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Zinc in PDB 5ylz: Cryo-Em Structure of the Post-Catalytic Spliceosome From Saccharomyces Cerevisiae at 3.6 Angstrom

Enzymatic activity of Cryo-Em Structure of the Post-Catalytic Spliceosome From Saccharomyces Cerevisiae at 3.6 Angstrom

All present enzymatic activity of Cryo-Em Structure of the Post-Catalytic Spliceosome From Saccharomyces Cerevisiae at 3.6 Angstrom:
2.3.2.27; 3.6.4.13;

Other elements in 5ylz:

The structure of Cryo-Em Structure of the Post-Catalytic Spliceosome From Saccharomyces Cerevisiae at 3.6 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 Post-Catalytic Spliceosome From Saccharomyces Cerevisiae at 3.6 Angstrom (pdb code 5ylz). 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 Post-Catalytic Spliceosome From Saccharomyces Cerevisiae at 3.6 Angstrom, PDB code: 5ylz:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5ylz

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Zinc binding site 1 out of 6 in the Cryo-Em Structure of the Post-Catalytic Spliceosome From Saccharomyces Cerevisiae at 3.6 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 Post-Catalytic Spliceosome From Saccharomyces Cerevisiae at 3.6 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn1000

b:82.3
occ:1.00
 SG L:CYS108 2.1 79.6 1.0
SG L:CYS148 2.3 72.1 1.0
SG L:CYS105 2.4 86.2 1.0
CB L:CYS104 2.4 67.1 1.0
SG L:CYS104 2.5 76.5 1.0
CB L:CYS105 3.1 68.5 1.0
CB L:CYS148 3.3 71.2 1.0
CB L:CYS108 3.5 88.5 1.0
ZN L:ZN1002 3.6 73.8 1.0
CA L:CYS104 3.8 63.2 1.0
N L:CYS105 3.8 75.2 1.0
C L:CYS104 4.0 70.5 1.0
ZN L:ZN1001 4.0 67.8 1.0
CA L:CYS105 4.1 68.7 1.0
SG L:CYS122 4.2 75.3 1.0
SG L:CYS145 4.6 49.4 1.0
N L:CYS108 4.6 72.8 1.0
CA L:CYS108 4.7 79.4 1.0
CA L:CYS148 4.7 70.5 1.0
O L:CYS104 4.7 69.3 1.0
CB L:CYS150 4.7 0.7 1.0
N L:CYS104 4.9 58.5 1.0
C L:CYS105 4.9 64.2 1.0

Zinc binding site 2 out of 6 in 5ylz

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Zinc binding site 2 out of 6 in the Cryo-Em Structure of the Post-Catalytic Spliceosome From Saccharomyces Cerevisiae at 3.6 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 Post-Catalytic Spliceosome From Saccharomyces Cerevisiae at 3.6 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn1001

b:67.8
occ:1.00
 SG L:CYS122 2.1 75.3 1.0
SG L:CYS104 2.2 76.5 1.0
SG L:CYS153 2.3 83.5 1.0
CB L:CYS153 2.4 95.7 1.0
SG L:CYS150 2.5 0.2 1.0
CB L:CYS150 2.8 0.7 1.0
CB L:CYS104 3.1 67.1 1.0
CB L:CYS122 3.7 71.9 1.0
CA L:CYS153 3.7 91.5 1.0
O L:CYS122 3.9 68.3 1.0
N L:CYS104 4.0 58.5 1.0
ZN L:ZN1000 4.0 82.3 1.0
CA L:CYS104 4.0 63.2 1.0
ZN L:ZN1002 4.1 73.8 1.0
C L:CYS122 4.2 73.6 1.0
CA L:CYS150 4.2 96.5 1.0
N L:CYS153 4.3 93.0 1.0
CA L:CYS122 4.4 73.3 1.0
SG L:CYS108 4.5 79.6 1.0
CB L:CYS108 4.5 88.5 1.0
C L:CYS153 4.9 90.2 1.0
CD L:ARG123 4.9 74.0 1.0
N L:ARG123 4.9 80.0 1.0

Zinc binding site 3 out of 6 in 5ylz

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Zinc binding site 3 out of 6 in the Cryo-Em Structure of the Post-Catalytic Spliceosome From Saccharomyces Cerevisiae at 3.6 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 Post-Catalytic Spliceosome From Saccharomyces Cerevisiae at 3.6 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn1002

b:73.8
occ:1.00
 SG L:CYS145 2.1 49.4 1.0
SG L:CYS108 2.3 79.6 1.0
SG L:CYS120 2.4 91.7 1.0
SG L:CYS122 2.4 75.3 1.0
CB L:CYS122 2.7 71.9 1.0
CB L:CYS108 2.9 88.5 1.0
CB L:CYS120 3.3 75.1 1.0
CB L:CYS145 3.4 68.7 1.0
ZN L:ZN1000 3.6 82.3 1.0
CA L:CYS108 3.9 79.4 1.0
SG L:CYS148 4.1 72.1 1.0
ZN L:ZN1001 4.1 67.8 1.0
CD2 L:HIS147 4.2 72.5 1.0
CA L:CYS122 4.2 73.3 1.0
SG L:CYS104 4.3 76.5 1.0
CB L:CYS150 4.4 0.7 1.0
CA L:CYS120 4.7 72.8 1.0
CB L:CYS148 4.7 71.2 1.0
N L:CYS108 4.7 72.8 1.0
CA L:CYS145 4.8 70.2 1.0
CB L:HIS147 4.8 87.7 1.0
N L:CYS122 4.8 75.6 1.0
CG L:HIS147 4.9 83.1 1.0
O L:CYS108 5.0 76.0 1.0

