Zinc in PDB 8z9e: Cryo-Em Structure of Ntr-Bound Type 7 Crispr-Cas Complex at Substrate- Engaged State 2

The binding sites of Zinc atom in the Cryo-Em Structure of Ntr-Bound Type 7 Crispr-Cas Complex at Substrate- Engaged State 2 (pdb code 8z9e). 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 Ntr-Bound Type 7 Crispr-Cas Complex at Substrate- Engaged State 2, PDB code: 8z9e:
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 Ntr-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 Ntr-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:175.6 occ:1.00 SG B:CYS81 2.3 132.1 1.0 SG B:CYS84 2.3 133.4 1.0 SG B:CYS87 2.3 136.1 1.0 SG B:CYS71 2.3 142.2 1.0 CB B:CYS87 3.2 129.2 1.0 CB B:CYS84 3.3 126.0 1.0 CB B:CYS81 3.3 126.0 1.0 CB B:CYS71 3.6 139.8 1.0 N B:CYS81 3.6 125.7 1.0 N B:CYS84 3.9 125.8 1.0 N B:CYS71 3.9 140.1 1.0 CA B:CYS81 4.0 126.9 1.0 N B:GLY82 4.1 121.2 1.0 CA B:CYS84 4.2 125.7 1.0 N B:CYS87 4.2 131.2 1.0 CA B:CYS87 4.3 130.6 1.0 OG1 B:THR86 4.4 124.1 1.0 CA B:CYS71 4.4 141.3 1.0 C B:CYS81 4.6 128.2 1.0 NH2 B:ARG56 4.6 124.3 1.0 C B:PRO80 4.7 124.1 1.0 N B:ARG83 4.8 122.2 1.0 C B:CYS84 4.8 127.5 1.0 CA B:PRO80 4.9 125.0 1.0 O B:CYS84 4.9 128.1 1.0 C B:VAL70 5.0 134.7 1.0

Zinc binding site 2 out of 7 in the Cryo-Em Structure of Ntr-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 Ntr-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:143.2 occ:1.00 SG C:CYS87 2.3 81.4 1.0 SG C:CYS84 2.3 80.7 1.0 SG C:CYS71 2.3 88.6 1.0 SG C:CYS81 2.3 88.8 1.0 CB C:CYS81 3.3 73.9 1.0 N C:CYS81 3.3 74.2 1.0 CB C:CYS87 3.5 58.9 1.0 N C:GLY82 3.5 65.0 1.0 CB C:CYS84 3.7 68.6 1.0 CB C:CYS71 3.7 89.5 1.0 CA C:CYS81 3.7 73.1 1.0 N C:CYS84 3.9 72.5 1.0 N C:CYS71 3.9 82.8 1.0 C C:CYS81 4.1 77.4 1.0 N C:ARG83 4.3 74.3 1.0 CA C:CYS84 4.3 70.7 1.0 C C:PRO80 4.4 75.1 1.0 CA C:CYS71 4.4 86.5 1.0 N C:CYS87 4.5 51.6 1.0 CA C:CYS87 4.5 54.8 1.0 CA C:GLY82 4.6 59.6 1.0 CA C:PRO80 4.7 70.2 1.0 OG1 C:THR86 4.7 63.7 1.0 C C:GLY82 4.8 67.0 1.0 CB C:PRO80 4.9 58.9 1.0 O C:CYS71 4.9 83.2 1.0 O C:CYS84 4.9 74.5 1.0 C C:CYS84 4.9 71.6 1.0 C C:ARG83 5.0 71.7 1.0 C C:VAL70 5.0 80.7 1.0

Zinc binding site 3 out of 7 in the Cryo-Em Structure of Ntr-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 Ntr-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:132.1 occ:1.00 SG D:CYS84 2.3 80.0 1.0 SG D:CYS71 2.3 50.8 1.0 SG D:CYS87 2.3 54.6 1.0 SG D:CYS81 2.8 90.3 1.0 N D:CYS81 3.0 70.1 1.0 N D:GLY82 3.2 70.5 1.0 CB D:CYS71 3.5 52.1 1.0 CB D:CYS87 3.6 48.2 1.0 CB D:CYS81 3.6 75.2 1.0 CA D:CYS81 3.6 74.7 1.0 CB D:CYS84 3.6 56.5 1.0 N D:CYS84 3.8 65.9 1.0 C D:PRO80 3.9 52.3 1.0 C D:CYS81 3.9 73.5 1.0 N D:ARG83 4.0 76.0 1.0 CA D:PRO80 4.0 44.7 1.0 CB D:PRO80 4.2 42.6 1.0 CA D:GLY82 4.2 66.5 1.0 N D:CYS71 4.4 57.3 1.0 CA D:CYS84 4.4 62.3 1.0 C D:GLY82 4.5 73.7 1.0 CA D:CYS71 4.6 50.3 1.0 CA D:CYS87 4.8 46.6 1.0 C D:ARG83 4.9 75.5 1.0 O D:PRO80 4.9 61.4 1.0

