Zinc in PDB 8drp: Focus/Local Refined Map in C4 of Signal Subtracted RYR1 Particles

The binding sites of Zinc atom in the Focus/Local Refined Map in C4 of Signal Subtracted RYR1 Particles (pdb code 8drp). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Focus/Local Refined Map in C4 of Signal Subtracted RYR1 Particles, PDB code: 8drp:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Focus/Local Refined Map in C4 of Signal Subtracted RYR1 Particles


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Focus/Local Refined Map in C4 of Signal Subtracted RYR1 Particles within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn5103 b:62.0 occ:1.00 NE2 A:HIS4978 2.0 59.5 1.0 ND1 A:HIS4983 2.0 49.1 1.0 SG A:CYS4961 2.3 57.0 1.0 SG A:CYS4958 2.3 58.4 1.0 CE1 A:HIS4978 2.7 56.0 1.0 CG A:HIS4983 3.0 46.6 1.0 CE1 A:HIS4983 3.1 50.9 1.0 CD2 A:HIS4978 3.1 59.3 1.0 CB A:HIS4983 3.3 43.2 1.0 N A:CYS4961 3.6 55.6 1.0 CB A:CYS4958 3.7 56.3 1.0 CB A:CYS4961 3.8 58.2 1.0 ND1 A:HIS4978 3.9 56.1 1.0 CB A:ILE4960 4.0 47.0 1.0 CG A:HIS4978 4.1 57.5 1.0 CD2 A:HIS4983 4.1 46.1 1.0 NE2 A:HIS4983 4.1 47.4 1.0 CA A:CYS4961 4.2 54.9 1.0 CG2 A:ILE4960 4.5 48.1 1.0 N A:GLY4962 4.5 55.4 1.0 C A:ILE4960 4.6 52.7 1.0 CA A:ILE4960 4.6 47.6 1.0 N A:ILE4960 4.6 51.0 1.0 CA A:HIS4983 4.8 40.2 1.0 C A:CYS4961 4.8 55.4 1.0 CG1 A:ILE4960 4.9 44.0 1.0

Zinc binding site 2 out of 4 in the Focus/Local Refined Map in C4 of Signal Subtracted RYR1 Particles


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Focus/Local Refined Map in C4 of Signal Subtracted RYR1 Particles within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn5103 b:62.0 occ:1.00 NE2 B:HIS4978 2.0 59.5 1.0 ND1 B:HIS4983 2.0 49.1 1.0 SG B:CYS4961 2.3 57.0 1.0 SG B:CYS4958 2.3 58.4 1.0 CE1 B:HIS4978 2.7 56.0 1.0 CG B:HIS4983 3.0 46.6 1.0 CE1 B:HIS4983 3.1 50.9 1.0 CD2 B:HIS4978 3.1 59.3 1.0 CB B:HIS4983 3.3 43.2 1.0 N B:CYS4961 3.6 55.6 1.0 CB B:CYS4958 3.7 56.3 1.0 CB B:CYS4961 3.8 58.2 1.0 ND1 B:HIS4978 3.9 56.1 1.0 CB B:ILE4960 4.0 47.0 1.0 CG B:HIS4978 4.1 57.5 1.0 CD2 B:HIS4983 4.1 46.1 1.0 NE2 B:HIS4983 4.1 47.4 1.0 CA B:CYS4961 4.2 54.9 1.0 CG2 B:ILE4960 4.5 48.1 1.0 N B:GLY4962 4.5 55.4 1.0 C B:ILE4960 4.6 52.7 1.0 CA B:ILE4960 4.6 47.6 1.0 N B:ILE4960 4.6 51.0 1.0 CA B:HIS4983 4.8 40.2 1.0 C B:CYS4961 4.8 55.4 1.0 CG1 B:ILE4960 4.9 44.0 1.0

Zinc binding site 3 out of 4 in the Focus/Local Refined Map in C4 of Signal Subtracted RYR1 Particles


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Focus/Local Refined Map in C4 of Signal Subtracted RYR1 Particles within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn5103 b:62.0 occ:1.00 NE2 C:HIS4978 2.0 59.5 1.0 ND1 C:HIS4983 2.0 49.1 1.0 SG C:CYS4961 2.3 57.0 1.0 SG C:CYS4958 2.3 58.4 1.0 CE1 C:HIS4978 2.7 56.0 1.0 CG C:HIS4983 3.0 46.6 1.0 CE1 C:HIS4983 3.1 50.9 1.0 CD2 C:HIS4978 3.1 59.3 1.0 CB C:HIS4983 3.3 43.2 1.0 N C:CYS4961 3.6 55.6 1.0 CB C:CYS4958 3.7 56.3 1.0 CB C:CYS4961 3.8 58.2 1.0 ND1 C:HIS4978 3.9 56.1 1.0 CB C:ILE4960 4.0 47.0 1.0 CG C:HIS4978 4.1 57.5 1.0 CD2 C:HIS4983 4.1 46.1 1.0 NE2 C:HIS4983 4.1 47.4 1.0 CA C:CYS4961 4.2 54.9 1.0 CG2 C:ILE4960 4.5 48.1 1.0 N C:GLY4962 4.5 55.4 1.0 C C:ILE4960 4.6 52.7 1.0 CA C:ILE4960 4.6 47.6 1.0 N C:ILE4960 4.6 51.0 1.0 CA C:HIS4983 4.8 40.2 1.0 C C:CYS4961 4.8 55.4 1.0 CG1 C:ILE4960 4.9 44.0 1.0

Zinc binding site 4 out of 4 in the Focus/Local Refined Map in C4 of Signal Subtracted RYR1 Particles


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Focus/Local Refined Map in C4 of Signal Subtracted RYR1 Particles within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn5103 b:62.0 occ:1.00 NE2 D:HIS4978 2.0 59.5 1.0 ND1 D:HIS4983 2.0 49.1 1.0 SG D:CYS4961 2.3 57.0 1.0 SG D:CYS4958 2.3 58.4 1.0 CE1 D:HIS4978 2.7 56.0 1.0 CG D:HIS4983 3.0 46.6 1.0 CE1 D:HIS4983 3.1 50.9 1.0 CD2 D:HIS4978 3.1 59.3 1.0 CB D:HIS4983 3.3 43.2 1.0 N D:CYS4961 3.6 55.6 1.0 CB D:CYS4958 3.7 56.3 1.0 CB D:CYS4961 3.8 58.2 1.0 ND1 D:HIS4978 3.9 56.1 1.0 CB D:ILE4960 4.0 47.0 1.0 CG D:HIS4978 4.1 57.5 1.0 CD2 D:HIS4983 4.1 46.1 1.0 NE2 D:HIS4983 4.1 47.4 1.0 CA D:CYS4961 4.2 54.9 1.0 CG2 D:ILE4960 4.5 48.1 1.0 N D:GLY4962 4.5 55.4 1.0 C D:ILE4960 4.6 52.7 1.0 CA D:ILE4960 4.6 47.6 1.0 N D:ILE4960 4.6 51.0 1.0 CA D:HIS4983 4.8 40.2 1.0 C D:CYS4961 4.8 55.4 1.0 CG1 D:ILE4960 4.9 44.0 1.0

O.Haji-Ghassemi, S.Y.Chen, G.B.Gurrola, W.Cai, C.R.Valdivia, H.H.Valdivia, F.Van Petegem. Cryo-Em Analysis of Calcin Binding to Ryanodine Receptors Reveals A Subconductance State That Is Abolished By Pka Phosphorylation. Sci Adv 2023.
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