Manganese in PDB 2wym: Structure of A Metallo-B-Lactamase

The structure of Structure of A Metallo-B-Lactamase, PDB code: 2wym was solved by F.Garces, F.J.Fernandez, E.Penya-Soler, J.Aguilar, L.Baldoma, M.Coll, J.Badia, M.C.Vega, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	14.97 / 2.60
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	103.221, 178.212, 111.559, 90.00, 103.96, 90.00
R / Rfree (%)	20.7 / 25.5

The binding sites of Manganese atom in the Structure of A Metallo-B-Lactamase (pdb code 2wym). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Structure of A Metallo-B-Lactamase, PDB code: 2wym:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in the Structure of A Metallo-B-Lactamase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structure of A Metallo-B-Lactamase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1341 b:67.0 occ:0.80 NE2 A:HIS122 2.3 43.3 1.0 NE2 A:HIS281 2.5 33.4 1.0 OD2 A:ASP226 3.0 46.7 1.0 CD2 A:HIS122 3.0 43.0 1.0 OD2 A:ASP121 3.3 45.2 1.0 CE1 A:HIS281 3.4 33.4 1.0 CE1 A:HIS122 3.4 43.0 1.0 CD2 A:HIS281 3.5 32.1 1.0 CG A:ASP226 3.6 46.2 1.0 CB A:ASP121 3.6 44.5 1.0 ND1 A:HIS119 3.8 48.8 1.0 CG A:ASP121 3.8 45.0 1.0 CB A:ASP226 3.9 45.8 1.0 CE1 A:HIS119 4.1 49.3 1.0 CG A:HIS122 4.2 43.0 1.0 NZ A:LYS259 4.3 37.1 1.0 CG A:HIS119 4.4 47.9 1.0 ND1 A:HIS122 4.4 42.9 1.0 OD1 A:ASP226 4.4 46.6 1.0 ND1 A:HIS281 4.5 32.7 1.0 CG A:HIS281 4.6 31.6 1.0 CE A:LYS259 4.7 36.9 1.0 CA A:ASP121 4.7 44.4 1.0 CE1 A:HIS117 4.7 46.4 1.0 NE2 A:HIS119 4.8 49.6 1.0 NE2 A:HIS117 4.8 46.6 1.0 CB A:HIS119 4.8 46.8 1.0 N A:ASP121 4.9 44.9 1.0 CD2 A:HIS119 4.9 48.9 1.0 OD1 A:ASP121 4.9 45.5 1.0 SG A:CYS45 4.9 30.9 1.0 C A:ASP121 5.0 44.0 1.0

Manganese binding site 2 out of 6 in the Structure of A Metallo-B-Lactamase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structure of A Metallo-B-Lactamase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn1338 b:63.1 occ:0.60 NE2 B:HIS122 2.2 49.2 1.0 NE2 B:HIS281 2.3 31.0 1.0 OD2 B:ASP226 2.3 42.9 1.0 CD2 B:HIS122 3.1 49.4 1.0 CE1 B:HIS281 3.2 30.5 1.0 OD2 B:ASP121 3.3 51.7 1.0 CE1 B:HIS122 3.3 49.2 1.0 CD2 B:HIS281 3.3 30.5 1.0 CG B:ASP226 3.3 42.2 1.0 CB B:ASP121 3.4 50.8 1.0 O B:HOH2004 3.6 26.6 1.0 CG B:ASP121 3.7 51.3 1.0 OD1 B:ASP226 4.0 42.9 1.0 ND1 B:HIS119 4.2 52.1 1.0 CG B:HIS122 4.3 49.6 1.0 NZ B:LYS259 4.3 38.8 1.0 ND1 B:HIS122 4.3 49.1 1.0 ND1 B:HIS281 4.3 30.5 1.0 CB B:ASP226 4.3 41.6 1.0 CG B:HIS281 4.4 30.4 1.0 SG B:CYS45 4.6 29.2 1.0 CE B:LYS259 4.6 39.0 1.0 CA B:ASP121 4.7 50.6 1.0 NE2 B:HIS117 4.8 50.3 1.0 CE1 B:HIS119 4.9 52.2 1.0 CE1 B:HIS117 4.9 50.4 1.0 OD1 B:ASP121 4.9 51.9 1.0

