Samarium in PDB 6nbt: Crispr Complex Subunit CSM3 From Staphylococcus Epidermidis RP62A

The structure of Crispr Complex Subunit CSM3 From Staphylococcus Epidermidis RP62A, PDB code: 6nbt was solved by B.W.Dorsey, A.Mondragon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 2.40
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	104.612, 50.979, 83.018, 90.00, 97.05, 90.00
R / Rfree (%)	23 / 26.7

The structure of Crispr Complex Subunit CSM3 From Staphylococcus Epidermidis RP62A also contains other interesting chemical elements:

Calcium

(Ca)

3 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Samarium atom in the Crispr Complex Subunit CSM3 From Staphylococcus Epidermidis RP62A (pdb code 6nbt). This binding sites where shown within 5.0 Angstroms radius around Samarium atom.
In total 13 binding sites of Samarium where determined in the Crispr Complex Subunit CSM3 From Staphylococcus Epidermidis RP62A, PDB code: 6nbt:
Jump to Samarium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Samarium binding site 1 out of 13 in the Crispr Complex Subunit CSM3 From Staphylococcus Epidermidis RP62A


Mono view


Stereo pair view

A full contact list of Samarium with other atoms in the Sm binding site number 1 of Crispr Complex Subunit CSM3 From Staphylococcus Epidermidis RP62A within 5.0Å range: probe atom residue distance (Å) B Occ A:Sm303 b:0.4 occ:1.00 O A:PHE194 2.6 44.0 1.0 OE2 A:GLU177 3.1 42.3 1.0 OE1 A:GLN193 3.7 62.6 1.0 C A:PHE194 3.7 41.6 1.0 OE1 A:GLU177 3.8 47.4 1.0 CD A:GLU177 3.8 42.1 1.0 N A:PHE194 4.3 41.1 1.0 SM A:SM307 4.4 0.1 1.0 CA A:PHE194 4.5 43.8 1.0 CB A:PHE194 4.7 42.5 1.0 N A:LYS195 4.7 45.7 1.0 CA A:LYS195 4.8 44.7 1.0 CD A:GLN193 4.8 58.5 1.0 CB A:LYS195 4.9 49.1 1.0 CG A:LYS214 4.9 0.0 1.0

Samarium binding site 2 out of 13 in the Crispr Complex Subunit CSM3 From Staphylococcus Epidermidis RP62A


Mono view


Stereo pair view

A full contact list of Samarium with other atoms in the Sm binding site number 2 of Crispr Complex Subunit CSM3 From Staphylococcus Epidermidis RP62A within 5.0Å range: probe atom residue distance (Å) B Occ A:Sm304 b:0.7 occ:1.00 OE1 A:GLU170 3.4 55.9 1.0 OE2 A:GLU170 3.5 61.5 1.0 CD A:GLU170 3.8 53.5 1.0 O A:HOH402 4.3 46.6 1.0 CG A:GLU167 4.7 61.8 1.0 O A:LYS212 4.9 54.9 1.0

Samarium binding site 3 out of 13 in the Crispr Complex Subunit CSM3 From Staphylococcus Epidermidis RP62A


Mono view


Stereo pair view

A full contact list of Samarium with other atoms in the Sm binding site number 3 of Crispr Complex Subunit CSM3 From Staphylococcus Epidermidis RP62A within 5.0Å range: probe atom residue distance (Å) B Occ A:Sm305 b:0.5 occ:1.00 OE1 A:GLU87 2.9 84.8 1.0 OD1 A:ASP75 2.9 95.6 1.0 CG A:ASP75 3.8 90.5 1.0 OD2 A:ASP75 3.9 90.1 1.0 CD A:GLU87 4.2 86.1 1.0 NE2 B:GLN40 4.8 93.5 1.0 O A:GLN74 4.9 0.3 1.0 OE2 A:GLU87 4.9 99.0 1.0

Samarium binding site 4 out of 13 in the Crispr Complex Subunit CSM3 From Staphylococcus Epidermidis RP62A


Mono view


Stereo pair view

A full contact list of Samarium with other atoms in the Sm binding site number 4 of Crispr Complex Subunit CSM3 From Staphylococcus Epidermidis RP62A within 5.0Å range: probe atom residue distance (Å) B Occ A:Sm306 b:0.3 occ:1.01 O A:HOH432 1.5 51.2 1.0 O A:LEU175 2.0 41.7 1.0 C A:ASN178 2.8 55.0 1.0 N A:ASP179 2.9 48.5 1.0 C A:LEU175 3.0 39.7 1.0 O A:ASN178 3.1 60.1 1.0 CB A:ASN178 3.2 57.6 1.0 CA A:ASN178 3.2 55.1 1.0 CB A:ASP179 3.3 53.0 1.0 CA A:LEU175 3.4 40.3 1.0 N A:ASN178 3.5 51.2 1.0 CA A:ASP179 3.6 50.5 1.0 CB A:LEU175 4.2 41.2 1.0 O A:HIS174 4.2 45.1 1.0 N A:LEU176 4.2 36.9 1.0 CG A:ASP179 4.5 57.3 1.0 CG A:ASN178 4.6 67.4 1.0 N A:LEU175 4.6 39.4 1.0 CD2 A:LEU175 4.6 40.4 1.0 C A:LEU176 4.6 37.7 1.0 CA A:LEU176 4.7 35.7 1.0 C A:GLU177 4.7 43.2 1.0 C A:HIS174 4.8 41.9 1.0 N A:GLU177 4.8 37.0 1.0 OD1 A:ASP179 4.9 60.1 1.0 CD1 A:LEU58 4.9 45.2 1.0 ND2 A:ASN178 4.9 63.9 1.0 O A:LEU176 5.0 43.5 1.0 C A:ASP179 5.0 49.8 1.0

