Zinc in PDB 8rhf: Lytic Transglycosylase Mltd of Pseudomonas Aeruginosa Bound to the Natural Product Bulgecin A, with Two Lysm Domains

The structure of Lytic Transglycosylase Mltd of Pseudomonas Aeruginosa Bound to the Natural Product Bulgecin A, with Two Lysm Domains, PDB code: 8rhf 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)	60.62 / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	46.753, 116.527, 121.101, 90, 90, 90
R / Rfree (%)	18.6 / 22.8

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc atom in the Lytic Transglycosylase Mltd of Pseudomonas Aeruginosa Bound to the Natural Product Bulgecin A, with Two Lysm Domains (pdb code 8rhf). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the Lytic Transglycosylase Mltd of Pseudomonas Aeruginosa Bound to the Natural Product Bulgecin A, with Two Lysm Domains, PDB code: 8rhf:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in the Lytic Transglycosylase Mltd of Pseudomonas Aeruginosa Bound to the Natural Product Bulgecin A, with Two Lysm Domains


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, with Two Lysm Domains within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn403 b:27.5 occ:1.00 NE2 A:HIS170 2.0 27.7 1.0 NE2 B:HIS64 2.0 26.2 1.0 NE2 B:HIS62 2.1 40.6 1.0 O A:HOH670 2.2 13.1 1.0 CD2 B:HIS62 2.8 49.7 1.0 CD2 A:HIS170 3.0 25.9 1.0 CE1 A:HIS170 3.0 29.9 1.0 CE1 B:HIS64 3.0 26.9 1.0 CD2 B:HIS64 3.0 28.2 1.0 CE1 B:HIS62 3.3 51.5 1.0 ND1 A:HIS170 4.1 28.0 1.0 CG B:HIS62 4.1 51.4 1.0 CG A:HIS170 4.1 27.6 1.0 ND1 B:HIS64 4.1 24.4 1.0 CG B:HIS64 4.1 26.9 1.0 CE1 A:PHE171 4.1 20.7 1.0 C2 A:PEG401 4.2 52.4 1.0 ND1 B:HIS62 4.3 53.7 1.0 NH1 A:ARG198 4.4 32.7 1.0 CZ A:PHE171 4.4 21.9 1.0 OD1 B:ASN132 4.7 22.8 1.0 CD1 A:PHE171 4.7 21.1 1.0 O B:HIS62 4.9 45.6 1.0 O1 A:PEG401 4.9 58.6 1.0

Zinc binding site 2 out of 12 in the Lytic Transglycosylase Mltd of Pseudomonas Aeruginosa Bound to the Natural Product Bulgecin A, with Two Lysm Domains


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, with Two Lysm Domains within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn404 b:32.9 occ:1.00 OD2 B:ASP82 1.8 29.6 1.0 NE2 B:HIS63 2.0 33.4 1.0 OE1 B:GLU69 2.0 31.1 1.0 ND1 B:HIS65 2.3 28.7 1.0 CD B:GLU69 2.7 33.7 1.0 CG B:ASP82 2.8 29.4 1.0 OE2 B:GLU69 2.8 31.8 1.0 CD2 B:HIS63 2.9 28.4 1.0 CE1 B:HIS63 3.0 32.6 1.0 OD1 B:ASP82 3.1 30.5 1.0 CE1 B:HIS65 3.2 28.6 1.0 CG B:HIS65 3.3 28.9 1.0 CB B:HIS65 3.6 28.3 1.0 CA B:HIS65 3.6 28.8 1.0 O B:HOH622 3.7 26.7 1.0 O B:HOH527 3.9 42.1 1.0 ND1 B:HIS63 4.1 28.0 1.0 CG B:HIS63 4.1 27.8 1.0 CG B:GLU69 4.1 34.7 1.0 CB B:ASP82 4.2 30.2 1.0 NE2 B:HIS65 4.3 28.0 1.0 CD2 B:HIS65 4.4 28.8 1.0 N B:SER66 4.4 32.7 1.0 O B:HOH585 4.4 33.3 1.0 CB B:GLU69 4.6 34.7 1.0 N B:HIS65 4.6 27.2 1.0 C B:HIS65 4.6 30.4 1.0 O B:ASP82 4.6 27.8 1.0 CZ B:PHE73 4.7 32.8 1.0 O B:HIS64 4.9 27.6 1.0 C B:ASP82 5.0 27.6 1.0

Zinc binding site 3 out of 12 in the Lytic Transglycosylase Mltd of Pseudomonas Aeruginosa Bound to the Natural Product Bulgecin A, with Two Lysm Domains


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, with Two Lysm Domains within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn405 b:53.3 occ:1.00 ND1 B:HIS383 2.1 51.9 1.0 CE1 B:HIS383 3.0 55.4 1.0 CG B:HIS383 3.1 52.7 1.0 CB B:HIS383 3.5 53.0 1.0 NE2 B:HIS383 4.1 55.8 1.0 CD2 B:HIS383 4.2 56.1 1.0

