Zinc in PDB 5o1j: Lytic Transglycosylase in Action

The structure of Lytic Transglycosylase in Action, PDB code: 5o1j was solved by A.H.Williams, L.Rateau, A.Hoauz, I.G.Boneca, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	71.66 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	68.135, 69.122, 143.321, 90.00, 90.00, 90.00
R / Rfree (%)	20.1 / 24.9

The binding sites of Zinc atom in the Lytic Transglycosylase in Action (pdb code 5o1j). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Lytic Transglycosylase in Action, PDB code: 5o1j:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Lytic Transglycosylase in Action


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Lytic Transglycosylase in Action within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn704 b:31.1 occ:1.00 OD1 A:ASP523 2.0 31.8 1.0 NE2 A:HIS463 2.1 19.6 1.0 O A:HOH1196 2.4 30.0 1.0 CG A:ASP523 2.9 32.8 1.0 CD2 A:HIS463 2.9 22.7 1.0 CE1 A:HIS463 3.2 27.4 1.0 OD2 A:ASP523 3.2 30.3 1.0 O A:HOH1055 3.9 39.2 1.0 NH2 A:ARG527 4.1 34.3 1.0 NE A:ARG527 4.1 35.8 1.0 CG A:HIS463 4.2 24.1 1.0 ND1 A:HIS463 4.2 22.6 1.0 CG2 A:THR459 4.3 33.0 1.0 CB A:ASP523 4.3 29.6 1.0 CD A:ARG462 4.3 31.9 1.0 CZ A:ARG527 4.5 38.2 1.0 NH1 A:ARG462 4.6 33.9 1.0 CA A:THR459 5.0 30.4 1.0

Zinc binding site 2 out of 4 in the Lytic Transglycosylase in Action


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Lytic Transglycosylase in Action within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn705 b:47.0 occ:1.00 O A:HOH1190 2.0 44.9 1.0 O A:HOH802 2.0 51.2 1.0 O A:HOH1212 2.0 49.2 1.0 O A:HOH871 2.0 43.0 1.0 OE1 A:GLU481 2.0 38.5 1.0 O A:HOH1175 2.1 48.4 1.0 O6 A:Z4S702 3.0 76.3 1.0 CD A:GLU481 3.2 34.8 1.0 C1 A:Z4S702 3.4 71.7 1.0 OE2 A:GLU481 3.6 35.5 1.0 C6 A:Z4S702 4.1 72.7 1.0 CG A:GLN499 4.2 27.0 1.0 OE1 A:GLN499 4.2 27.3 1.0 CB A:GLN499 4.3 26.3 1.0 O5 A:Z4S702 4.3 74.0 1.0 O A:GLU481 4.4 27.1 1.0 CG A:GLU481 4.4 30.9 1.0 C2 A:Z4S702 4.5 61.9 1.0 CA A:GLU481 4.5 28.9 1.0 O7 A:Z4S702 4.5 58.5 1.0 CB A:GLU481 4.7 28.4 1.0 OD1 A:ASN552 4.7 38.8 1.0 CD A:GLN499 4.7 25.5 1.0 CE2 A:TYR584 4.8 29.9 1.0 N2 A:Z4S702 4.8 71.9 1.0 OE2 A:GLU580 4.8 64.3 1.0 C7 A:Z4S702 4.8 66.5 1.0 C A:GLU481 4.9 26.6 1.0

Zinc binding site 3 out of 4 in the Lytic Transglycosylase in Action


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Lytic Transglycosylase in Action within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn706 b:48.8 occ:1.00 O A:HOH1158 1.9 37.4 1.0 O A:HOH970 2.0 43.4 1.0 NE2 A:HIS303 2.2 38.3 1.0 O A:HOH1203 2.4 41.0 1.0 O A:HOH1198 2.6 53.2 1.0 O A:HOH1269 2.8 48.2 1.0 CE1 A:HIS303 3.0 39.1 1.0 CD2 A:HIS303 3.3 35.9 1.0 O A:HOH1035 3.5 30.3 1.0 ND1 A:HIS303 4.1 39.1 1.0 CG A:HIS303 4.3 33.9 1.0 NH2 A:ARG274 4.6 47.0 1.0

Zinc binding site 4 out of 4 in the Lytic Transglycosylase in Action


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Lytic Transglycosylase in Action within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn707 b:46.3 occ:1.00 O A:HOH1236 2.1 54.9 1.0 O A:HOH1219 2.1 45.1 1.0 NE2 A:HIS429 2.2 32.2 1.0 O A:HOH1264 2.5 53.5 1.0 O A:HOH1205 3.0 45.4 1.0 CE1 A:HIS429 3.1 36.1 1.0 O A:HOH1226 3.2 49.2 1.0 CD2 A:HIS429 3.2 31.6 1.0 ND1 A:HIS429 4.2 33.8 1.0 CG A:HIS429 4.3 33.5 1.0 NE2 A:GLN389 4.4 55.4 1.0 CB A:ALA376 4.6 26.2 1.0 CD1 A:LEU385 4.7 32.1 1.0

A.H.Williams, R.Wheeler, L.Rateau, C.Malosse, J.Chamot-Rooke, A.Haouz, M.K.Taha, I.G.Boneca. A Step-By-Stepin Crystalloguide to Bond Cleavage and 1,6-Anhydro-Sugar Product Synthesis By A Peptidoglycan-Degrading Lytic Transglycosylase. J. Biol. Chem. V. 293 6000 2018.
ISSN: ESSN 1083-351X
PubMed: 29483188
DOI: 10.1074/JBC.RA117.001095