Zinc in PDB 4y7l: T6SS Protein Tssm C-Terminal Domain (869-1107) From Eaec

The structure of T6SS Protein Tssm C-Terminal Domain (869-1107) From Eaec, PDB code: 4y7l was solved by V.S.Nguyen, S.Spinelli, E.Durand, A.Roussel, C.Cambillau, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	22.11 / 1.51
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	64.030, 64.030, 249.660, 90.00, 90.00, 90.00
R / Rfree (%)	19.1 / 20.3

The binding sites of Zinc atom in the T6SS Protein Tssm C-Terminal Domain (869-1107) From Eaec (pdb code 4y7l). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the T6SS Protein Tssm C-Terminal Domain (869-1107) From Eaec, PDB code: 4y7l:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the T6SS Protein Tssm C-Terminal Domain (869-1107) From Eaec


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of T6SS Protein Tssm C-Terminal Domain (869-1107) From Eaec within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1203 b:0.1 occ:1.00 O A:HOH1310 1.9 51.9 1.0 OD2 A:ASP916 2.1 43.1 1.0 O A:HOH1302 2.2 49.9 1.0 O A:HOH1474 2.3 37.8 1.0 CG A:ASP916 2.9 36.1 1.0 OD1 A:ASP916 3.0 39.1 1.0 ND2 B:ASN998 3.8 38.9 1.0 O B:HOH1332 4.2 32.9 1.0 O B:HOH1457 4.2 36.0 1.0 CB A:ASP916 4.3 21.1 1.0 O B:ASP1018 4.5 21.7 1.0 O B:HOH1514 4.5 47.8 1.0 CG B:ASN998 4.9 44.6 1.0 CG2 A:THR915 4.9 23.4 1.0 CB B:ASN998 5.0 23.1 1.0

Zinc binding site 2 out of 4 in the T6SS Protein Tssm C-Terminal Domain (869-1107) From Eaec


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of T6SS Protein Tssm C-Terminal Domain (869-1107) From Eaec within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1204 b:66.2 occ:1.00 OE2 A:GLU1085 2.1 51.9 1.0 O B:HOH1301 2.1 28.7 1.0 OE1 B:GLU1085 2.5 71.9 1.0 OE2 B:GLU1085 2.7 64.5 1.0 CD B:GLU1085 2.9 74.5 1.0 CD A:GLU1085 2.9 68.0 1.0 ND1 A:HIS978 3.0 42.1 1.0 OE1 A:GLU1085 3.1 64.5 1.0 CG A:HIS978 3.3 38.1 1.0 CB A:HIS978 3.5 31.4 1.0 CE1 A:HIS978 3.6 42.4 1.0 NE A:ARG1012 3.7 64.1 1.0 ND1 B:HIS978 3.8 39.7 1.0 O A:HOH1409 4.0 46.4 1.0 O A:HOH1469 4.0 51.1 1.0 CD2 A:HIS978 4.0 41.9 1.0 NE2 A:HIS978 4.2 42.5 1.0 CD A:ARG1012 4.3 52.8 1.0 CG B:GLU1085 4.3 49.5 1.0 CG A:GLU1085 4.4 50.4 1.0 CE1 B:HIS978 4.4 40.3 1.0 CG B:HIS978 4.5 35.6 1.0 CB B:HIS978 4.7 28.6 1.0

Zinc binding site 3 out of 4 in the T6SS Protein Tssm C-Terminal Domain (869-1107) From Eaec


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of T6SS Protein Tssm C-Terminal Domain (869-1107) From Eaec within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1202 b:69.5 occ:1.00 O B:HOH1538 2.2 34.7 1.0 O B:HOH1541 2.2 28.0 1.0 OE2 B:GLU1052 2.3 25.8 1.0 O B:HOH1520 2.4 31.5 1.0 CD B:GLU1052 3.2 27.6 1.0 CG B:GLU1052 3.3 26.2 1.0 NE B:ARG1097 4.0 19.0 1.0 O B:HOH1350 4.1 48.1 1.0 CG B:ARG1097 4.3 19.0 1.0 OE1 B:GLU1052 4.4 21.3 1.0 NH2 B:ARG1097 4.6 21.4 1.0 CD B:ARG1097 4.6 18.6 1.0 CZ B:ARG1097 4.7 25.4 1.0 CB B:GLU1052 4.8 19.1 1.0 CB B:ARG1097 4.8 17.4 1.0 O B:HOH1557 4.9 61.4 1.0

Zinc binding site 4 out of 4 in the T6SS Protein Tssm C-Terminal Domain (869-1107) From Eaec


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of T6SS Protein Tssm C-Terminal Domain (869-1107) From Eaec within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1203 b:0.9 occ:1.00 O B:HOH1326 2.2 48.4 1.0 OD2 B:ASP916 2.2 48.6 1.0 CG B:ASP916 3.1 38.5 1.0 OD1 B:ASP916 3.2 39.7 1.0 ND2 A:ASN998 3.8 57.3 1.0 O A:HOH1381 4.3 33.1 1.0 O A:ASP1018 4.3 24.7 1.0 CG2 A:THR1019 4.4 35.1 0.5 CB B:ASP916 4.5 24.1 1.0 CG2 B:THR915 4.7 27.8 1.0 OG1 A:THR1019 4.7 39.6 0.5 CG A:ASN998 4.8 62.0 1.0 CB A:ASN998 4.8 26.5 1.0

E.Durand, V.S.Nguyen, A.Zoued, L.Logger, G.Pehau-Arnaudet, M.S.Aschtgen, S.Spinelli, A.Desmyter, B.Bardiaux, A.Dujeancourt, A.Roussel, C.Cambillau, E.Cascales, R.Fronzes. Biogenesis and Structure of A Type VI Secretion Membrane Core Complex. Nature V. 523 555 2015.
ISSN: ESSN 1476-4687
PubMed: 26200339
DOI: 10.1038/NATURE14667