Zinc binding site 4 out of 6 in 5ylz

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Zinc binding site 4 out of 6 in the Cryo-Em Structure of the Post-Catalytic Spliceosome From Saccharomyces Cerevisiae at 3.6 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 Post-Catalytic Spliceosome From Saccharomyces Cerevisiae at 3.6 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn400

b:0.1
occ:1.00
 SG M:CYS74 1.9 0.5 1.0
SG M:CYS13 2.2 0.6 1.0
SG M:CYS73 2.3 0.2 1.0
SG M:CYS71 2.4 0.3 1.0
CB M:CYS13 2.5 1.0 1.0
CB M:CYS74 2.9 0.7 1.0
N M:CYS74 3.2 0.6 1.0
CB M:CYS16 3.4 0.0 1.0
CB M:CYS71 3.4 0.2 1.0
CA M:CYS74 3.6 0.5 1.0
N M:CYS13 3.6 0.4 1.0
CA M:CYS13 3.7 0.2 1.0
CB M:CYS73 3.9 0.6 1.0
SG M:CYS16 4.1 0.3 1.0
C M:CYS73 4.3 0.4 1.0
CA M:CYS73 4.5 0.0 1.0
CA M:CYS16 4.5 0.7 1.0
N M:CYS73 4.6 0.4 1.0
N M:CYS16 4.7 0.6 1.0
C M:CYS13 4.7 0.7 1.0
N M:LEU17 4.7 0.7 1.0
CG2 M:ILE12 4.8 0.0 1.0
CA M:CYS71 4.8 0.1 1.0
O M:CYS71 4.9 0.9 1.0
C M:ILE12 4.9 0.6 1.0
C M:CYS71 4.9 0.6 1.0
C M:CYS16 4.9 0.0 1.0
C M:CYS74 5.0 0.5 1.0

Zinc binding site 5 out of 6 in 5ylz

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Zinc binding site 5 out of 6 in the Cryo-Em Structure of the Post-Catalytic Spliceosome From Saccharomyces Cerevisiae at 3.6 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 Post-Catalytic Spliceosome From Saccharomyces Cerevisiae at 3.6 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn401

b:0.7
occ:1.00
 SG M:CYS37 2.1 0.2 1.0
SG M:CYS64 2.2 0.2 1.0
SG M:CYS34 2.5 0.0 1.0
SG M:CYS61 2.5 1.0 1.0
CB M:CYS37 2.9 0.3 1.0
CB M:CYS61 3.1 0.3 1.0
CB M:CYS34 3.3 0.5 1.0
CB M:CYS64 3.3 0.8 1.0
N M:CYS37 3.6 0.0 1.0
CA M:CYS37 3.8 0.5 1.0
N M:CYS61 4.1 0.8 1.0
CA M:CYS61 4.2 0.7 1.0
NH1 M:ARG63 4.2 0.6 1.0
N M:CYS64 4.4 0.1 1.0
CA M:CYS64 4.4 0.2 1.0
CB M:ILE36 4.6 0.2 1.0
C M:CYS37 4.6 0.3 1.0
CA M:CYS34 4.7 0.3 1.0
N M:THR38 4.7 0.6 1.0
C M:ILE36 4.8 0.7 1.0
CZ M:ARG63 4.8 0.6 1.0
CB M:SER114 4.9 0.7 1.0
CG2 M:ILE36 4.9 0.6 1.0

Zinc binding site 6 out of 6 in 5ylz

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Zinc binding site 6 out of 6 in the Cryo-Em Structure of the Post-Catalytic Spliceosome From Saccharomyces Cerevisiae at 3.6 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 Post-Catalytic Spliceosome From Saccharomyces Cerevisiae at 3.6 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn400

b:0.1
occ:1.00
 SG N:CYS73 2.2 0.1 1.0
SG N:CYS81 2.3 1.0 1.0
NE2 N:HIS91 2.3 0.4 1.0
SG N:CYS87 2.4 0.6 1.0
CB N:CYS87 3.0 0.0 1.0
CB N:CYS73 3.1 0.1 1.0
CE1 N:HIS91 3.1 0.5 1.0
CD2 N:HIS91 3.1 0.6 1.0
CB N:CYS81 3.2 0.6 1.0
O N:TYR89 4.0 0.0 1.0
N6 D:A35 4.1 0.3 1.0
ND1 N:HIS91 4.1 0.1 1.0
CG N:HIS91 4.1 0.4 1.0
CB N:PHE76 4.3 0.2 1.0
N N:PHE76 4.4 0.7 1.0
CA N:CYS87 4.5 0.5 1.0
CA N:CYS73 4.5 0.6 1.0
CA N:CYS81 4.6 0.9 1.0
CA N:PHE76 4.8 0.6 1.0
C N:PHE75 5.0 0.5 1.0

Reference:

R.Bai, C.Yan, R.Wan, J.Lei, Y.Shi. Structure of the Post-Catalytic Spliceosome From Saccharomyces Cerevisiae Cell V. 171 1589 2017.
ISSN: ISSN 1097-4172
PubMed: 29153833
DOI: 10.1016/J.CELL.2017.10.038
Page generated: Mon Oct 28 15:59:54 2024

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