Magnesium in PDB 7qoc: Se-Met Derivative Structure of A Small Alarmone Hydrolase (Relh) From Corynebacterium Glutamicum

All present enzymatic activity of Se-Met Derivative Structure of A Small Alarmone Hydrolase (Relh) From Corynebacterium Glutamicum:
3.1.7.2;

The structure of Se-Met Derivative Structure of A Small Alarmone Hydrolase (Relh) From Corynebacterium Glutamicum, PDB code: 7qoc was solved by F.Bisiak, D.E.Brodersen, A.Chrenkova, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.01 / 2.30
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	96.01, 96.01, 80.47, 90, 90, 120
R / Rfree (%)	19.2 / 21.5

The binding sites of Magnesium atom in the Se-Met Derivative Structure of A Small Alarmone Hydrolase (Relh) From Corynebacterium Glutamicum (pdb code 7qoc). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Se-Met Derivative Structure of A Small Alarmone Hydrolase (Relh) From Corynebacterium Glutamicum, PDB code: 7qoc:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Se-Met Derivative Structure of A Small Alarmone Hydrolase (Relh) From Corynebacterium Glutamicum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Se-Met Derivative Structure of A Small Alarmone Hydrolase (Relh) From Corynebacterium Glutamicum within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:77.8 occ:1.00 OD1 A:ASP122 2.0 78.1 1.0 NE2 A:HIS58 2.5 76.2 1.0 OD2 A:ASP59 2.5 91.3 1.0 NE2 A:HIS34 2.6 62.8 1.0 CG A:ASP122 2.8 75.7 1.0 OD2 A:ASP122 3.2 78.2 1.0 OH A:TYR31 3.3 78.2 1.0 CD2 A:HIS34 3.4 61.9 1.0 CD2 A:HIS58 3.4 74.8 1.0 CG A:ASP59 3.5 88.9 1.0 CE1 A:HIS58 3.5 75.8 1.0 CE1 A:HIS34 3.6 63.5 1.0 OD1 A:ASP59 3.8 91.4 1.0 CB A:ASP122 4.1 68.7 1.0 ND2 A:ASN126 4.3 68.0 1.0 CZ A:TYR31 4.5 75.3 1.0 CG A:HIS34 4.5 61.9 1.0 CG A:HIS58 4.6 74.5 1.0 OD1 A:ASN126 4.6 69.0 1.0 ND1 A:HIS58 4.7 75.5 1.0 ND1 A:HIS34 4.7 63.5 1.0 CB A:ASP59 4.8 80.3 1.0 CA A:ASP122 4.8 65.7 1.0 CG A:ASN126 4.9 68.1 1.0 CE2 A:TYR31 5.0 73.9 1.0

Magnesium binding site 2 out of 2 in the Se-Met Derivative Structure of A Small Alarmone Hydrolase (Relh) From Corynebacterium Glutamicum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Se-Met Derivative Structure of A Small Alarmone Hydrolase (Relh) From Corynebacterium Glutamicum within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg201 b:122.2 occ:1.00 OD1 B:ASP122 2.0 83.1 1.0 NE2 B:HIS58 2.5 100.9 1.0 OD2 B:ASP59 2.6 110.9 1.0 NE2 B:HIS34 2.6 71.0 1.0 CG B:ASP122 2.8 81.7 1.0 OD2 B:ASP122 3.2 84.7 1.0 OH B:TYR31 3.3 76.6 1.0 CD2 B:HIS34 3.3 70.3 1.0 CD2 B:HIS58 3.4 99.9 1.0 CE1 B:HIS58 3.5 100.6 1.0 CG B:ASP59 3.6 107.6 1.0 CE1 B:HIS34 3.6 71.4 1.0 OD1 B:ASP59 3.8 109.1 1.0 CB B:ASP122 4.1 77.1 1.0 ND2 B:ASN126 4.4 82.1 1.0 CZ B:TYR31 4.5 73.3 1.0 CG B:HIS34 4.5 70.0 1.0 CG B:HIS58 4.6 98.2 1.0 ND1 B:HIS58 4.7 100.1 1.0 OD1 B:ASN126 4.7 83.9 1.0 ND1 B:HIS34 4.7 71.3 1.0 CA B:ASP122 4.8 75.8 1.0 CB B:ASP59 4.9 99.8 1.0 CE2 B:TYR31 4.9 71.7 1.0 CG B:ASN126 5.0 81.6 1.0

F.Bisiak, A.Chrenkova, S.D.Zhang, J.N.Pedersen, D.E.Otzen, Y.E.Zhang, D.E.Brodersen. Structural Variations Between Small Alarmone Hydrolase Dimers Support Different Modes of Regulation of the Stringent Response. J.Biol.Chem. V. 298 02142 2022.
ISSN: ESSN 1083-351X
PubMed: 35714769
DOI: 10.1016/J.JBC.2022.102142