Manganese in PDB 3myy: Structure of E. Coli Chey Mutant A113P Bound to Beryllium Fluoride

The structure of Structure of E. Coli Chey Mutant A113P Bound to Beryllium Fluoride, PDB code: 3myy was solved by R.M.Immormino, L.R.Mcdonald, R.B.Bourret, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.59 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	53.445, 53.547, 161.082, 90.00, 90.00, 90.00
R / Rfree (%)	17.3 / 20.2

The structure of Structure of E. Coli Chey Mutant A113P Bound to Beryllium Fluoride also contains other interesting chemical elements:

Fluorine

(F)

12 atoms

The binding sites of Manganese atom in the Structure of E. Coli Chey Mutant A113P Bound to Beryllium Fluoride (pdb code 3myy). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 7 binding sites of Manganese where determined in the Structure of E. Coli Chey Mutant A113P Bound to Beryllium Fluoride, PDB code: 3myy:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7;

Manganese binding site 1 out of 7 in the Structure of E. Coli Chey Mutant A113P Bound to Beryllium Fluoride


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structure of E. Coli Chey Mutant A113P Bound to Beryllium Fluoride within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn131 b:36.6 occ:1.00 OD2 A:ASP57 2.1 25.9 1.0 OD1 A:ASP13 2.2 29.9 1.0 O A:HOH174 2.2 35.1 1.0 O A:ASN59 2.2 25.7 1.0 O A:HOH139 2.3 28.0 1.0 F2 A:BEF130 2.3 33.6 1.0 CG A:ASP13 3.1 27.7 1.0 CG A:ASP57 3.1 27.1 1.0 BE A:BEF130 3.3 34.1 1.0 C A:ASN59 3.4 30.1 1.0 OD2 A:ASP13 3.4 33.8 1.0 OD1 A:ASP57 3.4 26.6 1.0 OD1 A:ASP12 4.0 26.5 1.0 CB A:ASN59 4.0 31.7 0.5 CA A:ASN59 4.0 31.3 0.5 CA A:ASN59 4.1 31.3 0.5 CB A:ASN59 4.1 31.7 0.5 O A:HOH182 4.1 51.7 1.0 CG A:MET60 4.2 24.8 1.0 F1 A:BEF130 4.2 27.8 1.0 N A:ASN59 4.2 26.2 1.0 F3 A:BEF130 4.3 27.3 1.0 O A:HOH169 4.3 47.4 1.0 N A:ASP13 4.4 25.2 1.0 CD2 A:PHE14 4.4 40.5 1.0 CB A:ASP57 4.5 25.2 1.0 N A:MET60 4.5 29.3 1.0 CB A:ASP13 4.5 30.0 1.0 CG A:ASP12 4.6 31.1 1.0 O A:HOH250 4.6 45.8 1.0 O A:HOH252 4.6 42.1 1.0 NZ A:LYS109 4.7 30.7 1.0 OD2 A:ASP12 4.7 26.9 1.0 CA A:MET60 4.7 26.3 1.0 CG A:ASN59 4.8 36.7 0.5 CE2 A:PHE14 4.8 46.0 1.0 CA A:ASP13 4.9 27.5 1.0

Manganese binding site 2 out of 7 in the Structure of E. Coli Chey Mutant A113P Bound to Beryllium Fluoride


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structure of E. Coli Chey Mutant A113P Bound to Beryllium Fluoride within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn133 b:81.1 occ:1.00 O A:HOH386 2.8 65.0 1.0 OG A:SER15 3.3 60.0 1.0 O A:HOH149 3.6 46.2 1.0 O A:HOH155 3.6 48.5 1.0 N A:SER15 3.7 33.0 1.0 O A:HOH246 3.8 54.3 1.0 CB A:SER15 4.0 46.2 1.0 O A:ASP13 4.3 39.6 1.0 O A:HOH353 4.3 59.8 1.0 CA A:PHE14 4.4 34.6 1.0 CD1 A:PHE14 4.5 54.8 1.0 CA A:SER15 4.5 40.8 1.0 C A:PHE14 4.6 35.5 1.0 O A:HOH173 4.9 50.6 1.0

