Zinc in PDB 7y80: Cryoem Structure of Type III-E Crispr Craspase Gramp-Crrna Binary Complex

The structure of Cryoem Structure of Type III-E Crispr Craspase Gramp-Crrna Binary Complex 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 Binary Complex (pdb code 7y80). 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 Binary Complex, PDB code: 7y80:
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 Binary Complex


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 Binary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1801 b:114.4 occ:1.00 SG A:CYS127 2.3 72.1 1.0 SG A:CYS130 2.3 73.3 1.0 SG A:CYS121 2.3 74.4 1.0 SG A:CYS88 2.3 73.0 1.0 CB A:CYS130 3.1 65.6 1.0 CB A:CYS88 3.3 71.8 1.0 CB A:CYS121 3.3 80.5 1.0 CB A:CYS127 3.6 71.7 1.0 N A:CYS130 4.0 70.5 1.0 N A:CYS88 4.1 72.9 1.0 CA A:CYS130 4.1 65.0 1.0 CA A:CYS88 4.2 72.2 1.0 N A:CYS127 4.2 70.2 1.0 NH2 A:ARG135 4.2 70.6 1.0 CA A:CYS127 4.4 67.9 1.0 N A:GLY90 4.6 67.6 1.0 C A:CYS88 4.6 71.1 1.0 CA A:GLY90 4.7 66.8 1.0 CA A:CYS121 4.8 82.2 1.0 CB A:PHE129 4.9 60.1 1.0 NE A:ARG135 4.9 65.6 1.0 O A:CYS127 5.0 68.2 1.0

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


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 Binary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1802 b:109.3 occ:1.00 SG A:CYS491 2.3 73.8 1.0 SG A:CYS503 2.3 57.4 1.0 SG A:CYS501 2.3 62.4 1.0 SG A:CYS506 2.3 54.0 1.0 CB A:CYS501 3.2 56.2 1.0 CB A:CYS506 3.2 41.0 1.0 CB A:CYS491 3.3 62.8 1.0 CB A:CYS503 3.7 56.0 1.0 N A:CYS506 4.2 56.9 1.0 N A:CYS503 4.3 52.6 1.0 CA A:CYS506 4.3 35.8 1.0 CA A:CYS491 4.4 59.2 1.0 N A:CYS491 4.4 55.8 1.0 CA A:CYS503 4.5 50.3 1.0 CA A:CYS501 4.5 57.4 1.0 C A:CYS501 4.6 57.8 1.0 O A:CYS503 4.6 48.2 1.0 O A:CYS501 4.8 56.0 1.0 C A:CYS503 4.8 49.8 1.0 C A:CYS491 4.9 63.2 1.0

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


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 Binary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1803 b:88.0 occ:1.00 ND1 A:HIS747 2.1 63.0 1.0 SG A:CYS752 2.3 61.9 1.0 SG A:CYS755 2.3 49.5 1.0 SG A:CYS750 2.3 74.1 1.0 CE1 A:HIS747 2.4 60.6 1.0 CB A:CYS755 2.9 42.0 1.0 CB A:CYS752 3.0 45.6 1.0 CB A:CYS750 3.2 61.6 1.0 CG A:HIS747 3.4 60.4 1.0 NE2 A:HIS747 3.7 57.0 1.0 N A:CYS755 3.9 50.7 1.0 CA A:CYS755 3.9 41.2 1.0 N A:CYS752 4.1 47.6 1.0 CA A:CYS752 4.1 45.0 1.0 CD A:LYS744 4.1 62.6 1.0 CD2 A:HIS747 4.2 60.8 1.0 CB A:HIS747 4.2 58.4 1.0 CA A:CYS750 4.5 62.1 1.0 C A:CYS750 4.6 61.8 1.0 C A:CYS752 4.7 50.4 1.0 CE A:LYS744 4.7 62.5 1.0 O A:CYS750 4.8 59.5 1.0 CA A:HIS747 4.8 61.8 1.0 O A:CYS752 4.8 53.2 1.0 C A:MET754 5.0 38.0 1.0

Zinc binding site 4 out of 4 in the Cryoem Structure of Type III-E Crispr Craspase Gramp-Crrna Binary Complex


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 Binary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1804 b:72.7 occ:1.00 SG A:CYS1018 2.3 60.2 1.0 SG A:CYS1414 2.3 57.2 1.0 SG A:CYS1417 2.3 53.1 1.0 SG A:CYS1406 2.3 64.0 1.0 CB A:CYS1417 2.8 40.6 1.0 CB A:CYS1414 3.1 46.0 1.0 CB A:CYS1406 3.4 53.7 1.0 CB A:CYS1018 3.5 50.3 1.0 N A:CYS1406 3.8 56.7 1.0 N A:CYS1414 3.8 49.2 1.0 CA A:CYS1417 4.0 36.9 1.0 N A:CYS1417 4.0 43.4 1.0 CA A:CYS1414 4.0 37.6 1.0 CA A:CYS1406 4.2 54.9 1.0 NH2 A:ARG935 4.3 53.9 1.0 CA A:CYS1018 4.5 51.7 1.0 N A:CYS1018 4.6 43.0 1.0 CB A:ALA1020 4.6 51.9 1.0 O A:CYS1414 4.6 56.1 1.0 C A:CYS1414 4.6 47.0 1.0 C A:PRO1405 4.8 55.6 1.0 O A:CYS1018 4.8 55.2 1.0 C A:CYS1018 4.9 53.2 1.0 CA A:PRO1405 4.9 47.5 1.0 CA A:ALA1020 4.9 50.2 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