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Calcium in PDB 5zc0: Crystal Structure of Xenopus Embryonic Epidermal Lectin in Complex with Samarium Ions

Protein crystallography data

The structure of Crystal Structure of Xenopus Embryonic Epidermal Lectin in Complex with Samarium Ions, PDB code: 5zc0 was solved by K.Wangkanont, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.19 / 2.75
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 124.300, 111.410, 124.360, 90.00, 119.94, 90.00
R / Rfree (%) 19.6 / 23.8

Other elements in 5zc0:

The structure of Crystal Structure of Xenopus Embryonic Epidermal Lectin in Complex with Samarium Ions also contains other interesting chemical elements:

Samarium (Sm) 27 atoms

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of Xenopus Embryonic Epidermal Lectin in Complex with Samarium Ions (pdb code 5zc0). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 12 binding sites of Calcium where determined in the Crystal Structure of Xenopus Embryonic Epidermal Lectin in Complex with Samarium Ions, PDB code: 5zc0:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 12 in 5zc0

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Calcium binding site 1 out of 12 in the Crystal Structure of Xenopus Embryonic Epidermal Lectin in Complex with Samarium Ions


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Xenopus Embryonic Epidermal Lectin in Complex with Samarium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:7.4
occ:1.00
 O A:GLY121 2.3 13.5 1.0
O A:HOH525 2.3 7.9 1.0
OE2 A:GLU116 2.3 13.5 1.0
O A:HOH508 2.4 8.0 1.0
OD1 A:ASP127 2.5 11.0 1.0
O A:ASN118 2.5 18.8 1.0
OD2 A:ASP127 2.6 10.4 1.0
CG A:ASP127 2.9 12.8 1.0
CD A:GLU116 3.3 15.6 1.0
C A:GLY121 3.4 15.7 1.0
C A:ASN118 3.5 11.0 1.0
OE1 A:GLU116 3.8 11.7 1.0
CA A:GLY121 4.1 11.4 1.0
OD1 A:ASN117 4.1 14.3 1.0
N A:ASN118 4.1 14.9 1.0
N A:GLY121 4.2 27.2 1.0
CA A:ASN118 4.3 12.7 1.0
OG1 A:THR124 4.3 6.4 1.0
O A:HOH501 4.4 10.1 1.0
N A:MET119 4.4 9.6 1.0
CB A:ASP127 4.5 11.2 1.0
CB A:ASN118 4.5 14.2 1.0
N A:LYS122 4.5 9.3 1.0
CG A:GLU116 4.5 10.1 1.0
N A:CYS123 4.6 13.1 1.0
CA A:MET119 4.6 11.4 1.0
CA A:GLY310 4.6 8.5 1.0
C A:MET119 4.7 13.9 1.0
N A:ASP311 4.7 7.2 1.0
CA A:LYS122 4.8 11.2 1.0
O A:MET119 4.9 14.5 1.0
N A:THR124 4.9 16.3 1.0
O A:HOH513 4.9 17.5 1.0

Calcium binding site 2 out of 12 in 5zc0

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Calcium binding site 2 out of 12 in the Crystal Structure of Xenopus Embryonic Epidermal Lectin in Complex with Samarium Ions


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Xenopus Embryonic Epidermal Lectin in Complex with Samarium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:8.3
occ:1.00
 OD2 A:ASP311 2.3 8.4 1.0
OD1 A:ASP162 2.3 15.9 1.0
O A:HIS115 2.4 16.2 1.0
O A:GLY126 2.4 13.0 1.0
O A:HOH530 2.4 7.3 1.0
OD2 A:ASP162 2.5 8.0 1.0
O A:HOH501 2.6 10.1 1.0
CG A:ASP162 2.7 10.0 1.0
CG A:ASP311 3.4 11.1 1.0
C A:HIS115 3.6 11.6 1.0
C A:GLY126 3.6 12.5 1.0
N A:ARG128 4.1 10.3 1.0
CB A:ASP311 4.1 6.1 1.0
CA A:ASP127 4.2 13.3 1.0
CB A:ASP162 4.2 9.3 1.0
N A:HIS115 4.3 9.4 1.0
N A:ASP127 4.3 9.0 1.0
OD1 A:ASN117 4.3 14.3 1.0
OD1 A:ASP311 4.4 7.7 1.0
CA A:HIS115 4.4 8.8 1.0
N A:GLU116 4.5 7.4 1.0
CA A:GLU116 4.5 7.4 1.0
CD1 A:TRP129 4.6 6.7 1.0
CA A:GLY126 4.6 5.6 1.0
C A:ASP127 4.6 12.5 1.0
N A:ASN117 4.6 14.7 1.0
N A:ASP162 4.7 8.3 1.0
CB A:HIS115 4.7 9.1 1.0
ND1 A:HIS115 4.8 7.8 1.0
CA A:ASP162 4.8 12.4 1.0
OD1 A:ASP127 4.9 11.0 1.0

