Magnesium in PDB 5odz: Crystal Structure of the Beta-Lactamase Oxa-163

All present enzymatic activity of Crystal Structure of the Beta-Lactamase Oxa-163:
3.5.2.6;

The structure of Crystal Structure of the Beta-Lactamase Oxa-163, PDB code: 5odz was solved by B.A.Lund, T.J.O.Carlsen, H.K.S.Leiros, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.49 / 2.07
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	121.920, 121.920, 160.426, 90.00, 90.00, 120.00
R / Rfree (%)	14.5 / 18.7

The structure of Crystal Structure of the Beta-Lactamase Oxa-163 also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Magnesium atom in the Crystal Structure of the Beta-Lactamase Oxa-163 (pdb code 5odz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of the Beta-Lactamase Oxa-163, PDB code: 5odz:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of the Beta-Lactamase Oxa-163


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Beta-Lactamase Oxa-163 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg303 b:39.8 occ:1.00 HH21 B:ARG100 2.1 32.7 1.0 HD2 B:ARG100 2.5 40.4 1.0 HE1 B:TRP95 2.5 36.8 1.0 OD1 B:ASN106 2.6 28.7 1.0 HA B:ASN106 2.8 30.0 1.0 NH2 B:ARG100 2.9 27.2 1.0 O B:TRP105 2.9 28.8 1.0 HB2 B:ARG100 3.1 36.5 1.0 NE1 B:TRP95 3.1 30.6 1.0 HG3 B:ARG100 3.1 38.4 1.0 HB3 B:TRP105 3.2 26.9 1.0 O B:GLN98 3.2 32.4 1.0 HD1 B:TRP95 3.3 34.5 1.0 HH22 B:ARG100 3.3 32.7 1.0 CD B:ARG100 3.3 33.6 1.0 C B:TRP105 3.3 27.9 1.0 H B:ARG100 3.5 42.1 1.0 CD1 B:TRP95 3.5 28.8 1.0 CG B:ARG100 3.5 32.0 1.0 CA B:ASN106 3.6 25.0 1.0 N B:ASN106 3.7 23.5 1.0 HB2 B:TRP105 3.7 26.9 1.0 CG B:ASN106 3.7 35.6 1.0 CB B:ARG100 3.8 30.4 1.0 CB B:TRP105 3.8 22.4 1.0 CZ B:ARG100 3.9 32.4 1.0 HD3 B:ARG100 4.0 40.4 1.0 O B:HOH486 4.0 30.9 1.0 NE B:ARG100 4.0 29.8 1.0 N B:ARG100 4.1 35.1 1.0 CA B:TRP105 4.2 24.9 1.0 CB B:ASN106 4.2 30.4 1.0 HG2 B:PRO121 4.3 33.1 1.0 H B:ASN106 4.3 28.2 1.0 CE2 B:TRP95 4.3 33.6 1.0 C B:GLN98 4.4 38.9 1.0 H B:ARG107 4.5 28.9 1.0 HG2 B:ARG100 4.5 38.4 1.0 HE3 B:TRP105 4.5 28.3 1.0 O B:HOH481 4.5 29.7 1.0 HA B:THR99 4.5 50.0 1.0 HB3 B:ARG100 4.5 36.5 1.0 HB3 B:ASN106 4.6 36.5 1.0 CA B:ARG100 4.6 32.8 1.0 OD1 B:ASP96 4.7 33.1 1.0 HB2 B:GLN98 4.7 48.6 1.0 HA B:TRP105 4.7 29.9 1.0 C B:ASN106 4.8 26.4 1.0 CG B:TRP95 4.8 29.7 1.0 ND2 B:ASN106 4.8 34.3 1.0 HZ2 B:TRP95 4.8 39.8 1.0 HE B:ARG100 4.9 35.7 1.0 N B:ARG107 4.9 24.1 1.0 HD21 B:ASN106 5.0 41.1 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of the Beta-Lactamase Oxa-163


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Beta-Lactamase Oxa-163 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg304 b:50.7 occ:1.00 H B:GLY151 2.3 30.4 1.0 O B:HOH493 2.7 42.4 1.0 HA B:SER150 2.9 26.6 1.0 N B:GLY151 3.1 25.3 1.0 O B:HOH555 3.2 41.0 1.0 O B:HOH554 3.3 53.6 1.0 O B:GLY151 3.5 21.3 1.0 CA B:SER150 3.7 22.2 1.0 HB3 B:SER150 3.9 27.4 1.0 C B:SER150 3.9 25.0 1.0 CA B:GLY151 4.0 23.6 1.0 HA2 B:GLY151 4.1 28.3 1.0 C B:GLY151 4.2 22.3 1.0 CB B:SER150 4.2 22.8 1.0 OG B:SER150 4.6 35.2 1.0 O B:HOH436 4.7 26.0 1.0 O B:ILE149 4.8 24.1 1.0 N B:SER150 4.8 23.3 1.0 HA3 B:GLY151 4.9 28.3 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of the Beta-Lactamase Oxa-163


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the Beta-Lactamase Oxa-163 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg304 b:61.5 occ:1.00 HA D:HIS109 3.7 27.4 1.0 HG22 D:VAL92 3.8 37.0 1.0 HA B:ASP230 4.0 50.1 1.0 H D:ASN110 4.0 22.1 1.0 O D:ASP108 4.1 24.4 1.0 HG13 D:VAL92 4.1 35.2 1.0 HD22 D:ASN110 4.2 30.8 1.0 N D:ASN110 4.3 18.4 1.0 HB2 D:ASP108 4.3 27.2 1.0 HB3 D:ASN110 4.3 27.4 1.0 O B:ASP229 4.3 35.1 1.0 O D:HOH406 4.3 27.0 1.0 C D:HIS109 4.3 21.5 1.0 CA D:HIS109 4.3 22.9 1.0 ND2 D:ASN110 4.4 25.7 1.0 C D:ASP108 4.4 18.9 1.0 O D:HOH527 4.4 56.0 1.0 HB3 D:ASP108 4.4 27.2 1.0 HG21 D:THR113 4.5 28.7 1.0 N D:HIS109 4.5 22.8 1.0 HD21 D:ASN110 4.6 30.8 1.0 HB3 B:ASP230 4.6 71.4 1.0 CG2 D:VAL92 4.7 30.8 1.0 HG21 D:VAL92 4.7 37.0 1.0 CG D:ASN110 4.7 27.8 1.0 CB D:ASP108 4.8 22.7 1.0 OG1 D:THR113 4.9 20.4 1.0 O D:HIS109 4.9 24.9 1.0 CB D:ASN110 4.9 22.9 1.0 CA B:ASP230 4.9 41.7 1.0 CG1 D:VAL92 4.9 29.4 1.0 HG11 D:VAL92 4.9 35.2 1.0

B.A.Lund, A.M.Thomassen, T.J.O.Carlsen, H.K.S.Leiros. Structure, Activity and Thermostability Investigations of Oxa-163, Oxa-181 and Oxa-245 Using Biochemical Analysis, Crystal Structures and Differential Scanning Calorimetry Analysis. Acta Crystallogr F Struct V. 73 579 2017BIOL Commun.
ISSN: ESSN 2053-230X
PubMed: 28994407
DOI: 10.1107/S2053230X17013838