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Samarium in PDB 1exz: Structure of Stem Cell Factor

Protein crystallography data

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

Other elements in 1exz:

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

Calcium (Ca) 2 atoms

Samarium Binding Sites:

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 1exz

Go back to Samarium Binding Sites List in 1exz
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 1exz

Go back to Samarium Binding Sites List in 1exz
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 1exz

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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 1exz

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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

Reference:

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
Page generated: Wed Dec 16 02:09:47 2020

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