Manganese binding site 3 out of 7 in the Structure of E. Coli Chey Mutant A113P Bound to Beryllium Fluoride


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Structure of E. Coli Chey Mutant A113P Bound to Beryllium Fluoride within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn134 b:0.3 occ:1.00 N A:GLY50 3.1 42.4 1.0 O A:HOH387 3.6 67.6 1.0 O A:HOH260 3.7 57.9 1.0 CA A:GLY50 3.9 45.9 1.0 CA A:GLY49 4.0 43.0 1.0 C A:GLY49 4.0 40.6 1.0 O A:HOH318 4.4 56.4 1.0 O A:HOH200 4.7 40.3 1.0 C A:GLY50 4.8 42.7 1.0 O A:HOH286 5.0 59.5 1.0

Manganese binding site 4 out of 7 in the Structure of E. Coli Chey Mutant A113P Bound to Beryllium Fluoride


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Structure of E. Coli Chey Mutant A113P Bound to Beryllium Fluoride within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn131 b:38.1 occ:1.00 O B:HOH142 2.2 28.7 1.0 O B:ASN59 2.2 31.6 1.0 OD2 B:ASP57 2.2 28.4 1.0 F2 B:BEF130 2.3 31.3 1.0 OD1 B:ASP13 2.3 26.5 1.0 O B:HOH137 2.3 27.5 1.0 CG B:ASP13 3.2 30.4 1.0 CG B:ASP57 3.2 27.4 1.0 C B:ASN59 3.4 32.7 1.0 BE B:BEF130 3.4 35.4 1.0 OD2 B:ASP13 3.4 30.4 1.0 OD1 B:ASP57 3.5 29.2 1.0 OD1 B:ASP12 3.9 28.8 1.0 O B:HOH148 4.1 46.5 1.0 CA B:ASN59 4.1 30.1 1.0 CB B:ASN59 4.2 31.9 1.0 F1 B:BEF130 4.2 31.0 1.0 CG B:MET60 4.3 26.0 1.0 CD2 B:PHE14 4.3 35.6 1.0 F3 B:BEF130 4.3 29.7 1.0 N B:ASN59 4.3 28.5 1.0 N B:MET60 4.4 27.4 1.0 O B:HOH231 4.4 51.1 1.0 N B:ASP13 4.5 25.6 1.0 O B:HOH153 4.5 46.5 1.0 CB B:ASP57 4.5 24.3 1.0 CB B:ASP13 4.6 26.2 1.0 CE2 B:PHE14 4.6 38.3 1.0 CG B:ASP12 4.6 28.9 1.0 CA B:MET60 4.7 26.5 1.0 NZ B:LYS109 4.7 29.0 1.0 OD2 B:ASP12 4.7 30.9 1.0 CG B:ASN59 4.8 43.5 1.0 O B:HOH228 4.9 43.9 1.0 O B:HOH254 5.0 46.0 1.0

Manganese binding site 5 out of 7 in the Structure of E. Coli Chey Mutant A113P Bound to Beryllium Fluoride


