Atomistry » Zinc » PDB 5yhx-5ynz » 5ylz
Atomistry »
  Zinc »
    PDB 5yhx-5ynz »
      5ylz »

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

Go back to Zinc Binding Sites List in 5ylz
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

Go back to Zinc Binding Sites List in 5ylz
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

Go back to Zinc Binding Sites List in 5ylz
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

Go back to Zinc Binding Sites List in 5ylz
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

Go back to Zinc Binding Sites List in 5ylz
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

Go back to Zinc Binding Sites List in 5ylz
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

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy