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Zinc in PDB 6id0: Cryo-Em Structure of A Human Intron Lariat Spliceosome Prior to PRP43 Loaded (ILS1 Complex) at 2.9 Angstrom Resolution

Enzymatic activity of Cryo-Em Structure of A Human Intron Lariat Spliceosome Prior to PRP43 Loaded (ILS1 Complex) at 2.9 Angstrom Resolution

All present enzymatic activity of Cryo-Em Structure of A Human Intron Lariat Spliceosome Prior to PRP43 Loaded (ILS1 Complex) at 2.9 Angstrom Resolution:
2.3.2.27; 3.6.4.13; 5.2.1.8;

Other elements in 6id0:

The structure of Cryo-Em Structure of A Human Intron Lariat Spliceosome Prior to PRP43 Loaded (ILS1 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 Prior to PRP43 Loaded (ILS1 Complex) at 2.9 Angstrom Resolution (pdb code 6id0). 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 Prior to PRP43 Loaded (ILS1 Complex) at 2.9 Angstrom Resolution, PDB code: 6id0:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 6id0

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Zinc binding site 1 out of 7 in the Cryo-Em Structure of A Human Intron Lariat Spliceosome Prior to PRP43 Loaded (ILS1 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 Prior to PRP43 Loaded (ILS1 Complex) at 2.9 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn201

b:43.4
occ:1.00
 SG N:CYS134 2.3 14.2 1.0
SG N:CYS117 2.3 17.9 1.0
SG N:CYS105 2.3 8.7 1.0
SG N:CYS119 2.3 19.8 1.0
CB N:CYS119 2.4 19.8 1.0
CB N:CYS105 2.9 8.7 1.0
CB N:CYS134 3.3 14.2 1.0
CB N:CYS117 3.5 17.9 1.0
CA N:CYS119 3.9 19.8 1.0
CA N:CYS105 3.9 8.7 1.0
ZN N:ZN202 3.9 22.2 1.0
ZN N:ZN203 4.1 29.0 1.0
N N:CYS119 4.3 19.8 1.0
CB N:CYS137 4.4 16.2 1.0
SG N:CYS101 4.5 15.1 1.0
O N:CYS105 4.6 8.7 1.0
CB N:CYS139 4.6 18.2 1.0
CA N:CYS134 4.7 14.2 1.0
C N:CYS119 4.7 19.8 1.0
CD2 N:HIS136 4.7 8.9 1.0
C N:CYS105 4.8 8.7 1.0
CA N:CYS117 4.8 17.9 1.0
N N:CYS105 4.9 8.7 1.0
N N:ARG120 5.0 11.2 1.0

Zinc binding site 2 out of 7 in 6id0

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Zinc binding site 2 out of 7 in the Cryo-Em Structure of A Human Intron Lariat Spliceosome Prior to PRP43 Loaded (ILS1 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 Prior to PRP43 Loaded (ILS1 Complex) at 2.9 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn202

b:22.2
occ:1.00
 SG N:CYS137 2.3 16.2 1.0
SG N:CYS102 2.3 11.4 1.0
SG N:CYS101 2.3 15.1 1.0
SG N:CYS105 2.3 8.7 1.0
CB N:CYS137 2.4 16.2 1.0
CB N:CYS101 2.6 15.1 1.0
CB N:CYS102 3.2 11.4 1.0
N N:CYS102 3.5 11.4 1.0
CB N:CYS105 3.6 8.7 1.0
CA N:CYS137 3.8 16.2 1.0
CA N:CYS101 3.9 15.1 1.0
ZN N:ZN201 3.9 43.4 1.0
CA N:CYS102 3.9 11.4 1.0
C N:CYS101 4.0 15.1 1.0
ZN N:ZN203 4.0 29.0 1.0
CB N:CYS139 4.3 18.2 1.0
SG N:CYS119 4.3 19.8 1.0
N N:CYS101 4.4 15.1 1.0
N N:CYS137 4.5 16.2 1.0
C N:CYS137 4.7 16.2 1.0
CA N:CYS105 4.8 8.7 1.0
N N:CYS105 4.8 8.7 1.0
O N:CYS101 4.9 15.1 1.0
C N:CYS102 4.9 11.4 1.0

