Zinc in PDB 6o7e: Cryo-Em Structure of Csm-Crrna-Target Rna Ternary Complex in Complex with Amppnp in Type III-A Crispr-Cas System

The structure of Cryo-Em Structure of Csm-Crrna-Target Rna Ternary Complex in Complex with Amppnp in Type III-A Crispr-Cas System also contains other interesting chemical elements:

Manganese

(Mn)

3 atoms

The binding sites of Zinc atom in the Cryo-Em Structure of Csm-Crrna-Target Rna Ternary Complex in Complex with Amppnp in Type III-A Crispr-Cas System (pdb code 6o7e). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Cryo-Em Structure of Csm-Crrna-Target Rna Ternary Complex in Complex with Amppnp in Type III-A Crispr-Cas System, PDB code: 6o7e:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Cryo-Em Structure of Csm-Crrna-Target Rna Ternary Complex in Complex with Amppnp in Type III-A Crispr-Cas System


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 Csm-Crrna-Target Rna Ternary Complex in Complex with Amppnp in Type III-A Crispr-Cas System within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn801 b:84.9 occ:1.00 SG A:CYS389 2.5 31.9 1.0 SG A:CYS416 2.5 40.8 1.0 SG A:CYS413 2.5 39.6 1.0 SG A:CYS392 2.5 29.6 1.0 CB A:CYS389 3.3 31.9 1.0 CB A:CYS416 3.3 40.8 1.0 CB A:CYS392 3.7 29.6 1.0 N A:CYS392 3.9 29.6 1.0 CB A:CYS413 4.0 39.6 1.0 CB A:VAL391 4.3 30.1 1.0 CA A:CYS392 4.4 29.6 1.0 OH A:TYR258 4.4 27.4 1.0 N A:CYS413 4.5 39.6 1.0 CA A:CYS416 4.6 40.8 1.0 N A:CYS416 4.7 40.8 1.0 CA A:CYS389 4.7 31.9 1.0 CA A:CYS413 4.8 39.6 1.0 C A:VAL391 4.9 30.1 1.0 N A:VAL391 4.9 30.1 1.0 CA A:VAL391 4.9 30.1 1.0 O A:CYS413 5.0 39.6 1.0

Zinc binding site 2 out of 3 in the Cryo-Em Structure of Csm-Crrna-Target Rna Ternary Complex in Complex with Amppnp in Type III-A Crispr-Cas System


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 Csm-Crrna-Target Rna Ternary Complex in Complex with Amppnp in Type III-A Crispr-Cas System within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:35.4 occ:1.00 NE2 C:HIS111 2.2 27.7 1.0 SG C:CYS125 2.4 28.2 1.0 SG C:CYS122 2.5 24.9 1.0 SG C:CYS113 2.5 32.1 1.0 CB C:CYS125 2.9 28.2 1.0 CD2 C:HIS111 3.0 27.7 1.0 CB C:CYS122 3.2 24.9 1.0 CE1 C:HIS111 3.2 27.7 1.0 N C:CYS125 3.3 28.2 1.0 CA C:CYS125 3.7 28.2 1.0 CB C:CYS113 3.7 32.1 1.0 N C:CYS113 4.0 32.1 1.0 CG C:HIS111 4.1 27.7 1.0 ND1 C:HIS111 4.2 27.7 1.0 CB C:VAL124 4.2 27.1 1.0 C C:VAL124 4.4 27.1 1.0 CA C:CYS113 4.4 32.1 1.0 N C:VAL124 4.6 27.1 1.0 CA C:VAL124 4.6 27.1 1.0 CA C:CYS122 4.6 24.9 1.0 CG1 C:VAL124 4.8 27.1 1.0 C C:CYS125 4.9 28.2 1.0 C C:VAL112 4.9 27.5 1.0

Zinc binding site 3 out of 3 in the Cryo-Em Structure of Csm-Crrna-Target Rna Ternary Complex in Complex with Amppnp in Type III-A Crispr-Cas System


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 Csm-Crrna-Target Rna Ternary Complex in Complex with Amppnp in Type III-A Crispr-Cas System within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn301 b:62.9 occ:1.00 NE2 D:HIS111 2.2 42.2 1.0 SG D:CYS122 2.5 40.2 1.0 SG D:CYS125 2.5 35.1 1.0 SG D:CYS113 2.5 44.5 1.0 CD2 D:HIS111 2.8 42.2 1.0 CB D:CYS125 3.2 35.1 1.0 CE1 D:HIS111 3.2 42.2 1.0 CB D:CYS122 3.3 40.2 1.0 N D:CYS125 3.7 35.1 1.0 CB D:CYS113 3.9 44.5 1.0 CG D:HIS111 3.9 42.2 1.0 N D:CYS113 4.0 44.5 1.0 CA D:CYS125 4.1 35.1 1.0 ND1 D:HIS111 4.1 42.2 1.0 CB D:VAL124 4.3 34.3 1.0 CA D:CYS113 4.4 44.5 1.0 O D:HIS111 4.7 42.2 1.0 C D:VAL112 4.7 40.9 1.0 C D:VAL124 4.7 34.3 1.0 CG1 D:VAL124 4.7 34.3 1.0 CA D:CYS122 4.8 40.2 1.0 CA D:VAL112 4.9 40.9 1.0 CA D:VAL124 4.9 34.3 1.0 C D:HIS111 5.0 42.2 1.0

N.Jia, R.Jones, G.Sukenick, D.J.Patel. Second Messenger CA4FORMATION Within the Composite CSM1 Palm Pocket of Type III-A Crispr-Cas Csm Complex and Its Release Path. Mol.Cell V. 75 933 2019.
ISSN: ISSN 1097-2765
PubMed: 31326272
DOI: 10.1016/J.MOLCEL.2019.06.013