Zinc in PDB 4y7o: 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: 4y7o 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)	49.34 / 2.24
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	85.470, 85.470, 256.370, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 22.4

The binding sites of Zinc atom in the T6SS Protein Tssm C-Terminal Domain (869-1107) From Eaec (pdb code 4y7o). 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: 4y7o:
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:Zn1201 b:1.0 occ:1.00 O A:GLY930 2.0 67.2 1.0 NE2 A:HIS933 2.1 78.7 1.0 OD2 A:ASP942 2.5 81.8 1.0 CE1 A:HIS933 2.8 78.2 1.0 C A:GLY930 3.2 67.3 1.0 CD2 A:HIS933 3.3 78.7 1.0 CG A:ASP942 3.4 75.7 1.0 CB A:ASP942 3.8 65.9 1.0 CA A:GLY930 3.9 63.3 1.0 ND1 A:HIS933 4.0 78.6 1.0 CG A:HIS933 4.2 76.7 1.0 N A:VAL931 4.3 64.1 1.0 OD1 A:ASP942 4.3 76.7 1.0 O A:SER929 4.4 65.0 1.0 CA A:VAL931 4.6 63.7 1.0 C A:VAL931 5.0 64.0 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:Zn1202 b:47.8 occ:1.00 ND1 A:HIS978 1.9 47.0 1.0 ND1 B:HIS978 2.1 48.0 1.0 OE2 A:GLU1085 2.1 46.5 1.0 OE2 B:GLU1085 2.1 42.7 1.0 CE1 A:HIS978 2.9 46.6 1.0 CD A:GLU1085 3.0 58.4 1.0 CG A:HIS978 3.0 44.3 1.0 CE1 B:HIS978 3.0 47.4 1.0 CD B:GLU1085 3.0 69.2 1.0 CG B:HIS978 3.1 45.1 1.0 OE1 A:GLU1085 3.2 38.6 1.0 OE1 B:GLU1085 3.2 39.9 1.0 CB A:HIS978 3.4 40.2 1.0 CB B:HIS978 3.5 40.4 1.0 O B:HOH1444 3.5 67.5 1.0 NE2 A:HIS978 4.1 46.3 1.0 CD2 A:HIS978 4.1 46.1 1.0 NE2 B:HIS978 4.2 47.7 1.0 CD2 B:HIS978 4.2 47.5 1.0 NH1 B:ARG1012 4.3 93.7 1.0 N A:HIS978 4.3 39.4 1.0 CG A:GLU1085 4.4 46.1 1.0 NH2 B:ARG1012 4.4 0.8 1.0 CG B:GLU1085 4.4 57.2 1.0 CA A:HIS978 4.5 39.3 1.0 N B:HIS978 4.5 39.6 1.0 NH2 A:ARG1012 4.5 87.5 1.0 CA B:HIS978 4.6 39.4 1.0 CZ B:ARG1012 4.8 0.9 1.0 CB A:GLU1085 4.9 42.9 1.0 CB B:GLU1085 4.9 50.1 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:Zn1201 b:89.6 occ:1.00 OE2 B:GLU964 1.9 50.6 1.0 CD B:GLU964 2.9 55.6 1.0 CG B:GLU964 3.4 40.6 1.0 CG B:GLU1088 3.5 59.3 1.0 CD B:GLU1088 3.9 96.0 1.0 OE1 B:GLU964 4.0 60.1 1.0 OE2 B:GLU1088 4.0 0.9 1.0 N B:GLU1088 4.1 41.0 1.0 CG2 B:VAL1092 4.4 39.0 1.0 CA B:GLY1087 4.4 45.2 1.0 NZ B:LYS1095 4.4 70.3 1.0 CB B:GLU1088 4.5 43.8 1.0 C B:GLY1087 4.7 47.2 1.0 OE1 B:GLU1088 4.7 88.8 1.0 CB B:GLU964 4.9 36.3 1.0 CA B:GLU1088 4.9 41.4 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 C:Zn201 b:83.0 occ:1.00 OD2 C:ASP135 2.0 95.3 1.0 CG C:ASP135 2.7 88.3 1.0 OD1 C:ASP135 2.8 90.2 1.0 CB C:ASP135 4.1 74.4 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