Zinc binding site 3 out of 7 in 6id0

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Zinc binding site 3 out of 7 in the Cryo-Em Structure of A Human Intron Lariat Spliceosome Prior to PRP43 Loaded (ILS1 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 Prior to PRP43 Loaded (ILS1 Complex) at 2.9 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn203

b:29.0
occ:1.00
 SG N:CYS119 2.2 19.8 1.0
SG N:CYS101 2.3 15.1 1.0
SG N:CYS142 2.3 17.2 1.0
SG N:CYS139 2.3 18.2 1.0
CB N:CYS139 2.7 18.2 1.0
CB N:CYS142 3.6 17.2 1.0
N N:CYS142 3.6 17.2 1.0
CB N:CYS101 3.8 15.1 1.0
CB N:CYS119 3.8 19.8 1.0
ZN N:ZN202 4.0 22.2 1.0
CA N:CYS142 4.0 17.2 1.0
ZN N:ZN201 4.1 43.4 1.0
CA N:CYS139 4.1 18.2 1.0
N N:CYS101 4.2 15.1 1.0
O N:CYS119 4.5 19.8 1.0
CA N:CYS101 4.6 15.1 1.0
CA N:CYS119 4.6 19.8 1.0
SG N:CYS137 4.6 16.2 1.0
SG N:CYS105 4.6 8.7 1.0
C N:GLY141 4.6 16.4 1.0
C N:CYS119 4.6 19.8 1.0
C N:CYS139 4.7 18.2 1.0
N N:GLY141 4.8 16.4 1.0
CB W:PRO195 4.8 14.6 1.0
CB N:CYS105 4.9 8.7 1.0
N N:ARG140 4.9 18.7 1.0

Zinc binding site 4 out of 7 in 6id0

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Zinc binding site 4 out of 7 in the Cryo-Em Structure of A Human Intron Lariat Spliceosome Prior to PRP43 Loaded (ILS1 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 Prior to PRP43 Loaded (ILS1 Complex) at 2.9 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Zn501

b:44.7
occ:1.00
 SG O:CYS81 2.5 17.3 1.0
SG O:CYS27 2.5 23.1 1.0
SG O:CYS84 2.5 21.8 1.0
SG O:CYS24 2.5 18.9 1.0
CB O:CYS84 3.0 21.8 1.0
N O:CYS84 3.2 21.8 1.0
CB O:CYS27 3.2 23.1 1.0
CB O:CYS81 3.4 17.3 1.0
CG2 O:THR83 3.4 13.5 1.0
CA O:CYS84 3.7 21.8 1.0
CB O:CYS24 3.9 18.9 1.0
C O:THR83 4.2 13.5 1.0
N O:CYS24 4.4 18.9 1.0
N O:THR83 4.4 13.5 1.0
CA O:CYS27 4.5 23.1 1.0
N O:CYS27 4.6 23.1 1.0
CB O:THR83 4.6 13.5 1.0
CA O:THR83 4.6 13.5 1.0
C O:CYS84 4.7 21.8 1.0
CA O:CYS24 4.7 18.9 1.0
CA O:CYS81 4.8 17.3 1.0
NZ O:LYS66 4.9 14.9 1.0
CG2 O:THR26 4.9 19.4 1.0
N O:LEU85 4.9 14.6 1.0

Zinc binding site 5 out of 7 in 6id0

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Zinc binding site 5 out of 7 in the Cryo-Em Structure of A Human Intron Lariat Spliceosome Prior to PRP43 Loaded (ILS1 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 Prior to PRP43 Loaded (ILS1 Complex) at 2.9 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Zn502

