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

The binding sites of Calcium atom in the Cryo-Em Structure of CHCAS12B-Sgrna-Extended Non-Target Dna Ternary Complex (Complex-C) (pdb code 9klp). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Cryo-Em Structure of CHCAS12B-Sgrna-Extended Non-Target Dna Ternary Complex (Complex-C), PDB code: 9klp:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Cryo-Em Structure of CHCAS12B-Sgrna-Extended Non-Target Dna Ternary Complex (Complex-C)


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-C) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1501 b:124.6 occ:1.00 CA A:CA1502 2.0 124.4 1.0 O A:LEU768 2.6 99.5 1.0 C A:LEU768 3.8 91.8 1.0 OD1 A:ASP767 3.8 92.7 1.0 OD2 A:ASP767 4.1 89.7 1.0 CA A:GLY769 4.2 92.4 1.0 CG A:ASP767 4.3 90.1 1.0 N A:GLY769 4.4 88.6 1.0 OG1 A:THR1230 4.5 129.5 1.0 ND1 A:HIS770 4.7 112.2 1.0 OE2 A:GLU1220 4.8 97.9 1.0 CE1 A:HIS770 4.8 113.2 1.0 CA A:LEU768 4.9 85.2 1.0 N A:LEU768 5.0 83.2 1.0

Calcium binding site 2 out of 6 in the Cryo-Em Structure of CHCAS12B-Sgrna-Extended Non-Target Dna Ternary Complex (Complex-C)


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-C) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1502 b:124.4 occ:1.00 CA A:CA1501 2.0 124.6 1.0 O A:LEU768 2.7 99.5 1.0 OD1 A:ASP767 2.8 92.7 1.0 OE2 A:GLU1220 2.9 97.9 1.0 OE1 A:GLU1220 3.5 95.8 1.0 CD A:GLU1220 3.6 94.5 1.0 CG A:ASP767 3.7 90.1 1.0 C A:LEU768 3.9 91.8 1.0 OD2 A:ASP767 4.0 89.7 1.0 N A:LEU768 4.1 83.2 1.0 CB A:PRO1227 4.4 107.7 1.0 CA A:LEU768 4.4 85.2 1.0 N A:GLU1228 4.6 113.5 1.0 CB A:LEU768 4.6 85.2 1.0 CA A:PRO1227 4.8 114.1 1.0 OH A:TYR1225 4.9 108.6 1.0 C A:ASP767 4.9 81.9 1.0 CG A:GLU1220 4.9 84.0 1.0 N A:GLY769 5.0 88.6 1.0

Calcium binding site 3 out of 6 in the Cryo-Em Structure of CHCAS12B-Sgrna-Extended Non-Target Dna Ternary Complex (Complex-C)


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-C) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca201 b:90.4 occ:1.00 CA B:CA203 1.9 73.9 1.0 OP2 B:U33 2.4 66.5 1.0 P B:U33 3.7 59.5 1.0 OP2 B:G55 3.7 79.3 1.0 OP1 B:U33 4.0 51.5 1.0 O5' B:G55 4.1 77.3 1.0 O5' B:G32 4.5 53.5 1.0 C2' B:G55 4.6 65.0 1.0 P B:G55 4.6 80.5 1.0 O5' B:U33 4.7 51.4 1.0 O2' B:C31 4.7 66.8 1.0 O3' B:G32 4.7 47.4 1.0 N7 B:G56 4.8 56.5 1.0 NH1 A:ARG14 4.8 67.5 1.0 C3' B:G55 4.9 68.4 1.0 O2' B:G55 5.0 64.2 1.0

Calcium binding site 4 out of 6 in the Cryo-Em Structure of CHCAS12B-Sgrna-Extended Non-Target Dna Ternary Complex (Complex-C)


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-C) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca202 b:66.9 occ:1.00 CA B:CA204 1.8 76.5 1.0 OP2 B:C39 2.7 62.1 1.0 OP2 B:U38 2.7 56.4 1.0 P B:C39 4.0 62.2 1.0 P B:U38 4.1 54.1 1.0 OP1 B:C39 4.4 57.7 1.0 OP1 B:U35 4.5 57.7 1.0 C5' B:U38 4.7 47.0 1.0 OP1 B:U38 4.8 43.7 1.0 O5' B:U38 4.8 45.7 1.0 NH2 A:ARG1129 4.8 63.5 1.0 O3' B:U38 4.9 55.8 1.0 OP1 B:C36 4.9 46.9 1.0 CB A:ALA1168 4.9 70.8 1.0 OP2 B:C36 4.9 41.1 1.0

Calcium binding site 5 out of 6 in the Cryo-Em Structure of CHCAS12B-Sgrna-Extended Non-Target Dna Ternary Complex (Complex-C)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Cryo-Em Structure of CHCAS12B-Sgrna-Extended Non-Target Dna Ternary Complex (Complex-C) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca203 b:73.9 occ:1.00 CA B:CA201 1.9 90.4 1.0 OP2 B:U33 2.4 66.5 1.0 O6 B:G56 3.4 60.7 1.0 N7 B:G56 3.7 56.5 1.0 P B:U33 3.8 59.5 1.0 O5' B:G32 4.1 53.5 1.0 C6 B:G56 4.2 55.5 1.0 OP1 B:G32 4.2 57.3 1.0 C5 B:G56 4.3 54.3 1.0 O5' B:U33 4.3 51.4 1.0 C5 B:U33 4.4 44.9 1.0 OP1 B:U33 4.7 51.5 1.0 P B:G32 4.7 59.7 1.0 C6 B:U33 4.8 49.2 1.0 C8 B:G56 4.8 57.0 1.0 O3' B:G32 4.9 47.4 1.0 O3' B:C31 4.9 53.9 1.0 N4 B:C57 5.0 55.9 1.0 C3' B:G32 5.0 41.0 1.0

Calcium binding site 6 out of 6 in the Cryo-Em Structure of CHCAS12B-Sgrna-Extended Non-Target Dna Ternary Complex (Complex-C)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Cryo-Em Structure of CHCAS12B-Sgrna-Extended Non-Target Dna Ternary Complex (Complex-C) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca204 b:76.5 occ:1.00 CA B:CA202 1.8 66.9 1.0 OP2 B:U38 2.3 56.4 1.0 OP2 B:C39 2.4 62.1 1.0 OP2 B:C36 3.7 41.1 1.0 P B:U38 3.8 54.1 1.0 P B:C39 3.8 62.2 1.0 OP1 B:U35 3.8 57.7 1.0 C5 B:C39 3.9 48.6 1.0 C6 B:C39 4.1 55.4 1.0 O3' B:U37 4.3 50.4 1.0 OP2 B:U35 4.4 49.0 1.0 O5' B:U38 4.4 45.7 1.0 O5' B:C39 4.4 54.7 1.0 P B:U35 4.5 53.9 1.0 P B:C36 4.6 43.4 1.0 OP1 B:C36 4.6 46.9 1.0 C5' B:U38 4.7 47.0 1.0 O3' B:U38 4.7 55.8 1.0 OP1 B:C39 4.7 57.7 1.0 C3' B:U38 4.8 52.2 1.0 O5' B:U35 4.8 44.1 1.0 OP1 B:U38 4.9 43.7 1.0 C3' B:U37 5.0 43.2 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