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

Protein crystallography data

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

Other elements in 6nbt:

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

Samarium (Sm) 13 atoms

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total 3 binding sites of Calcium where determined in the Crispr Complex Subunit CSM3 From Staphylococcus Epidermidis RP62A, PDB code: 6nbt:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 6nbt

Go back to Calcium Binding Sites List in 6nbt
Calcium binding site 1 out of 3 in the Crispr Complex Subunit CSM3 From Staphylococcus Epidermidis RP62A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca301

b:37.3
occ:1.00
O A:THR201 2.2 34.2 1.0
C A:THR201 3.4 36.5 1.0
CA A:VAL202 4.1 36.5 1.0
N A:VAL202 4.1 32.9 1.0
C A:VAL202 4.3 38.6 1.0
O A:GLY204 4.4 43.8 1.0
O A:VAL202 4.4 39.5 1.0
CA A:THR201 4.5 36.8 1.0
CB A:THR201 4.5 32.2 1.0
CG2 A:THR201 4.9 34.0 1.0
N A:VAL203 4.9 35.0 1.0
N A:THR201 5.0 37.9 1.0

Calcium binding site 2 out of 3 in 6nbt

Go back to Calcium Binding Sites List in 6nbt
Calcium binding site 2 out of 3 in the Crispr Complex Subunit CSM3 From Staphylococcus Epidermidis RP62A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca302

b:57.0
occ:1.00
O A:HOH420 2.3 52.1 1.0
O A:HOH408 2.3 42.5 1.0
O A:HOH437 2.3 53.2 1.0
O A:ILE199 2.5 34.4 1.0
C A:ILE199 3.5 39.5 1.0
CA A:ILE199 4.3 38.7 1.0
N A:ILE199 4.4 39.6 1.0
O A:SER208 4.4 39.2 1.0
CB A:ILE199 4.4 36.0 1.0
CA A:THR209 4.4 48.2 1.0
OD1 A:ASN198 4.4 60.9 1.0
N A:GLU200 4.5 41.1 1.0
CA A:GLU200 4.7 41.1 1.0
OG A:SER208 4.7 31.9 1.0
CG2 A:THR209 4.8 52.5 1.0
C A:SER208 4.9 40.1 1.0
O A:THR209 4.9 42.9 1.0

Calcium binding site 3 out of 3 in 6nbt

Go back to Calcium Binding Sites List in 6nbt
Calcium binding site 3 out of 3 in the Crispr Complex Subunit CSM3 From Staphylococcus Epidermidis RP62A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crispr Complex Subunit CSM3 From Staphylococcus Epidermidis RP62A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca308

b:89.4
occ:1.00
O B:ASN178 2.3 65.6 1.0
C B:ASN178 3.5 55.9 1.0
CA B:ASN178 4.5 53.8 1.0
N B:ASP179 4.5 53.5 1.0
CA B:ASP179 4.5 51.5 1.0
CB B:ASN178 4.7 54.2 1.0

Reference:

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
Page generated: Sat Dec 12 07:22:46 2020

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