Atomistry » Zinc » PDB 5y1r-5yhg » 5y88
Atomistry »
  Zinc »
    PDB 5y1r-5yhg »
      5y88 »

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

Go back to Zinc Binding Sites List in 5y88
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

Go back to Zinc Binding Sites List in 5y88
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

Go back to Zinc Binding Sites List in 5y88
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

Go back to Zinc Binding Sites List in 5y88
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

Go back to Zinc Binding Sites List in 5y88
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy