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Zinc in PDB 6icz: Cryo-Em Structure of A Human Post-Catalytic Spliceosome (P Complex) at 3.0 Angstrom

Enzymatic activity of Cryo-Em Structure of A Human Post-Catalytic Spliceosome (P Complex) at 3.0 Angstrom

All present enzymatic activity of Cryo-Em Structure of A Human Post-Catalytic Spliceosome (P Complex) at 3.0 Angstrom:
2.3.2.27; 3.6.4.13; 5.2.1.8;

Other elements in 6icz:

The structure of Cryo-Em Structure of A Human Post-Catalytic Spliceosome (P Complex) at 3.0 Angstrom also contains other interesting chemical elements:

Magnesium (Mg) 9 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Cryo-Em Structure of A Human Post-Catalytic Spliceosome (P Complex) at 3.0 Angstrom (pdb code 6icz). 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 Post-Catalytic Spliceosome (P Complex) at 3.0 Angstrom, PDB code: 6icz:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 6icz

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Zinc binding site 1 out of 7 in the Cryo-Em Structure of A Human Post-Catalytic Spliceosome (P Complex) at 3.0 Angstrom


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 Post-Catalytic Spliceosome (P Complex) at 3.0 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn201

b:24.5
occ:1.00
 SG N:CYS117 2.3 15.0 1.0
SG N:CYS134 2.3 15.3 1.0
SG N:CYS105 2.3 9.0 1.0
SG N:CYS119 2.3 14.4 1.0
CB N:CYS119 2.8 14.4 1.0
CB N:CYS105 2.9 9.0 1.0
CB N:CYS134 3.4 15.3 1.0
CB N:CYS117 3.6 15.0 1.0
ZN N:ZN202 3.9 19.8 1.0
CA N:CYS105 4.0 9.0 1.0
CA N:CYS119 4.0 14.4 1.0
ZN N:ZN203 4.1 29.8 1.0
N N:CYS119 4.2 14.4 1.0
SG N:CYS101 4.4 11.5 1.0
CB N:CYS139 4.4 18.0 1.0
CB N:CYS137 4.5 14.7 1.0
O N:CYS105 4.5 9.0 1.0
C N:CYS119 4.7 14.4 1.0
N N:ARG120 4.8 12.0 1.0
CA N:CYS134 4.8 15.3 1.0
C N:CYS105 4.8 9.0 1.0
CA N:CYS117 4.8 15.0 1.0
CD2 N:HIS136 4.9 11.0 1.0
CB N:HIS136 5.0 11.0 1.0

Zinc binding site 2 out of 7 in 6icz

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Zinc binding site 2 out of 7 in the Cryo-Em Structure of A Human Post-Catalytic Spliceosome (P Complex) at 3.0 Angstrom


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 Post-Catalytic Spliceosome (P Complex) at 3.0 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn202

b:19.8
occ:1.00
 CB N:CYS137 2.1 14.7 1.0
SG N:CYS101 2.3 11.5 1.0
SG N:CYS102 2.3 9.3 1.0
SG N:CYS137 2.3 14.7 1.0
SG N:CYS105 2.3 9.0 1.0
CB N:CYS102 2.9 9.3 1.0
CB N:CYS101 3.3 11.5 1.0
CB N:CYS105 3.4 9.0 1.0
N N:CYS102 3.5 9.3 1.0
CA N:CYS137 3.6 14.7 1.0
CA N:CYS102 3.8 9.3 1.0
C N:CYS101 3.9 11.5 1.0
ZN N:ZN201 3.9 24.5 1.0
ZN N:ZN203 3.9 29.8 1.0
N N:CYS137 4.2 14.7 1.0
CA N:CYS101 4.2 11.5 1.0
CB N:CYS139 4.3 18.0 1.0
SG N:CYS119 4.4 14.4 1.0
O N:CYS101 4.5 11.5 1.0
C N:CYS137 4.5 14.7 1.0
N N:CYS105 4.6 9.0 1.0
CA N:CYS105 4.6 9.0 1.0
N N:CYS101 4.9 11.5 1.0
C N:CYS102 4.9 9.3 1.0
CB N:HIS136 4.9 11.0 1.0

