Manganese in PDB 7qod: Native Structure of A Small Alarmone Hydrolase (Relh) From Corynebacterium Glutamicum

All present enzymatic activity of Native Structure of A Small Alarmone Hydrolase (Relh) From Corynebacterium Glutamicum:
3.1.7.2;

The structure of Native Structure of A Small Alarmone Hydrolase (Relh) From Corynebacterium Glutamicum, PDB code: 7qod 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)	36.43 / 1.85
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	94.332, 94.332, 80.561, 90, 90, 120
R / Rfree (%)	17.7 / 20.6

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

Manganese binding site 1 out of 2 in the Native Structure of A Small Alarmone Hydrolase (Relh) From Corynebacterium Glutamicum


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Native Structure of A Small Alarmone Hydrolase (Relh) From Corynebacterium Glutamicum within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn201 b:34.4 occ:1.00 O A:HOH313 2.1 37.0 1.0 O A:HOH352 2.2 37.4 1.0 OD1 A:ASP122 2.2 33.2 1.0 NE2 A:HIS58 2.2 35.7 1.0 NE2 A:HIS34 2.3 32.5 1.0 OD2 A:ASP59 2.3 34.1 1.0 CG A:ASP122 3.0 40.2 1.0 CE1 A:HIS34 3.2 36.1 1.0 CG A:ASP59 3.2 40.1 1.0 CE1 A:HIS58 3.2 31.9 1.0 CD2 A:HIS58 3.2 37.6 1.0 CD2 A:HIS34 3.3 31.3 1.0 OD2 A:ASP122 3.4 43.5 1.0 OD1 A:ASP59 3.4 37.0 1.0 OH A:TYR31 3.7 39.6 1.0 CB A:ASP122 4.2 35.5 1.0 ND2 A:ASN126 4.2 37.4 1.0 ND1 A:HIS58 4.3 34.7 1.0 ND1 A:HIS34 4.3 35.0 1.0 CG A:HIS58 4.3 37.3 1.0 CG A:HIS34 4.4 34.6 1.0 CB A:ASP59 4.6 34.5 1.0 CZ A:TYR31 4.7 36.1 1.0 OD1 A:ASN126 4.8 42.3 1.0 CA A:ASP122 4.8 32.0 1.0 NH2 A:ARG24 4.9 44.5 0.5 CG A:ASN126 5.0 37.4 1.0 CE2 A:TYR31 5.0 32.0 1.0

Manganese binding site 2 out of 2 in the Native Structure of A Small Alarmone Hydrolase (Relh) From Corynebacterium Glutamicum


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Native Structure of A Small Alarmone Hydrolase (Relh) From Corynebacterium Glutamicum within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn201 b:39.9 occ:1.00 OD1 B:ASP122 2.2 40.3 1.0 O B:HOH328 2.2 40.4 1.0 NE2 B:HIS58 2.2 38.4 1.0 NE2 B:HIS34 2.3 36.4 1.0 O B:HOH303 2.3 45.5 1.0 OD2 B:ASP59 2.4 43.3 1.0 CG B:ASP122 3.0 41.5 1.0 CE1 B:HIS58 3.1 39.0 1.0 CE1 B:HIS34 3.2 37.4 1.0 CD2 B:HIS34 3.2 34.4 1.0 CG B:ASP59 3.3 43.8 1.0 OD2 B:ASP122 3.3 46.9 1.0 CD2 B:HIS58 3.3 41.2 1.0 OD1 B:ASP59 3.5 43.9 1.0 OH B:TYR31 3.7 37.0 1.0 CB B:ASP122 4.2 40.8 1.0 ND1 B:HIS58 4.3 38.6 1.0 ND1 B:HIS34 4.3 35.6 1.0 CG B:HIS34 4.4 35.8 1.0 CG B:HIS58 4.4 42.2 1.0 ND2 B:ASN126 4.4 51.7 1.0 CB B:ASP59 4.6 44.2 1.0 OD1 B:ASN126 4.7 54.0 1.0 CZ B:TYR31 4.8 32.5 1.0 CA B:ASP122 4.8 40.9 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