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Zinc in PDB 8s8k: Structure of A Yeast 48S-Auc Preinitiation Complex in Swivelled Conformation (Model PY48S-Auc-Swiv-EIF1)

Enzymatic activity of Structure of A Yeast 48S-Auc Preinitiation Complex in Swivelled Conformation (Model PY48S-Auc-Swiv-EIF1)

All present enzymatic activity of Structure of A Yeast 48S-Auc Preinitiation Complex in Swivelled Conformation (Model PY48S-Auc-Swiv-EIF1):
3.6.5.3;

Other elements in 8s8k:

The structure of Structure of A Yeast 48S-Auc Preinitiation Complex in Swivelled Conformation (Model PY48S-Auc-Swiv-EIF1) also contains other interesting chemical elements:

Magnesium (Mg) 96 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of A Yeast 48S-Auc Preinitiation Complex in Swivelled Conformation (Model PY48S-Auc-Swiv-EIF1) (pdb code 8s8k). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of A Yeast 48S-Auc Preinitiation Complex in Swivelled Conformation (Model PY48S-Auc-Swiv-EIF1), PDB code: 8s8k:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 8s8k

Go back to Zinc Binding Sites List in 8s8k
Zinc binding site 1 out of 4 in the Structure of A Yeast 48S-Auc Preinitiation Complex in Swivelled Conformation (Model PY48S-Auc-Swiv-EIF1)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of A Yeast 48S-Auc Preinitiation Complex in Swivelled Conformation (Model PY48S-Auc-Swiv-EIF1) within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Zn500

b:127.4
occ:1.00
 SG a:CYS23 2.1 51.0 1.0
SG a:CYS26 2.1 51.0 1.0
SG a:CYS77 2.4 40.6 1.0
SG a:CYS74 2.5 41.2 1.0
N a:CYS26 2.6 51.0 1.0
CB a:CYS26 2.9 51.0 1.0
CB a:CYS23 3.1 51.0 1.0
CA a:CYS26 3.2 51.0 1.0
CB a:CYS77 3.3 40.6 1.0
CB a:CYS74 3.3 41.2 1.0
N a:CYS74 3.7 41.2 1.0
C a:ASN25 3.8 54.6 1.0
CB a:ASN25 3.9 54.6 1.0
C a:CYS26 4.0 51.0 1.0
CA a:CYS74 4.1 41.2 1.0
N a:SER27 4.1 47.2 1.0
N a:ASN25 4.1 54.6 1.0
CA a:ASN25 4.2 54.6 1.0
CA a:CYS23 4.5 51.0 1.0
CA a:CYS77 4.5 40.6 1.0
N a:CYS77 4.6 40.6 1.0
N a:ARG28 4.7 41.7 1.0
C a:CYS74 4.8 41.2 1.0
O a:CYS74 4.8 41.2 1.0
O a:CYS26 4.9 51.0 1.0
C a:CYS23 4.9 51.0 1.0
O a:ASN25 4.9 54.6 1.0
C a:TYR73 4.9 37.7 1.0
CB a:ARG28 4.9 41.7 1.0
N a:VAL24 5.0 50.5 1.0

Zinc binding site 2 out of 4 in 8s8k

Go back to Zinc Binding Sites List in 8s8k
Zinc binding site 2 out of 4 in the Structure of A Yeast 48S-Auc Preinitiation Complex in Swivelled Conformation (Model PY48S-Auc-Swiv-EIF1)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of A Yeast 48S-Auc Preinitiation Complex in Swivelled Conformation (Model PY48S-Auc-Swiv-EIF1) within 5.0Å range:
probe atom residue distance (Å) B Occ
b:Zn101

b:187.6
occ:1.00
 CB b:CYS56 2.0 136.2 1.0
SG b:CYS59 2.3 136.1 1.0
SG b:CYS56 2.3 136.2 1.0
O b:CYS59 3.3 136.1 1.0
CA b:CYS56 3.5 136.2 1.0
OG1 b:THR61 3.5 103.3 1.0
OG b:SER58 3.7 142.6 1.0
N b:CYS59 3.8 136.1 1.0
CB b:CYS59 3.8 136.1 1.0
SG b:CYS37 3.9 131.3 1.0
SG b:CYS40 4.0 132.1 1.0
C b:CYS59 4.1 136.1 1.0
CA b:CYS59 4.1 136.1 1.0
N b:CYS56 4.1 136.2 1.0
C b:CYS56 4.2 136.2 1.0
CB b:CYS37 4.4 131.3 1.0
O b:CYS56 4.5 136.2 1.0
CB b:THR61 4.8 103.3 1.0
C b:SER58 4.9 142.6 1.0
N b:SER58 4.9 142.6 1.0
N b:GLU57 4.9 142.7 1.0
CB b:SER58 4.9 142.6 1.0

