Manganese in PDB 3rvl: Structure of the Chey-BEF3 Complex with Substitutions at 59 and 89: N59D and E89R

The structure of Structure of the Chey-BEF3 Complex with Substitutions at 59 and 89: N59D and E89R, PDB code: 3rvl was solved by C.A.Starbird, R.M.Immormino, R.E.Silversmith, R.B.Bourret, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.92 / 1.55
Space group	P 21 2 21
Cell size a, b, c (Å), α, β, γ (°)	37.630, 72.436, 107.280, 90.00, 90.00, 90.00
R / Rfree (%)	15.6 / 18.2

The structure of Structure of the Chey-BEF3 Complex with Substitutions at 59 and 89: N59D and E89R also contains other interesting chemical elements:

Fluorine

(F)

6 atoms

The binding sites of Manganese atom in the Structure of the Chey-BEF3 Complex with Substitutions at 59 and 89: N59D and E89R (pdb code 3rvl). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Structure of the Chey-BEF3 Complex with Substitutions at 59 and 89: N59D and E89R, PDB code: 3rvl:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the Structure of the Chey-BEF3 Complex with Substitutions at 59 and 89: N59D and E89R


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structure of the Chey-BEF3 Complex with Substitutions at 59 and 89: N59D and E89R within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn131 b:15.2 occ:1.00 OD1 A:ASP13 2.1 11.7 1.0 O A:HOH145 2.1 11.1 1.0 OD2 A:ASP57 2.1 11.8 1.0 O A:HOH135 2.1 12.9 1.0 F2 A:BEF130 2.2 12.4 1.0 O A:ASP59 2.2 10.3 1.0 CG A:ASP57 3.2 10.4 1.0 CG A:ASP13 3.2 11.9 1.0 BE A:BEF130 3.3 10.2 1.0 C A:ASP59 3.4 10.9 1.0 OD1 A:ASP57 3.5 11.5 1.0 OD2 A:ASP13 3.5 15.4 1.0 HG2 A:MET60 3.6 10.6 1.0 H A:ASP13 3.7 14.0 1.0 HB2 A:ASP59 3.7 13.2 1.0 OD1 A:ASP12 3.9 12.8 1.0 HG3 A:MET60 4.0 10.6 1.0 HZ1 A:LYS109 4.0 15.3 1.0 HA A:MET60 4.1 13.2 1.0 H A:ASP59 4.2 12.7 1.0 CA A:ASP59 4.2 9.5 1.0 F1 A:BEF130 4.2 13.1 1.0 CG A:MET60 4.2 8.8 1.0 F3 A:BEF130 4.3 12.4 1.0 N A:ASP59 4.3 10.6 1.0 CB A:ASP59 4.3 11.0 1.0 O A:HOH260 4.4 23.8 1.0 N A:MET60 4.4 11.4 1.0 HB3 A:ASP59 4.4 13.2 1.0 CB A:ASP57 4.4 11.5 1.0 N A:ASP13 4.5 11.7 1.0 HB3 A:ASP57 4.5 13.8 1.0 O A:HOH151 4.5 15.1 1.0 CB A:ASP13 4.5 11.9 1.0 H A:PHE14 4.6 16.3 1.0 HB2 A:PHE14 4.7 20.3 1.0 CA A:MET60 4.7 11.0 1.0 HB2 A:ASP57 4.8 13.8 1.0 NZ A:LYS109 4.8 12.8 1.0 CG A:ASP12 4.8 11.2 1.0 HB3 A:ASP13 4.8 14.2 1.0 HZ2 A:LYS109 4.8 15.3 1.0 CA A:ASP13 4.9 11.3 1.0 HA A:ASP12 4.9 11.5 1.0 H A:TRP58 4.9 13.3 1.0

Manganese binding site 2 out of 3 in the Structure of the Chey-BEF3 Complex with Substitutions at 59 and 89: N59D and E89R


