Zinc in PDB 7y82: Cryoem Structure of Type III-E Crispr Craspase Gramp-Crrna Complex Bound to Self Rna Target

The structure of Cryoem Structure of Type III-E Crispr Craspase Gramp-Crrna Complex Bound to Self Rna Target also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Zinc atom in the Cryoem Structure of Type III-E Crispr Craspase Gramp-Crrna Complex Bound to Self Rna Target (pdb code 7y82). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Cryoem Structure of Type III-E Crispr Craspase Gramp-Crrna Complex Bound to Self Rna Target, PDB code: 7y82:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Cryoem Structure of Type III-E Crispr Craspase Gramp-Crrna Complex Bound to Self Rna Target


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryoem Structure of Type III-E Crispr Craspase Gramp-Crrna Complex Bound to Self Rna Target within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1801 b:87.8 occ:1.00 ND1 A:HIS747 2.1 52.7 1.0 SG A:CYS752 2.3 49.5 1.0 SG A:CYS755 2.3 47.6 1.0 SG A:CYS750 2.3 50.1 1.0 CE1 A:HIS747 2.7 49.5 1.0 CB A:CYS755 3.1 32.0 1.0 CB A:CYS752 3.3 35.0 1.0 CG A:HIS747 3.3 50.5 1.0 CB A:CYS750 3.4 42.9 1.0 N A:CYS752 3.9 41.8 1.0 CB A:HIS747 3.9 46.9 1.0 NE2 A:HIS747 3.9 52.9 1.0 N A:CYS755 4.0 32.4 1.0 CA A:CYS755 4.1 30.3 1.0 CA A:CYS752 4.1 35.5 1.0 CD2 A:HIS747 4.2 50.7 1.0 CD A:LYS744 4.3 47.3 1.0 ND2 A:ASN760 4.5 40.6 1.0 CE A:LYS744 4.6 46.1 1.0 CA A:HIS747 4.6 50.8 1.0 NZ A:LYS744 4.6 45.3 1.0 C A:CYS752 4.7 38.7 1.0 N A:THR751 4.7 41.3 1.0 CA A:CYS750 4.7 45.1 1.0 O A:CYS752 4.8 39.9 1.0 CE A:MET754 4.8 27.4 1.0 C A:CYS750 4.8 45.2 1.0 CB A:ASP741 5.0 31.4 1.0

Zinc binding site 2 out of 4 in the Cryoem Structure of Type III-E Crispr Craspase Gramp-Crrna Complex Bound to Self Rna Target


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryoem Structure of Type III-E Crispr Craspase Gramp-Crrna Complex Bound to Self Rna Target within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1802 b:107.8 occ:1.00 SG A:CYS506 2.3 45.1 1.0 SG A:CYS491 2.3 51.3 1.0 SG A:CYS503 2.3 55.1 1.0 O A:CYS491 3.3 39.8 1.0 CB A:CYS491 3.4 41.9 1.0 N A:CYS491 3.6 39.2 1.0 CB A:CYS503 3.7 41.0 1.0 CB A:CYS506 3.7 33.3 1.0 C A:CYS491 3.8 36.5 1.0 CA A:CYS491 3.8 40.1 1.0 N A:CYS506 3.9 29.8 1.0 NH1 A:ARG480 4.0 21.8 1.0 SG A:CYS501 4.3 54.1 1.0 CA A:CYS506 4.3 26.9 1.0 CB A:VAL505 4.3 33.1 1.0 C A:VAL505 4.8 35.0 1.0 C A:GLY490 4.8 34.6 1.0 CB A:CYS501 4.9 46.5 1.0 N A:ASN492 4.9 31.9 1.0 CG1 A:VAL505 5.0 30.6 1.0

Zinc binding site 3 out of 4 in the Cryoem Structure of Type III-E Crispr Craspase Gramp-Crrna Complex Bound to Self Rna Target


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cryoem Structure of Type III-E Crispr Craspase Gramp-Crrna Complex Bound to Self Rna Target within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1803 b:67.7 occ:1.00 SG A:CYS1018 2.3 16.2 1.0 SG A:CYS1414 2.3 27.5 1.0 SG A:CYS1417 2.3 31.7 1.0 SG A:CYS1406 2.3 14.5 1.0 CB A:CYS1417 2.7 7.6 1.0 CB A:CYS1018 3.5 7.9 1.0 CB A:CYS1414 3.5 2.5 1.0 CB A:CYS1406 3.7 5.8 1.0 N A:CYS1406 3.8 9.7 1.0 CA A:CYS1417 3.9 2.0 1.0 N A:CYS1414 4.0 0.1 1.0 N A:CYS1417 4.1 0.0 1.0 N A:CYS1018 4.3 0.0 1.0 CA A:CYS1414 4.3 0.0 1.0 CA A:CYS1018 4.4 3.9 1.0 CA A:CYS1406 4.4 9.5 1.0 O A:CYS1018 4.8 18.0 1.0 NH2 A:ARG935 4.8 17.6 1.0 C A:PRO1405 4.8 9.3 1.0 CA A:PRO1405 4.8 0.0 1.0 C A:CYS1018 4.8 5.5 1.0 OE2 A:GLU1012 4.8 20.4 1.0 NH2 A:ARG1008 4.9 17.0 1.0 O A:CYS1414 4.9 25.2 1.0 C A:CYS1414 5.0 4.0 1.0

Zinc binding site 4 out of 4 in the Cryoem Structure of Type III-E Crispr Craspase Gramp-Crrna Complex Bound to Self Rna Target


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Cryoem Structure of Type III-E Crispr Craspase Gramp-Crrna Complex Bound to Self Rna Target within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1805 b:98.3 occ:1.00 SG A:CYS127 2.3 55.4 1.0 SG A:CYS88 2.3 53.9 1.0 SG A:CYS130 2.3 56.8 1.0 SG A:CYS121 2.3 66.5 1.0 CB A:CYS88 3.3 46.3 1.0 CB A:CYS121 3.4 54.6 1.0 CB A:CYS127 3.5 46.3 1.0 CB A:CYS130 3.6 46.6 1.0 N A:CYS127 3.9 49.5 1.0 N A:CYS88 4.0 46.0 1.0 CA A:CYS88 4.2 48.1 1.0 N A:CYS130 4.2 51.0 1.0 CA A:CYS127 4.2 48.0 1.0 NH1 A:ARG135 4.3 46.6 1.0 CA A:CYS130 4.5 47.0 1.0 O A:CYS127 4.7 51.8 1.0 C A:CYS88 4.7 49.4 1.0 C A:CYS127 4.8 49.7 1.0 CA A:CYS121 4.8 55.3 1.0 O A:CYS88 4.9 46.6 1.0 N A:GLY90 5.0 45.8 1.0 C A:ALA126 5.0 47.9 1.0

N.Cui, J.T.Zhang, Z.Li, X.Y.Liu, C.Wang, H.Huang, N.Jia. Structural Basis For the Non-Self Rna-Activated Protease Activity of the Type III-E Crispr Nuclease-Protease Craspase Nat Commun V. 13 7549 2022.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-022-35275-5