Zinc in PDB 5abx: Complex of C. Elegans EIF4E-3 with the 4E-Binding Protein Mextli and Cap Analog

The structure of Complex of C. Elegans EIF4E-3 with the 4E-Binding Protein Mextli and Cap Analog, PDB code: 5abx was solved by D.Peter, O.Weichenrieder, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.282 / 1.66
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	71.040, 71.040, 85.280, 90.00, 90.00, 90.00
R / Rfree (%)	17.33 / 19.38

The structure of Complex of C. Elegans EIF4E-3 with the 4E-Binding Protein Mextli and Cap Analog also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Zinc atom in the Complex of C. Elegans EIF4E-3 with the 4E-Binding Protein Mextli and Cap Analog (pdb code 5abx). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Complex of C. Elegans EIF4E-3 with the 4E-Binding Protein Mextli and Cap Analog, PDB code: 5abx:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Complex of C. Elegans EIF4E-3 with the 4E-Binding Protein Mextli and Cap Analog


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Complex of C. Elegans EIF4E-3 with the 4E-Binding Protein Mextli and Cap Analog within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1217 b:25.8 occ:0.71 ND1 A:HIS126 1.9 25.1 1.0 OE2 A:GLU130 2.1 30.9 1.0 CL A:CL1219 2.3 26.9 0.7 CE1 A:HIS126 2.6 21.8 1.0 HE1 A:HIS126 2.6 26.2 1.0 HG2 A:GLU130 2.8 27.3 1.0 CD A:GLU130 3.0 25.2 1.0 HH21 B:ARG475 3.0 40.6 1.0 CG A:HIS126 3.1 23.8 1.0 HG3 A:GLU130 3.1 27.3 1.0 CG A:GLU130 3.2 22.8 1.0 HB2 A:HIS126 3.5 27.1 1.0 HA A:HIS126 3.6 25.7 1.0 CB A:HIS126 3.7 22.6 1.0 NH2 B:ARG475 3.8 33.8 1.0 NE2 A:HIS126 3.8 27.9 1.0 HH22 B:ARG475 4.0 40.6 1.0 CD2 A:HIS126 4.1 26.9 1.0 O A:HIS126 4.1 20.2 1.0 CA A:HIS126 4.1 21.4 1.0 OE1 A:GLU130 4.2 22.1 1.0 C A:HIS126 4.5 22.4 1.0 HE B:ARG475 4.5 37.8 1.0 HE2 A:HIS126 4.5 33.5 1.0 HB3 A:HIS126 4.7 27.1 1.0 CB A:GLU130 4.7 20.9 1.0 O A:HOH2077 4.7 28.1 1.0 H A:GLU130 4.8 22.9 1.0 CZ B:ARG475 4.9 30.9 1.0 HD2 A:HIS126 5.0 32.3 1.0

Zinc binding site 2 out of 4 in the Complex of C. Elegans EIF4E-3 with the 4E-Binding Protein Mextli and Cap Analog


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Complex of C. Elegans EIF4E-3 with the 4E-Binding Protein Mextli and Cap Analog within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1218 b:24.0 occ:0.15 OD2 A:ASP62 2.1 29.3 1.0 O A:HOH2014 2.1 40.1 1.0 CG A:ASP62 2.9 25.3 1.0 OD1 A:ASP62 3.0 21.0 1.0 O A:HOH2005 3.4 35.8 1.0 O A:HOH2013 3.4 34.3 1.0 HE A:ARG37 3.9 32.4 1.0 HD2 A:ARG37 3.9 29.2 1.0 HH21 A:ARG31 4.2 33.2 1.0 CB A:ASP62 4.2 18.6 1.0 NE A:ARG37 4.2 27.0 1.0 HB3 A:ASP62 4.3 22.3 1.0 HH22 A:ARG31 4.3 33.2 1.0 CD A:ARG37 4.6 24.4 1.0 NH2 A:ARG31 4.6 27.6 1.0 HB2 A:ASP62 4.7 22.3 1.0 HH21 A:ARG37 4.8 38.8 1.0 O A:HOH2035 4.8 22.8 1.0 CZ A:ARG37 4.9 31.2 1.0

Zinc binding site 3 out of 4 in the Complex of C. Elegans EIF4E-3 with the 4E-Binding Protein Mextli and Cap Analog


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Complex of C. Elegans EIF4E-3 with the 4E-Binding Protein Mextli and Cap Analog within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1508 b:36.4 occ:0.39 NE2 B:HIS469 2.1 49.6 1.0 CD2 B:HIS469 2.9 49.9 1.0 HD2 B:HIS469 2.9 59.9 1.0 CE1 B:HIS469 3.2 58.3 1.0 HE1 B:HIS469 3.5 70.0 1.0 CG B:HIS469 4.1 52.0 1.0 ND1 B:HIS469 4.2 52.4 1.0

Zinc binding site 4 out of 4 in the Complex of C. Elegans EIF4E-3 with the 4E-Binding Protein Mextli and Cap Analog


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Complex of C. Elegans EIF4E-3 with the 4E-Binding Protein Mextli and Cap Analog within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1509 b:36.3 occ:0.22 O B:HOH2004 2.1 51.0 1.0 HD1 B:HIS469 2.9 62.9 1.0 ND1 B:HIS469 3.4 52.4 1.0 HB2 B:HIS469 4.0 45.3 1.0 HE1 B:HIS469 4.0 70.0 1.0 CE1 B:HIS469 4.0 58.3 1.0 CG B:HIS469 4.3 52.0 1.0 CB B:HIS469 4.7 37.7 1.0 H B:HIS469 4.9 41.9 1.0

D.Peter, R.Weber, C.Koene, M.-Y.Chung, L.Ebertsch, V.Truffault, O.Weichenrieder, C.Igreja, E.Izaurralde. Mextli Proteins Use Both Canonical Bipartite and Novel Tripartite Binding Modes to Form EIF4E Complexes That Display Differential Sensitivity to 4E-Bp Regulation Genes Dev. V. 29 1835 2015.
ISSN: ISSN 0890-9369
PubMed: 26294658
DOI: 10.1101/GAD.269068.115