Calcium binding site 3 out of 12 in 5zc0

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Calcium binding site 3 out of 12 in the Crystal Structure of Xenopus Embryonic Epidermal Lectin in Complex with Samarium Ions


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Xenopus Embryonic Epidermal Lectin in Complex with Samarium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca401

b:18.7
occ:1.00
 O B:HOH518 2.2 10.9 1.0
O B:HOH508 2.2 23.2 1.0
O B:GLY121 2.4 17.1 1.0
OD1 B:ASP127 2.4 16.0 1.0
OD2 B:ASP127 2.5 18.7 1.0
OE2 B:GLU116 2.6 23.3 1.0
O B:ASN118 2.6 16.8 1.0
CG B:ASP127 2.8 12.9 1.0
CD B:GLU116 3.4 17.9 1.0
OE1 B:GLU116 3.4 19.0 1.0
C B:GLY121 3.6 15.2 1.0
C B:ASN118 3.6 16.1 1.0
O B:HOH509 4.2 8.1 1.0
OD1 B:ASN117 4.3 19.0 1.0
N B:ASN118 4.3 12.0 1.0
CB B:ASP127 4.3 8.8 1.0
CA B:GLY121 4.3 8.0 1.0
CA B:ASN118 4.4 12.9 1.0
CA B:GLY310 4.4 11.5 1.0
N B:GLY121 4.4 17.5 1.0
N B:CYS123 4.5 12.1 1.0
N B:ASP311 4.5 12.4 1.0
N B:MET119 4.5 21.0 1.0
CA B:MET119 4.6 16.6 1.0
N B:LYS122 4.6 14.6 1.0
OG1 B:THR124 4.6 9.2 1.0
CB B:ASN118 4.6 10.2 1.0
C B:MET119 4.7 15.9 1.0
CG B:GLU116 4.8 15.9 1.0
CA B:LYS122 4.8 10.7 1.0
O B:MET119 4.9 20.2 1.0

Calcium binding site 4 out of 12 in 5zc0

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Calcium binding site 4 out of 12 in the Crystal Structure of Xenopus Embryonic Epidermal Lectin in Complex with Samarium Ions


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Xenopus Embryonic Epidermal Lectin in Complex with Samarium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca402

b:6.7
occ:1.00
 O B:HIS115 2.1 11.8 1.0
O B:HOH520 2.3 19.3 1.0
OD2 B:ASP311 2.4 8.8 1.0
OD1 B:ASP162 2.4 8.1 1.0
O B:HOH509 2.4 8.1 1.0
O B:GLY126 2.5 20.2 1.0
OD2 B:ASP162 2.6 13.9 1.0
CG B:ASP162 2.8 12.0 1.0
C B:HIS115 3.4 9.9 1.0
CG B:ASP311 3.5 13.3 1.0
C B:GLY126 3.6 18.7 1.0
OD1 B:ASN117 4.2 19.0 1.0
CB B:ASP311 4.2 13.1 1.0
CA B:HIS115 4.2 7.2 1.0
N B:HIS115 4.2 9.3 1.0
CB B:ASP162 4.3 8.6 1.0
N B:GLU116 4.3 9.0 1.0
CA B:ASP127 4.3 9.4 1.0
N B:ARG128 4.3 9.4 1.0
CA B:GLU116 4.4 8.5 1.0
N B:ASP127 4.4 14.4 1.0
CB B:HIS115 4.4 4.3 1.0
N B:ASN117 4.5 12.7 1.0
CD2 B:HIS115 4.5 7.8 1.0
OD1 B:ASP311 4.5 10.3 1.0
CA B:GLY126 4.6 12.2 1.0
N B:ASP162 4.7 9.6 1.0
CD1 B:TRP129 4.7 5.4 1.0
OD1 B:ASP127 4.8 16.0 1.0
CG B:HIS115 4.8 9.4 1.0
C B:ASP127 4.8 8.4 1.0
CA B:ASP162 4.9 8.6 1.0
C B:GLU116 4.9 14.8 1.0
CG B:ASN117 4.9 13.1 1.0
OD2 B:ASP161 4.9 28.0 1.0

