Zinc in PDB 7y81: Cryoem Structure of Type III-E Crispr Craspase Gramp-Crrna Complex Bound to Non-Self Rna Target

The structure of Cryoem Structure of Type III-E Crispr Craspase Gramp-Crrna Complex 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 Complex Bound to Non-Self Rna Target (pdb code 7y81). 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 Non-Self Rna Target, PDB code: 7y81:
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 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 Complex Bound to Non-Self Rna Target within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1801 b:81.1 occ:1.00 ND1 A:HIS747 2.1 54.3 1.0 SG A:CYS752 2.3 46.8 1.0 SG A:CYS755 2.3 46.3 1.0 SG A:CYS750 2.3 60.9 1.0 CE1 A:HIS747 2.6 50.8 1.0 CB A:CYS755 3.0 33.0 1.0 CB A:CYS752 3.1 39.5 1.0 CG A:HIS747 3.3 52.6 1.0 CB A:CYS750 3.4 47.5 1.0 NE2 A:HIS747 3.8 47.7 1.0 N A:CYS755 4.0 40.6 1.0 CA A:CYS755 4.0 34.0 1.0 CB A:HIS747 4.0 51.4 1.0 N A:CYS752 4.1 40.5 1.0 CA A:CYS752 4.1 36.3 1.0 CD A:LYS744 4.2 52.7 1.0 CD2 A:HIS747 4.2 49.3 1.0 CA A:CYS750 4.6 50.7 1.0 CA A:HIS747 4.7 50.8 1.0 C A:CYS750 4.7 51.5 1.0 C A:CYS752 4.8 42.3 1.0 CE A:MET754 4.8 35.8 1.0 CE A:LYS744 4.8 54.7 1.0 O A:CYS750 4.8 51.6 1.0 O A:CYS752 4.9 48.3 1.0 NZ A:LYS744 5.0 53.2 1.0

Zinc binding site 2 out of 4 in the Cryoem Structure of Type III-E Crispr Craspase Gramp-Crrna Complex 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 Complex Bound to Non-Self Rna Target within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1802 b:91.6 occ:1.00 SG A:CYS501 2.3 42.9 1.0 SG A:CYS491 2.3 56.0 1.0 SG A:CYS503 2.3 44.0 1.0 SG A:CYS506 2.3 41.7 1.0 CB A:CYS506 2.9 25.2 1.0 CB A:CYS491 3.3 41.2 1.0 CB A:CYS503 3.3 33.1 1.0 CB A:CYS501 3.3 34.0 1.0 CA A:CYS506 4.0 28.3 1.0 N A:CYS506 4.0 37.5 1.0 CA A:CYS503 4.3 30.6 1.0 N A:CYS503 4.3 36.6 1.0 CA A:CYS491 4.4 42.1 1.0 N A:CYS491 4.4 39.6 1.0 NH1 A:ARG480 4.5 23.1 1.0 CA A:CYS501 4.6 39.1 1.0 O A:CYS503 4.7 38.1 1.0 C A:CYS503 4.8 35.1 1.0 C A:CYS501 4.8 41.1 1.0 C A:CYS491 4.9 43.9 1.0 O A:CYS491 4.9 47.2 1.0 O A:CYS501 4.9 42.7 1.0

Zinc binding site 3 out of 4 in the Cryoem Structure of Type III-E Crispr Craspase Gramp-Crrna Complex 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 Complex Bound to Non-Self Rna Target within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1803 b:64.5 occ:1.00 SG A:CYS1414 2.3 29.6 1.0 SG A:CYS1018 2.3 37.9 1.0 SG A:CYS1417 2.3 46.2 1.0 SG A:CYS1406 2.3 27.1 1.0 CB A:CYS1417 2.7 22.7 1.0 CB A:CYS1414 3.2 25.9 1.0 CB A:CYS1406 3.4 33.6 1.0 CB A:CYS1018 3.4 34.5 1.0 N A:CYS1406 3.8 34.8 1.0 CA A:CYS1417 4.0 17.6 1.0 N A:CYS1414 4.0 28.4 1.0 N A:CYS1417 4.1 26.1 1.0 CA A:CYS1414 4.2 29.7 1.0 CA A:CYS1406 4.2 32.7 1.0 OE2 A:GLU1012 4.3 44.1 1.0 N A:CYS1018 4.4 40.5 1.0 CA A:CYS1018 4.4 35.5 1.0 CB A:ALA1020 4.8 31.0 1.0 C A:PRO1405 4.8 41.2 1.0 O A:CYS1414 4.8 44.8 1.0 C A:CYS1414 4.8 32.6 1.0 NH2 A:ARG935 4.8 30.6 1.0 CA A:PRO1405 4.8 36.3 1.0 C A:CYS1018 4.9 38.1 1.0 NH2 A:ARG1008 4.9 24.5 1.0

Zinc binding site 4 out of 4 in the Cryoem Structure of Type III-E Crispr Craspase Gramp-Crrna Complex 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 Complex Bound to Non-Self Rna Target within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1805 b:97.5 occ:1.00 SG A:CYS130 2.3 59.9 1.0 SG A:CYS127 2.3 56.0 1.0 SG A:CYS121 2.3 73.5 1.0 SG A:CYS88 2.3 58.7 1.0 CB A:CYS130 3.2 48.8 1.0 CB A:CYS121 3.3 70.9 1.0 CB A:CYS88 3.4 54.9 1.0 CB A:CYS127 3.5 51.9 1.0 N A:CYS130 4.0 51.3 1.0 N A:CYS127 4.1 55.9 1.0 N A:CYS88 4.1 54.9 1.0 CA A:CYS130 4.2 48.5 1.0 CA A:CYS88 4.3 56.6 1.0 CA A:CYS127 4.3 52.1 1.0 NH1 A:ARG135 4.6 47.3 1.0 N A:GLY90 4.7 56.9 1.0 CA A:CYS121 4.7 71.1 1.0 C A:CYS88 4.7 56.5 1.0 O A:CYS127 4.9 54.5 1.0 CA A:GLY90 4.9 48.8 1.0 C A:CYS127 4.9 53.0 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