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

Other elements in 3jap:

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

Magnesium (Mg) 81 atoms

Zinc Binding Sites:

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 3jap

Go back to Zinc Binding Sites List in 3jap
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 3jap

Go back to Zinc Binding Sites List in 3jap
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 3jap

Go back to Zinc Binding Sites List in 3jap
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 3jap

Go back to Zinc Binding Sites List in 3jap
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

Reference:

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
Page generated: Wed Dec 16 04:27:51 2020

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