Zinc binding site 4 out of 7 in the Cryo-Em Structure of Ntr-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 Ntr-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:145.7 occ:1.00 SG E:CYS71 2.1 94.4 1.0 SG E:CYS84 2.3 99.4 1.0 SG E:CYS81 2.3 82.3 1.0 SG E:CYS87 2.3 61.1 1.0 CB E:CYS71 3.2 81.3 1.0 N E:CYS81 3.2 69.2 1.0 CB E:CYS81 3.5 80.2 1.0 N E:GLY82 3.6 76.4 1.0 CB E:CYS87 3.6 61.6 1.0 CB E:CYS84 3.7 78.7 1.0 CA E:CYS81 3.8 74.1 1.0 N E:CYS71 4.0 78.6 1.0 N E:CYS84 4.0 78.1 1.0 C E:CYS81 4.2 76.3 1.0 C E:PRO80 4.2 63.4 1.0 CA E:CYS71 4.2 78.5 1.0 N E:ARG83 4.3 84.5 1.0 CA E:PRO80 4.4 62.4 1.0 CA E:CYS84 4.5 81.2 1.0 CA E:GLY82 4.6 74.0 1.0 CA E:CYS87 4.8 55.0 1.0 CB E:PRO80 4.8 67.1 1.0 C E:GLY82 5.0 77.0 1.0 N E:CYS87 5.0 57.8 1.0

Zinc binding site 5 out of 7 in the Cryo-Em Structure of Ntr-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 Ntr-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:180.5 occ:1.00 SG F:CYS84 2.3 105.7 1.0 SG F:CYS71 2.3 104.1 1.0 SG F:CYS87 2.3 93.8 1.0 SG F:CYS81 2.3 116.1 1.0 N F:CYS81 3.3 107.6 1.0 CB F:CYS81 3.3 111.3 1.0 CB F:CYS84 3.4 97.4 1.0 CB F:CYS87 3.4 86.5 1.0 N F:GLY82 3.6 108.8 1.0 N F:CYS84 3.6 99.9 1.0 CA F:CYS81 3.8 110.0 1.0 CB F:CYS71 3.9 100.9 1.0 CA F:CYS84 4.1 97.6 1.0 C F:CYS81 4.2 111.2 1.0 N F:ARG83 4.2 114.0 1.0 N F:CYS71 4.2 100.7 1.0 OG1 F:THR86 4.3 79.5 1.0 N F:CYS87 4.3 84.4 1.0 C F:PRO80 4.4 110.0 1.0 CA F:CYS87 4.5 84.0 1.0 CA F:PRO80 4.6 109.9 1.0 CA F:GLY82 4.6 108.5 1.0 CA F:CYS71 4.7 100.6 1.0 C F:ARG83 4.8 113.3 1.0 CB F:PRO80 4.8 108.1 1.0 C F:CYS84 4.8 97.5 1.0 C F:GLY82 4.8 112.0 1.0 C F:VAL70 5.0 97.1 1.0

Zinc binding site 6 out of 7 in the Cryo-Em Structure of Ntr-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 Ntr-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:110.5 occ:1.00 OD2 H:ASP169 2.1 85.0 1.0 ND1 H:HIS64 2.3 77.5 1.0 NE2 H:HIS62 2.3 65.6 1.0 NE2 H:HIS148 2.3 83.0 1.0 CD2 H:HIS62 2.7 56.6 1.0 CD2 H:HIS148 3.0 73.6 1.0 CE1 H:HIS64 3.1 77.6 1.0 CG H:ASP169 3.3 83.5 1.0 CE1 H:HIS148 3.4 80.4 1.0 CG H:HIS64 3.4 76.2 1.0 CE1 H:HIS62 3.4 69.0 1.0 OP2 N:A-15 3.6 121.7 1.0 CB H:HIS64 3.8 77.5 1.0 CB H:ASP169 3.9 79.2 1.0 CG H:HIS62 3.9 56.5 1.0 NE2 H:HIS373 4.1 103.9 1.0 CG H:HIS148 4.1 64.0 1.0 ND1 H:HIS62 4.2 64.6 1.0 NE2 H:HIS64 4.3 78.0 1.0 ND1 H:HIS148 4.3 71.8 1.0 OD1 H:ASP169 4.3 84.5 1.0 CD2 H:HIS64 4.4 77.8 1.0 CD2 H:HIS373 4.6 102.7 1.0 P N:A-15 4.9 129.8 1.0 O5' N:A-15 4.9 120.8 1.0 CE1 H:HIS373 4.9 101.2 1.0

Zinc binding site 7 out of 7 in the Cryo-Em Structure of Ntr-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 Ntr-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:143.2 occ:1.00 SG J:CYS87 2.3 63.3 1.0 SG J:CYS81 2.3 63.2 1.0 SG J:CYS84 2.3 76.9 1.0 SG J:CYS71 2.3 77.6 1.0 CB J:CYS71 3.2 66.1 1.0 CB J:CYS84 3.4 54.7 1.0 CB J:CYS87 3.5 45.6 1.0 N J:CYS81 3.6 68.0 1.0 N J:CYS71 3.7 58.7 1.0 CB J:CYS81 3.8 68.5 1.0 N J:GLY82 4.0 58.1 1.0 N J:CYS84 4.0 62.1 1.0 N J:CYS87 4.0 31.2 1.0 CA J:CYS71 4.0 62.2 1.0 CA J:CYS81 4.1 67.8 1.0 CA J:CYS84 4.3 59.1 1.0 CA J:CYS87 4.3 35.9 1.0 C J:CYS81 4.6 66.4 1.0 C J:PRO80 4.6 65.9 1.0 N J:ARG83 4.7 61.6 1.0 CA J:PRO80 4.7 59.8 1.0 CB J:PRO80 4.8 54.6 1.0 C J:VAL70 4.8 59.6 1.0 C J:CYS84 4.9 63.4 1.0 C J:CYS71 4.9 67.2 1.0 CA J:VAL70 4.9 60.2 1.0 O J:CYS71 5.0 68.9 1.0 CA J:GLY82 5.0 55.5 1.0

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