Zinc binding site 3 out of 4 in 8s8k

Go back to Zinc Binding Sites List in 8s8k
Zinc binding site 3 out of 4 in the Structure of A Yeast 48S-Auc Preinitiation Complex in Swivelled Conformation (Model PY48S-Auc-Swiv-EIF1)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of A Yeast 48S-Auc Preinitiation Complex in Swivelled Conformation (Model PY48S-Auc-Swiv-EIF1) within 5.0Å range:
probe atom residue distance (Å) B Occ
f:Zn501

b:244.4
occ:1.00
 SG f:CYS139 2.3 189.7 1.0
SG f:CYS124 2.3 162.8 1.0
N f:CYS142 2.8 183.4 1.0
CB f:LYS141 2.9 177.3 1.0
SG f:CYS142 3.1 183.4 1.0
SG f:CYS121 3.1 164.4 1.0
CB f:CYS142 3.4 183.4 1.0
CA f:LYS141 3.5 177.3 1.0
C f:LYS141 3.5 177.3 1.0
CB f:CYS139 3.6 189.7 1.0
N f:LYS141 3.6 177.3 1.0
CA f:CYS142 3.6 183.4 1.0
CB f:CYS124 4.0 162.8 1.0
CB f:CYS121 4.1 164.4 1.0
CD2 f:PHE146 4.2 168.6 1.0
CG f:LYS141 4.3 177.3 1.0
N f:CYS124 4.4 162.8 1.0
C f:CYS142 4.6 183.4 1.0
O f:LYS141 4.7 177.3 1.0
CA f:CYS124 4.7 162.8 1.0
N f:GLY140 4.8 183.3 1.0
CE2 f:PHE146 4.8 168.6 1.0
CB f:ASN123 4.8 149.8 1.0
C f:GLY140 4.8 183.3 1.0
CA f:CYS139 4.9 189.7 1.0
CG2 f:ILE128 5.0 157.8 1.0

Zinc binding site 4 out of 4 in 8s8k

Go back to Zinc Binding Sites List in 8s8k
Zinc binding site 4 out of 4 in the Structure of A Yeast 48S-Auc Preinitiation Complex in Swivelled Conformation (Model PY48S-Auc-Swiv-EIF1)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of A Yeast 48S-Auc Preinitiation Complex in Swivelled Conformation (Model PY48S-Auc-Swiv-EIF1) within 5.0Å range:
probe atom residue distance (Å) B Occ
l:Zn301

b:269.6
occ:1.00
 SG l:CYS239 2.3 180.9 1.0
SG l:CYS236 2.3 178.3 1.0
SG l:CYS262 2.3 186.0 1.0
CB l:CYS236 3.3 178.3 1.0
CB l:CYS262 3.5 186.0 1.0
SG l:CYS259 3.6 177.1 1.0
OG l:SER264 3.7 185.0 1.0
CB l:CYS259 3.9 177.1 1.0
NH2 l:ARG266 4.0 183.1 1.0
CB l:CYS239 4.0 180.9 1.0
NH1 l:ARG266 4.1 183.1 1.0
CZ l:ARG266 4.1 183.1 1.0
CB l:SER241 4.2 172.7 1.0
CA l:CYS262 4.7 186.0 1.0
CA l:CYS236 4.7 178.3 1.0
OG l:SER241 4.7 172.7 1.0
N l:CYS262 4.8 186.0 1.0
CB l:SER264 4.9 185.0 1.0
NE l:ARG266 4.9 183.1 1.0
OG l:SER261 4.9 175.0 1.0

Reference:

L.Villamayor-Belinchon, P.Sharma, Y.Gordiyenko, J.L.Llacer, T.Hussain. Structural Basis of Auc Codon Discrimination During Translation Initiation in Yeast. Nucleic Acids Res. V. 52 11317 2024.
ISSN: ESSN 1362-4962
PubMed: 39193907
DOI: 10.1093/NAR/GKAE737
Page generated: Wed Nov 13 13:42:42 2024

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