Zinc in PDB 8rhe: Lytic Transglycosylase Mltd of Pseudomonas Aeruginosa Bound to the Natural Product Bulgecin A

The structure of Lytic Transglycosylase Mltd of Pseudomonas Aeruginosa Bound to the Natural Product Bulgecin A, PDB code: 8rhe 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)	42.18 / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.224, 113.408, 116.858, 90, 90, 90
R / Rfree (%)	19.1 / 21.3

The binding sites of Zinc atom in the Lytic Transglycosylase Mltd of Pseudomonas Aeruginosa Bound to the Natural Product Bulgecin A (pdb code 8rhe). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Lytic Transglycosylase Mltd of Pseudomonas Aeruginosa Bound to the Natural Product Bulgecin A, PDB code: 8rhe:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Lytic Transglycosylase Mltd of Pseudomonas Aeruginosa Bound to the Natural Product Bulgecin A


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 Bound to the Natural Product Bulgecin A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:43.1 occ:1.00 NE2 A:HIS64 1.9 35.4 1.0 NE2 A:HIS62 2.1 53.6 1.0 NE2 B:HIS170 2.3 43.8 1.0 O A:HOH636 2.3 28.3 1.0 CD2 A:HIS62 2.7 55.1 1.0 CE1 A:HIS64 2.9 37.8 1.0 CD2 A:HIS64 2.9 36.1 1.0 CD2 B:HIS170 3.0 43.0 1.0 CE1 A:HIS62 3.3 56.7 1.0 CE1 B:HIS170 3.4 45.6 1.0 CE1 B:PHE171 3.8 41.5 1.0 CG A:HIS62 4.0 56.0 1.0 ND1 A:HIS64 4.0 36.6 1.0 CG A:HIS64 4.0 35.7 1.0 CZ B:PHE171 4.1 42.8 1.0 ND1 A:HIS62 4.2 58.5 1.0 CG B:HIS170 4.2 44.9 1.0 ND1 B:HIS170 4.4 48.4 1.0 OD1 A:ASN132 4.4 38.0 1.0 CD1 B:PHE171 4.5 42.1 1.0 CD B:ARG198 4.8 57.1 1.0 CE2 B:PHE171 4.9 41.7 1.0 CG A:ASN132 4.9 33.1 1.0 NE B:ARG198 5.0 63.9 1.0

Zinc binding site 2 out of 5 in the Lytic Transglycosylase Mltd of Pseudomonas Aeruginosa Bound to the Natural Product Bulgecin A


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 Bound to the Natural Product Bulgecin A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:25.8 occ:1.00 NE2 A:HIS63 1.9 29.8 1.0 OD1 A:ASP82 2.0 25.7 1.0 NE2 A:HIS65 2.0 32.6 1.0 CG A:ASP82 2.6 25.2 1.0 OD2 A:ASP82 2.6 24.9 1.0 CD2 A:HIS63 2.7 35.6 1.0 CD2 A:HIS65 3.0 34.8 1.0 CE1 A:HIS65 3.0 33.3 1.0 CE1 A:HIS63 3.0 34.6 1.0 O A:HOH563 3.9 28.9 1.0 CG A:HIS63 3.9 36.8 1.0 ND1 A:HIS63 4.0 35.3 1.0 CB A:ASP82 4.1 24.6 1.0 ND1 A:HIS65 4.1 32.3 1.0 CG A:HIS65 4.1 35.4 1.0 CZ A:PHE73 4.5 30.9 1.0 O A:ASP82 4.5 25.4 1.0 CA A:ASP82 4.8 24.5 1.0 C A:ASP82 5.0 24.7 1.0

Zinc binding site 3 out of 5 in the Lytic Transglycosylase Mltd of Pseudomonas Aeruginosa Bound to the Natural Product Bulgecin A


