Zinc in PDB 8y7e: Cryo-Em Structure of the Human Minor Pre-B Complex (Pre-Precatalytic Spliceosome) U12 Snrnp Part

Zinc Binding Sites:

The binding sites of Zinc atom in the Cryo-Em Structure of the Human Minor Pre-B Complex (Pre-Precatalytic Spliceosome) U12 Snrnp Part (pdb code 8y7e). 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 the Human Minor Pre-B Complex (Pre-Precatalytic Spliceosome) U12 Snrnp Part, PDB code: 8y7e:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 8y7e

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Zinc binding site 1 out of 4 in the Cryo-Em Structure of the Human Minor Pre-B Complex (Pre-Precatalytic Spliceosome) U12 Snrnp Part


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 the Human Minor Pre-B Complex (Pre-Precatalytic Spliceosome) U12 Snrnp Part within 5.0Å range:
probe atom residue distance (Å) B Occ
6:Zn201

b:59.3
occ:1.00
 SG 6:CYS61 2.3 28.4 1.0
SG 6:CYS23 2.3 22.3 1.0
SG 6:CYS26 2.3 23.6 1.0
SG 6:CYS58 2.3 22.6 1.0
CB 6:CYS58 3.2 22.6 1.0
CB 6:CYS23 3.3 22.3 1.0
CB 6:CYS26 3.4 23.6 1.0
CB 6:CYS61 3.4 28.4 1.0
N 6:CYS23 3.8 22.3 1.0
N 6:CYS61 3.9 28.4 1.0
CA 6:CYS23 4.1 22.3 1.0
CA 6:CYS61 4.2 28.4 1.0
N 6:CYS26 4.2 23.6 1.0
O 6:CYS23 4.4 22.3 1.0
CA 6:CYS26 4.4 23.6 1.0
N 6:GLY62 4.4 35.1 1.0
C 6:CYS23 4.6 22.3 1.0
N 6:GLY63 4.6 35.1 1.0
CA 6:CYS58 4.6 22.6 1.0
C 6:CYS61 4.8 28.4 1.0
C 6:LEU22 4.9 16.6 1.0
C 6:ILE60 4.9 18.4 1.0
CB 6:LYS25 4.9 29.3 1.0
CB 6:ILE60 5.0 18.4 1.0

Zinc binding site 2 out of 4 in 8y7e

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Zinc binding site 2 out of 4 in the Cryo-Em Structure of the Human Minor Pre-B Complex (Pre-Precatalytic Spliceosome) U12 Snrnp Part


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 the Human Minor Pre-B Complex (Pre-Precatalytic Spliceosome) U12 Snrnp Part within 5.0Å range:
probe atom residue distance (Å) B Occ
6:Zn202

b:50.5
occ:1.00
 SG 6:CYS49 2.3 27.9 1.0
SG 6:CYS11 2.3 13.9 1.0
SG 6:CYS46 2.3 22.6 1.0
SG 6:CYS85 2.3 15.6 1.0
CB 6:CYS11 3.1 13.9 1.0
CB 6:CYS85 3.2 15.6 1.0
CB 6:CYS49 3.3 27.9 1.0
CB 6:CYS46 3.4 22.6 1.0
N 6:CYS46 4.1 22.6 1.0
CA 6:CYS46 4.3 22.6 1.0
N 6:CYS49 4.3 27.9 1.0
CB 6:LYS87 4.4 15.1 1.0
CA 6:CYS49 4.4 27.9 1.0
O 6:CYS46 4.5 22.6 1.0
CA 6:CYS11 4.6 13.9 1.0
CA 6:CYS85 4.7 15.6 1.0
C 6:CYS46 4.7 22.6 1.0
CB 6:LYS13 4.8 18.4 1.0
N 6:LYS13 4.9 18.4 1.0

Zinc binding site 3 out of 4 in 8y7e

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Zinc binding site 3 out of 4 in the Cryo-Em Structure of the Human Minor Pre-B Complex (Pre-Precatalytic Spliceosome) U12 Snrnp Part


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 the Human Minor Pre-B Complex (Pre-Precatalytic Spliceosome) U12 Snrnp Part within 5.0Å range:
probe atom residue distance (Å) B Occ
6:Zn203

b:54.6
occ:1.00
 SG 6:CYS33 2.3 35.1 1.0
SG 6:CYS72 2.3 17.2 1.0
SG 6:CYS30 2.3 15.4 1.0
SG 6:CYS75 2.3 35.1 1.0
CB 6:CYS33 3.4 35.1 1.0
CB 6:CYS75 3.4 35.1 1.0
CB 6:CYS30 3.4 15.4 1.0
CB 6:CYS72 3.5 17.2 1.0
N 6:CYS33 3.7 35.1 1.0
N 6:CYS72 3.8 17.2 1.0
CA 6:CYS33 4.1 35.1 1.0
N 6:CYS75 4.2 35.1 1.0
CA 6:CYS72 4.2 17.2 1.0
CA 6:CYS75 4.4 35.1 1.0
C 6:CYS33 4.6 35.1 1.0
CB 6:ILE32 4.7 11.8 1.0
N 6:ASP34 4.7 16.4 1.0
C 6:CYS72 4.8 17.2 1.0
CA 6:CYS30 4.8 15.4 1.0
C 6:ILE32 4.9 11.8 1.0
N 6:ILE32 5.0 11.8 1.0

Zinc binding site 4 out of 4 in 8y7e

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Zinc binding site 4 out of 4 in the Cryo-Em Structure of the Human Minor Pre-B Complex (Pre-Precatalytic Spliceosome) U12 Snrnp Part


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 the Human Minor Pre-B Complex (Pre-Precatalytic Spliceosome) U12 Snrnp Part within 5.0Å range:
probe atom residue distance (Å) B Occ
v:Zn300

b:39.0
occ:1.00
 ND1 v:HIS68 2.3 30.1 1.0
SG v:CYS44 2.3 27.0 1.0
NE2 v:HIS62 2.3 19.9 1.0
SG v:CYS47 2.3 37.4 1.0
CE1 v:HIS68 3.1 30.1 1.0
CD2 v:HIS62 3.2 19.9 1.0
CB v:CYS44 3.2 27.0 1.0
CE1 v:HIS62 3.2 19.9 1.0
CG v:HIS68 3.3 30.1 1.0
CB v:CYS47 3.6 37.4 1.0
CB v:HIS68 3.7 30.1 1.0
N v:CYS47 4.1 37.4 1.0
CA v:HIS68 4.2 30.1 1.0
NE2 v:HIS68 4.3 30.1 1.0
ND1 v:HIS62 4.3 19.9 1.0
CG v:HIS62 4.3 19.9 1.0
CD2 v:HIS68 4.4 30.1 1.0
CA v:CYS47 4.4 37.4 1.0
CB v:ILE46 4.6 32.5 1.0
CA v:CYS44 4.6 27.0 1.0
CG2 v:ILE46 4.9 32.5 1.0
CG v:PRO51 4.9 23.4 1.0

Reference:

R.Bai, M.Yuan, P.Zhang, T.Luo, Y.Shi, R.Wan. Structural Basis of U12-Type Intron Engagement By the Fully Assembled Human Minor Spliceosome Science 2024.
ISSN: ESSN 1095-9203
DOI: 10.1126/SCIENCE.ADN7272
Page generated: Thu Oct 31 13:58:28 2024

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