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Zinc in PDB 9dtr: Structure of the Yeast Post-Catalytic P Complex Spliceosome at 2.3 Angstrom Resolution

Enzymatic activity of Structure of the Yeast Post-Catalytic P Complex Spliceosome at 2.3 Angstrom Resolution

All present enzymatic activity of Structure of the Yeast Post-Catalytic P Complex Spliceosome at 2.3 Angstrom Resolution:
2.3.2.27; 3.6.4.13;

Other elements in 9dtr:

The structure of Structure of the Yeast Post-Catalytic P Complex Spliceosome at 2.3 Angstrom Resolution also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Potassium (K) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of the Yeast Post-Catalytic P Complex Spliceosome at 2.3 Angstrom Resolution (pdb code 9dtr). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Structure of the Yeast Post-Catalytic P Complex Spliceosome at 2.3 Angstrom Resolution, PDB code: 9dtr:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 9dtr

Go back to Zinc Binding Sites List in 9dtr
Zinc binding site 1 out of 7 in the Structure of the Yeast Post-Catalytic P Complex Spliceosome at 2.3 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the Yeast Post-Catalytic P Complex Spliceosome at 2.3 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn1000

b:29.9
occ:1.00
 SG L:CYS104 2.3 28.7 1.0
SG L:CYS148 2.3 41.4 1.0
SG L:CYS108 2.3 37.2 1.0
SG L:CYS105 2.3 41.0 1.0
CB L:CYS108 3.3 35.9 1.0
CB L:CYS104 3.5 33.8 1.0
CB L:CYS105 3.6 36.6 1.0
CB L:CYS148 3.7 47.7 1.0
N L:CYS105 3.7 27.0 1.0
ZN L:ZN1002 3.8 30.1 1.0
CA L:CYS105 4.1 28.4 1.0
ZN L:ZN1001 4.1 27.9 1.0
C L:CYS104 4.2 28.4 1.0
N L:CYS108 4.3 38.2 1.0
O L:CYS105 4.3 36.5 1.0
CA L:CYS108 4.4 35.6 1.0
SG L:CYS145 4.4 33.0 1.0
CB L:CYS150 4.4 33.0 1.0
CA L:CYS104 4.4 29.6 1.0
C L:CYS105 4.5 27.2 1.0
N L:CYS148 4.6 36.5 1.0
SG L:CYS122 4.6 33.2 1.0
CA L:CYS148 4.7 35.7 1.0
O L:CYS104 4.9 39.7 1.0
CB L:HIS147 4.9 45.8 1.0

Zinc binding site 2 out of 7 in 9dtr

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Zinc binding site 2 out of 7 in the Structure of the Yeast Post-Catalytic P Complex Spliceosome at 2.3 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the Yeast Post-Catalytic P Complex Spliceosome at 2.3 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn1001

b:27.9
occ:1.00
 SG L:CYS150 2.3 32.6 1.0
SG L:CYS122 2.3 33.2 1.0
SG L:CYS104 2.3 28.7 1.0
SG L:CYS153 2.3 30.5 1.0
CB L:CYS104 3.1 33.8 1.0
CB L:CYS153 3.2 33.4 1.0
CB L:CYS150 3.2 33.0 1.0
CB L:CYS122 3.4 37.7 1.0
O L:CYS122 4.0 34.0 1.0
ZN L:ZN1002 4.0 30.1 1.0
N L:CYS153 4.0 34.3 1.0
N L:CYS104 4.0 33.5 1.0
ZN L:ZN1000 4.1 29.9 1.0
CA L:CYS104 4.2 29.6 1.0
CA L:CYS153 4.2 31.7 1.0
C L:CYS122 4.2 29.1 1.0
CA L:CYS122 4.5 30.9 1.0
SG L:CYS108 4.5 37.2 1.0
CB L:CYS108 4.6 35.9 1.0
CA L:CYS150 4.7 33.4 1.0
C L:GLY152 4.7 34.1 1.0
CD L:ARG123 4.7 39.9 1.0
N L:ARG123 4.9 30.8 1.0
SG L:CYS148 4.9 41.4 1.0

