Zinc in PDB 7y83: Cryoem Structure of Type III-E Crispr Craspase Gramp-Crrna in Complex with Tpr-Chat Protease Bound to Non-Self Rna Target

The structure of Cryoem Structure of Type III-E Crispr Craspase Gramp-Crrna in Complex with Tpr-Chat Protease Bound to Non-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 in Complex with Tpr-Chat Protease Bound to Non-Self Rna Target (pdb code 7y83). 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 Bound to Non-Self Rna Target, PDB code: 7y83:
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 Bound to Non-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 in Complex with Tpr-Chat Protease Bound to Non-Self Rna Target within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1801 b:136.8 occ:1.00 ND1 A:HIS747 2.1 57.5 1.0 SG A:CYS750 2.3 61.5 1.0 CE1 A:HIS747 2.3 57.2 1.0 SG A:CYS752 2.3 70.6 1.0 SG A:CYS755 2.3 55.6 1.0 CB A:CYS752 2.9 58.1 1.0 CD A:LYS744 3.5 65.8 1.0 CG A:HIS747 3.5 55.2 1.0 NE2 A:HIS747 3.6 55.5 1.0 N A:CYS752 3.7 57.4 1.0 CE A:LYS744 3.7 67.2 1.0 CB A:CYS750 3.8 63.5 1.0 CA A:CYS752 3.9 57.4 1.0 CB A:CYS755 4.0 46.0 1.0 CD2 A:HIS747 4.2 58.6 1.0 NZ A:LYS744 4.3 67.8 1.0 CG A:LYS744 4.3 67.9 1.0 CB A:HIS747 4.3 52.5 1.0 CA A:HIS747 4.6 55.1 1.0 N A:THR751 4.7 61.2 1.0 C A:CYS750 4.8 58.8 1.0 CA A:CYS750 4.8 61.5 1.0 C A:THR751 4.9 61.6 1.0 C A:CYS752 5.0 60.9 1.0 O A:ASP746 5.0 65.3 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 Bound to Non-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 in Complex with Tpr-Chat Protease Bound to Non-Self Rna Target within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1802 b:101.8 occ:1.00 CB A:CYS501 2.3 38.4 1.0 SG A:CYS491 2.3 58.6 1.0 SG A:CYS506 2.3 19.2 1.0 SG A:CYS503 2.3 34.8 1.0 SG A:CYS501 2.3 52.2 1.0 CB A:CYS506 3.1 15.6 1.0 CB A:CYS491 3.4 41.7 1.0 CA A:CYS501 3.7 27.1 1.0 CB A:CYS503 4.1 21.3 1.0 C A:CYS501 4.3 28.9 1.0 CA A:CYS506 4.3 17.9 1.0 O A:CYS501 4.5 31.1 1.0 N A:CYS506 4.6 29.8 1.0 CA A:CYS491 4.6 37.1 1.0 N A:CYS503 4.7 23.4 1.0 N A:CYS501 4.7 29.8 1.0 N A:CYS491 4.8 39.1 1.0 CA A:CYS503 4.9 21.7 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 Bound to Non-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 in Complex with Tpr-Chat Protease Bound to Non-Self Rna Target within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1803 b:118.9 occ:1.00 SG A:CYS1414 2.3 66.7 1.0 SG A:CYS1417 2.3 69.5 1.0 SG A:CYS1018 2.3 73.9 1.0 SG A:CYS1406 2.3 67.7 1.0 CB A:CYS1417 3.2 54.4 1.0 CB A:CYS1414 3.5 60.4 1.0 CB A:CYS1018 3.5 75.5 1.0 CB A:CYS1406 3.7 69.2 1.0 N A:CYS1406 3.9 71.6 1.0 N A:CYS1414 3.9 60.0 1.0 N A:CYS1417 4.2 51.3 1.0 CA A:CYS1414 4.3 59.6 1.0 CA A:CYS1417 4.3 52.1 1.0 N A:CYS1018 4.3 73.0 1.0 CA A:CYS1406 4.4 69.5 1.0 CA A:CYS1018 4.5 74.9 1.0 NH2 A:ARG935 4.6 68.8 1.0 CB A:ALA1020 4.7 69.0 1.0 O A:CYS1018 4.8 73.5 1.0 O A:CYS1414 4.8 63.6 1.0 C A:PRO1405 4.9 72.8 1.0 C A:CYS1018 4.9 73.7 1.0 O A:HIS1404 4.9 79.2 1.0 C A:CYS1414 4.9 59.4 1.0 CA A:PRO1405 4.9 73.5 1.0 CA A:ALA1020 4.9 70.2 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 Bound to Non-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 in Complex with Tpr-Chat Protease Bound to Non-Self Rna Target within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1805 b:66.4 occ:1.00 SG A:CYS88 2.3 45.0 1.0 SG A:CYS127 2.3 57.0 1.0 SG A:CYS130 2.3 42.2 1.0 SG A:CYS121 2.3 67.6 1.0 CB A:CYS121 3.3 60.1 1.0 CB A:CYS130 3.5 36.6 1.0 CB A:CYS127 3.5 45.1 1.0 CB A:CYS88 3.5 47.0 1.0 N A:CYS127 3.9 49.3 1.0 N A:CYS88 4.1 51.3 1.0 N A:CYS130 4.1 37.5 1.0 CA A:CYS127 4.2 45.8 1.0 CA A:CYS88 4.3 49.1 1.0 CA A:CYS130 4.3 36.0 1.0 O A:CYS127 4.6 44.2 1.0 CA A:CYS121 4.8 62.9 1.0 C A:CYS127 4.8 45.3 1.0 NH1 A:ARG135 4.8 34.7 1.0 C A:CYS88 4.9 44.2 1.0 N A:GLY90 4.9 29.0 1.0 C A:ALA126 5.0 52.9 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