Manganese in PDB 6a53: Crystal Structure of Dddk

The structure of Crystal Structure of Dddk, PDB code: 6a53 was solved by Y.Z.Zhang, C.Y.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.78 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	35.284, 57.395, 55.788, 90.00, 94.22, 90.00
R / Rfree (%)	17.2 / 21.3

The binding sites of Manganese atom in the Crystal Structure of Dddk (pdb code 6a53). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Crystal Structure of Dddk, PDB code: 6a53:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Crystal Structure of Dddk


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Dddk within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn200 b:23.6 occ:1.00 OE1 A:GLU62 2.2 18.9 1.0 O A:HOH355 2.2 25.2 1.0 NE2 A:HIS58 2.3 20.4 1.0 NE2 A:HIS96 2.3 16.8 1.0 NE2 A:HIS56 2.5 18.6 1.0 CE1 A:HIS58 3.1 20.1 1.0 CE1 A:HIS96 3.2 16.3 1.0 CD A:GLU62 3.2 21.4 1.0 OH A:TYR64 3.3 28.3 1.0 CD2 A:HIS58 3.3 23.0 1.0 CD2 A:HIS96 3.4 17.9 1.0 CE1 A:HIS56 3.4 17.7 1.0 OE2 A:GLU62 3.5 22.4 1.0 CD2 A:HIS56 3.5 17.2 1.0 CZ A:TYR64 4.3 22.4 1.0 ND1 A:HIS58 4.3 23.6 1.0 ND1 A:HIS96 4.3 16.5 1.0 CE2 A:TYR122 4.4 31.9 1.0 CG A:HIS58 4.4 23.9 1.0 CG A:HIS96 4.5 21.1 1.0 CE1 A:TYR64 4.5 21.0 1.0 ND1 A:HIS56 4.5 20.4 1.0 OH A:TYR122 4.5 32.7 1.0 CG A:GLU62 4.6 14.8 1.0 CG A:HIS56 4.6 20.8 1.0 CZ A:TYR122 4.7 31.6 1.0 CZ A:PHE112 4.7 15.6 1.0 CB A:GLU62 4.9 15.1 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of Dddk


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Dddk within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn200 b:39.6 occ:1.00 NE2 B:HIS96 2.2 32.3 1.0 OE1 B:GLU62 2.2 35.7 1.0 NE2 B:HIS58 2.3 39.4 1.0 O B:HOH304 2.3 49.5 1.0 NE2 B:HIS56 2.6 37.1 1.0 CE1 B:HIS96 3.0 34.8 1.0 OH B:TYR64 3.1 48.4 1.0 CD B:GLU62 3.1 36.0 1.0 CE1 B:HIS58 3.2 38.1 1.0 OE2 B:GLU62 3.3 42.3 1.0 CD2 B:HIS96 3.4 33.2 1.0 CD2 B:HIS58 3.4 42.4 1.0 CE1 B:HIS56 3.5 42.2 1.0 CD2 B:HIS56 3.5 41.8 1.0 CZ B:TYR64 4.1 39.1 1.0 ND1 B:HIS96 4.2 31.7 1.0 CE2 B:TYR122 4.3 40.9 1.0 ND1 B:HIS58 4.4 34.1 1.0 CG B:HIS96 4.4 29.2 1.0 CG B:HIS58 4.5 38.2 1.0 CE1 B:TYR64 4.5 34.0 1.0 CG B:GLU62 4.5 30.0 1.0 OH B:TYR122 4.6 45.0 1.0 ND1 B:HIS56 4.6 46.8 1.0 CG B:HIS56 4.6 44.7 1.0 CZ B:TYR122 4.8 41.2 1.0 CD1 B:ILE90 4.9 29.8 1.0 CZ B:PHE112 4.9 37.0 1.0 CB B:GLU62 5.0 27.2 1.0

M.Peng, X.L.Chen, D.Zhang, X.J.Wang, N.Wang, P.Wang, J.D.Todd, Y.Z.Zhang, C.Y.Li. Structure-Function Analysis Indicates That An Active-Site Water Molecule Participates in Dimethylsulfoniopropionate Cleavage By Dddk. Appl. Environ. Microbiol. V. 85 2019.
ISSN: ESSN 1098-5336
PubMed: 30770407
DOI: 10.1128/AEM.03127-18