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

Zinc Binding Sites:

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 8sex

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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 8sex

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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 8sex

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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 8sex

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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

Reference:

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
Page generated: Fri Jul 28 07:27:56 2023

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