Zinc binding site 3 out of 7 in 6icz

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Zinc binding site 3 out of 7 in the Cryo-Em Structure of A Human Post-Catalytic Spliceosome (P Complex) at 3.0 Angstrom


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 Post-Catalytic Spliceosome (P Complex) at 3.0 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn203

b:29.8
occ:1.00
 SG N:CYS119 2.3 14.4 1.0
SG N:CYS142 2.3 18.3 1.0
SG N:CYS139 2.3 18.0 1.0
SG N:CYS101 2.3 11.5 1.0
CB N:CYS139 2.8 18.0 1.0
CB N:CYS101 2.8 11.5 1.0
CB N:CYS142 3.7 18.3 1.0
N N:CYS101 3.7 11.5 1.0
CB N:CYS119 3.9 14.4 1.0
CA N:CYS101 3.9 11.5 1.0
ZN N:ZN202 3.9 19.8 1.0
N N:CYS142 4.0 18.3 1.0
ZN N:ZN201 4.1 24.5 1.0
CA N:CYS142 4.2 18.3 1.0
CA N:CYS139 4.3 18.0 1.0
CB N:CYS105 4.5 9.0 1.0
SG N:CYS105 4.5 9.0 1.0
SG N:CYS137 4.6 14.7 1.0
C N:CYS119 4.8 14.4 1.0
O N:CYS119 4.8 14.4 1.0
C N:LEU100 4.9 9.8 1.0
C N:CYS101 4.9 11.5 1.0
N N:CYS102 4.9 9.3 1.0
CA N:CYS119 4.9 14.4 1.0
C N:CYS139 5.0 18.0 1.0
C N:GLY141 5.0 22.4 1.0
O N:ASN99 5.0 20.9 1.0

Zinc binding site 4 out of 7 in 6icz

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Zinc binding site 4 out of 7 in the Cryo-Em Structure of A Human Post-Catalytic Spliceosome (P Complex) at 3.0 Angstrom


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 Post-Catalytic Spliceosome (P Complex) at 3.0 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Zn501

b:56.6
occ:1.00
 CB O:CYS84 2.5 28.7 1.0
SG O:CYS27 2.5 23.8 1.0
SG O:CYS81 2.5 22.9 1.0
SG O:CYS24 2.5 27.6 1.0
SG O:CYS84 2.6 28.7 1.0
CB O:CYS81 3.0 22.9 1.0
N O:CYS84 3.1 28.7 1.0
CA O:CYS84 3.3 28.7 1.0
OG1 O:THR83 3.4 22.1 1.0
CB O:CYS24 3.4 27.6 1.0
CB O:CYS27 4.0 23.8 1.0
N O:CYS24 4.2 27.6 1.0
C O:THR83 4.3 22.1 1.0
CA O:CYS24 4.4 27.6 1.0
CA O:CYS81 4.4 22.9 1.0
C O:CYS84 4.5 28.7 1.0
N O:THR83 4.6 22.1 1.0
CB O:THR83 4.6 22.1 1.0
NZ O:LYS66 4.6 18.2 1.0
N O:LEU85 4.7 21.7 1.0
CA O:THR83 4.8 22.1 1.0
OG1 O:THR26 4.8 26.8 1.0
N O:CYS27 4.9 23.8 1.0
C O:CYS81 4.9 22.9 1.0
CA O:CYS27 5.0 23.8 1.0

Zinc binding site 5 out of 7 in 6icz

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Zinc binding site 5 out of 7 in the Cryo-Em Structure of A Human Post-Catalytic Spliceosome (P Complex) at 3.0 Angstrom