Samarium binding site 5 out of 13 in the Crispr Complex Subunit CSM3 From Staphylococcus Epidermidis RP62A


Mono view


Stereo pair view

A full contact list of Samarium with other atoms in the Sm binding site number 5 of Crispr Complex Subunit CSM3 From Staphylococcus Epidermidis RP62A within 5.0Å range: probe atom residue distance (Å) B Occ A:Sm307 b:0.1 occ:1.00 OE1 A:GLN193 3.3 62.6 1.0 OE1 A:GLU177 3.4 47.4 1.0 NE2 A:GLN193 4.0 55.4 1.0 CD A:GLU177 4.0 42.1 1.0 CD A:GLN193 4.0 58.5 1.0 SM A:SM303 4.4 0.4 1.0 CB A:GLU177 4.4 40.0 1.0 OE2 A:GLU177 4.5 42.3 1.0 CG A:GLU177 4.7 41.2 1.0

Samarium binding site 6 out of 13 in the Crispr Complex Subunit CSM3 From Staphylococcus Epidermidis RP62A


Mono view


Stereo pair view

A full contact list of Samarium with other atoms in the Sm binding site number 6 of Crispr Complex Subunit CSM3 From Staphylococcus Epidermidis RP62A within 5.0Å range: probe atom residue distance (Å) B Occ A:Sm308 b:0.8 occ:1.00 OD2 A:ASP164 3.9 61.9 1.0 OD1 A:ASP164 3.9 75.5 1.0 CG A:ASP164 4.3 59.0 1.0

Samarium binding site 7 out of 13 in the Crispr Complex Subunit CSM3 From Staphylococcus Epidermidis RP62A


Mono view


Stereo pair view

A full contact list of Samarium with other atoms in the Sm binding site number 7 of Crispr Complex Subunit CSM3 From Staphylococcus Epidermidis RP62A within 5.0Å range: probe atom residue distance (Å) B Occ B:Sm301 b:0.6 occ:1.00 O B:PHE194 2.6 37.0 1.0 OE2 B:GLU177 2.7 43.2 1.0 CD B:GLU177 3.4 46.6 1.0 OE1 B:GLN193 3.4 68.2 1.0 OE1 B:GLU177 3.5 50.5 1.0 C B:PHE194 3.7 40.3 1.0 N B:PHE194 4.1 35.9 1.0 CA B:PHE194 4.4 39.4 1.0 CD B:GLN193 4.5 61.8 1.0 CB B:PHE194 4.6 38.9 1.0 N B:LYS195 4.8 40.0 1.0 CG B:GLU177 4.8 47.5 1.0 CB B:GLN193 4.9 49.0 1.0 C B:GLN193 5.0 38.7 1.0

Samarium binding site 8 out of 13 in the Crispr Complex Subunit CSM3 From Staphylococcus Epidermidis RP62A


Mono view


Stereo pair view

A full contact list of Samarium with other atoms in the Sm binding site number 8 of Crispr Complex Subunit CSM3 From Staphylococcus Epidermidis RP62A within 5.0Å range: probe atom residue distance (Å) B Occ B:Sm302 b:0.4 occ:1.00 OE1 B:GLU170 2.4 66.6 1.0 CD B:GLU170 3.4 53.4 1.0 OE2 B:GLU170 3.6 61.8 1.0 CG B:GLU170 4.7 50.4 1.0

Samarium binding site 9 out of 13 in the Crispr Complex Subunit CSM3 From Staphylococcus Epidermidis RP62A


Mono view


Stereo pair view

A full contact list of Samarium with other atoms in the Sm binding site number 9 of Crispr Complex Subunit CSM3 From Staphylococcus Epidermidis RP62A within 5.0Å range: probe atom residue distance (Å) B Occ B:Sm303 b:0.6 occ:1.00 OE2 B:GLU158 2.6 99.2 1.0 OE1 B:GLU158 2.7 84.7 1.0 CD B:GLU158 2.9 80.8 1.0 CG B:GLU158 4.4 72.0 1.0

Samarium binding site 10 out of 13 in the Crispr Complex Subunit CSM3 From Staphylococcus Epidermidis RP62A


Mono view


Stereo pair view

A full contact list of Samarium with other atoms in the Sm binding site number 10 of Crispr Complex Subunit CSM3 From Staphylococcus Epidermidis RP62A within 5.0Å range: probe atom residue distance (Å) B Occ B:Sm304 b:0.4 occ:1.00 OE2 B:GLU147 2.9 62.9 1.0 NZ B:LYS195 3.2 44.4 1.0 NZ B:LYS106 3.4 80.6 1.0 OE1 B:GLU147 3.6 56.4 1.0 CD B:GLU147 3.6 52.2 1.0 CE B:LYS106 3.8 79.9 1.0 CE B:LYS195 4.2 42.9 1.0 O B:HOH429 4.6 53.3 1.0 CD B:LYS106 5.0 74.6 1.0

B.W.Dorsey, L.Huang, A.Mondragon. Structural Organization of A Type III-A Crispr Effector Subcomplex Determined By X-Ray Crystallography and Cryo-Em. Nucleic Acids Res. V. 47 3765 2019.
ISSN: ESSN 1362-4962
PubMed: 30759237
DOI: 10.1093/NAR/GKZ079