Zinc in PDB 8sex: Cryo-Em Structure of RYR1 + Amp (Local Refinement of Tmd)

The binding sites of Zinc atom in the Cryo-Em Structure of RYR1 + Amp (Local Refinement of Tmd) (pdb code 8sex). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Cryo-Em Structure of RYR1 + Amp (Local Refinement of Tmd), PDB code: 8sex:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Cryo-Em Structure of RYR1 + Amp (Local Refinement of Tmd)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryo-Em Structure of RYR1 + Amp (Local Refinement of Tmd) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn5102 b:98.1 occ:1.00 ND1 A:HIS4983 2.0 41.9 1.0 NE2 A:HIS4978 2.0 47.6 1.0 SG A:CYS4958 2.3 45.5 1.0 SG A:CYS4961 2.3 43.9 1.0 CE1 A:HIS4978 2.9 47.6 1.0 CE1 A:HIS4983 3.0 41.9 1.0 CG A:HIS4983 3.0 41.9 1.0 CD2 A:HIS4978 3.1 47.6 1.0 CB A:CYS4958 3.2 45.5 1.0 CB A:CYS4961 3.3 43.9 1.0 CB A:HIS4983 3.4 41.9 1.0 N A:CYS4961 3.7 43.9 1.0 NE2 A:HIS4983 4.0 41.9 1.0 CA A:CYS4961 4.1 43.9 1.0 CD2 A:HIS4983 4.1 41.9 1.0 ND1 A:HIS4978 4.1 47.6 1.0 CG A:HIS4978 4.2 47.6 1.0 CZ A:PHE4968 4.5 58.1 1.0 CB A:ILE4960 4.6 40.1 1.0 CA A:CYS4958 4.7 45.5 1.0 C A:ILE4960 4.7 40.1 1.0 N A:ILE4960 4.8 40.1 1.0 N A:GLY4962 4.8 46.9 1.0 C A:CYS4961 4.8 43.9 1.0 CA A:HIS4983 4.9 41.9 1.0 CA A:ILE4960 4.9 40.1 1.0

Zinc binding site 2 out of 4 in the Cryo-Em Structure of RYR1 + Amp (Local Refinement of Tmd)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryo-Em Structure of RYR1 + Amp (Local Refinement of Tmd) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn5102 b:98.1 occ:1.00 ND1 B:HIS4983 2.0 41.9 1.0 NE2 B:HIS4978 2.0 47.6 1.0 SG B:CYS4958 2.3 45.5 1.0 SG B:CYS4961 2.3 43.9 1.0 CE1 B:HIS4978 2.9 47.6 1.0 CE1 B:HIS4983 3.0 41.9 1.0 CG B:HIS4983 3.0 41.9 1.0 CD2 B:HIS4978 3.1 47.6 1.0 CB B:CYS4958 3.2 45.5 1.0 CB B:CYS4961 3.3 43.9 1.0 CB B:HIS4983 3.4 41.9 1.0 N B:CYS4961 3.7 43.9 1.0 NE2 B:HIS4983 4.0 41.9 1.0 CA B:CYS4961 4.1 43.9 1.0 CD2 B:HIS4983 4.1 41.9 1.0 ND1 B:HIS4978 4.1 47.6 1.0 CG B:HIS4978 4.2 47.6 1.0 CZ B:PHE4968 4.5 58.1 1.0 CB B:ILE4960 4.6 40.1 1.0 CA B:CYS4958 4.7 45.5 1.0 C B:ILE4960 4.7 40.1 1.0 N B:ILE4960 4.8 40.1 1.0 N B:GLY4962 4.8 46.9 1.0 C B:CYS4961 4.8 43.9 1.0 CA B:HIS4983 4.9 41.9 1.0 CA B:ILE4960 4.9 40.1 1.0

Zinc binding site 3 out of 4 in the Cryo-Em Structure of RYR1 + Amp (Local Refinement of Tmd)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cryo-Em Structure of RYR1 + Amp (Local Refinement of Tmd) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn5102 b:98.1 occ:1.00 ND1 C:HIS4983 2.0 41.9 1.0 NE2 C:HIS4978 2.0 47.6 1.0 SG C:CYS4958 2.3 45.5 1.0 SG C:CYS4961 2.3 43.9 1.0 CE1 C:HIS4978 2.9 47.6 1.0 CE1 C:HIS4983 3.0 41.9 1.0 CG C:HIS4983 3.0 41.9 1.0 CD2 C:HIS4978 3.1 47.6 1.0 CB C:CYS4958 3.2 45.5 1.0 CB C:CYS4961 3.3 43.9 1.0 CB C:HIS4983 3.4 41.9 1.0 N C:CYS4961 3.7 43.9 1.0 NE2 C:HIS4983 4.0 41.9 1.0 CA C:CYS4961 4.1 43.9 1.0 CD2 C:HIS4983 4.1 41.9 1.0 ND1 C:HIS4978 4.1 47.6 1.0 CG C:HIS4978 4.2 47.6 1.0 CZ C:PHE4968 4.5 58.1 1.0 CB C:ILE4960 4.6 40.1 1.0 CA C:CYS4958 4.7 45.5 1.0 C C:ILE4960 4.7 40.1 1.0 N C:ILE4960 4.8 40.1 1.0 N C:GLY4962 4.8 46.9 1.0 C C:CYS4961 4.8 43.9 1.0 CA C:HIS4983 4.9 41.9 1.0 CA C:ILE4960 4.9 40.1 1.0

Zinc binding site 4 out of 4 in the Cryo-Em Structure of RYR1 + Amp (Local Refinement of Tmd)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Cryo-Em Structure of RYR1 + Amp (Local Refinement of Tmd) within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn5102 b:98.1 occ:1.00 ND1 D:HIS4983 2.0 41.9 1.0 NE2 D:HIS4978 2.0 47.6 1.0 SG D:CYS4958 2.3 45.5 1.0 SG D:CYS4961 2.3 43.9 1.0 CE1 D:HIS4978 2.9 47.6 1.0 CE1 D:HIS4983 3.0 41.9 1.0 CG D:HIS4983 3.0 41.9 1.0 CD2 D:HIS4978 3.1 47.6 1.0 CB D:CYS4958 3.2 45.5 1.0 CB D:CYS4961 3.3 43.9 1.0 CB D:HIS4983 3.4 41.9 1.0 N D:CYS4961 3.7 43.9 1.0 NE2 D:HIS4983 4.0 41.9 1.0 CA D:CYS4961 4.1 43.9 1.0 CD2 D:HIS4983 4.1 41.9 1.0 ND1 D:HIS4978 4.1 47.6 1.0 CG D:HIS4978 4.2 47.6 1.0 CZ D:PHE4968 4.5 58.1 1.0 CB D:ILE4960 4.6 40.1 1.0 CA D:CYS4958 4.7 45.5 1.0 C D:ILE4960 4.7 40.1 1.0 N D:ILE4960 4.8 40.1 1.0 N D:GLY4962 4.8 46.9 1.0 C D:CYS4961 4.8 43.9 1.0 CA D:HIS4983 4.9 41.9 1.0 CA D:ILE4960 4.9 40.1 1.0

S.Cholak, J.W.Saville, X.Zhu, A.M.Berezuk, K.S.Tuttle, O.Haji-Ghassemi, F.J.Alvarado, F.Van Petegem, S.Subramaniam. Allosteric Modulation of Ryanodine Receptor RYR1 By Nucleotide Derivatives Structure 2023.
ISSN: ISSN 0969-2126
DOI: 10.1016/J.STR.2023.04.009