Zinc in PDB 7dvq: Cryo-Em Structure of the Activated Human Minor Spliceosome (Minor Bact Complex)

Enzymatic activity of Cryo-Em Structure of the Activated Human Minor Spliceosome (Minor Bact Complex)

All present enzymatic activity of Cryo-Em Structure of the Activated Human Minor Spliceosome (Minor Bact Complex):
2.3.2.27; 3.6.4.13; 5.2.1.8;

Other elements in 7dvq:

The structure of Cryo-Em Structure of the Activated Human Minor Spliceosome (Minor Bact Complex) also contains other interesting chemical elements:

Magnesium (Mg) 5 atoms
Potassium (K) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Cryo-Em Structure of the Activated Human Minor Spliceosome (Minor Bact Complex) (pdb code 7dvq). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Cryo-Em Structure of the Activated Human Minor Spliceosome (Minor Bact Complex), PDB code: 7dvq:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 7dvq

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Zinc binding site 1 out of 7 in the Cryo-Em Structure of the Activated Human Minor Spliceosome (Minor Bact Complex)


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 Activated Human Minor Spliceosome (Minor Bact Complex) 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
CG v:HIS62 4.3 19.9 1.0
ND1 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

Zinc binding site 2 out of 7 in 7dvq

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Zinc binding site 2 out of 7 in the Cryo-Em Structure of the Activated Human Minor Spliceosome (Minor Bact Complex)


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 Activated Human Minor Spliceosome (Minor Bact Complex) 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 3 out of 7 in 7dvq

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Zinc binding site 3 out of 7 in the Cryo-Em Structure of the Activated Human Minor Spliceosome (Minor Bact Complex)


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 Activated Human Minor Spliceosome (Minor Bact Complex) 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 4 out of 7 in 7dvq

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Zinc binding site 4 out of 7 in the Cryo-Em Structure of the Activated Human Minor Spliceosome (Minor Bact Complex)


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 Activated Human Minor Spliceosome (Minor Bact Complex) 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:CYS75 2.3 35.1 1.0
SG 6:CYS30 2.3 15.4 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 3.9 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 5 out of 7 in 7dvq

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Zinc binding site 5 out of 7 in the Cryo-Em Structure of the Activated Human Minor Spliceosome (Minor Bact Complex)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Cryo-Em Structure of the Activated Human Minor Spliceosome (Minor Bact Complex) within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn500

b:31.2
occ:1.00
 SG M:CYS211 2.3 9.6 1.0
SG M:CYS217 2.3 14.0 1.0
NE2 M:HIS221 2.3 15.3 1.0
SG M:CYS202 2.3 17.1 1.0
CB M:CYS217 3.0 14.0 1.0
CD2 M:HIS221 3.1 15.3 1.0
CB M:CYS202 3.1 17.1 1.0
CB M:CYS211 3.2 9.6 1.0
CE1 M:HIS221 3.4 15.3 1.0
CG M:HIS221 4.3 15.3 1.0
ND1 M:HIS221 4.4 15.3 1.0
CA M:CYS202 4.4 17.1 1.0
CA M:CYS217 4.5 14.0 1.0
CA M:CYS211 4.5 9.6 1.0
CB M:TYR205 4.5 10.5 1.0
CB M:PHE213 4.9 16.9 1.0
CD2 M:PHE213 5.0 16.9 1.0

Zinc binding site 6 out of 7 in 7dvq

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Zinc binding site 6 out of 7 in the Cryo-Em Structure of the Activated Human Minor Spliceosome (Minor Bact Complex)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Cryo-Em Structure of the Activated Human Minor Spliceosome (Minor Bact Complex) within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Zn200

b:65.2
occ:1.00
 SG 0:CYS86 2.3 39.6 1.0
SG 0:CYS3 2.3 40.2 1.0
SG 0:CYS6 2.3 40.8 1.0
SG 0:CYS83 2.3 35.3 1.0
CB 0:CYS83 3.2 35.3 1.0
CB 0:CYS6 3.3 40.8 1.0
CB 0:CYS86 3.4 39.6 1.0
CB 0:CYS3 3.5 40.2 1.0
N 0:CYS86 3.7 39.6 1.0
N 0:CYS3 3.8 40.2 1.0
CA 0:CYS86 4.1 39.6 1.0
CA 0:CYS3 4.2 40.2 1.0
N 0:CYS6 4.5 40.8 1.0
CA 0:CYS6 4.5 40.8 1.0
CB 0:MET85 4.6 33.3 1.0
CA 0:CYS83 4.6 35.3 1.0
C 0:CYS3 4.7 40.2 1.0
C 0:MET85 4.7 33.3 1.0
N 0:GLY87 4.9 36.9 1.0
C 0:CYS86 4.9 39.6 1.0
O 0:CYS3 4.9 40.2 1.0
N 0:MET85 4.9 33.3 1.0
C 0:VAL2 5.0 31.2 1.0

Zinc binding site 7 out of 7 in 7dvq

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Zinc binding site 7 out of 7 in the Cryo-Em Structure of the Activated Human Minor Spliceosome (Minor Bact Complex)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Cryo-Em Structure of the Activated Human Minor Spliceosome (Minor Bact Complex) within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Zn201

b:63.2
occ:1.00
 SG 0:CYS73 2.3 28.4 1.0
SG 0:CYS61 2.3 38.4 1.0
SG 0:CYS76 2.3 29.7 1.0
SG 0:CYS58 2.3 36.1 1.0
CB 0:CYS58 3.0 36.1 1.0
CB 0:CYS76 3.1 29.7 1.0
CB 0:CYS61 3.3 38.4 1.0
CB 0:CYS73 3.4 28.4 1.0
N 0:CYS61 3.7 38.4 1.0
N 0:CYS73 4.0 28.4 1.0
CA 0:CYS61 4.1 38.4 1.0
CA 0:CYS73 4.2 28.4 1.0
N 0:CYS76 4.2 29.7 1.0
CA 0:CYS76 4.3 29.7 1.0
O 0:CYS73 4.4 28.4 1.0
OG 0:SER63 4.5 36.8 1.0
CA 0:CYS58 4.5 36.1 1.0
CB 0:ILE60 4.6 33.8 1.0
C 0:CYS73 4.7 28.4 1.0
C 0:ILE60 4.8 33.8 1.0
C 0:CYS61 4.9 38.4 1.0

Reference:

R.Bai, R.Wan, L.Wang, K.Xu, Q.Zhang, J.Lei, Y.Shi. Structure of the Activated Human Minor Spliceosome. Science V. 371 2021.
ISSN: ESSN 1095-9203
PubMed: 33509932
DOI: 10.1126/SCIENCE.ABG0879
Page generated: Tue Oct 29 19:26:55 2024

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