Zinc in PDB 7y84: Cryoem Structure of Type III-E Crispr Craspase Gramp-Crrna in Complex with Tpr-Chat Protease

The structure of Cryoem Structure of Type III-E Crispr Craspase Gramp-Crrna in Complex with Tpr-Chat Protease 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 in Complex with Tpr-Chat Protease (pdb code 7y84). 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 in Complex with Tpr-Chat Protease, PDB code: 7y84:
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 in Complex with Tpr-Chat Protease


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 in Complex with Tpr-Chat Protease within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1801 b:83.0 occ:1.00 SG A:CYS88 2.3 39.2 1.0 SG A:CYS130 2.3 37.1 1.0 SG A:CYS127 2.3 34.5 1.0 SG A:CYS121 2.3 48.4 1.0 CB A:CYS130 3.2 24.2 1.0 CB A:CYS127 3.3 27.8 1.0 CB A:CYS121 3.3 44.5 1.0 CB A:CYS88 3.4 27.2 1.0 N A:CYS127 3.8 31.0 1.0 N A:CYS88 3.9 22.4 1.0 N A:CYS130 4.0 27.2 1.0 CA A:CYS127 4.1 23.9 1.0 CA A:CYS130 4.2 17.4 1.0 CA A:CYS88 4.2 26.8 1.0 NH1 A:ARG135 4.5 23.7 1.0 O A:CYS127 4.6 33.3 1.0 C A:CYS127 4.7 26.9 1.0 C A:CYS88 4.7 28.5 1.0 CA A:CYS121 4.7 47.9 1.0 O A:CYS88 4.9 28.5 1.0 N A:GLY90 4.9 11.9 1.0 ND2 A:ASN117 4.9 57.6 1.0 C A:ALA126 4.9 39.7 1.0 CA A:GLY90 5.0 16.5 1.0

Zinc binding site 2 out of 4 in the Cryoem Structure of Type III-E Crispr Craspase Gramp-Crrna in Complex with Tpr-Chat Protease


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 in Complex with Tpr-Chat Protease within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1802 b:73.8 occ:1.00 SG A:CYS501 2.3 29.5 1.0 SG A:CYS503 2.3 30.8 1.0 SG A:CYS506 2.3 38.3 1.0 SG A:CYS491 2.3 36.1 1.0 CB A:CYS506 2.8 10.2 1.0 CB A:CYS491 3.1 28.5 1.0 CB A:CYS501 3.2 19.1 1.0 CB A:CYS503 3.4 16.8 1.0 N A:CYS506 3.9 14.8 1.0 CA A:CYS506 3.9 6.8 1.0 N A:CYS491 4.1 21.4 1.0 CA A:CYS491 4.2 25.1 1.0 NH1 A:ARG480 4.3 16.4 1.0 N A:CYS503 4.4 15.0 1.0 CA A:CYS503 4.4 4.1 1.0 CA A:CYS501 4.5 14.8 1.0 O A:CYS501 4.5 29.6 1.0 C A:CYS501 4.6 16.8 1.0 O A:CYS503 4.8 19.9 1.0 C A:CYS491 4.8 26.1 1.0 C A:CYS503 4.9 9.4 1.0 O A:CYS491 4.9 33.0 1.0

Zinc binding site 3 out of 4 in the Cryoem Structure of Type III-E Crispr Craspase Gramp-Crrna in Complex with Tpr-Chat Protease


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 in Complex with Tpr-Chat Protease within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1803 b:73.7 occ:1.00 ND1 A:HIS747 2.1 48.2 1.0 SG A:CYS752 2.3 42.0 1.0 SG A:CYS750 2.3 46.3 1.0 SG A:CYS755 2.3 33.9 1.0 CE1 A:HIS747 2.7 47.8 1.0 CB A:CYS755 3.1 22.0 1.0 CB A:CYS750 3.1 41.4 1.0 CG A:HIS747 3.3 44.9 1.0 CB A:CYS752 3.3 30.5 1.0 CB A:HIS747 3.8 46.2 1.0 N A:CYS755 3.9 25.9 1.0 NE2 A:HIS747 4.0 47.6 1.0 N A:CYS752 4.0 34.9 1.0 CA A:CYS755 4.1 20.2 1.0 CA A:CYS752 4.2 31.3 1.0 CD2 A:HIS747 4.2 48.1 1.0 CD A:LYS744 4.3 49.8 1.0 CA A:CYS750 4.4 43.1 1.0 C A:CYS750 4.5 45.7 1.0 CA A:HIS747 4.5 46.6 1.0 CE A:LYS744 4.6 52.8 1.0 O A:CYS750 4.7 47.6 1.0 NZ A:LYS744 4.7 52.0 1.0 C A:CYS752 4.7 36.8 1.0 O A:CYS752 4.8 40.2 1.0 CE A:MET754 4.9 23.6 1.0 C A:MET754 4.9 23.4 1.0 N A:THR751 4.9 43.9 1.0

Zinc binding site 4 out of 4 in the Cryoem Structure of Type III-E Crispr Craspase Gramp-Crrna in Complex with Tpr-Chat Protease


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 in Complex with Tpr-Chat Protease within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1804 b:67.9 occ:1.00 SG A:CYS1414 2.3 42.7 1.0 SG A:CYS1417 2.3 47.6 1.0 SG A:CYS1018 2.3 48.4 1.0 SG A:CYS1406 2.3 42.5 1.0 CB A:CYS1417 3.0 26.6 1.0 CB A:CYS1414 3.3 33.3 1.0 CB A:CYS1406 3.3 42.7 1.0 CB A:CYS1018 3.3 42.3 1.0 N A:CYS1406 3.7 42.1 1.0 N A:CYS1417 4.0 27.2 1.0 N A:CYS1414 4.0 31.6 1.0 CA A:CYS1406 4.1 43.7 1.0 CA A:CYS1417 4.1 21.7 1.0 N A:CYS1018 4.2 40.7 1.0 CA A:CYS1414 4.2 32.3 1.0 CA A:CYS1018 4.3 40.8 1.0 NH2 A:ARG935 4.5 41.0 1.0 C A:PRO1405 4.7 47.8 1.0 OE2 A:GLU1012 4.7 42.0 1.0 C A:CYS1018 4.8 45.6 1.0 O A:CYS1018 4.8 47.6 1.0 C A:CYS1414 4.8 36.0 1.0 O A:CYS1414 4.9 38.7 1.0 CA A:PRO1405 4.9 46.8 1.0 O A:HIS1404 5.0 56.1 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