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Zinc in PDB 6id1: Cryo-Em Structure of A Human Intron Lariat Spliceosome After PRP43 Loaded (ILS2 Complex) at 2.9 Angstrom Resolution

Enzymatic activity of Cryo-Em Structure of A Human Intron Lariat Spliceosome After PRP43 Loaded (ILS2 Complex) at 2.9 Angstrom Resolution

All present enzymatic activity of Cryo-Em Structure of A Human Intron Lariat Spliceosome After PRP43 Loaded (ILS2 Complex) at 2.9 Angstrom Resolution:
2.3.2.27; 3.6.4.13; 5.2.1.8;

Other elements in 6id1:

The structure of Cryo-Em Structure of A Human Intron Lariat Spliceosome After PRP43 Loaded (ILS2 Complex) at 2.9 Angstrom Resolution also contains other interesting chemical elements:

Magnesium (Mg) 7 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Cryo-Em Structure of A Human Intron Lariat Spliceosome After PRP43 Loaded (ILS2 Complex) at 2.9 Angstrom Resolution (pdb code 6id1). 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 A Human Intron Lariat Spliceosome After PRP43 Loaded (ILS2 Complex) at 2.9 Angstrom Resolution, PDB code: 6id1:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 6id1

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Zinc binding site 1 out of 7 in the Cryo-Em Structure of A Human Intron Lariat Spliceosome After PRP43 Loaded (ILS2 Complex) at 2.9 Angstrom Resolution


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 A Human Intron Lariat Spliceosome After PRP43 Loaded (ILS2 Complex) at 2.9 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn201

b:27.4
occ:1.00
 SG N:CYS117 2.3 9.3 1.0
SG N:CYS134 2.3 11.7 1.0
SG N:CYS105 2.3 2.1 1.0
SG N:CYS119 2.3 8.0 1.0
CB N:CYS119 2.4 8.0 1.0
CB N:CYS105 2.9 2.1 1.0
CB N:CYS134 3.4 11.7 1.0
CB N:CYS117 3.6 9.3 1.0
ZN N:ZN202 3.8 22.4 1.0
CA N:CYS105 3.9 2.1 1.0
CA N:CYS119 3.9 8.0 1.0
ZN N:ZN203 4.2 15.3 1.0
SG N:CYS101 4.2 8.4 1.0
CB N:CYS137 4.3 10.2 1.0
N N:CYS119 4.4 8.0 1.0
O N:CYS105 4.6 2.1 1.0
CB N:CYS139 4.6 14.1 1.0
CA N:CYS134 4.7 11.7 1.0
C N:CYS105 4.8 2.1 1.0
CD2 N:HIS136 4.8 6.6 1.0
C N:CYS119 4.9 8.0 1.0
CB N:HIS136 4.9 6.6 1.0
CA N:CYS117 4.9 9.3 1.0
N N:CYS105 5.0 2.1 1.0

Zinc binding site 2 out of 7 in 6id1

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Zinc binding site 2 out of 7 in the Cryo-Em Structure of A Human Intron Lariat Spliceosome After PRP43 Loaded (ILS2 Complex) at 2.9 Angstrom Resolution


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 A Human Intron Lariat Spliceosome After PRP43 Loaded (ILS2 Complex) at 2.9 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn202

b:22.4
occ:1.00
 CB N:CYS101 2.2 8.4 1.0
SG N:CYS137 2.3 10.2 1.0
SG N:CYS102 2.3 3.2 1.0
SG N:CYS105 2.3 2.1 1.0
SG N:CYS101 2.3 8.4 1.0
CB N:CYS137 2.4 10.2 1.0
CB N:CYS102 3.4 3.2 1.0
CB N:CYS105 3.6 2.1 1.0
CA N:CYS101 3.7 8.4 1.0
N N:CYS102 3.7 3.2 1.0
ZN N:ZN201 3.8 27.4 1.0
CA N:CYS137 3.8 10.2 1.0
C N:CYS101 4.0 8.4 1.0
CA N:CYS102 4.2 3.2 1.0
ZN N:ZN203 4.2 15.3 1.0
CB N:CYS139 4.3 14.1 1.0
SG N:CYS119 4.3 8.0 1.0
N N:CYS101 4.5 8.4 1.0
N N:CYS137 4.5 10.2 1.0
C N:CYS137 4.7 10.2 1.0
CA N:CYS105 4.8 2.1 1.0
O N:CYS101 4.8 8.4 1.0
SG N:CYS134 4.8 11.7 1.0
N N:CYS105 4.9 2.1 1.0