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Structure of E. Coli Chey Mutant A113P Bound to Beryllium Fluoride within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn132 b:55.4 occ:0.48 MN B:MN132 0.0 55.4 0.5 O A:HOH220 2.0 47.2 1.0 O A:HOH241 2.6 50.7 1.0 O A:HOH245 2.7 52.0 1.0 O B:HOH162 2.8 45.0 1.0 NZ B:LYS92 3.2 31.9 1.0 CE B:LYS92 3.3 28.3 1.0 O B:HOH225 3.5 51.8 1.0 O B:HOH218 3.6 40.7 1.0 MN B:MN132 4.1 45.0 0.5 CB B:LYS92 4.2 34.9 1.0 O2 A:SO4135 4.2 53.8 1.0 O B:HOH366 4.3 61.2 1.0 NZ A:LYS119 4.3 38.2 1.0 CE A:LYS119 4.5 37.3 1.0 O A:HOH208 4.5 41.3 1.0 CD B:LYS92 4.6 33.2 1.0 CG B:LYS92 4.6 32.2 1.0 N B:GLU93 4.7 28.2 1.0 O3 A:SO4135 4.7 67.1 1.0 O B:HOH362 4.8 62.5 1.0 S A:SO4135 4.9 61.1 1.0 O1 A:SO4135 4.9 45.3 1.0 O A:HOH136 4.9 25.1 1.0 CB B:GLU93 4.9 40.6 1.0

Manganese binding site 6 out of 7 in the Structure of E. Coli Chey Mutant A113P Bound to Beryllium Fluoride


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Structure of E. Coli Chey Mutant A113P Bound to Beryllium Fluoride within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn132 b:45.0 occ:0.52 MN B:MN132 0.0 45.0 0.5 O A:HOH308 2.1 57.0 1.0 O A:HOH220 2.6 47.2 1.0 O A:HOH168 3.1 33.6 1.0 NZ B:LYS92 3.2 31.9 1.0 O B:HOH164 3.2 34.3 1.0 NZ A:LYS119 3.4 38.2 1.0 CB B:GLU93 3.4 40.6 1.0 CA B:GLU93 3.5 34.3 1.0 CE A:LYS119 3.6 37.3 1.0 N B:GLU93 3.8 28.2 1.0 CD1 B:ILE96 4.0 29.9 1.0 MN B:MN132 4.1 55.4 0.5 CD A:LYS119 4.1 37.8 1.0 CG B:LYS92 4.1 32.2 1.0 CE B:LYS92 4.3 28.3 1.0 C B:LYS92 4.4 28.8 1.0 O A:TYR106 4.5 25.3 1.0 O B:HOH162 4.5 45.0 1.0 CB B:LYS92 4.7 34.9 1.0 CD B:LYS92 4.7 33.2 1.0 O B:LYS92 4.7 27.3 1.0 O A:HOH245 4.7 52.0 1.0 CG B:GLU93 4.8 54.7 1.0 CE A:LYS122 4.9 39.5 1.0 C B:GLU93 4.9 35.0 1.0 O B:HOH218 5.0 40.7 1.0 O A:HOH138 5.0 25.9 1.0 O B:HOH367 5.0 61.7 1.0

Manganese binding site 7 out of 7 in the Structure of E. Coli Chey Mutant A113P Bound to Beryllium Fluoride


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Structure of E. Coli Chey Mutant A113P Bound to Beryllium Fluoride within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn133 b:76.1 occ:1.00 OG B:SER15 3.4 35.6 0.4 O B:HOH211 3.5 39.6 1.0 N B:SER15 3.6 31.3 1.0 O B:HOH204 3.6 50.5 1.0 O B:HOH259 3.9 44.1 1.0 OG B:SER15 3.9 35.5 0.2 O B:HOH144 3.9 47.5 1.0 CB B:SER15 4.0 36.5 0.4 CB B:SER15 4.0 36.5 0.4 CB B:SER15 4.0 36.5 0.2 O B:HOH243 4.2 42.1 1.0 CA B:PHE14 4.2 35.0 1.0 O B:ASP13 4.2 33.1 1.0 CA B:SER15 4.4 35.1 0.4 CA B:SER15 4.4 35.1 0.4 CA B:SER15 4.4 35.0 0.2 C B:PHE14 4.4 31.4 1.0 CD1 B:PHE14 4.5 51.0 1.0 CB B:PHE14 4.9 32.3 1.0 CG B:PHE14 5.0 43.0 1.0

R.M.Immormino, L.R.Mcdonald, A.L.Lee, R.B.Bourret. Activation of Chey By Mutation at An Allosteric Site To Be Published.