Zinc in PDB 8rhi: Lytic Transglycosylase Mltd of Pseudomonas Aeruginosa in A Ternary Complex Bound to Bulgecin A and Chito-Tetraose

The structure of Lytic Transglycosylase Mltd of Pseudomonas Aeruginosa in A Ternary Complex Bound to Bulgecin A and Chito-Tetraose, PDB code: 8rhi was solved by V.Miguel-Ruano, J.A.Hermoso, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	83.84 / 1.98
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.248, 117.036, 120.146, 90, 90, 90
R / Rfree (%)	19 / 21.6

The binding sites of Zinc atom in the Lytic Transglycosylase Mltd of Pseudomonas Aeruginosa in A Ternary Complex Bound to Bulgecin A and Chito-Tetraose (pdb code 8rhi). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Lytic Transglycosylase Mltd of Pseudomonas Aeruginosa in A Ternary Complex Bound to Bulgecin A and Chito-Tetraose, PDB code: 8rhi:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in the Lytic Transglycosylase Mltd of Pseudomonas Aeruginosa in A Ternary Complex Bound to Bulgecin A and Chito-Tetraose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Lytic Transglycosylase Mltd of Pseudomonas Aeruginosa in A Ternary Complex Bound to Bulgecin A and Chito-Tetraose within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:34.9 occ:1.00 OE2 B:GLU197 1.9 34.6 1.0 OD2 A:ASP201 1.9 33.5 1.0 OE2 A:GLU197 2.0 37.0 1.0 OD2 B:ASP201 2.0 31.8 1.0 CG A:ASP201 2.6 34.2 1.0 CG B:ASP201 2.6 32.9 1.0 OD1 A:ASP201 2.7 33.4 1.0 OD1 B:ASP201 2.7 33.6 1.0 CD B:GLU197 3.0 35.9 1.0 CD A:GLU197 3.0 36.9 1.0 CG B:GLU197 3.4 34.3 1.0 CG A:GLU197 3.4 36.3 1.0 CB A:ASP201 4.1 35.0 1.0 OE1 B:GLU197 4.1 36.0 1.0 CB B:ASP201 4.1 32.6 1.0 OE1 A:GLU197 4.1 41.0 1.0 O A:GLU197 4.3 32.1 1.0 O B:GLU197 4.3 33.8 1.0 ND1 B:HIS200 4.5 43.0 1.0 CE1 B:HIS200 4.6 44.9 1.0 ND1 A:HIS200 4.6 39.9 1.0 CE1 A:HIS200 4.6 38.3 1.0 O A:HOH549 4.7 43.4 1.0 O B:HOH539 4.8 42.5 1.0 CB B:GLU197 4.9 35.1 1.0 C A:GLU197 4.9 33.2 1.0 CB A:GLU197 4.9 34.9 1.0 C B:GLU197 4.9 36.2 1.0

Zinc binding site 2 out of 9 in the Lytic Transglycosylase Mltd of Pseudomonas Aeruginosa in A Ternary Complex Bound to Bulgecin A and Chito-Tetraose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Lytic Transglycosylase Mltd of Pseudomonas Aeruginosa in A Ternary Complex Bound to Bulgecin A and Chito-Tetraose within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:47.6 occ:1.00 NE2 B:HIS170 2.1 48.5 1.0 ND1 A:HIS63 2.1 66.0 1.0 NE2 A:HIS65 2.1 43.0 1.0 O A:HOH606 2.5 36.5 1.0 CE1 A:HIS63 3.0 67.8 1.0 CD2 B:HIS170 3.0 47.4 1.0 CE1 B:HIS170 3.0 51.7 1.0 CG A:HIS63 3.0 66.1 1.0 CE1 A:HIS65 3.1 44.7 1.0 CD2 A:HIS65 3.1 45.2 1.0 CB A:HIS63 3.5 64.3 1.0 NE2 A:HIS63 4.0 69.5 1.0 CD2 A:HIS63 4.1 68.8 1.0 CA A:HIS63 4.1 59.5 1.0 ND1 B:HIS170 4.1 50.3 1.0 CG B:HIS170 4.2 49.1 1.0 ND1 A:HIS65 4.2 42.6 1.0 CE1 B:PHE171 4.2 42.1 1.0 CG A:HIS65 4.2 44.5 1.0 CZ B:PHE171 4.3 42.0 1.0 ND2 A:ASN132 4.7 37.1 1.0 CD1 B:PHE171 4.8 43.9 1.0 NH1 B:ARG198 5.0 76.5 1.0