Zinc binding site 3 out of 7 in 6id1

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Zinc binding site 3 out of 7 in the Cryo-Em Structure of A Human Intron Lariat Spliceosome After PRP43 Loaded (ILS2 Complex) at 2.9 Angstrom Resolution


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 A Human Intron Lariat Spliceosome After PRP43 Loaded (ILS2 Complex) at 2.9 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn203

b:15.3
occ:1.00
 SG N:CYS101 2.2 8.4 1.0
SG N:CYS119 2.2 8.0 1.0
SG N:CYS142 2.3 12.9 1.0
SG N:CYS139 2.3 14.1 1.0
CB N:CYS139 2.7 14.1 1.0
N N:CYS142 3.5 12.9 1.0
CB N:CYS142 3.6 12.9 1.0
CB N:CYS101 3.7 8.4 1.0
CB N:CYS119 3.8 8.0 1.0
CA N:CYS142 4.0 12.9 1.0
CA N:CYS139 4.1 14.1 1.0
ZN N:ZN201 4.2 27.4 1.0
N N:CYS101 4.2 8.4 1.0
ZN N:ZN202 4.2 22.4 1.0
O N:CYS119 4.3 8.0 1.0
CA N:CYS119 4.4 8.0 1.0
CA N:CYS101 4.4 8.4 1.0
C N:GLY141 4.4 13.6 1.0
C N:CYS119 4.5 8.0 1.0
CB W:PRO195 4.6 16.4 1.0
N N:GLY141 4.6 13.6 1.0
C N:CYS139 4.6 14.1 1.0
N N:ARG140 4.8 17.5 1.0
SG N:CYS105 4.9 2.1 1.0
SG N:CYS137 4.9 10.2 1.0
CA N:GLY141 4.9 13.6 1.0

Zinc binding site 4 out of 7 in 6id1

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Zinc binding site 4 out of 7 in the Cryo-Em Structure of A Human Intron Lariat Spliceosome After PRP43 Loaded (ILS2 Complex) at 2.9 Angstrom Resolution


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 A Human Intron Lariat Spliceosome After PRP43 Loaded (ILS2 Complex) at 2.9 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Zn501

b:32.8
occ:1.00
 SG O:CYS81 2.4 13.1 1.0
SG O:CYS84 2.5 27.3 1.0
SG O:CYS27 2.5 19.0 1.0
SG O:CYS24 2.5 20.0 1.0
CB O:CYS81 3.1 13.1 1.0
CB O:CYS27 3.2 19.0 1.0
CB O:CYS84 3.4 27.3 1.0
CB O:CYS24 3.7 20.0 1.0
N O:CYS84 3.8 27.3 1.0
CG2 O:THR83 3.9 20.1 1.0
N O:CYS24 4.0 20.0 1.0
CA O:CYS84 4.2 27.3 1.0
CA O:CYS24 4.4 20.0 1.0
CA O:CYS27 4.4 19.0 1.0
N O:CYS27 4.5 19.0 1.0
CA O:CYS81 4.5 13.1 1.0
C O:THR83 4.8 20.1 1.0
N O:THR83 4.9 20.1 1.0
NZ O:LYS66 4.9 20.1 1.0
NH2 O:ARG159 4.9 18.9 1.0
C O:CYS81 5.0 13.1 1.0

Zinc binding site 5 out of 7 in 6id1

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Zinc binding site 5 out of 7 in the Cryo-Em Structure of A Human Intron Lariat Spliceosome After PRP43 Loaded (ILS2 Complex) at 2.9 Angstrom Resolution


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 A Human Intron Lariat Spliceosome After PRP43 Loaded (ILS2 Complex) at 2.9 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Zn502

b:36.3
occ:1.00
 SG O:CYS74 2.5 20.1 1.0
SG O:CYS45 2.6 22.1 1.0
SG O:CYS71 2.7 15.9 1.0
CB O:CYS71 2.7 15.9 1.0
CB O:CYS48 2.9 18.3 1.0
CB O:CYS45 3.2 22.1 1.0
N O:CYS71 3.3 15.9 1.0
CB O:CYS74 3.3 20.1 1.0
CA O:CYS71 3.6 15.9 1.0
SG O:CYS48 3.9 18.3 1.0
N O:CYS48 4.0 18.3 1.0
N O:CYS74 4.0 20.1 1.0
CA O:CYS48 4.1 18.3 1.0
CA O:CYS74 4.3 20.1 1.0
C O:VAL70 4.5 20.1 1.0
C O:CYS71 4.6 15.9 1.0
CA O:CYS45 4.7 22.1 1.0
CB O:VAL70 4.7 20.1 1.0
CA O:VAL70 4.8 20.1 1.0
O O:CYS71 4.8 15.9 1.0