Zinc binding site 4 out of 12 in the Lytic Transglycosylase Mltd of Pseudomonas Aeruginosa Bound to the Natural Product Bulgecin A, with Two Lysm Domains


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, with Two Lysm Domains within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn406 b:29.9 occ:0.70 OE2 B:GLU372 1.9 42.7 1.0 OE1 B:GLU372 2.3 35.5 1.0 CD B:GLU372 2.5 37.3 1.0 CG B:GLU372 3.9 38.5 1.0 O B:HOH566 4.4 41.8 1.0 CG2 B:THR369 4.6 44.6 1.0 N B:THR369 4.9 45.1 1.0 CA B:ILE368 4.9 45.6 1.0 CB B:GLU372 4.9 39.4 1.0

Zinc binding site 5 out of 12 in the Lytic Transglycosylase Mltd of Pseudomonas Aeruginosa Bound to the Natural Product Bulgecin A, with Two Lysm Domains


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, with Two Lysm Domains within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn407 b:32.1 occ:0.60 OE2 B:GLU328 2.0 44.9 1.0 O B:HOH511 2.1 43.0 1.0 O B:HOH535 2.2 36.8 1.0 CD B:GLU328 2.7 48.0 1.0 OE1 B:GLU328 2.7 47.3 1.0 OE1 B:GLU303 4.1 43.3 1.0 CG B:GLU328 4.2 42.1 1.0 OE2 B:GLU303 4.3 41.2 1.0 O B:HOH593 4.6 32.3 1.0 CD B:GLU303 4.7 43.5 1.0 CB B:PRO326 4.9 26.9 1.0

Zinc binding site 6 out of 12 in the Lytic Transglycosylase Mltd of Pseudomonas Aeruginosa Bound to the Natural Product Bulgecin A, with Two Lysm Domains


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 Bound to the Natural Product Bulgecin A, with Two Lysm Domains within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn408 b:33.0 occ:0.50 N B:BLG402 1.9 29.1 1.0 OE1 B:GLU144 2.0 32.3 1.0 O B:HOH654 2.2 22.9 1.0 O B:HOH549 2.3 29.2 1.0 O9 B:BLG402 2.6 24.6 1.0 C9 B:BLG402 2.9 26.5 1.0 CA B:BLG402 2.9 27.6 1.0 CD B:GLU144 2.9 29.9 1.0 CD B:BLG402 3.0 31.0 1.0 OE2 B:GLU144 3.2 29.4 1.0 C10 B:BLG402 3.8 35.3 1.0 CB B:GLN162 3.9 27.6 1.0 O10 B:BLG402 4.0 34.8 1.0 CB B:BLG402 4.0 27.7 1.0 ND2 B:ASN215 4.2 29.4 1.0 CG B:BLG402 4.2 30.6 1.0 CG B:GLU144 4.3 29.2 1.0 CG B:GLN162 4.3 26.7 1.0 N3 B:BLG402 4.6 38.6 1.0 OE1 B:GLN162 4.7 29.3 1.0 CA B:GLU144 4.7 29.6 1.0 CB B:GLU144 4.7 29.4 1.0 OE2 B:GLU245 4.7 36.4 1.0 O B:GLU144 4.8 29.9 1.0 O B:GLN162 4.8 27.6 1.0 CE1 B:TYR249 4.9 27.5 1.0 CD B:GLN162 5.0 28.2 1.0

Zinc binding site 7 out of 12 in the Lytic Transglycosylase Mltd of Pseudomonas Aeruginosa Bound to the Natural Product Bulgecin A, with Two Lysm Domains


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 Bound to the Natural Product Bulgecin A, with Two Lysm Domains within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn409 b:59.2 occ:1.00 O B:HOH518 2.3 37.6 1.0 CE1 B:HIS200 2.4 27.6 1.0 O B:HOH612 2.8 38.7 1.0 NE2 B:HIS200 2.9 25.7 1.0 ND1 B:HIS200 3.6 28.5 1.0 NE1 B:TRP207 3.9 23.3 1.0 CD2 B:HIS200 4.2 27.6 1.0 O B:GLY205 4.3 29.4 1.0 O B:HOH607 4.3 37.2 1.0 CG B:HIS200 4.5 24.7 1.0 O A:HOH544 4.6 40.2 1.0 CD1 B:TRP207 4.6 23.3 1.0 CA B:GLY205 4.7 28.1 1.0 CE2 B:TRP207 4.8 23.5 1.0 C B:GLY205 5.0 28.4 1.0

Zinc binding site 8 out of 12 in the Lytic Transglycosylase Mltd of Pseudomonas Aeruginosa Bound to the Natural Product Bulgecin A, with Two Lysm Domains


