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

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

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

Calcium

(Ca)

12 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 27;

Binding sites:

The binding sites of Samarium 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 Samarium atom.
In total 27 binding sites of Samarium where determined in the Crystal Structure of Xenopus Embryonic Epidermal Lectin in Complex with Samarium Ions, PDB code: 5zc0:
Jump to Samarium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Samarium binding site 1 out of 27 in the Crystal Structure of Xenopus Embryonic Epidermal Lectin in Complex with Samarium Ions


Mono view


Stereo pair view

A full contact list of Samarium with other atoms in the Sm 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:Sm403 b:22.6 occ:1.00 OE2 A:GLU291 2.2 34.2 1.0 O A:HOH521 2.6 30.6 1.0 OE2 A:GLU303 2.6 33.6 1.0 O A:HOH503 2.7 24.9 1.0 OD1 A:ASN289 2.7 21.0 1.0 OE1 A:GLU303 2.7 37.1 1.0 O A:HOH528 3.0 14.5 1.0 CD A:GLU303 3.0 27.5 1.0 CD A:GLU291 3.1 26.0 1.0 O A:HOH531 3.1 11.5 1.0 OE1 A:GLU291 3.3 26.0 1.0 CG A:ASN289 3.7 20.4 1.0 CB A:ASN289 4.2 19.4 1.0 NE2 A:GLN308 4.3 22.1 1.0 OE1 A:GLU273 4.4 26.3 1.0 CG A:GLU291 4.4 22.2 1.0 CA A:ASN289 4.4 18.5 1.0 CG A:GLU303 4.5 25.1 1.0 NE2 A:HIS292 4.6 14.7 1.0 OG A:SER272 4.7 34.0 1.0 ND2 A:ASN289 4.8 28.2 1.0 OE2 A:GLU273 4.8 37.4 1.0

Samarium binding site 2 out of 27 in the Crystal Structure of Xenopus Embryonic Epidermal Lectin in Complex with Samarium Ions


Mono view


Stereo pair view

A full contact list of Samarium with other atoms in the Sm 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:Sm404 b:35.6 occ:1.00 OE2 A:GLU172 2.4 57.0 1.0 OE2 A:GLU214 2.4 53.1 1.0 O A:GLY209 2.6 33.8 1.0 OE1 A:GLU172 2.8 36.2 1.0 CD A:GLU172 2.9 29.8 1.0 OE1 A:GLU214 3.0 64.0 1.0 CD A:GLU214 3.0 45.0 1.0 C A:GLY209 3.7 25.0 1.0 CA A:GLY209 4.2 11.3 1.0 CG A:GLU172 4.4 20.2 1.0 CG A:GLU214 4.5 29.4 1.0 N A:GLY210 4.8 26.7 1.0 ND2 A:ASN211 4.8 16.7 1.0 CA A:GLY210 5.0 16.9 1.0

Samarium binding site 3 out of 27 in the Crystal Structure of Xenopus Embryonic Epidermal Lectin in Complex with Samarium Ions


Mono view


Stereo pair view

A full contact list of Samarium with other atoms in the Sm 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 A:Sm405 b:26.3 occ:1.00 OE2 A:GLU207 2.6 25.5 1.0 O A:HOH509 2.6 18.9 1.0 O A:HOH532 2.7 9.1 1.0 OE1 A:GLU207 2.7 26.0 1.0 O A:HOH523 2.7 15.0 1.0 CD A:GLU207 2.9 30.8 1.0 CG A:GLU207 4.3 34.6 1.0 OD1 A:ASN202 4.7 18.6 1.0 CA A:PHE204 4.8 13.0 1.0 O A:ASN202 4.9 25.1 1.0 CG A:ASN202 4.9 18.2 1.0

Samarium binding site 4 out of 27 in the Crystal Structure of Xenopus Embryonic Epidermal Lectin in Complex with Samarium Ions


Mono view


Stereo pair view

A full contact list of Samarium with other atoms in the Sm 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 A:Sm406 b:86.2 occ:0.55 OE2 A:GLU90 4.1 67.5 1.0 CD A:GLU90 4.3 68.5 1.0 CG A:GLU90 4.4 50.8 1.0 CB A:GLU90 4.8 38.9 1.0

Samarium binding site 5 out of 27 in the Crystal Structure of Xenopus Embryonic Epidermal Lectin in Complex with Samarium Ions


Mono view


Stereo pair view

A full contact list of Samarium with other atoms in the Sm 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 A:Sm407 b:75.0 occ:0.56 O A:GLU90 3.9 32.0 1.0 OD2 A:ASP91 4.1 55.2 1.0 OE1 A:GLU90 4.2 89.8 1.0 C A:GLU90 4.7 37.5 1.0

Samarium binding site 6 out of 27 in the Crystal Structure of Xenopus Embryonic Epidermal Lectin in Complex with Samarium Ions


Mono view


Stereo pair view

A full contact list of Samarium with other atoms in the Sm 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 B:Sm403 b:26.0 occ:1.00 ND2 B:ASN289 2.1 35.6 1.0 OE1 B:GLU291 2.3 27.9 1.0 O B:HOH502 2.6 26.6 1.0 OE1 B:GLU303 2.7 29.6 1.0 O B:HOH503 2.7 25.8 1.0 OE2 B:GLU303 2.8 29.2 1.0 O B:HOH519 2.9 17.5 1.0 CG B:ASN289 3.0 26.7 1.0 CD B:GLU303 3.1 26.6 1.0 CD B:GLU291 3.4 29.1 1.0 O B:HOH521 3.4 16.5 1.0 OD1 B:ASN289 3.5 35.9 1.0 CB B:ASN289 3.9 17.1 1.0 OE2 B:GLU291 3.9 31.3 1.0 OE1 B:GLU273 4.4 22.7 1.0 NE2 B:GLN308 4.4 30.9 1.0 NE2 B:HIS292 4.4 21.0 1.0 CG B:GLU291 4.4 20.3 1.0 OE2 B:GLU273 4.5 44.7 1.0 CA B:ASN289 4.6 25.1 1.0 CG B:GLU303 4.6 29.8 1.0 OG B:SER272 4.6 41.1 1.0 CD B:GLU273 4.9 29.7 1.0

Samarium binding site 7 out of 27 in the Crystal Structure of Xenopus Embryonic Epidermal Lectin in Complex with Samarium Ions


Mono view


Stereo pair view

A full contact list of Samarium with other atoms in the Sm 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 B:Sm404 b:35.0 occ:1.00 OE2 B:GLU214 2.5 45.6 1.0 O B:GLY209 2.6 26.1 1.0 OE1 B:GLU172 2.7 28.1 1.0 OE2 B:GLU172 2.7 54.2 1.0 CD B:GLU172 3.0 34.9 1.0 CD B:GLU214 3.2 37.5 1.0 OE1 B:GLU214 3.3 61.8 1.0 C B:GLY209 3.8 17.1 1.0 CA B:GLY209 4.4 14.2 1.0 CG B:GLU172 4.5 28.0 1.0 CG B:GLU214 4.6 28.6 1.0 N B:GLY210 4.8 24.2 1.0 ND2 B:ASN211 4.8 12.5 1.0 CA B:GLY210 4.9 16.0 1.0

Samarium binding site 8 out of 27 in the Crystal Structure of Xenopus Embryonic Epidermal Lectin in Complex with Samarium Ions


Mono view


Stereo pair view

A full contact list of Samarium with other atoms in the Sm 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 B:Sm405 b:28.0 occ:1.00 O B:HOH507 2.6 26.6 1.0 OE1 B:GLU207 2.6 29.4 1.0 O B:HOH513 2.6 30.0 1.0 OE2 B:GLU207 2.7 26.5 1.0 CD B:GLU207 3.0 28.9 1.0 CG B:GLU207 4.4 37.4 1.0 OD1 B:ASN202 4.7 19.1 1.0 ND2 B:ASN202 4.7 17.0 1.0 CG B:ASN202 4.7 13.8 1.0 O B:ASN202 4.8 22.4 1.0 CA B:PHE204 4.9 15.6 1.0

Samarium binding site 9 out of 27 in the Crystal Structure of Xenopus Embryonic Epidermal Lectin in Complex with Samarium Ions


Mono view


Stereo pair view

A full contact list of Samarium with other atoms in the Sm 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 B:Sm406 b:90.1 occ:0.51 OE2 B:GLU90 3.6 75.1 1.0 OE2 B:GLU172 4.3 54.2 1.0 CD B:GLU90 4.5 89.0 1.0 CG B:GLU90 4.7 67.9 1.0 CB B:GLU90 4.8 38.8 1.0 NH2 B:ARG68 4.8 37.4 1.0 O B:ASP170 4.9 31.5 1.0

Samarium binding site 10 out of 27 in the Crystal Structure of Xenopus Embryonic Epidermal Lectin in Complex with Samarium Ions


Mono view


Stereo pair view

A full contact list of Samarium with other atoms in the Sm 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 B:Sm407 b:67.6 occ:0.55 OE1 B:GLU90 2.5 65.0 1.0 CD B:GLU90 3.6 89.0 1.0 OD1 B:ASP91 3.8 43.8 1.0 O B:GLU90 4.0 50.4 1.0 CG B:GLU90 4.0 67.9 1.0 OE2 B:GLU90 4.7 75.1 1.0 C B:GLU90 4.7 38.4 1.0 OD2 B:ASP62 4.9 61.6 1.0 CG B:ASP91 5.0 51.5 1.0

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