Zinc binding site 6 out of 7 in 6id1

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Zinc binding site 6 out of 7 in the Cryo-Em Structure of A Human Intron Lariat Spliceosome After PRP43 Loaded (ILS2 Complex) at 2.9 Angstrom Resolution


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 A Human Intron Lariat Spliceosome After PRP43 Loaded (ILS2 Complex) at 2.9 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Zn503

b:35.6
occ:1.00
 NE2 O:HIS183 2.2 22.3 1.0
SG O:CYS179 2.5 21.7 1.0
SG O:CYS173 2.5 23.2 1.0
SG O:CYS165 2.5 22.7 1.0
CB O:CYS165 2.9 22.7 1.0
CD2 O:HIS183 2.9 22.3 1.0
CB O:CYS179 3.1 21.7 1.0
CE1 O:HIS183 3.3 22.3 1.0
CB O:CYS173 3.7 23.2 1.0
O O:TYR181 4.1 15.5 1.0
CG O:HIS183 4.2 22.3 1.0
CB O:TRP168 4.3 24.2 1.0
ND1 O:HIS183 4.3 22.3 1.0
CA O:CYS165 4.4 22.7 1.0
CB O:TYR181 4.6 15.5 1.0
CA O:CYS179 4.6 21.7 1.0
C O:TYR181 4.8 15.5 1.0
O O:GLY176 4.8 23.8 1.0
CA O:CYS173 4.9 23.2 1.0
N6 F:A28 5.0 19.2 1.0
CG O:TRP168 5.0 24.2 1.0

Zinc binding site 7 out of 7 in 6id1

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Zinc binding site 7 out of 7 in the Cryo-Em Structure of A Human Intron Lariat Spliceosome After PRP43 Loaded (ILS2 Complex) at 2.9 Angstrom Resolution


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 A Human Intron Lariat Spliceosome After PRP43 Loaded (ILS2 Complex) at 2.9 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Zn900

b:34.3
occ:1.00
 ND1 U:HIS765 2.3 29.6 1.0
NE2 U:HIS718 2.4 31.0 1.0
SG U:CYS678 2.6 38.0 1.0
SG U:CYS675 2.6 34.3 1.0
CD2 U:HIS718 2.7 31.0 1.0
CB U:CYS678 2.8 38.0 1.0
CE1 U:HIS765 3.0 29.6 1.0
CG U:HIS765 3.2 29.6 1.0
C U:TYR677 3.2 29.2 1.0
N U:CYS678 3.2 38.0 1.0
CE1 U:HIS718 3.3 31.0 1.0
O U:TYR677 3.4 29.2 1.0
CB U:CYS675 3.5 34.3 1.0
CA U:CYS678 3.6 38.0 1.0
CB U:TYR677 3.6 29.2 1.0
CG U:HIS718 3.6 31.0 1.0
CB U:HIS765 3.7 29.6 1.0
CA U:TYR677 3.9 29.2 1.0
ND1 U:HIS718 3.9 31.0 1.0
NE2 U:HIS765 4.1 29.6 1.0
CD2 U:HIS765 4.2 29.6 1.0
N U:TYR677 4.3 29.2 1.0
N U:HIS718 4.6 31.0 1.0
CB U:HIS718 4.7 31.0 1.0
CA U:HIS718 4.8 31.0 1.0
C U:CYS678 4.8 38.0 1.0
CA U:HIS765 4.8 29.6 1.0
CG U:TYR677 4.9 29.2 1.0
CA U:CYS675 4.9 34.3 1.0

Reference:

X.Zhang, X.Zhan, C.Yan, W.Zhang, D.Liu, J.Lei, Y.Shi. Structures of the Human Spliceosomes Before and After Release of the Ligated Exon. Cell Res. V. 29 274 2019.
ISSN: ISSN 1748-7838
PubMed: 30728453
DOI: 10.1038/S41422-019-0143-X
Page generated: Mon Oct 28 23:43:53 2024

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