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 Bound to the Natural Product Bulgecin A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:31.8 occ:1.00 OD2 A:ASP201 1.9 28.5 1.0 OE2 B:GLU197 1.9 34.2 1.0 OE2 A:GLU197 2.0 37.7 1.0 OD2 B:ASP201 2.0 32.3 1.0 OD1 B:ASP201 2.5 30.2 1.0 CG A:ASP201 2.5 27.3 1.0 OD1 A:ASP201 2.5 28.4 1.0 CG B:ASP201 2.6 29.9 1.0 CD B:GLU197 3.0 34.6 1.0 CD A:GLU197 3.1 38.1 1.0 CG B:GLU197 3.4 33.1 1.0 CG A:GLU197 3.5 33.6 1.0 O B:HOH504 3.9 45.2 1.0 CB A:ASP201 4.0 28.1 1.0 NH2 A:ARG198 4.0 67.4 1.0 CB B:ASP201 4.1 29.7 1.0 OE1 B:GLU197 4.1 35.5 1.0 OE1 A:GLU197 4.2 41.2 1.0 O B:GLU197 4.3 28.3 1.0 O A:GLU197 4.4 27.0 1.0 ND1 B:HIS200 4.4 37.2 1.0 ND1 A:HIS200 4.6 34.0 1.0 O B:HOH520 4.6 33.9 1.0 CE1 B:HIS200 4.6 38.2 1.0 CE1 A:HIS200 4.7 34.3 1.0 O A:HOH582 4.8 36.4 1.0 CB B:GLU197 4.8 31.2 1.0 C B:GLU197 5.0 28.9 1.0 CA A:ASP201 5.0 28.5 1.0 CB A:GLU197 5.0 29.4 1.0

Zinc binding site 4 out of 5 in the Lytic Transglycosylase Mltd of Pseudomonas Aeruginosa Bound to the Natural Product Bulgecin A


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 Bound to the Natural Product Bulgecin A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn403 b:51.4 occ:1.00 NE2 B:HIS64 1.9 43.4 1.0 NE2 A:HIS170 2.1 47.9 1.0 O B:HOH575 2.2 34.2 1.0 ND1 B:HIS62 2.3 87.8 1.0 CE1 B:HIS64 2.9 46.3 1.0 CD2 B:HIS64 2.9 46.2 1.0 CD2 A:HIS170 3.0 45.2 1.0 CE1 B:HIS62 3.0 87.1 1.0 CE1 A:HIS170 3.1 46.5 1.0 CG B:HIS62 3.2 86.8 1.0 CB B:HIS62 3.7 86.1 1.0 ND1 B:HIS64 4.0 45.6 1.0 NE2 B:HIS62 4.0 89.9 1.0 CG B:HIS64 4.0 47.6 1.0 CZ A:PHE171 4.1 32.2 1.0 CG A:HIS170 4.1 44.1 1.0 CD2 B:HIS62 4.2 88.2 1.0 ND1 A:HIS170 4.2 45.0 1.0 CE1 A:PHE171 4.4 32.0 1.0 CE2 A:PHE171 4.7 32.3 1.0 ND2 B:ASN132 4.8 42.2 1.0

Zinc binding site 5 out of 5 in the Lytic Transglycosylase Mltd of Pseudomonas Aeruginosa Bound to the Natural Product Bulgecin A


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 Bound to the Natural Product Bulgecin A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn404 b:104.1 occ:1.00 OD2 B:ASP82 2.1 60.3 1.0 ND1 B:HIS63 2.5 99.0 1.0 CG B:ASP82 2.9 60.4 1.0 CE1 B:HIS63 3.0 99.6 1.0 OD1 B:ASP82 3.1 58.1 1.0 NE2 B:HIS65 3.2 75.9 1.0 OE2 B:GLU69 3.6 104.3 1.0 CG B:HIS63 3.8 91.5 1.0 CD2 B:HIS65 3.8 79.0 1.0 CE1 B:HIS65 4.2 80.3 1.0 NE2 B:HIS63 4.3 99.9 1.0 CB B:ASP82 4.3 57.4 1.0 CB B:HIS63 4.3 82.7 1.0 CD2 B:HIS63 4.7 96.6 1.0 O B:ASP82 4.8 53.6 1.0 CD B:GLU69 4.8 108.0 1.0 CG B:HIS65 5.0 80.0 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