Zinc binding site 3 out of 7 in 9dtr

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Zinc binding site 3 out of 7 in the Structure of the Yeast Post-Catalytic P Complex Spliceosome at 2.3 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of the Yeast Post-Catalytic P Complex Spliceosome at 2.3 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn1002

b:30.1
occ:1.00
 SG L:CYS122 2.3 33.2 1.0
SG L:CYS108 2.3 37.2 1.0
SG L:CYS120 2.3 35.1 1.0
SG L:CYS145 2.3 33.0 1.0
CB L:CYS145 3.1 31.9 1.0
CB L:CYS122 3.2 37.7 1.0
CB L:CYS120 3.2 34.1 1.0
CB L:CYS108 3.4 35.9 1.0
ZN L:ZN1000 3.8 29.9 1.0
ZN L:ZN1001 4.0 27.9 1.0
N L:CYS122 4.3 30.4 1.0
SG L:CYS104 4.3 28.7 1.0
CA L:CYS122 4.3 30.9 1.0
CB L:CYS150 4.3 33.0 1.0
SG L:CYS148 4.5 41.4 1.0
CA L:CYS108 4.5 35.6 1.0
CA L:CYS120 4.6 28.3 1.0
CA L:CYS145 4.6 27.3 1.0
C L:CYS120 4.9 29.7 1.0
SG L:CYS150 4.9 32.6 1.0
O L:CYS148 5.0 60.9 1.0

Zinc binding site 4 out of 7 in 9dtr

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Zinc binding site 4 out of 7 in the Structure of the Yeast Post-Catalytic P Complex Spliceosome at 2.3 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of the Yeast Post-Catalytic P Complex Spliceosome at 2.3 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn1000

b:34.7
occ:1.00
 NE2 M:HIS91 2.0 39.0 1.0
SG M:CYS73 2.3 42.9 1.0
SG M:CYS81 2.3 36.1 1.0
SG M:CYS87 2.3 48.7 1.0
CE1 M:HIS91 2.8 44.8 1.0
CD2 M:HIS91 3.1 41.5 1.0
CB M:CYS73 3.1 35.2 1.0
CB M:CYS87 3.3 47.8 1.0
CB M:CYS81 3.4 39.0 1.0
ND1 M:HIS91 4.0 45.1 1.0
CG M:HIS91 4.2 41.5 1.0
N6 6:A35 4.4 48.7 1.0
CB M:PHE76 4.5 43.7 1.0
N M:PHE76 4.5 33.9 1.0
CA M:CYS73 4.5 30.7 1.0
CA M:CYS87 4.6 44.4 1.0
CA M:CYS81 4.7 39.1 1.0
O M:TYR89 4.7 71.7 1.0
CB M:TYR89 4.9 51.4 1.0
CA M:PHE76 5.0 36.9 1.0
CB M:LEU83 5.0 61.5 1.0

Zinc binding site 5 out of 7 in 9dtr

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Zinc binding site 5 out of 7 in the Structure of the Yeast Post-Catalytic P Complex Spliceosome at 2.3 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of the Yeast Post-Catalytic P Complex Spliceosome at 2.3 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn401

b:34.4
occ:1.00
 SG N:CYS34 2.3 35.0 1.0
SG N:CYS64 2.3 47.9 1.0
SG N:CYS37 2.3 38.5 1.0
SG N:CYS61 2.3 39.0 1.0
CB N:CYS34 3.0 33.2 1.0
CB N:CYS37 3.2 37.3 1.0
CB N:CYS64 3.4 40.4 1.0
CB N:CYS61 3.6 38.5 1.0
N N:CYS37 3.7 31.9 1.0
N N:CYS61 4.0 32.0 1.0
CA N:CYS37 4.1 32.3 1.0
N N:CYS64 4.2 33.3 1.0
CA N:CYS61 4.3 31.4 1.0
CA N:CYS64 4.4 35.3 1.0
CA N:CYS34 4.5 31.6 1.0
CB N:SER114 4.5 33.8 1.0
NH1 N:ARG63 4.6 152.5 1.0
CB N:ILE36 4.7 34.3 1.0
C N:ILE36 4.8 34.2 1.0
C N:CYS37 4.9 31.8 1.0
O N:CYS61 4.9 27.4 1.0
C N:CYS61 4.9 28.3 1.0
OG N:SER114 5.0 42.6 1.0

