Manganese in PDB 6a54: Crystal Structure of Dddk Mutant Y64A

The structure of Crystal Structure of Dddk Mutant Y64A, PDB code: 6a54 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)	28.69 / 2.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	35.142, 57.378, 55.377, 90.00, 94.09, 90.00
R / Rfree (%)	22.4 / 29.4

The binding sites of Manganese atom in the Crystal Structure of Dddk Mutant Y64A (pdb code 6a54). 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 Mutant Y64A, PDB code: 6a54:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Crystal Structure of Dddk Mutant Y64A


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 Mutant Y64A within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn200 b:48.4 occ:1.00 O A:HOH331 2.3 48.4 1.0 NE2 A:HIS56 2.4 38.8 1.0 NE2 A:HIS96 2.4 37.6 1.0 NE2 A:HIS58 2.4 48.2 1.0 OE1 A:GLU62 2.4 39.9 1.0 CE1 A:HIS56 3.3 40.2 1.0 CE1 A:HIS96 3.3 37.4 1.0 CD A:GLU62 3.3 40.1 1.0 CD2 A:HIS58 3.3 45.0 1.0 CD2 A:HIS56 3.4 32.2 1.0 CD2 A:HIS96 3.4 38.4 1.0 CE1 A:HIS58 3.4 45.8 1.0 OE2 A:GLU62 3.5 46.1 1.0 OH A:TYR122 3.8 69.6 1.0 CZ A:TYR122 4.3 64.2 1.0 CE2 A:TYR122 4.3 61.1 1.0 ND1 A:HIS56 4.4 42.9 1.0 ND1 A:HIS96 4.4 36.0 1.0 CZ A:PHE112 4.5 36.3 1.0 CG A:HIS56 4.5 35.1 1.0 CG A:HIS96 4.5 41.5 1.0 ND1 A:HIS58 4.5 41.9 1.0 CG A:HIS58 4.5 45.2 1.0 CG A:GLU62 4.7 36.6 1.0 CD1 A:ILE90 4.9 42.4 1.0 CE1 A:PHE112 4.9 39.8 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of Dddk Mutant Y64A


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 Mutant Y64A within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn200 b:64.6 occ:1.00 NE2 B:HIS96 2.1 49.1 1.0 O B:HOH307 2.2 67.7 1.0 NE2 B:HIS58 2.4 63.1 1.0 NE2 B:HIS56 2.6 61.2 1.0 OE1 B:GLU62 2.7 67.6 1.0 OE2 B:GLU62 2.7 66.1 1.0 CE1 B:HIS96 2.9 57.6 1.0 CD B:GLU62 3.0 62.1 1.0 CD2 B:HIS96 3.2 51.8 1.0 CE1 B:HIS56 3.3 62.3 1.0 CE1 B:HIS58 3.3 57.3 1.0 CD2 B:HIS58 3.4 59.6 1.0 CD2 B:HIS56 3.7 65.3 1.0 ND1 B:HIS96 4.1 55.7 1.0 CE2 B:TYR122 4.1 67.2 1.0 CG B:HIS96 4.2 52.0 1.0 CD1 B:ILE90 4.3 70.4 1.0 ND1 B:HIS56 4.4 64.1 1.0 OH B:TYR122 4.4 62.2 1.0 ND1 B:HIS58 4.5 53.5 1.0 CG B:GLU62 4.5 52.9 1.0 CG B:HIS58 4.5 60.6 1.0 CZ B:TYR122 4.6 63.9 1.0 CZ B:PHE112 4.6 63.0 1.0 CG B:HIS56 4.6 67.8 1.0 CD2 B:TYR122 4.9 70.7 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