Calcium binding site 5 out of 12 in 5zc0

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Calcium binding site 5 out of 12 in the Crystal Structure of Xenopus Embryonic Epidermal Lectin in Complex with Samarium Ions


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Xenopus Embryonic Epidermal Lectin in Complex with Samarium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca401

b:10.6
occ:1.00
 O C:GLY121 2.3 18.5 1.0
O C:HOH507 2.4 9.5 1.0
O C:HOH502 2.4 10.2 1.0
O C:ASN118 2.5 10.4 1.0
OD2 C:ASP127 2.5 9.6 1.0
OE2 C:GLU116 2.5 13.9 1.0
OD1 C:ASP127 2.5 12.8 1.0
CG C:ASP127 2.9 9.0 1.0
CD C:GLU116 3.4 14.8 1.0
C C:GLY121 3.4 19.1 1.0
C C:ASN118 3.5 9.9 1.0
OE1 C:GLU116 3.5 8.8 1.0
CA C:GLY121 4.0 15.6 1.0
N C:ASN118 4.1 13.5 1.0
N C:GLY121 4.2 19.4 1.0
CA C:ASN118 4.2 14.4 1.0
OG1 C:THR124 4.2 12.6 1.0
OD1 C:ASN117 4.3 9.8 1.0
O C:HOH503 4.3 3.8 1.0
N C:MET119 4.4 14.2 1.0
CB C:ASP127 4.4 8.5 1.0
CB C:ASN118 4.4 9.8 1.0
N C:LYS122 4.5 13.2 1.0
CA C:MET119 4.6 12.6 1.0
CA C:GLY310 4.6 6.8 1.0
N C:CYS123 4.7 12.6 1.0
CG C:GLU116 4.7 14.8 1.0
C C:MET119 4.7 17.9 1.0
N C:ASP311 4.8 6.5 1.0
O C:MET119 4.8 25.3 1.0
CA C:LYS122 4.9 11.6 1.0
O C:HOH513 5.0 11.7 1.0

Calcium binding site 6 out of 12 in 5zc0

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Calcium binding site 6 out of 12 in the Crystal Structure of Xenopus Embryonic Epidermal Lectin in Complex with Samarium Ions


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Xenopus Embryonic Epidermal Lectin in Complex with Samarium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca402

b:9.2
occ:1.00
 OD1 C:ASP311 2.3 8.0 1.0
O C:GLY126 2.3 12.6 1.0
O C:HIS115 2.4 11.2 1.0
OD2 C:ASP162 2.4 8.2 1.0
O C:HOH503 2.4 3.8 1.0
O C:HOH525 2.5 11.8 1.0
OD1 C:ASP162 2.6 10.0 1.0
CG C:ASP162 2.8 7.1 1.0
CG C:ASP311 3.5 15.9 1.0
C C:GLY126 3.5 13.9 1.0
C C:HIS115 3.6 12.2 1.0
N C:ARG128 4.1 15.6 1.0
CA C:ASP127 4.2 7.8 1.0
CB C:ASP311 4.2 9.5 1.0
OD1 C:ASN117 4.2 9.8 1.0
N C:HIS115 4.2 10.0 1.0
N C:ASP127 4.3 10.9 1.0
CB C:ASP162 4.3 6.3 1.0
CA C:HIS115 4.4 9.1 1.0
OD2 C:ASP311 4.5 12.1 1.0
CA C:GLY126 4.5 8.9 1.0
N C:GLU116 4.6 7.5 1.0
CB C:HIS115 4.6 4.9 1.0
CD1 C:TRP129 4.6 7.8 1.0
CA C:GLU116 4.6 7.7 1.0
C C:ASP127 4.6 13.8 1.0
ND1 C:HIS115 4.7 10.2 1.0
N C:ASN117 4.7 9.8 1.0
OD1 C:ASP127 4.8 12.8 1.0
N C:ASP162 4.8 11.7 1.0
OD2 C:ASP161 4.9 27.3 1.0

