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Zinc in PDB 5y88: Cryo-Em Structure of the Intron-Lariat Spliceosome Ready For Disassembly From S.Cerevisiae at 3.5 Angstrom

Enzymatic activity of Cryo-Em Structure of the Intron-Lariat Spliceosome Ready For Disassembly From S.Cerevisiae at 3.5 Angstrom

All present enzymatic activity of Cryo-Em Structure of the Intron-Lariat Spliceosome Ready For Disassembly From S.Cerevisiae at 3.5 Angstrom:
2.3.2.27; 3.6.4.13;

Other elements in 5y88:

The structure of Cryo-Em Structure of the Intron-Lariat Spliceosome Ready For Disassembly From S.Cerevisiae at 3.5 Angstrom also contains other interesting chemical elements:

Magnesium (Mg) 6 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Cryo-Em Structure of the Intron-Lariat Spliceosome Ready For Disassembly From S.Cerevisiae at 3.5 Angstrom (pdb code 5y88). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Cryo-Em Structure of the Intron-Lariat Spliceosome Ready For Disassembly From S.Cerevisiae at 3.5 Angstrom, PDB code: 5y88:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5y88

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Zinc binding site 1 out of 6 in the Cryo-Em Structure of the Intron-Lariat Spliceosome Ready For Disassembly From S.Cerevisiae at 3.5 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 the Intron-Lariat Spliceosome Ready For Disassembly From S.Cerevisiae at 3.5 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn1000

b:60.0
occ:1.00
 SG L:CYS108 2.2 56.4 1.0
SG L:CYS148 2.2 58.4 1.0
CB L:CYS104 2.2 55.5 1.0
SG L:CYS105 2.3 85.3 1.0
SG L:CYS104 2.3 74.3 1.0
CB L:CYS148 3.1 54.1 1.0
CB L:CYS105 3.3 60.5 1.0
CA L:CYS104 3.6 53.8 1.0
N L:CYS105 3.7 63.1 1.0
ZN L:ZN1002 3.7 51.5 1.0
CB L:CYS108 3.7 65.4 1.0
ZN L:ZN1001 3.9 46.5 1.0
C L:CYS104 3.9 60.2 1.0
CA L:CYS105 4.1 59.9 1.0
SG L:CYS122 4.3 55.9 1.0
SG L:CYS145 4.4 45.7 1.0
CA L:CYS148 4.4 55.9 1.0
CB L:CYS150 4.6 73.6 1.0
O L:CYS104 4.7 58.1 1.0
N L:CYS104 4.7 51.6 1.0
N L:CYS108 4.8 70.0 1.0
SG L:CYS153 4.8 63.1 1.0
CA L:CYS108 4.8 63.5 1.0
N L:CYS148 4.9 58.1 1.0

Zinc binding site 2 out of 6 in 5y88

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Zinc binding site 2 out of 6 in the Cryo-Em Structure of the Intron-Lariat Spliceosome Ready For Disassembly From S.Cerevisiae at 3.5 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 the Intron-Lariat Spliceosome Ready For Disassembly From S.Cerevisiae at 3.5 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn1001

b:46.5
occ:1.00
 SG L:CYS153 2.1 63.1 1.0
SG L:CYS122 2.2 55.9 1.0
SG L:CYS104 2.3 74.3 1.0
SG L:CYS150 2.3 96.8 1.0
CB L:CYS150 2.4 73.6 1.0
CB L:CYS104 3.2 55.5 1.0
CB L:CYS153 3.4 71.3 1.0
CB L:CYS122 3.7 53.4 1.0
O L:CYS122 3.7 54.6 1.0
N L:CYS153 3.9 66.9 1.0
ZN L:ZN1000 3.9 60.0 1.0
CA L:CYS150 3.9 67.0 1.0
CA L:CYS153 4.0 65.6 1.0
ZN L:ZN1002 4.0 51.5 1.0
CA L:CYS104 4.1 53.8 1.0
N L:CYS104 4.2 51.6 1.0
SG L:CYS108 4.2 56.4 1.0
C L:CYS122 4.3 50.7 1.0
CA L:CYS122 4.5 50.4 1.0
C L:CYS150 4.6 68.3 1.0
N L:CYS150 4.7 62.1 1.0
CB L:CYS108 4.9 65.4 1.0
N L:ARG151 4.9 68.2 1.0
C L:GLY152 5.0 66.6 1.0

Zinc binding site 3 out of 6 in 5y88

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Zinc binding site 3 out of 6 in the Cryo-Em Structure of the Intron-Lariat Spliceosome Ready For Disassembly From S.Cerevisiae at 3.5 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 the Intron-Lariat Spliceosome Ready For Disassembly From S.Cerevisiae at 3.5 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn1002

b:51.5
occ:1.00
 SG L:CYS145 2.1 45.7 1.0
SG L:CYS120 2.3 69.2 1.0
SG L:CYS108 2.3 56.4 1.0
SG L:CYS122 2.4 55.9 1.0
CB L:CYS122 2.8 53.4 1.0
CB L:CYS108 3.1 65.4 1.0
CB L:CYS120 3.2 51.6 1.0
CB L:CYS145 3.3 54.0 1.0
ZN L:ZN1000 3.7 60.0 1.0
SG L:CYS148 3.8 58.4 1.0
CA L:CYS108 3.9 63.5 1.0
ZN L:ZN1001 4.0 46.5 1.0
CA L:CYS122 4.3 50.4 1.0
CD2 L:HIS147 4.4 75.2 1.0
SG L:CYS104 4.5 74.3 1.0
CA L:CYS120 4.6 51.4 1.0
CA L:CYS145 4.6 56.0 1.0
N L:CYS108 4.8 70.0 1.0
CB L:CYS150 4.8 73.6 1.0
N L:CYS122 4.8 52.4 1.0
CB L:CYS148 4.9 54.1 1.0
C L:CYS108 4.9 55.8 1.0
O L:CYS108 4.9 54.9 1.0
C L:CYS122 4.9 50.7 1.0
CB L:CYS104 5.0 55.5 1.0

