Zinc in PDB 8z4j: Cryo-Em Structure of Ctr-Bound Type 7 Crispr-Cas Complex at Substrate- Engaged State 2

The binding sites of Zinc atom in the Cryo-Em Structure of Ctr-Bound Type 7 Crispr-Cas Complex at Substrate- Engaged State 2 (pdb code 8z4j). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Cryo-Em Structure of Ctr-Bound Type 7 Crispr-Cas Complex at Substrate- Engaged State 2, PDB code: 8z4j:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in the Cryo-Em Structure of Ctr-Bound Type 7 Crispr-Cas Complex at Substrate- Engaged State 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryo-Em Structure of Ctr-Bound Type 7 Crispr-Cas Complex at Substrate- Engaged State 2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:155.9 occ:1.00 SG B:CYS71 2.3 97.5 1.0 SG B:CYS87 2.3 88.6 1.0 SG B:CYS84 2.3 88.1 1.0 SG B:CYS81 2.3 92.6 1.0 CB B:CYS71 3.0 91.1 1.0 CB B:CYS84 3.2 85.1 1.0 CB B:CYS87 3.3 84.8 1.0 N B:CYS81 3.5 87.1 1.0 CB B:CYS81 3.6 87.7 1.0 N B:CYS84 3.7 84.0 1.0 N B:GLY82 4.0 77.0 1.0 CA B:CYS81 4.0 87.8 1.0 N B:CYS71 4.0 90.9 1.0 CA B:CYS84 4.0 84.8 1.0 N B:CYS87 4.0 86.7 1.0 CA B:CYS71 4.1 91.4 1.0 CA B:CYS87 4.2 86.5 1.0 C B:CYS81 4.4 88.3 1.0 N B:ARG83 4.4 83.5 1.0 O B:ASN69 4.5 89.2 1.0 C B:PRO80 4.6 79.1 1.0 C B:CYS84 4.6 84.8 1.0 CA B:PRO80 4.8 79.9 1.0 O B:CYS84 4.9 84.5 1.0 C B:ARG83 4.9 82.9 1.0 C B:CYS71 5.0 92.3 1.0 O B:CYS71 5.0 90.9 1.0

Zinc binding site 2 out of 7 in the Cryo-Em Structure of Ctr-Bound Type 7 Crispr-Cas Complex at Substrate- Engaged State 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryo-Em Structure of Ctr-Bound Type 7 Crispr-Cas Complex at Substrate- Engaged State 2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:85.7 occ:1.00 SG C:CYS71 2.3 51.7 1.0 SG C:CYS87 2.3 43.7 1.0 SG C:CYS84 2.3 50.7 1.0 SG C:CYS81 2.3 51.5 1.0 CB C:CYS81 3.3 40.1 1.0 CB C:CYS87 3.4 33.5 1.0 N C:CYS81 3.4 41.4 1.0 CB C:CYS71 3.6 55.7 1.0 CB C:CYS84 3.6 40.8 1.0 N C:GLY82 3.6 48.7 1.0 CA C:CYS81 3.8 39.8 1.0 N C:CYS84 3.8 43.5 1.0 N C:CYS71 4.0 45.4 1.0 C C:CYS81 4.1 45.5 1.0 N C:CYS87 4.2 30.8 1.0 N C:ARG83 4.2 51.6 1.0 CA C:CYS84 4.3 42.5 1.0 OG1 C:THR86 4.3 45.6 1.0 CA C:CYS87 4.3 27.6 1.0 CA C:CYS71 4.4 50.3 1.0 C C:PRO80 4.4 35.4 1.0 CA C:GLY82 4.6 47.3 1.0 CA C:PRO80 4.8 28.5 1.0 NH2 C:ARG56 4.8 34.5 1.0 C C:GLY82 4.9 51.3 1.0 C C:ARG83 4.9 49.8 1.0 C C:CYS84 4.9 44.4 1.0 CB C:PRO80 5.0 26.3 1.0