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 Post-Catalytic Spliceosome (P Complex) at 3.0 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Zn502

b:59.6
occ:1.00
 SG O:CYS74 2.2 21.7 1.0
SG O:CYS71 2.4 14.0 1.0
SG O:CYS45 2.5 17.4 1.0
SG O:CYS48 2.6 17.8 1.0
CB O:CYS74 3.3 21.7 1.0
N O:CYS48 3.4 17.8 1.0
CB O:CYS48 3.5 17.8 1.0
CB O:CYS45 3.5 17.4 1.0
CB O:CYS71 3.6 14.0 1.0
N O:CYS71 3.8 14.0 1.0
CA O:CYS48 4.0 17.8 1.0
CB O:ILE47 4.1 18.1 1.0
CA O:CYS71 4.3 14.0 1.0
CA O:CYS74 4.4 21.7 1.0
C O:ILE47 4.4 18.1 1.0
N O:CYS74 4.5 21.7 1.0
N O:ILE47 4.6 18.1 1.0
CA O:ILE47 4.6 18.1 1.0
C O:CYS48 4.7 17.8 1.0
CG2 O:ILE47 4.8 18.1 1.0
N O:ALA49 4.9 16.5 1.0
O O:CYS71 4.9 14.0 1.0
C O:VAL70 4.9 17.0 1.0
C O:CYS71 4.9 14.0 1.0
CA O:CYS45 4.9 17.4 1.0

Zinc binding site 6 out of 7 in 6icz

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Zinc binding site 6 out of 7 in the Cryo-Em Structure of A Human Post-Catalytic Spliceosome (P Complex) at 3.0 Angstrom


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 Post-Catalytic Spliceosome (P Complex) at 3.0 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Zn503

b:53.5
occ:1.00
 NE2 O:HIS183 2.3 41.3 1.0
SG O:CYS165 2.4 31.9 1.0
SG O:CYS179 2.4 39.8 1.0
SG O:CYS173 2.4 33.0 1.0
CB O:CYS179 3.0 39.8 1.0
CD2 O:HIS183 3.2 41.3 1.0
CB O:CYS165 3.2 31.9 1.0
CE1 O:HIS183 3.3 41.3 1.0
CB O:CYS173 3.8 33.0 1.0
CG O:HIS183 4.3 41.3 1.0
ND1 O:HIS183 4.4 41.3 1.0
CB O:TRP168 4.4 40.1 1.0
CA O:CYS179 4.5 39.8 1.0
O O:TYR181 4.6 37.6 1.0
N6 F:A28 4.6 33.1 1.0
CA O:CYS165 4.6 31.9 1.0
N O:TRP168 4.9 40.1 1.0
O O:GLY176 4.9 42.5 1.0
CB O:ARG175 4.9 35.4 1.0

Zinc binding site 7 out of 7 in 6icz

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Zinc binding site 7 out of 7 in the Cryo-Em Structure of A Human Post-Catalytic Spliceosome (P Complex) at 3.0 Angstrom


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 Post-Catalytic Spliceosome (P Complex) at 3.0 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Zn601

b:63.6
occ:1.00
 NE2 Z:HIS128 2.2 32.3 1.0
SG Z:CYS120 2.4 43.0 1.0
SG Z:CYS133 2.4 22.8 1.0
SG Z:CYS123 2.5 37.7 1.0
CD2 Z:HIS128 2.7 32.3 1.0
CB Z:CYS133 3.2 22.8 1.0
CE1 Z:HIS128 3.4 32.3 1.0
N Z:CYS123 3.5 37.7 1.0
CB Z:CYS123 3.7 37.7 1.0
CB Z:CYS120 3.8 43.0 1.0
CB Z:ASN122 3.9 31.3 1.0
CG Z:HIS128 4.0 32.3 1.0
CA Z:CYS133 4.0 22.8 1.0
CA Z:CYS123 4.1 37.7 1.0
O Z:LYS129 4.2 30.5 1.0
O Z:CYS123 4.3 37.7 1.0
ND1 Z:HIS128 4.3 32.3 1.0
C Z:ASN122 4.5 31.3 1.0
C Z:CYS123 4.6 37.7 1.0
CA Z:ASN122 4.7 31.3 1.0
N Z:PHE134 4.7 17.7 1.0
N Z:ASN122 4.8 31.3 1.0
CG Z:ASN122 4.8 31.3 1.0
O Z:HIS128 4.9 32.3 1.0
C Z:LYS129 4.9 30.5 1.0
C Z:CYS133 4.9 22.8 1.0
CA Z:LYS130 5.0 28.8 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 23:42:15 2024

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