Calcium binding site 7 out of 12 in 5zc0

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Calcium binding site 7 out of 12 in the Crystal Structure of Xenopus Embryonic Epidermal Lectin in Complex with Samarium Ions


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Xenopus Embryonic Epidermal Lectin in Complex with Samarium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca401

b:7.8
occ:1.00
 O D:GLY121 2.2 14.0 1.0
OE2 D:GLU116 2.3 15.0 1.0
O D:HOH517 2.4 13.5 1.0
O D:HOH507 2.4 12.9 1.0
OD2 D:ASP127 2.5 9.9 1.0
O D:ASN118 2.5 16.8 1.0
OD1 D:ASP127 2.7 11.3 1.0
CG D:ASP127 2.9 10.0 1.0
CD D:GLU116 3.2 14.2 1.0
C D:GLY121 3.4 16.6 1.0
OE1 D:GLU116 3.4 14.2 1.0
C D:ASN118 3.6 16.3 1.0
CA D:GLY121 3.9 15.8 1.0
N D:GLY121 4.1 19.5 1.0
CG2 D:THR124 4.2 10.1 1.0
O D:HOH504 4.2 12.8 1.0
N D:ASN118 4.3 12.6 1.0
CA D:ASN118 4.3 12.6 1.0
CB D:ASN118 4.4 9.5 1.0
CB D:ASP127 4.4 13.8 1.0
N D:LYS122 4.5 10.3 1.0
OD1 D:ASN117 4.5 20.3 1.0
N D:MET119 4.5 13.1 1.0
CG D:GLU116 4.6 12.4 1.0
CA D:GLY310 4.6 9.9 1.0
N D:CYS123 4.6 12.5 1.0
N D:ASP311 4.7 14.1 1.0
CA D:MET119 4.7 14.5 1.0
C D:MET119 4.8 16.9 1.0
O D:MET119 4.8 16.3 1.0
O D:HOH513 4.8 12.8 1.0
CA D:LYS122 4.8 12.6 1.0
N D:THR124 4.9 12.8 1.0

Calcium binding site 8 out of 12 in 5zc0

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Calcium binding site 8 out of 12 in the Crystal Structure of Xenopus Embryonic Epidermal Lectin in Complex with Samarium Ions


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Xenopus Embryonic Epidermal Lectin in Complex with Samarium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca402

b:12.3
occ:1.00
 O D:HIS115 2.2 14.1 1.0
OD2 D:ASP311 2.2 12.7 1.0
O D:HOH511 2.4 20.6 1.0
O D:GLY126 2.4 14.4 1.0
OD1 D:ASP162 2.4 16.8 1.0
OD2 D:ASP162 2.5 7.9 1.0
O D:HOH504 2.6 12.8 1.0
CG D:ASP162 2.8 11.0 1.0
CG D:ASP311 3.4 15.5 1.0
C D:HIS115 3.4 13.5 1.0
C D:GLY126 3.6 18.5 1.0
CB D:ASP311 4.1 9.0 1.0
N D:ARG128 4.2 8.8 1.0
N D:HIS115 4.2 16.8 1.0
CA D:ASP127 4.2 15.5 1.0
CB D:ASP162 4.3 6.9 1.0
CA D:HIS115 4.3 12.4 1.0
OD1 D:ASN117 4.3 20.3 1.0
OD1 D:ASP311 4.4 12.2 1.0
N D:ASP127 4.4 13.5 1.0
N D:GLU116 4.4 10.2 1.0
CA D:GLU116 4.4 11.3 1.0
CB D:HIS115 4.6 7.4 1.0
N D:ASN117 4.6 11.5 1.0
ND1 D:HIS115 4.6 13.7 1.0
CD1 D:TRP129 4.7 6.0 1.0
OD1 D:ASP127 4.7 11.3 1.0
CA D:GLY126 4.7 9.4 1.0
C D:ASP127 4.7 11.0 1.0
N D:ASP162 4.8 8.8 1.0
NH1 D:ARG128 4.8 9.3 1.0
CA D:ASP162 4.9 8.7 1.0
C D:GLU116 5.0 11.7 1.0

Calcium binding site 9 out of 12 in 5zc0

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Calcium binding site 9 out of 12 in the Crystal Structure of Xenopus Embryonic Epidermal Lectin in Complex with Samarium Ions