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 Bound to the Natural Product Bulgecin A, with Two Lysm Domains within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn404 b:20.8 occ:1.00 OE2 B:GLU197 1.8 22.2 1.0 OD2 B:ASP201 2.0 19.2 1.0 OE2 A:GLU197 2.0 23.6 1.0 OD2 A:ASP201 2.0 20.0 1.0 OD1 A:ASP201 2.3 20.3 1.0 CG A:ASP201 2.5 19.7 1.0 CG B:ASP201 2.6 20.3 1.0 OD1 B:ASP201 2.6 18.6 1.0 CD B:GLU197 2.9 24.7 1.0 CD A:GLU197 3.0 25.8 1.0 CG A:GLU197 3.3 23.9 1.0 CG B:GLU197 3.4 22.6 1.0 O B:HOH508 3.8 48.0 1.0 O A:HOH576 4.0 39.3 1.0 CB A:ASP201 4.0 20.8 1.0 CB B:ASP201 4.1 21.6 1.0 OE1 B:GLU197 4.1 26.6 1.0 O A:HOH575 4.1 41.9 1.0 OE1 A:GLU197 4.1 25.4 1.0 O A:GLU197 4.3 19.4 1.0 O A:HOH544 4.3 40.2 1.0 O B:GLU197 4.3 19.3 1.0 ND1 A:HIS200 4.6 28.2 1.0 CD2 B:HIS200 4.6 27.6 1.0 CE1 A:HIS200 4.7 26.9 1.0 O B:HOH554 4.8 32.9 1.0 O A:HOH654 4.8 29.2 1.0 CB A:GLU197 4.8 21.9 1.0 CB B:GLU197 4.8 21.8 1.0 C A:GLU197 4.9 19.8 1.0 C B:GLU197 4.9 19.1 1.0

Zinc binding site 9 out of 12 in the Lytic Transglycosylase Mltd of Pseudomonas Aeruginosa Bound to the Natural Product Bulgecin A, with Two Lysm Domains


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 Bound to the Natural Product Bulgecin A, with Two Lysm Domains within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn405 b:29.4 occ:1.00 NE2 A:HIS61 1.9 54.5 1.0 NE2 B:HIS170 1.9 26.5 1.0 NE2 A:HIS64 2.0 25.3 1.0 O B:HOH658 2.3 11.8 1.0 CE1 A:HIS61 2.7 59.3 1.0 CD2 A:HIS61 2.9 60.3 1.0 CE1 B:HIS170 2.9 30.0 1.0 CD2 B:HIS170 3.0 27.5 1.0 CD2 A:HIS64 3.0 26.3 1.0 CE1 A:HIS64 3.1 25.5 1.0 O A:HOH555 3.7 41.3 1.0 ND1 A:HIS61 3.8 61.3 1.0 CG A:HIS61 3.9 59.2 1.0 ND1 B:HIS170 4.0 29.7 1.0 CG B:HIS170 4.1 29.0 1.0 CG A:HIS64 4.2 25.8 1.0 ND1 A:HIS64 4.2 24.8 1.0 CE1 B:PHE171 4.2 23.8 1.0 C1 B:PEG401 4.3 54.1 1.0 NH2 B:ARG198 4.4 33.0 1.0 CZ B:PHE171 4.5 24.5 1.0 CD1 B:PHE171 4.8 25.5 1.0 OD1 A:ASN132 4.8 20.6 1.0 O A:HIS62 4.9 39.1 1.0 O1 B:PEG401 5.0 54.1 1.0

Zinc binding site 10 out of 12 in the Lytic Transglycosylase Mltd of Pseudomonas Aeruginosa Bound to the Natural Product Bulgecin A, with Two Lysm Domains


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Lytic Transglycosylase Mltd of Pseudomonas Aeruginosa Bound to the Natural Product Bulgecin A, with Two Lysm Domains within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn406 b:25.3 occ:1.00 OD2 A:ASP82 1.8 23.4 1.0 NE2 A:HIS63 2.0 23.0 1.0 OE1 A:GLU69 2.0 30.4 1.0 ND1 A:HIS65 2.1 23.8 1.0 CD A:GLU69 2.7 27.7 1.0 OE2 A:GLU69 2.8 27.1 1.0 CG A:ASP82 2.8 24.8 1.0 CD2 A:HIS63 3.0 23.2 1.0 CE1 A:HIS63 3.0 25.7 1.0 CE1 A:HIS65 3.1 24.2 1.0 CG A:HIS65 3.2 23.7 1.0 OD1 A:ASP82 3.2 25.3 1.0 CB A:HIS65 3.6 24.6 1.0 O A:HOH628 3.6 21.5 1.0 CA A:HIS65 3.6 24.2 1.0 O A:HOH569 3.9 32.5 1.0 CG A:HIS63 4.1 23.9 1.0 ND1 A:HIS63 4.1 24.8 1.0 CG A:GLU69 4.1 26.3 1.0 NE2 A:HIS65 4.2 23.6 1.0 CB A:ASP82 4.2 23.2 1.0 CD2 A:HIS65 4.3 23.1 1.0 N A:SER66 4.4 26.7 1.0 CB A:GLU69 4.5 26.2 1.0 CZ A:PHE73 4.5 25.3 1.0 C A:HIS65 4.6 26.1 1.0 N A:HIS65 4.6 23.7 1.0 O A:ASP82 4.7 22.3 1.0 O A:HIS64 5.0 27.4 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