAL49 4.6 11.4 1.0
CA D:GLY84 4.6 14.1 1.0
CB D:GLU170 4.8 13.9 1.0
CB D:ASP82 4.8 12.7 1.0
O D:HOH471 4.8 12.4 1.0

Calcium binding site 5 out of 6 in 4rus

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Calcium binding site 5 out of 6 in the Carp Fishelectin, Holo Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Carp Fishelectin, Holo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca303

b:13.6
occ:1.00
 O E:HOH401 2.4 11.6 1.0
O E:HOH403 2.4 12.6 1.0
OD1 E:ASP82 2.4 13.9 1.0
OE2 E:GLU170 2.4 14.4 1.0
O E:HOH402 2.4 14.2 1.0
OD1 E:ASP14 2.5 11.9 1.0
OD2 E:ASP14 2.6 12.1 1.0
CG E:ASP14 2.9 11.8 1.0
CD E:GLU170 3.4 13.9 1.0
CG E:ASP82 3.4 14.0 1.0
OD2 E:ASP82 3.8 14.2 1.0
OE1 E:GLU170 3.9 14.1 1.0
OG E:SER127 4.0 15.9 1.0
OG E:SER48 4.1 11.3 1.0
O E:HOH479 4.1 16.1 1.0
OG E:SER216 4.4 12.7 1.0
O E:HOH408 4.4 16.7 1.0
CB E:ASP14 4.4 11.1 1.0
O E:VAL171 4.5 14.1 1.0
O E:ALA15 4.5 11.5 1.0
CG E:GLU170 4.5 13.8 1.0
N E:GLY84 4.6 14.2 1.0
O E:VAL49 4.6 12.4 1.0
CA E:GLY84 4.7 14.5 1.0
CB E:GLU170 4.7 14.0 1.0
CB E:ASP82 4.7 13.8 1.0
O E:HOH428 4.8 15.0 1.0

Calcium binding site 6 out of 6 in 4rus

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Calcium binding site 6 out of 6 in the Carp Fishelectin, Holo Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Carp Fishelectin, Holo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca303

b:15.4
occ:1.00
 O F:HOH401 2.3 16.1 1.0
O F:HOH402 2.4 15.9 1.0
OE1 F:GLU170 2.4 17.1 1.0
O F:HOH403 2.4 15.6 1.0
OD1 F:ASP82 2.4 14.9 1.0
OD1 F:ASP14 2.5 15.3 1.0
OD2 F:ASP14 2.6 14.7 1.0
CG F:ASP14 2.9 14.7 1.0
CD F:GLU170 3.3 17.2 1.0
CG F:ASP82 3.4 15.1 1.0
OD2 F:ASP82 3.7 15.6 1.0
OE2 F:GLU170 3.8 17.3 1.0
OG F:SER127 4.0 18.0 1.0
OG F:SER48 4.1 13.3 1.0
O F:HOH469 4.2 19.8 1.0
O F:HOH408 4.2 19.8 1.0
O F:VAL171 4.4 17.4 1.0
OG F:SER216 4.4 16.3 1.0
CB F:ASP14 4.4 14.3 1.0
CG F:GLU170 4.5 17.5 1.0
O F:ALA15 4.5 14.2 1.0
N F:GLY84 4.5 15.0 1.0
CA F:GLY84 4.6 15.4 1.0
O F:VAL49 4.6 12.9 1.0
CB F:GLU170 4.7 17.7 1.0
CB F:ASP82 4.8 15.0 1.0
O F:HOH454 4.9 20.8 1.0

Reference:

S.Capaldi, B.Faggion, M.E.Carrizo, L.Destefanis, M.C.Gonzalez, M.Perduca, M.Bovi, M.Galliano, H.L.Monaco. Three Dimensional Structure and Ligand-Binding Site of Carp Fishelectin (Fel) Acta Crystallogr.,Sect.D V. 71 2015.
ISSN: ESSN 1399-0047
DOI: 10.1107/S1399004715004174
Page generated: Sun Jul 14 12:48:50 2024

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