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of Xenopus Embryonic Epidermal Lectin in Complex with Samarium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca401

b:7.1
occ:1.00
 O E:GLY121 2.3 12.2 1.0
OD1 E:ASP127 2.4 9.8 1.0
O E:HOH517 2.5 6.6 1.0
O E:HOH516 2.5 13.3 1.0
OD2 E:ASP127 2.5 8.0 1.0
OE2 E:GLU116 2.5 7.3 1.0
O E:ASN118 2.6 13.7 1.0
CG E:ASP127 2.8 11.3 1.0
CD E:GLU116 3.3 11.6 1.0
C E:GLY121 3.4 26.5 1.0
OE1 E:GLU116 3.5 11.5 1.0
C E:ASN118 3.6 11.2 1.0
CA E:GLY121 4.1 13.7 1.0
N E:GLY121 4.2 19.6 1.0
N E:ASN118 4.3 11.7 1.0
CB E:ASP127 4.4 11.3 1.0
OD1 E:ASN117 4.4 15.6 1.0
CA E:ASN118 4.4 13.6 1.0
O E:HOH519 4.5 3.8 1.0
OG1 E:THR124 4.5 6.5 1.0
CA E:GLY310 4.5 7.1 1.0
N E:LYS122 4.5 15.8 1.0
N E:CYS123 4.5 9.1 1.0
N E:MET119 4.5 13.2 1.0
N E:ASP311 4.6 10.2 1.0
CA E:MET119 4.6 17.8 1.0
O E:MET119 4.6 23.8 1.0
CG E:GLU116 4.6 10.2 1.0
CB E:ASN118 4.7 10.1 1.0
C E:MET119 4.7 16.8 1.0
CA E:LYS122 4.8 9.8 1.0
O E:HOH507 4.8 13.3 1.0
N E:THR124 5.0 10.4 1.0

Calcium binding site 10 out of 12 in 5zc0

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Calcium binding site 10 out of 12 in the Crystal Structure of Xenopus Embryonic Epidermal Lectin in Complex with Samarium Ions


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure of Xenopus Embryonic Epidermal Lectin in Complex with Samarium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca402

b:8.1
occ:1.00
 O E:HIS115 2.2 12.6 1.0
OD1 E:ASP311 2.3 10.1 1.0
OD2 E:ASP162 2.3 10.7 1.0
O E:HOH519 2.3 3.8 1.0
O E:GLY126 2.4 22.7 1.0
OD1 E:ASP162 2.5 12.1 1.0
O E:HOH520 2.6 10.9 1.0
CG E:ASP162 2.8 7.4 1.0
C E:HIS115 3.4 13.4 1.0
CG E:ASP311 3.5 10.4 1.0
C E:GLY126 3.6 18.0 1.0
N E:HIS115 4.1 11.8 1.0
CB E:ASP311 4.2 8.5 1.0
CB E:ASP162 4.2 6.8 1.0
N E:ARG128 4.2 7.2 1.0
CA E:HIS115 4.2 10.8 1.0
CA E:ASP127 4.2 9.8 1.0
N E:ASP127 4.4 13.8 1.0
N E:GLU116 4.4 7.3 1.0
CB E:HIS115 4.5 5.0 1.0
OD2 E:ASP311 4.5 10.2 1.0
ND1 E:HIS115 4.5 14.1 1.0
CA E:GLU116 4.5 6.8 1.0
OD1 E:ASN117 4.5 15.6 1.0
CA E:GLY126 4.6 11.5 1.0
N E:ASN117 4.6 11.9 1.0
CD1 E:TRP129 4.6 10.8 1.0
N E:ASP162 4.6 9.3 1.0
C E:ASP127 4.7 9.3 1.0
NH2 E:ARG128 4.7 12.6 1.0
OD2 E:ASP161 4.8 21.4 1.0
OD1 E:ASP127 4.8 9.8 1.0
CA E:ASP162 4.8 7.9 1.0
CG E:HIS115 5.0 13.8 1.0

Reference:

J.J.Kozak, H.B.Gray, R.A.Garza-Lopez, K.Wangkanont. Structural Stabilities of Calcium Proteins: Human Intelectin-1 and Frog Lectin Xeel J. Inorg. Biochem. V. 185 86 2018.
ISSN: ISSN 1873-3344
PubMed: 29807191
DOI: 10.1016/J.JINORGBIO.2018.04.021
Page generated: Mon Jul 15 15:46:19 2024

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