Manganese binding site 3 out of 6 in the Structure of A Metallo-B-Lactamase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Structure of A Metallo-B-Lactamase within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn1338 b:61.1 occ:0.80 OD2 C:ASP226 2.2 44.1 1.0 NE2 C:HIS281 2.5 28.7 1.0 NE2 C:HIS122 2.6 47.3 1.0 CE1 C:HIS281 3.2 28.3 1.0 ND1 C:HIS119 3.2 49.8 1.0 CD2 C:HIS122 3.2 46.8 1.0 OD2 C:ASP121 3.2 48.6 1.0 CG C:ASP226 3.4 43.8 1.0 CB C:ASP121 3.4 47.5 1.0 CE1 C:HIS119 3.5 50.0 1.0 CD2 C:HIS281 3.7 28.0 1.0 CG C:ASP121 3.7 48.2 1.0 CE1 C:HIS122 3.8 47.4 1.0 CB C:ASP226 4.1 43.2 1.0 OD1 C:ASP226 4.4 44.2 1.0 ND1 C:HIS281 4.4 28.2 1.0 NZ C:LYS259 4.4 35.7 1.0 CG C:HIS122 4.5 46.8 1.0 CG C:HIS119 4.5 49.2 1.0 CG C:HIS281 4.7 27.8 1.0 CE1 C:HIS117 4.7 47.6 1.0 CA C:ASP121 4.7 47.3 1.0 ND1 C:HIS122 4.7 47.0 1.0 SG C:CYS45 4.8 30.5 1.0 NE2 C:HIS119 4.8 50.2 1.0 CE C:LYS259 4.9 35.6 1.0 OD1 C:ASP121 4.9 49.0 1.0 NE2 C:HIS117 5.0 47.7 1.0

Manganese binding site 4 out of 6 in the Structure of A Metallo-B-Lactamase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Structure of A Metallo-B-Lactamase within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn1340 b:69.2 occ:0.80 OD2 D:ASP226 2.2 40.7 1.0 NE2 D:HIS281 2.3 28.3 1.0 NE2 D:HIS122 2.3 35.0 1.0 OD2 D:ASP121 2.6 36.9 1.0 CE1 D:HIS281 3.1 28.2 1.0 CD2 D:HIS122 3.2 34.7 1.0 CE1 D:HIS122 3.3 34.6 1.0 CG D:ASP226 3.3 40.1 1.0 CD2 D:HIS281 3.4 27.8 1.0 CG D:ASP121 3.5 36.0 1.0 OD1 D:ASP121 3.6 37.2 1.0 ND1 D:HIS119 3.7 36.5 0.5 CB D:ASP226 3.8 39.5 1.0 O D:HOH2025 3.9 37.1 1.0 CE1 D:HIS119 4.0 36.4 0.5 NZ D:LYS259 4.1 37.1 1.0 ND1 D:HIS281 4.3 28.0 1.0 CG D:HIS122 4.3 34.2 1.0 ND1 D:HIS122 4.3 34.1 1.0 OD1 D:ASP226 4.3 40.3 1.0 CG D:HIS281 4.4 27.1 1.0 CG D:HIS119 4.6 36.5 0.5 CE D:LYS259 4.7 36.8 1.0 CE1 D:HIS117 4.8 38.3 1.0 SG D:CYS45 4.9 25.9 1.0 CB D:ASP121 4.9 35.3 1.0