Zinc binding site 3 out of 9 in the Lytic Transglycosylase Mltd of Pseudomonas Aeruginosa in A Ternary Complex Bound to Bulgecin A and Chito-Tetraose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Lytic Transglycosylase Mltd of Pseudomonas Aeruginosa in A Ternary Complex Bound to Bulgecin A and Chito-Tetraose within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn404 b:50.9 occ:1.00 NE2 B:HIS64 2.0 47.6 1.0 NE2 A:HIS170 2.0 50.8 1.0 O A:HOH573 2.2 60.7 1.0 O A:HOH562 2.4 44.4 1.0 O A:HOH605 2.5 68.0 1.0 CE1 B:HIS64 3.0 48.6 1.0 CE1 A:HIS170 3.0 51.2 1.0 CD2 B:HIS64 3.0 47.9 1.0 CD2 A:HIS170 3.0 47.8 1.0 NH2 A:ARG198 3.9 79.2 1.0 ND1 B:HIS64 4.1 47.0 1.0 ND1 A:HIS170 4.1 49.0 1.0 CG B:HIS64 4.1 48.4 1.0 CG A:HIS170 4.1 45.9 1.0 CE1 A:PHE171 4.4 35.5 1.0 CZ A:PHE171 4.4 35.9 1.0 OD1 B:ASN132 4.7 43.4 1.0 CZ A:ARG198 5.0 73.1 1.0 CD1 A:PHE171 5.0 35.2 1.0 CE2 A:PHE171 5.0 33.6 1.0

Zinc binding site 4 out of 9 in the Lytic Transglycosylase Mltd of Pseudomonas Aeruginosa in A Ternary Complex Bound to Bulgecin A and Chito-Tetraose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Lytic Transglycosylase Mltd of Pseudomonas Aeruginosa in A Ternary Complex Bound to Bulgecin A and Chito-Tetraose within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn405 b:32.5 occ:1.00 O A:HOH520 1.9 34.8 1.0 NE2 A:HIS64 1.9 37.8 1.0 OD1 A:ASP82 1.9 27.3 1.0 CG A:ASP82 2.6 27.5 1.0 OD2 A:ASP82 2.6 24.9 1.0 CE1 A:HIS64 2.8 43.2 1.0 CD2 A:HIS64 2.9 40.9 1.0 O A:HOH571 3.8 32.5 1.0 ND1 A:HIS64 3.9 43.2 1.0 CG A:HIS64 4.0 41.9 1.0 OE2 A:GLU69 4.1 73.9 1.0 CB A:ASP82 4.1 28.9 1.0 OD1 A:ASN70 4.3 44.8 1.0 O A:ASP82 4.6 28.1 1.0 CA A:ASP82 4.9 28.2 1.0 CZ A:PHE73 4.9 39.3 1.0

Zinc binding site 5 out of 9 in the Lytic Transglycosylase Mltd of Pseudomonas Aeruginosa in A Ternary Complex Bound to Bulgecin A and Chito-Tetraose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Lytic Transglycosylase Mltd of Pseudomonas Aeruginosa in A Ternary Complex Bound to Bulgecin A and Chito-Tetraose within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn406 b:56.8 occ:1.00 O A:HOH523 1.9 46.5 1.0 NE2 A:HIS200 2.2 40.0 1.0 O A:HOH553 2.3 46.1 1.0 O A:HOH617 2.7 54.3 1.0 CE1 A:HIS200 3.2 38.3 1.0 CD2 A:HIS200 3.2 37.8 1.0 NE1 A:TRP207 4.1 36.8 1.0 O A:GLY205 4.2 41.4 1.0 ND1 A:HIS200 4.3 39.9 1.0 CG A:HIS200 4.3 37.4 1.0 CA A:GLY205 4.5 42.7 1.0 CD1 A:TRP207 4.8 36.4 1.0 C A:GLY205 4.8 41.0 1.0 CE2 A:TRP207 4.9 37.0 1.0

Zinc binding site 6 out of 9 in the Lytic Transglycosylase Mltd of Pseudomonas Aeruginosa in A Ternary Complex Bound to Bulgecin A and Chito-Tetraose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Lytic Transglycosylase Mltd of Pseudomonas Aeruginosa in A Ternary Complex Bound to Bulgecin A and Chito-Tetraose within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn407 b:101.3 occ:1.00 OE2 A:GLU226 2.2 69.0 1.0 OE1 A:GLU229 2.4 79.2 1.0 OE2 A:GLU229 2.7 78.5 1.0 OE1 A:GLU226 2.7 68.7 1.0 CD A:GLU226 2.8 65.0 1.0 CD A:GLU229 2.8 75.0 1.0 CG A:GLU226 4.3 60.4 1.0 CG A:GLU229 4.4 70.2 1.0

