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Manganese in PDB 3rvn: Structure of the Chey-BEF3 Complex with Substitutions at 59 and 89: N59D and E89Y

Protein crystallography data

The structure of Structure of the Chey-BEF3 Complex with Substitutions at 59 and 89: N59D and E89Y, PDB code: 3rvn 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) 27.60 / 2.25
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 53.436, 53.613, 161.310, 90.00, 90.00, 90.00
R / Rfree (%) 18.6 / 22.5

Other elements in 3rvn:

The structure of Structure of the Chey-BEF3 Complex with Substitutions at 59 and 89: N59D and E89Y also contains other interesting chemical elements:

Fluorine (F) 6 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Structure of the Chey-BEF3 Complex with Substitutions at 59 and 89: N59D and E89Y (pdb code 3rvn). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Structure of the Chey-BEF3 Complex with Substitutions at 59 and 89: N59D and E89Y, PDB code: 3rvn:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 3rvn

Go back to Manganese Binding Sites List in 3rvn
Manganese binding site 1 out of 2 in the Structure of the Chey-BEF3 Complex with Substitutions at 59 and 89: N59D and E89Y


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 E89Y within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn130

b:31.9
occ:1.00
OD2 A:ASP57 2.1 24.3 1.0
F2 A:BEF131 2.2 26.2 1.0
OD1 A:ASP13 2.2 29.1 1.0
O A:HOH174 2.2 30.9 1.0
O A:ASP59 2.3 27.5 1.0
O A:HOH146 2.4 25.5 1.0
CG A:ASP57 3.1 23.8 1.0
CG A:ASP13 3.2 26.9 1.0
BE A:BEF131 3.3 29.5 1.0
OD1 A:ASP57 3.4 22.5 1.0
OD2 A:ASP13 3.4 30.2 1.0
C A:ASP59 3.5 30.5 1.0
CB A:ASP59 4.0 28.2 1.0
OD1 A:ASP12 4.1 27.0 1.0
CA A:ASP59 4.2 25.8 1.0
F1 A:BEF131 4.2 24.1 1.0
O A:HOH237 4.2 42.7 1.0
F3 A:BEF131 4.3 23.5 1.0
O A:HOH260 4.4 41.1 1.0
N A:ASP59 4.4 25.9 1.0
CG A:MET60 4.4 22.9 1.0
CB A:ASP57 4.4 22.0 1.0
N A:ASP13 4.5 26.9 1.0
CB A:ASP13 4.5 24.4 1.0
CG A:ASP59 4.5 31.4 1.0
N A:MET60 4.5 27.3 1.0
CE2 A:PHE14 4.6 47.4 1.0
CD2 A:PHE14 4.7 45.1 1.0
CG A:ASP12 4.7 25.6 1.0
NZ A:LYS109 4.7 22.2 1.0
OD2 A:ASP12 4.7 26.5 1.0
CA A:MET60 4.8 28.2 1.0
OD2 A:ASP59 4.8 33.0 1.0
CA A:ASP13 5.0 27.1 1.0

Manganese binding site 2 out of 2 in 3rvn

Go back to Manganese Binding Sites List in 3rvn
Manganese binding site 2 out of 2 in the Structure of the Chey-BEF3 Complex with Substitutions at 59 and 89: N59D and E89Y


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 E89Y within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn130

b:32.4
occ:1.00
OD2 B:ASP57 2.2 24.6 1.0
O B:ASP59 2.2 28.1 1.0
O B:HOH153 2.2 29.4 1.0
OD1 B:ASP13 2.2 28.6 1.0
F2 B:BEF131 2.2 28.2 1.0
O B:HOH137 2.3 23.3 1.0
CG B:ASP13 3.2 29.1 1.0
CG B:ASP57 3.2 23.8 1.0
BE B:BEF131 3.3 28.4 1.0
C B:ASP59 3.4 27.0 1.0
OD2 B:ASP13 3.5 32.3 1.0
OD1 B:ASP57 3.5 22.3 1.0
OD1 B:ASP12 4.0 22.4 1.0
CB B:ASP59 4.0 25.8 1.0
CA B:ASP59 4.1 26.9 1.0
CD2 B:PHE14 4.2 42.9 1.0
F1 B:BEF131 4.2 24.9 1.0
N B:ASP59 4.3 26.9 1.0
F3 B:BEF131 4.3 25.7 1.0
O B:HOH175 4.3 34.0 1.0
CG B:MET60 4.3 18.0 1.0
N B:MET60 4.4 28.0 1.0
N B:ASP13 4.5 24.3 1.0
CB B:ASP57 4.5 22.6 1.0
CG B:ASP59 4.5 27.8 1.0
CB B:ASP13 4.5 28.5 1.0
CE2 B:PHE14 4.6 44.2 1.0
O B:HOH193 4.6 47.2 1.0
CA B:MET60 4.6 27.6 1.0
CG B:ASP12 4.7 28.1 1.0
NZ B:LYS109 4.7 25.8 1.0
O B:HOH230 4.7 33.5 1.0
OD2 B:ASP12 4.8 27.3 1.0
OD2 B:ASP59 4.9 33.8 1.0

Reference:

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
Page generated: Sat Oct 5 17:50:48 2024

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