Manganese binding site 5 out of 6 in the Structure of A Metallo-B-Lactamase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Structure of A Metallo-B-Lactamase within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn1339 b:67.1 occ:0.60 OD2 E:ASP226 2.1 47.7 1.0 NE2 E:HIS122 2.4 53.0 1.0 NE2 E:HIS281 2.7 33.8 1.0 CD2 E:HIS122 3.1 52.6 1.0 CD2 E:HIS119 3.2 51.6 0.7 CG E:ASP226 3.4 47.6 1.0 CE1 E:HIS281 3.4 33.7 1.0 NE2 E:HIS119 3.4 51.3 0.7 CE1 E:HIS122 3.5 52.7 1.0 CB E:ASP121 3.5 52.2 1.0 OD2 E:ASP121 3.5 52.5 1.0 CD2 E:HIS281 3.9 33.4 1.0 CG E:ASP121 4.0 52.4 1.0 OD1 E:ASP226 4.2 48.2 1.0 CB E:ASP226 4.2 47.1 1.0 CG E:HIS119 4.2 51.7 0.7 CG E:HIS122 4.3 52.2 1.0 ND1 E:HIS122 4.4 52.3 1.0 CE1 E:HIS119 4.5 51.5 0.7 CA E:ASP121 4.6 52.1 1.0 ND1 E:HIS281 4.6 33.5 1.0 NZ E:LYS259 4.7 38.5 1.0 SG E:CYS45 4.8 36.6 1.0 CE1 E:HIS117 4.8 51.8 1.0 C E:ASP121 4.8 52.0 1.0 ND1 E:HIS119 4.9 51.8 0.7 CG E:HIS281 4.9 32.8 1.0 NE2 E:HIS117 4.9 51.7 1.0 O E:ASP121 5.0 52.0 1.0

Manganese binding site 6 out of 6 in the Structure of A Metallo-B-Lactamase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Structure of A Metallo-B-Lactamase within 5.0Å range: probe atom residue distance (Å) B Occ F:Mn1339 b:67.8 occ:0.80 NE2 F:HIS281 2.2 31.9 1.0 NE2 F:HIS122 2.4 55.8 1.0 OD2 F:ASP226 2.9 50.3 1.0 CD2 F:HIS281 3.2 31.6 1.0 CE1 F:HIS281 3.2 31.8 1.0 CG F:ASP226 3.3 49.6 1.0 CD2 F:HIS122 3.3 55.6 1.0 OD2 F:ASP121 3.4 56.0 1.0 CE1 F:HIS122 3.4 55.7 1.0 CB F:ASP121 3.6 56.3 1.0 CB F:ASP226 3.7 48.8 1.0 ND1 F:HIS119 3.8 58.1 1.0 OD1 F:ASP226 3.9 50.4 1.0 CG F:ASP121 3.9 56.4 1.0 CE1 F:HIS119 4.1 58.0 1.0 NZ F:LYS259 4.3 36.5 1.0 ND1 F:HIS281 4.3 31.7 1.0 CG F:HIS281 4.4 31.4 1.0 ND1 F:HIS122 4.4 55.5 1.0 CG F:HIS122 4.5 55.6 1.0 CE F:LYS259 4.7 36.7 1.0 SG F:CYS45 4.8 34.9 1.0 CG F:HIS119 4.8 57.8 1.0 CA F:ASP121 4.8 56.2 1.0 NE2 F:HIS117 4.9 56.6 1.0

F.Garces, F.J.Fernandez, C.Montella, E.Penya-Soler, R.Prohens, J.Aguilar, L.Baldoma, M.Coll, J.Badia, M.C.Vega. Molecular Architecture of the Mn(2+)Dependent Lactonase Ulag Reveals An Rnase-Like Metallo-Beta- Lactamase Fold and A Novel Quaternary Structure. J.Mol.Biol. V. 398 715 2010.
ISSN: ISSN 0022-2836
PubMed: 20359483
DOI: 10.1016/J.JMB.2010.03.041