Calcium in PDB 9klo: Cryo-Em Structure of CHCAS12B-Sgrna-Extended Non-Target Dna Ternary Complex (Complex-B)

The binding sites of Calcium atom in the Cryo-Em Structure of CHCAS12B-Sgrna-Extended Non-Target Dna Ternary Complex (Complex-B) (pdb code 9klo). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Cryo-Em Structure of CHCAS12B-Sgrna-Extended Non-Target Dna Ternary Complex (Complex-B), PDB code: 9klo:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Cryo-Em Structure of CHCAS12B-Sgrna-Extended Non-Target Dna Ternary Complex (Complex-B)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Cryo-Em Structure of CHCAS12B-Sgrna-Extended Non-Target Dna Ternary Complex (Complex-B) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1501 b:110.9 occ:1.00 O A:HOH1602 2.2 103.0 1.0 O D:HOH101 2.3 47.4 1.0 O D:HOH102 2.4 112.9 1.0 OD2 A:ASP767 2.4 97.5 1.0 OP1 D:DT29 2.5 37.0 1.0 OD1 A:ASP1364 2.8 110.3 1.0 CG A:ASP767 3.5 98.9 1.0 P D:DT29 3.9 38.1 1.0 OD1 A:ASP767 4.0 106.2 1.0 CG A:ASP1364 4.0 105.6 1.0 CA A:CA1502 4.0 123.6 1.0 O A:LEU768 4.4 104.4 1.0 C5' D:DT29 4.6 35.5 1.0 CA A:ASP1364 4.6 89.3 1.0 O5' D:DT29 4.6 33.8 1.0 OP2 D:DT29 4.7 40.8 1.0 CB A:ASP1364 4.7 93.9 1.0 CB A:ASP767 4.8 90.9 1.0 CB A:ALA1367 4.8 83.1 1.0 O3' D:DT28 4.9 38.1 1.0 OD2 A:ASP1364 4.9 109.8 1.0

Calcium binding site 2 out of 4 in the Cryo-Em Structure of CHCAS12B-Sgrna-Extended Non-Target Dna Ternary Complex (Complex-B)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Cryo-Em Structure of CHCAS12B-Sgrna-Extended Non-Target Dna Ternary Complex (Complex-B) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1502 b:123.6 occ:1.00 O A:HOH1601 2.3 99.3 1.0 OD1 A:ASP767 2.3 106.2 1.0 O3' D:DT28 2.8 38.1 1.0 OP1 D:DT29 2.9 37.0 1.0 OE1 A:GLU1220 2.9 105.3 1.0 OE2 A:GLU1220 3.2 102.4 1.0 CG A:ASP767 3.3 98.9 1.0 P D:DT29 3.4 38.1 1.0 CD A:GLU1220 3.4 105.8 1.0 OD2 A:ASP767 3.6 97.5 1.0 C3' D:DT28 3.9 36.9 1.0 CA A:CA1501 4.0 110.9 1.0 C4' D:DT28 4.1 35.3 1.0 O D:HOH101 4.1 47.4 1.0 OP2 D:DT29 4.3 40.8 1.0 CD1 A:ILE1371 4.5 89.4 1.0 O5' D:DT29 4.6 33.8 1.0 C5' D:DT28 4.6 33.4 1.0 O A:LEU768 4.7 104.4 1.0 CB A:ASP767 4.7 90.9 1.0 C2' D:DT28 4.7 35.0 1.0 OG1 A:THR1270 4.7 97.7 1.0 CB A:ALA1367 4.8 83.1 1.0 C5' D:DT29 4.8 35.5 1.0 CG A:GLU1220 5.0 101.3 1.0 N A:LEU768 5.0 97.3 1.0

Calcium binding site 3 out of 4 in the Cryo-Em Structure of CHCAS12B-Sgrna-Extended Non-Target Dna Ternary Complex (Complex-B)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Cryo-Em Structure of CHCAS12B-Sgrna-Extended Non-Target Dna Ternary Complex (Complex-B) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca201 b:60.0 occ:1.00 OP2 B:U33 2.3 64.8 1.0 P B:U33 3.7 57.2 1.0 N7 B:G56 4.3 55.8 1.0 O5' B:G32 4.3 53.9 1.0 OP2 B:G55 4.4 76.3 1.0 OP1 B:U33 4.5 52.4 1.0 O6 B:G56 4.5 57.0 1.0 O5' B:U33 4.5 55.5 1.0 O5' B:G55 4.6 75.7 1.0 O3' B:G32 4.7 47.3 1.0 C2' B:G55 4.7 65.4 1.0 OP1 B:G32 4.9 55.1 1.0 O2' B:G55 4.9 65.5 1.0 C3' B:G32 4.9 46.3 1.0

Calcium binding site 4 out of 4 in the Cryo-Em Structure of CHCAS12B-Sgrna-Extended Non-Target Dna Ternary Complex (Complex-B)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Cryo-Em Structure of CHCAS12B-Sgrna-Extended Non-Target Dna Ternary Complex (Complex-B) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca202 b:51.6 occ:1.00 OP2 B:C39 2.4 55.6 1.0 OP2 B:U38 2.4 51.6 1.0 P B:U38 3.7 52.5 1.0 P B:C39 3.8 55.6 1.0 O5' B:U38 3.9 50.4 1.0 OP2 B:C36 4.4 45.4 1.0 OP1 B:C39 4.4 57.2 1.0 OP1 B:U35 4.4 60.6 1.0 OP1 B:U38 4.6 45.9 1.0 O5' B:C39 4.6 53.8 1.0 OP1 B:C36 4.6 47.5 1.0 C5' B:U38 4.8 47.9 1.0 O3' B:U38 4.8 54.7 1.0 O3' B:U37 4.8 47.7 1.0 NH2 A:ARG1129 4.8 83.2 1.0 P B:C36 4.9 49.8 1.0 C6 B:C39 5.0 53.8 1.0 C5 B:C39 5.0 49.0 1.0

Y.Li, J.Li, X.Pei, J.Wei, J.Gan, J.Lin. Catalytic-State Structure of Candidatus Hydrogenedentes CAS12B Revealed By Cryo-Em Studies. Nucleic Acids Res. V. 53 2025.
ISSN: ESSN 1362-4962
PubMed: 40539514
DOI: 10.1093/NAR/GKAF519