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structure of the Chey-BEF3 Complex with Substitutions at 59 and 89: N59D and E89R within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn131 b:13.2 occ:1.00 OD2 B:ASP57 2.1 8.8 1.0 O B:HOH143 2.1 9.6 1.0 OD1 B:ASP13 2.1 10.4 1.0 O B:ASP59 2.2 10.4 1.0 O B:HOH136 2.2 10.2 1.0 F2 B:BEF130 2.2 10.6 1.0 CG B:ASP57 3.1 9.6 1.0 CG B:ASP13 3.2 10.8 1.0 BE B:BEF130 3.3 6.3 1.0 C B:ASP59 3.3 9.5 1.0 OD1 B:ASP57 3.5 9.8 1.0 OD2 B:ASP13 3.5 13.3 1.0 HG2 B:MET60 3.6 10.7 1.0 HB2 B:ASP59 3.6 9.2 1.0 H B:ASP13 3.7 11.6 1.0 OD1 B:ASP12 3.9 11.7 1.0 HG3 B:MET60 3.9 10.7 1.0 H B:ASP59 4.0 11.0 1.0 O B:HOH213 4.1 17.7 1.0 CA B:ASP59 4.1 9.8 1.0 HA B:MET60 4.1 11.8 1.0 F1 B:BEF130 4.2 10.1 1.0 CG B:MET60 4.2 8.9 1.0 CB B:ASP59 4.2 7.7 1.0 N B:ASP59 4.2 9.2 1.0 HZ2 B:LYS109 4.3 12.2 1.0 F3 B:BEF130 4.3 10.3 1.0 HB3 B:ASP59 4.4 9.2 1.0 N B:MET60 4.4 12.3 1.0 N B:ASP13 4.4 9.6 1.0 CB B:ASP57 4.4 9.6 1.0 CB B:ASP13 4.5 11.3 1.0 HB3 B:ASP57 4.5 11.5 1.0 O B:HOH233 4.5 13.1 1.0 HZ1 B:LYS109 4.6 12.2 1.0 H B:PHE14 4.6 13.4 1.0 CA B:MET60 4.7 9.8 1.0 HB2 B:PHE14 4.7 15.9 1.0 CG B:ASP12 4.7 9.9 1.0 HB3 B:ASP13 4.7 13.6 1.0 HB2 B:ASP57 4.8 11.5 1.0 NZ B:LYS109 4.8 10.2 1.0 CA B:ASP13 4.9 8.6 1.0 H B:TRP58 4.9 11.0 1.0 O B:HOH163 4.9 24.0 1.0 HA B:ASP12 5.0 11.0 1.0

Manganese binding site 3 out of 3 in the Structure of the Chey-BEF3 Complex with Substitutions at 59 and 89: N59D and E89R


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Structure of the Chey-BEF3 Complex with Substitutions at 59 and 89: N59D and E89R within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn132 b:71.9 occ:1.00 O B:HOH297 2.5 46.8 1.0 HD21 B:ASN62 2.8 24.1 1.0 O B:HOH181 3.2 23.8 1.0 HG2 B:PRO61 3.5 17.1 1.0 HB2 B:PRO61 3.5 17.4 1.0 ND2 B:ASN62 3.5 20.1 1.0 HG3 B:PRO61 3.6 17.1 1.0 O B:HOH192 3.6 39.5 1.0 CG B:PRO61 3.8 14.2 1.0 HD22 B:ASN62 3.9 24.1 1.0 CB B:PRO61 4.1 14.5 1.0 O B:HOH254 4.3 48.9 1.0 O B:HOH282 4.3 40.5 1.0 HB3 B:PRO61 4.4 17.4 1.0 CG B:ASN62 4.4 23.1 1.0 OD1 B:ASN62 4.5 21.3 1.0 O B:HOH330 4.9 45.8 1.0

R.M.Immormino, C.A.Starbird, R.E.Silversmith, R.B.Bourret. Probing Mechanistic Similarities Between Response Regulator Signaling Proteins and Haloacid Dehalogenase Phosphatases. Biochemistry V. 54 3514 2015.
ISSN: ISSN 0006-2960
PubMed: 25928369
DOI: 10.1021/ACS.BIOCHEM.5B00286