Zinc binding site 3 out of 7 in the Cryo-Em Structure of Ctr-Bound Type 7 Crispr-Cas Complex at Substrate- Engaged State 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cryo-Em Structure of Ctr-Bound Type 7 Crispr-Cas Complex at Substrate- Engaged State 2 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn301 b:87.7 occ:1.00 SG D:CYS87 2.3 40.2 1.0 SG D:CYS84 2.3 59.2 1.0 SG D:CYS71 2.3 54.1 1.0 CB D:CYS84 3.3 41.0 1.0 N D:CYS81 3.4 31.5 1.0 CB D:CYS87 3.5 24.4 1.0 CB D:CYS71 3.5 53.9 1.0 SG D:CYS81 3.7 53.7 1.0 N D:GLY82 3.7 39.6 1.0 N D:CYS84 4.0 44.4 1.0 CB D:PRO80 4.0 17.9 1.0 CA D:PRO80 4.1 16.1 1.0 C D:PRO80 4.1 19.1 1.0 N D:CYS71 4.2 50.0 1.0 CA D:CYS84 4.3 41.0 1.0 CA D:CYS81 4.3 42.4 1.0 CB D:CYS81 4.4 43.7 1.0 CA D:CYS71 4.4 49.3 1.0 CA D:CYS87 4.5 13.6 1.0 N D:CYS87 4.5 25.4 1.0 C D:CYS81 4.5 47.8 1.0 NH2 D:ARG56 4.5 15.8 1.0 N D:ARG83 4.5 51.6 1.0 CA D:GLY82 4.6 36.8 1.0 OG1 D:THR86 4.8 28.4 1.0

Zinc binding site 4 out of 7 in the Cryo-Em Structure of Ctr-Bound Type 7 Crispr-Cas Complex at Substrate- Engaged State 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Cryo-Em Structure of Ctr-Bound Type 7 Crispr-Cas Complex at Substrate- Engaged State 2 within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn301 b:132.6 occ:1.00 SG E:CYS84 2.3 73.1 1.0 SG E:CYS71 2.3 60.4 1.0 SG E:CYS87 2.3 47.7 1.0 SG E:CYS81 2.3 71.7 1.0 N E:CYS81 3.2 52.0 1.0 CB E:CYS71 3.2 57.9 1.0 CB E:CYS81 3.4 59.5 1.0 CB E:CYS87 3.4 39.0 1.0 CB E:CYS84 3.6 53.3 1.0 N E:GLY82 3.6 50.7 1.0 CA E:CYS81 3.7 56.0 1.0 N E:CYS84 3.9 52.1 1.0 N E:CYS71 4.0 58.1 1.0 C E:CYS81 4.0 59.9 1.0 CA E:CYS71 4.2 55.7 1.0 C E:PRO80 4.2 44.7 1.0 N E:ARG83 4.2 58.2 1.0 CA E:CYS84 4.4 52.8 1.0 CA E:PRO80 4.5 41.3 1.0 CA E:CYS87 4.5 28.2 1.0 CA E:GLY82 4.7 47.5 1.0 N E:CYS87 4.7 33.0 1.0 C E:ARG83 4.9 65.2 1.0 C E:GLY82 5.0 46.9 1.0 OG1 E:THR86 5.0 38.0 1.0

Zinc binding site 5 out of 7 in the Cryo-Em Structure of Ctr-Bound Type 7 Crispr-Cas Complex at Substrate- Engaged State 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Cryo-Em Structure of Ctr-Bound Type 7 Crispr-Cas Complex at Substrate- Engaged State 2 within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn301 b:147.1 occ:1.00 SG F:CYS71 2.3 79.0 1.0 SG F:CYS87 2.3 63.4 1.0 SG F:CYS84 2.3 72.7 1.0 CB F:CYS81 2.7 68.7 1.0 N F:CYS81 2.8 68.0 1.0 CA F:CYS81 3.2 67.4 1.0 SG F:CYS81 3.4 73.4 1.0 N F:GLY82 3.7 76.5 1.0 CB F:CYS71 3.7 73.6 1.0 CB F:CYS87 3.8 53.6 1.0 C F:CYS81 4.0 64.9 1.0 CB F:CYS84 4.0 70.3 1.0 C F:PRO80 4.0 63.2 1.0 N F:CYS84 4.1 71.5 1.0 N F:CYS71 4.2 72.7 1.0 N F:ARG83 4.2 80.2 1.0 CA F:PRO80 4.4 60.5 1.0 CA F:CYS71 4.6 73.5 1.0 CA F:CYS84 4.7 72.1 1.0 CA F:GLY82 4.8 77.0 1.0 N F:CYS87 4.9 49.7 1.0 CA F:CYS87 4.9 47.2 1.0