Zinc binding site 4 out of 6 in 5y88

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Zinc binding site 4 out of 6 in the Cryo-Em Structure of the Intron-Lariat Spliceosome Ready For Disassembly From S.Cerevisiae at 3.5 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 the Intron-Lariat Spliceosome Ready For Disassembly From S.Cerevisiae at 3.5 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn400

b:0.5
occ:1.00
 SG M:CYS74 2.2 81.3 1.0
SG M:CYS71 2.3 0.1 1.0
SG M:CYS73 2.3 0.3 1.0
SG M:CYS13 2.3 0.8 1.0
CB M:CYS13 3.0 0.0 1.0
CB M:CYS74 3.1 73.0 1.0
N M:CYS74 3.3 72.4 1.0
CB M:CYS16 3.4 0.4 1.0
N M:CYS13 3.6 94.8 1.0
CB M:CYS71 3.6 89.3 1.0
CA M:CYS74 3.8 69.2 1.0
CA M:CYS13 3.9 0.9 1.0
CB M:CYS73 3.9 95.1 1.0
C M:CYS73 4.2 72.6 1.0
N M:CYS16 4.3 0.6 1.0
CG2 M:ILE12 4.4 0.8 1.0
CA M:CYS73 4.4 79.7 1.0
CA M:CYS16 4.5 0.5 1.0
N M:CYS73 4.5 77.1 1.0
SG M:CYS16 4.5 0.6 1.0
C M:CYS13 4.6 0.8 1.0
C M:ILE12 4.7 88.3 1.0
O M:CYS13 4.7 0.2 1.0
CA M:CYS71 4.9 78.3 1.0

Zinc binding site 5 out of 6 in 5y88

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Zinc binding site 5 out of 6 in the Cryo-Em Structure of the Intron-Lariat Spliceosome Ready For Disassembly From S.Cerevisiae at 3.5 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 the Intron-Lariat Spliceosome Ready For Disassembly From S.Cerevisiae at 3.5 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn401

b:70.8
occ:1.00
 SG M:CYS64 2.1 63.6 1.0
SG M:CYS34 2.3 62.6 1.0
SG M:CYS61 2.4 94.3 1.0
SG M:CYS37 2.4 76.3 1.0
CB M:CYS61 2.9 69.4 1.0
CB M:CYS37 3.0 58.6 1.0
CB M:CYS34 3.2 56.1 1.0
CB M:CYS64 3.3 68.6 1.0
N M:CYS61 3.8 55.5 1.0
CA M:CYS61 3.9 59.0 1.0
N M:CYS37 3.9 61.8 1.0
CA M:CYS37 4.0 53.7 1.0
N M:CYS64 4.4 65.1 1.0
CA M:CYS64 4.4 65.2 1.0
CA M:CYS34 4.5 56.2 1.0
CB M:SER114 4.8 79.1 1.0
NH1 M:ARG63 4.8 0.3 1.0
C M:CYS37 4.8 46.4 1.0
N M:CYS34 4.9 56.9 1.0
N M:THR38 4.9 46.4 1.0
OG M:SER114 4.9 78.8 1.0
O M:LEU39 4.9 53.5 1.0
C M:ILE60 5.0 51.9 1.0

Zinc binding site 6 out of 6 in 5y88

Go back to Zinc Binding Sites List in 5y88
Zinc binding site 6 out of 6 in the Cryo-Em Structure of the Intron-Lariat Spliceosome Ready For Disassembly From S.Cerevisiae at 3.5 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 the Intron-Lariat Spliceosome Ready For Disassembly From S.Cerevisiae at 3.5 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn400

b:36.1
occ:1.00
 SG N:CYS73 2.3 58.5 1.0
SG N:CYS81 2.3 57.9 1.0
CE1 N:HIS91 2.3 76.0 1.0
SG N:CYS87 2.3 55.6 1.0
NE2 N:HIS91 2.3 70.8 1.0
CB N:CYS81 3.1 58.4 1.0
CB N:CYS73 3.1 54.5 1.0
CB N:CYS87 3.3 69.0 1.0
ND1 N:HIS91 3.5 69.3 1.0
CD2 N:HIS91 3.6 65.4 1.0
CG N:HIS91 4.2 63.0 1.0
CB N:PHE76 4.5 67.6 1.0
N N:PHE76 4.5 57.4 1.0
CA N:CYS81 4.6 59.6 1.0
N6 D:A35 4.6 54.2 1.0
CA N:CYS73 4.6 53.2 1.0
CA N:CYS87 4.7 68.7 1.0
O N:TYR89 4.8 93.4 1.0
CB N:PHE75 5.0 56.3 1.0
CA N:PHE76 5.0 58.2 1.0

Reference:

R.Wan, C.Yan, R.Bai, J.Lei, Y.Shi. Structure of An Intron Lariat Spliceosome From Saccharomyces Cerevisiae Cell(Cambridge,Mass.) V. 171 120 2017.
ISSN: ISSN 0092-8674
PubMed: 28919079
DOI: 10.1016/J.CELL.2017.08.029
Page generated: Mon Oct 28 15:28:21 2024

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