Zinc binding site 7 out of 9 in the Lytic Transglycosylase Mltd of Pseudomonas Aeruginosa in A Ternary Complex Bound to Bulgecin A and Chito-Tetraose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Lytic Transglycosylase Mltd of Pseudomonas Aeruginosa in A Ternary Complex Bound to Bulgecin A and Chito-Tetraose within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:72.2 occ:1.00 OD2 B:ASP82 2.1 72.3 1.0 NE2 B:HIS63 2.2 73.9 1.0 ND1 B:HIS65 2.2 76.2 1.0 OE1 B:GLU69 2.3 95.3 1.0 CD B:GLU69 3.0 94.2 1.0 CE1 B:HIS63 3.1 75.8 1.0 CE1 B:HIS65 3.2 75.3 1.0 CD2 B:HIS63 3.2 73.4 1.0 CG B:HIS65 3.2 72.3 1.0 CG B:ASP82 3.2 65.9 1.0 OE2 B:GLU69 3.2 91.1 1.0 O B:HOH559 3.3 46.0 1.0 CB B:HIS65 3.5 67.8 1.0 CA B:HIS65 3.7 64.6 1.0 OD1 B:ASP82 3.8 69.9 1.0 O B:HOH502 3.8 63.5 1.0 ND1 B:HIS63 4.3 74.7 1.0 NE2 B:HIS65 4.3 73.6 1.0 CG B:HIS63 4.3 72.8 1.0 CD2 B:HIS65 4.3 73.6 1.0 CG B:GLU69 4.3 93.7 1.0 CB B:ASP82 4.4 61.4 1.0 CZ B:PHE73 4.6 74.7 1.0 N B:HIS65 4.6 59.9 1.0 N B:SER66 4.7 73.5 1.0 CB B:GLU69 4.7 93.1 1.0 C B:HIS65 4.7 67.0 1.0 CE2 B:PHE73 4.8 74.5 1.0 O B:HIS64 4.9 56.3 1.0

Zinc binding site 8 out of 9 in the Lytic Transglycosylase Mltd of Pseudomonas Aeruginosa in A Ternary Complex Bound to Bulgecin A and Chito-Tetraose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Lytic Transglycosylase Mltd of Pseudomonas Aeruginosa in A Ternary Complex Bound to Bulgecin A and Chito-Tetraose within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn403 b:60.9 occ:1.00 O B:HOH508 2.0 47.7 1.0 O B:HOH538 2.3 50.7 1.0 NE2 B:HIS200 2.3 44.8 1.0 CD2 B:HIS200 3.3 43.7 1.0 CE1 B:HIS200 3.3 44.9 1.0 NE1 B:TRP207 3.9 37.9 1.0 O B:HOH542 4.2 49.5 1.0 O B:GLY205 4.2 42.8 1.0 O B:HOH510 4.3 45.3 1.0 ND1 B:HIS200 4.4 43.0 1.0 CG B:HIS200 4.4 42.0 1.0 CD1 B:TRP207 4.6 37.7 1.0 CA B:GLY205 4.6 42.3 1.0 CE2 B:TRP207 4.8 37.6 1.0 C B:GLY205 4.9 42.4 1.0

Zinc binding site 9 out of 9 in the Lytic Transglycosylase Mltd of Pseudomonas Aeruginosa in A Ternary Complex Bound to Bulgecin A and Chito-Tetraose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Lytic Transglycosylase Mltd of Pseudomonas Aeruginosa in A Ternary Complex Bound to Bulgecin A and Chito-Tetraose within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn404 b:82.9 occ:1.00 OD2 B:ASP302 2.4 90.7 1.0 OD2 B:ASP300 2.5 90.4 1.0 OD1 B:ASP300 2.8 82.2 1.0 CG B:ASP300 3.0 86.1 1.0 CG B:ASP302 3.1 88.5 1.0 CB B:ASP302 3.5 81.1 1.0 OD1 B:ASP302 4.0 91.3 1.0 CB B:ASP300 4.5 84.9 1.0 N B:ASP302 4.7 77.6 1.0 CA B:ASP302 4.7 76.5 1.0

V.Miguel-Ruano, R.Feltzer, M.T.Batuecas, B.Ramachandran, A.M.El-Araby, L.F.Avila-Cobian, S.De Benedetti, S.Mobashery, J.A.Hermoso. Structural Characterization of Lytic Transglycosylase Mltd of Pseudomonas Aeruginosa, A Target For the Natural Product Bulgecin A. Int.J.Biol.Macromol. 31420 2024.
ISSN: ISSN 0141-8130
PubMed: 38583835
DOI: 10.1016/J.IJBIOMAC.2024.131420