Zinc binding site 6 out of 7 in 9dtr

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Zinc binding site 6 out of 7 in the Structure of the Yeast Post-Catalytic P Complex Spliceosome at 2.3 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of the Yeast Post-Catalytic P Complex Spliceosome at 2.3 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn402

b:58.8
occ:1.00
 SG N:CYS16 2.3 91.8 1.0
SG N:CYS71 2.3 44.3 1.0
SG N:CYS13 2.3 46.5 1.0
SG N:CYS74 2.3 45.9 1.0
CB N:CYS71 3.0 41.5 1.0
CB N:CYS74 3.3 47.1 1.0
CB N:CYS16 3.5 86.4 1.0
CB N:CYS13 3.7 46.6 1.0
N N:CYS74 3.8 46.3 1.0
N N:CYS13 4.1 56.8 1.0
CA N:CYS74 4.2 42.5 1.0
CB N:CYS73 4.4 58.7 1.0
NE2 N:HIS81 4.4 79.1 1.0
C N:CYS73 4.5 46.1 1.0
CA N:CYS71 4.5 39.0 1.0
CA N:CYS13 4.5 51.4 1.0
N N:CYS16 4.5 70.1 1.0
CA N:CYS16 4.6 73.2 1.0
N N:CYS73 4.8 43.7 1.0
CA N:CYS73 4.8 43.5 1.0
O N:CYS13 4.9 89.0 1.0
C N:CYS74 4.9 42.7 1.0
C N:CYS71 5.0 41.5 1.0

Zinc binding site 7 out of 7 in 9dtr

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Zinc binding site 7 out of 7 in the Structure of the Yeast Post-Catalytic P Complex Spliceosome at 2.3 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of the Yeast Post-Catalytic P Complex Spliceosome at 2.3 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
c:Zn400

b:96.8
occ:1.00
 NE2 c:HIS130 2.0 91.0 1.0
SG c:CYS125 2.3 99.2 1.0
SG c:CYS135 2.3 72.3 1.0
SG c:CYS122 2.3 109.7 1.0
CD2 c:HIS130 3.0 82.3 1.0
CE1 c:HIS130 3.0 85.8 1.0
CB c:CYS135 3.1 71.2 1.0
CB c:CYS122 3.2 136.4 1.0
CB c:CYS125 3.4 111.9 1.0
N c:CYS125 3.6 89.5 1.0
CA c:CYS135 3.8 63.6 1.0
CA c:CYS125 4.1 106.2 1.0
ND1 c:HIS130 4.1 78.9 1.0
CG c:HIS130 4.1 77.9 1.0
CB c:ASN124 4.3 91.5 1.0
C c:ASN124 4.6 81.6 1.0
OD1 c:ASN124 4.6 66.9 1.0
CA c:CYS122 4.6 133.5 1.0
N c:CYS135 4.7 58.2 1.0
C c:CYS135 4.8 64.8 1.0
C c:CYS125 4.8 116.0 1.0
CA c:ASN124 4.8 84.7 1.0
O c:GLU127 4.8 128.5 1.0
N c:ASN124 4.8 104.7 1.0
N c:MET136 4.8 57.8 1.0
CG c:ASN124 5.0 83.5 1.0

Reference:

K.A.Senn, K.A.Lipinski, N.J.Zeps, A.F.Griffin, M.E.Wilkinson, A.A.Hoskins. Control of 3' Splice Site Selection By the Yeast Splicing Factor FYV6. Elife 2024.
ISSN: ESSN 2050-084X
PubMed: 38746449
DOI: 10.1038/S41422-019-0143-X
Page generated: Sun Feb 9 01:05:10 2025

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