Samarium in PDB 1exz: Structure of Stem Cell Factor

The structure of Structure of Stem Cell Factor, PDB code: 1exz was solved by Z.Zhang, R.Zhang, A.Joachimiak, J.Schlessinger, X.Kong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 2.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	36.154, 87.526, 79.434, 90.00, 97.76, 90.00
R / Rfree (%)	22.3 / 29.4

The structure of Structure of Stem Cell Factor also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Samarium atom in the Structure of Stem Cell Factor (pdb code 1exz). This binding sites where shown within 5.0 Angstroms radius around Samarium atom.
In total 4 binding sites of Samarium where determined in the Structure of Stem Cell Factor, PDB code: 1exz:
Jump to Samarium binding site number: 1; 2; 3; 4;

Samarium binding site 1 out of 4 in the Structure of Stem Cell Factor


Mono view


Stereo pair view

A full contact list of Samarium with other atoms in the Sm binding site number 1 of Structure of Stem Cell Factor within 5.0Å range: probe atom residue distance (Å) B Occ B:Sm802 b:46.2 occ:1.00 OD1 D:ASP677 2.5 36.9 1.0 OE2 B:GLU288 2.9 77.2 1.0 OD2 D:ASP677 2.9 36.7 1.0 OD1 B:ASP285 3.1 62.4 1.0 NH1 B:ARG207 3.1 51.5 1.0 CG D:ASP677 3.1 33.9 1.0 CG B:ASP285 3.9 60.6 1.0 CZ B:ARG207 3.9 50.3 1.0 CD B:GLU288 4.1 76.9 1.0 NH2 B:ARG207 4.2 51.0 1.0 OD2 B:ASP285 4.3 62.9 1.0 CA B:ASP285 4.5 56.8 1.0 CB D:ASP677 4.6 34.6 1.0 N B:ASP285 4.7 53.5 1.0 ND2 D:ASN681 4.7 47.6 1.0 OD1 D:ASN681 4.7 46.7 1.0 O B:ASP284 4.7 50.1 1.0 C B:ASP284 4.8 51.4 1.0 CB B:ASP285 4.8 57.8 1.0 OE1 B:GLU288 4.9 76.6 1.0 O B:ASN281 4.9 40.5 1.0 NE B:ARG207 5.0 49.3 1.0 O B:HOH881 5.0 27.3 1.0

Samarium binding site 2 out of 4 in the Structure of Stem Cell Factor


Mono view


Stereo pair view

A full contact list of Samarium with other atoms in the Sm binding site number 2 of Structure of Stem Cell Factor within 5.0Å range: probe atom residue distance (Å) B Occ B:Sm803 b:31.9 occ:1.00 OD2 B:ASP337 2.2 52.1 1.0 O B:VAL339 2.3 57.2 1.0 O B:HOH859 2.5 23.4 1.0 CG B:ASP337 3.0 54.8 1.0 OD1 B:ASP337 3.1 56.0 1.0 C B:VAL339 3.5 58.2 1.0 N B:VAL339 4.2 57.3 1.0 N B:VAL340 4.4 58.7 1.0 CA B:VAL339 4.4 58.4 1.0 CB B:ASP337 4.4 55.5 1.0 CA B:VAL340 4.5 59.5 1.0 O B:ASP337 4.5 56.6 1.0 C B:ASP337 4.7 56.8 1.0 N B:ASP337 4.7 56.5 1.0 CD1 B:LEU239 4.7 50.4 1.0 OG B:SER336 4.8 61.0 1.0 CB B:SER336 4.8 60.0 1.0 CA B:ASP337 4.9 56.7 1.0 CB B:VAL339 5.0 59.5 1.0

Samarium binding site 3 out of 4 in the Structure of Stem Cell Factor


Mono view


Stereo pair view

A full contact list of Samarium with other atoms in the Sm binding site number 3 of Structure of Stem Cell Factor within 5.0Å range: probe atom residue distance (Å) B Occ C:Sm801 b:1.0 occ:1.00 O C:HOH946 1.9 41.8 1.0 OD2 C:ASP454 2.4 32.3 1.0 OD2 C:ASP458 2.5 28.0 1.0 OD1 C:ASP454 2.5 30.6 1.0 CG C:ASP454 2.8 28.3 1.0 OD1 C:ASP458 2.8 31.3 1.0 CG C:ASP458 3.0 27.8 1.0 O C:ASP454 4.2 18.3 1.0 CB C:ASP454 4.3 24.0 1.0 O C:HOH895 4.3 42.8 1.0 O C:HOH930 4.4 30.6 1.0 O C:HOH913 4.4 23.4 1.0 CB C:ASP458 4.5 26.3 1.0 NZ C:LYS431 4.6 36.9 1.0 C C:ASP454 4.7 23.4 1.0 CA C:ASP454 5.0 23.4 1.0

Samarium binding site 4 out of 4 in the Structure of Stem Cell Factor


Mono view


Stereo pair view

A full contact list of Samarium with other atoms in the Sm binding site number 4 of Structure of Stem Cell Factor within 5.0Å range: probe atom residue distance (Å) B Occ C:Sm804 b:29.2 occ:1.00 OD1 A:ASP124 2.5 55.3 1.0 OG C:SER533 2.5 65.9 1.0 OD2 A:ASP128 2.6 89.4 1.0 O C:VAL531 2.7 62.9 1.0 OD2 A:ASP124 2.7 54.5 1.0 CB C:SER533 2.8 64.8 1.0 CG A:ASP124 3.0 54.8 1.0 O C:PHE529 3.2 60.7 1.0 N C:SER533 3.3 65.2 1.0 CA C:SER533 3.7 65.3 1.0 CG A:ASP128 3.8 88.4 1.0 C C:PHE529 3.9 62.9 1.0 C C:VAL531 3.9 63.5 1.0 O C:VAL530 4.0 62.0 1.0 C C:VAL530 4.4 62.2 1.0 C C:ALA532 4.4 64.6 1.0 CA C:PHE529 4.4 62.9 1.0 CB A:ASP124 4.5 52.4 1.0 OD1 A:ASP128 4.6 87.9 1.0 N C:VAL530 4.7 62.9 1.0 CA C:ALA532 4.7 64.3 1.0 N C:ALA532 4.8 64.3 1.0 CB A:ASP128 4.8 87.2 1.0 N C:VAL531 4.8 62.0 1.0 O A:ASP124 4.8 55.5 1.0 C C:SER533 4.8 65.4 1.0 O C:SER533 4.9 65.6 1.0 CA C:VAL531 4.9 62.8 1.0 CB C:PHE529 5.0 59.2 1.0

Z.Zhang, R.Zhang, A.Joachimiak, J.Schlessinger, X.P.Kong. Crystal Structure of Human Stem Cell Factor: Implication For Stem Cell Factor Receptor Dimerization and Activation. Proc.Natl.Acad.Sci.Usa V. 97 7732 2000.
ISSN: ISSN 0027-8424
PubMed: 10884405
DOI: 10.1073/PNAS.97.14.7732