Zinc in PDB 3jap: Structure of A Partial Yeast 48S Preinitiation Complex in Closed Conformation

The structure of Structure of A Partial Yeast 48S Preinitiation Complex in Closed Conformation also contains other interesting chemical elements:

Magnesium

(Mg)

81 atoms

The binding sites of Zinc atom in the Structure of A Partial Yeast 48S Preinitiation Complex in Closed Conformation (pdb code 3jap). 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 Partial Yeast 48S Preinitiation Complex in Closed Conformation, PDB code: 3jap:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure of A Partial Yeast 48S Preinitiation Complex in Closed Conformation


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 Partial Yeast 48S Preinitiation Complex in Closed Conformation within 5.0Å range: probe atom residue distance (Å) B Occ a:Zn500 b:50.0 occ:1.00 SG a:CYS23 1.9 50.0 1.0 SG a:CYS77 2.7 50.0 1.0 SG a:CYS26 2.9 50.0 1.0 CB a:CYS77 3.2 50.0 1.0 SG a:CYS74 3.2 50.0 1.0 CB a:CYS23 3.3 50.0 1.0 N a:CYS74 3.3 50.0 1.0 N a:CYS26 3.4 50.0 1.0 CB a:CYS26 3.6 50.0 1.0 CB a:CYS74 3.8 50.0 1.0 CB a:ASN25 4.0 50.0 1.0 CA a:CYS26 4.1 50.0 1.0 CA a:TYR73 4.1 50.0 1.0 CA a:CYS74 4.1 50.0 1.0 C a:TYR73 4.2 50.0 1.0 N a:ASN25 4.3 50.0 1.0 C a:ASN25 4.4 50.0 1.0 CA a:ASN25 4.5 50.0 1.0 O a:CYS74 4.5 50.0 1.0 CB a:TYR73 4.6 50.0 1.0 CA a:CYS23 4.6 50.0 1.0 N a:SER27 4.6 50.0 1.0 CD1 a:TYR73 4.6 50.0 1.0 CA a:CYS77 4.7 50.0 1.0 C a:CYS26 4.7 50.0 1.0 O a:HIS72 4.8 50.0 1.0 C a:CYS74 4.8 50.0 1.0 CB a:ARG28 5.0 50.0 1.0 N a:CYS77 5.0 50.0 1.0

Zinc binding site 2 out of 4 in the Structure of A Partial Yeast 48S Preinitiation Complex in Closed Conformation


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 Partial Yeast 48S Preinitiation Complex in Closed Conformation within 5.0Å range: probe atom residue distance (Å) B Occ b:Zn101 b:50.0 occ:1.00 SG b:CYS59 2.2 50.0 1.0 O b:CYS59 2.6 50.0 1.0 CB b:CYS56 3.3 50.0 1.0 CG2 b:THR61 3.4 50.0 1.0 CB b:CYS59 3.4 50.0 1.0 SG b:CYS56 3.4 50.0 1.0 C b:CYS59 3.4 50.0 1.0 N b:CYS59 3.6 50.0 1.0 OG1 b:THR61 3.6 50.0 1.0 CA b:CYS59 3.6 50.0 1.0 SG b:CYS37 3.8 50.0 1.0 OG b:SER58 3.8 50.0 1.0 SG b:CYS40 4.0 50.0 1.0 CB b:THR61 4.1 50.0 1.0 CB b:CYS37 4.5 50.0 1.0 CA b:CYS56 4.6 50.0 1.0 N b:SER60 4.7 50.0 1.0 N b:THR61 4.7 50.0 1.0 C b:SER58 4.7 50.0 1.0 O b:CYS56 4.8 50.0 1.0 C b:CYS56 4.8 50.0 1.0

Zinc binding site 3 out of 4 in the Structure of A Partial Yeast 48S Preinitiation Complex in Closed Conformation


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 Partial Yeast 48S Preinitiation Complex in Closed Conformation within 5.0Å range: probe atom residue distance (Å) B Occ f:Zn501 b:50.0 occ:1.00 SG f:CYS121 2.0 50.0 1.0 SG f:CYS139 2.0 50.0 1.0 SG f:CYS124 2.6 50.0 1.0 CB f:CYS121 3.3 50.0 1.0 CB f:CYS124 3.3 50.0 1.0 CB f:CYS139 3.6 50.0 1.0 CG2 f:ILE128 4.0 50.0 1.0 N f:CYS124 4.2 50.0 1.0 CD1 f:ILE128 4.3 50.0 1.0 CA f:CYS124 4.4 50.0 1.0 CA f:CYS139 4.5 50.0 1.0 CB f:ILE128 4.6 50.0 1.0 CA f:CYS121 4.6 50.0 1.0 N f:CYS142 4.8 50.0 1.0 CB f:CYS142 4.8 50.0 1.0 N f:GLY140 4.9 50.0 1.0 CG1 f:ILE128 5.0 50.0 1.0

Zinc binding site 4 out of 4 in the Structure of A Partial Yeast 48S Preinitiation Complex in Closed Conformation


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 Partial Yeast 48S Preinitiation Complex in Closed Conformation within 5.0Å range: probe atom residue distance (Å) B Occ l:Zn301 b:50.0 occ:1.00 SG l:CYS236 1.6 50.0 1.0 SG l:CYS262 2.6 50.0 1.0 OG l:SER264 2.6 50.0 1.0 CB l:SER264 3.2 50.0 1.0 OG1 l:THR238 3.2 50.0 1.0 CB l:CYS259 3.3 50.0 1.0 CB l:CYS236 3.4 50.0 1.0 N l:SER264 3.9 50.0 1.0 SG l:CYS259 3.9 50.0 1.0 CA l:SER264 4.2 50.0 1.0 CA l:CYS236 4.4 50.0 1.0 CB l:CYS262 4.4 50.0 1.0 CB l:THR238 4.5 50.0 1.0 CA l:CYS259 4.6 50.0 1.0 N l:GLY263 4.6 50.0 1.0 CG2 l:THR238 4.7 50.0 1.0 O l:CYS239 4.7 50.0 1.0 N l:CYS259 4.7 50.0 1.0 C l:CYS236 5.0 50.0 1.0 N l:THR238 5.0 50.0 1.0 C l:GLY263 5.0 50.0 1.0

J.L.Llacer, T.Hussain, L.Marler, C.E.Aitken, A.Thakur, J.R.Lorsch, A.G.Hinnebusch, V.Ramakrishnan. Conformational Differences Between Open and Closed States of the Eukaryotic Translation Initiation Complex. Mol.Cell V. 59 399 2015.
ISSN: ISSN 1097-2765
PubMed: 26212456
DOI: 10.1016/J.MOLCEL.2015.06.033