Zinc binding site 6 out of 7 in the Cryo-Em Structure of Ctr-Bound Type 7 Crispr-Cas Complex at Substrate- Engaged State 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Cryo-Em Structure of Ctr-Bound Type 7 Crispr-Cas Complex at Substrate- Engaged State 2 within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn701 b:71.2 occ:1.00 OD2 H:ASP169 2.1 61.6 1.0 ND1 H:HIS64 2.3 58.7 1.0 NE2 H:HIS62 2.3 46.4 1.0 NE2 H:HIS148 2.3 54.3 1.0 CD2 H:HIS62 2.7 39.5 1.0 CD2 H:HIS148 2.9 49.8 1.0 CE1 H:HIS64 3.0 56.6 1.0 CG H:ASP169 3.1 59.0 1.0 CE1 H:HIS62 3.4 45.9 1.0 CG H:HIS64 3.4 56.5 1.0 CE1 H:HIS148 3.4 56.6 1.0 CG H:HIS62 3.8 38.1 1.0 CB H:ASP169 3.9 57.2 1.0 CB H:HIS64 3.9 56.3 1.0 OD1 H:ASP169 3.9 53.3 1.0 OP2 N:A-15 4.0 112.6 1.0 ND1 H:HIS62 4.1 40.9 1.0 CG H:HIS148 4.1 44.7 1.0 CE1 H:HIS373 4.1 78.3 1.0 NE2 H:HIS64 4.2 56.9 1.0 ND1 H:HIS148 4.3 50.9 1.0 CD2 H:HIS64 4.4 57.2 1.0 O5' N:A-15 4.4 113.5 1.0 ND1 H:HIS373 4.8 77.1 1.0 NE2 H:HIS373 4.8 80.1 1.0 P N:A-15 4.9 116.5 1.0

Zinc binding site 7 out of 7 in the Cryo-Em Structure of Ctr-Bound Type 7 Crispr-Cas Complex at Substrate- Engaged State 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Cryo-Em Structure of Ctr-Bound Type 7 Crispr-Cas Complex at Substrate- Engaged State 2 within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn301 b:92.8 occ:1.00 SG J:CYS71 2.3 42.7 1.0 SG J:CYS84 2.3 29.0 1.0 SG J:CYS87 2.3 44.2 1.0 SG J:CYS81 2.3 45.1 1.0 CB J:CYS87 3.0 22.3 1.0 N J:CYS81 3.5 33.1 1.0 N J:GLY82 3.6 29.6 1.0 CB J:CYS84 3.6 27.5 1.0 CB J:CYS81 3.7 37.2 1.0 CB J:CYS71 3.8 41.7 1.0 CA J:CYS81 4.0 30.7 1.0 CA J:CYS87 4.1 10.7 1.0 N J:CYS87 4.1 19.5 1.0 N J:ARG83 4.1 28.9 1.0 N J:CYS71 4.2 37.2 1.0 N J:CYS84 4.2 34.2 1.0 C J:CYS81 4.3 33.8 1.0 C J:ARG83 4.4 29.8 1.0 CA J:GLY82 4.4 25.4 1.0 CA J:CYS84 4.5 37.0 1.0 C J:GLY82 4.5 28.1 1.0 C J:PRO80 4.6 32.4 1.0 CA J:CYS71 4.6 39.6 1.0 O J:ARG83 4.7 34.2 1.0 CA J:PRO80 4.8 30.4 1.0 CB J:PRO80 4.8 20.6 1.0 CA J:ARG83 5.0 27.1 1.0

X.Li, Z.Deng, H.Zhang. Cryo-Em Structure of Ctr-Bound Type 7 Crispr-Cas Complex at Substrate-Engaged State 2 To Be Published.