b:40.9
occ:1.00
 SG O:CYS45 2.5 9.5 1.0
SG O:CYS74 2.5 12.6 1.0
SG O:CYS71 2.5 10.4 1.0
CB O:CYS71 2.8 10.4 1.0
CB O:CYS48 2.8 14.8 1.0
CB O:CYS74 3.0 12.6 1.0
N O:CYS71 3.1 10.4 1.0
CB O:CYS45 3.4 9.5 1.0
CA O:CYS71 3.6 10.4 1.0
N O:CYS48 3.8 14.8 1.0
SG O:CYS48 3.9 14.8 1.0
CA O:CYS48 4.0 14.8 1.0
N O:CYS74 4.1 12.6 1.0
CA O:CYS74 4.1 12.6 1.0
C O:VAL70 4.3 7.0 1.0
CB O:VAL70 4.5 7.0 1.0
CA O:VAL70 4.5 7.0 1.0
C O:CYS71 4.6 10.4 1.0
O O:CYS71 4.8 10.4 1.0
CA O:CYS45 4.8 9.5 1.0
CB O:ILE47 4.9 14.6 1.0

Zinc binding site 6 out of 7 in 6id0

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Zinc binding site 6 out of 7 in the Cryo-Em Structure of A Human Intron Lariat Spliceosome Prior to PRP43 Loaded (ILS1 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 Prior to PRP43 Loaded (ILS1 Complex) at 2.9 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Zn503

b:33.8
occ:1.00
 NE2 O:HIS183 2.2 30.3 1.0
SG O:CYS179 2.4 26.3 1.0
SG O:CYS173 2.5 26.8 1.0
SG O:CYS165 2.5 26.6 1.0
CB O:CYS179 2.7 26.3 1.0
CD2 O:HIS183 3.1 30.3 1.0
CB O:CYS165 3.1 26.6 1.0
CE1 O:HIS183 3.2 30.3 1.0
CB O:CYS173 3.8 26.8 1.0
O O:TYR181 4.2 20.6 1.0
CA O:CYS179 4.3 26.3 1.0
CG O:HIS183 4.3 30.3 1.0
ND1 O:HIS183 4.3 30.3 1.0
CB O:TRP168 4.6 34.4 1.0
CA O:CYS165 4.6 26.6 1.0
O O:GLY176 4.6 31.3 1.0
N6 F:A28 4.7 24.9 1.0
CB O:TYR181 4.8 20.6 1.0
C O:CYS179 4.8 26.3 1.0
C O:TYR181 4.9 20.6 1.0
O O:CYS179 4.9 26.3 1.0
CA O:CYS173 5.0 26.8 1.0

Zinc binding site 7 out of 7 in 6id0

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Zinc binding site 7 out of 7 in the Cryo-Em Structure of A Human Intron Lariat Spliceosome Prior to PRP43 Loaded (ILS1 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 Prior to PRP43 Loaded (ILS1 Complex) at 2.9 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Zn900

b:50.6
occ:1.00
 ND1 U:HIS765 2.3 33.7 1.0
NE2 U:HIS718 2.4 38.1 1.0
SG U:CYS675 2.5 39.5 1.0
SG U:CYS678 2.6 48.1 1.0
CB U:CYS678 2.7 48.1 1.0
CD2 U:HIS718 2.7 38.1 1.0
CE1 U:HIS765 2.7 33.7 1.0
C U:TYR677 3.2 39.8 1.0
N U:CYS678 3.2 48.1 1.0
CB U:CYS675 3.3 39.5 1.0
CG U:HIS765 3.3 33.7 1.0
O U:TYR677 3.3 39.8 1.0
CE1 U:HIS718 3.4 38.1 1.0
CA U:CYS678 3.5 48.1 1.0
CG U:HIS718 3.7 38.1 1.0
CB U:TYR677 3.8 39.8 1.0
NE2 U:HIS765 3.8 33.7 1.0
CA U:TYR677 3.9 39.8 1.0
CB U:HIS765 4.0 33.7 1.0
ND1 U:HIS718 4.0 38.1 1.0
CD2 U:HIS765 4.1 33.7 1.0
N U:TYR677 4.2 39.8 1.0
CA U:CYS675 4.7 39.5 1.0
N U:HIS718 4.7 38.1 1.0
C U:CYS678 4.7 48.1 1.0
CB U:HIS718 4.9 38.1 1.0
O U:CYS678 5.0 48.1 1.0
CA U:HIS718 5.0 38.1 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 23:43:54 2024

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