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Magnesium in PDB 3m6m: Crystal Structure of Rpff Complexed with Rec Domain of Rpfc

Enzymatic activity of Crystal Structure of Rpff Complexed with Rec Domain of Rpfc

All present enzymatic activity of Crystal Structure of Rpff Complexed with Rec Domain of Rpfc:
2.7.13.3;

Protein crystallography data

The structure of Crystal Structure of Rpff Complexed with Rec Domain of Rpfc, PDB code: 3m6m was solved by Z.Cheng, S.C.Lim, R.Qamra, H.Song, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.50
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 130.913, 130.913, 156.471, 90.00, 90.00, 120.00
R / Rfree (%) 25 / 27.1

Other elements in 3m6m:

The structure of Crystal Structure of Rpff Complexed with Rec Domain of Rpfc also contains other interesting chemical elements:

Iodine (I) 14 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Rpff Complexed with Rec Domain of Rpfc (pdb code 3m6m). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Rpff Complexed with Rec Domain of Rpfc, PDB code: 3m6m:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 3m6m

Go back to Magnesium Binding Sites List in 3m6m
Magnesium binding site 1 out of 3 in the Crystal Structure of Rpff Complexed with Rec Domain of Rpfc


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Rpff Complexed with Rec Domain of Rpfc within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg591

b:53.6
occ:1.00
O D:HIS514 2.3 47.1 1.0
OD2 D:ASP512 2.3 46.9 1.0
OD1 D:ASP469 2.5 59.0 1.0
CG D:ASP512 3.4 46.0 1.0
CG D:ASP469 3.5 59.7 1.0
C D:HIS514 3.5 46.9 1.0
OD2 D:ASP469 3.6 61.0 1.0
OD1 D:ASP512 3.7 46.6 1.0
ND1 D:HIS470 4.0 61.9 1.0
CA D:HIS514 4.3 46.9 1.0
OD1 D:ASP468 4.4 58.1 1.0
CE1 D:HIS470 4.4 62.9 1.0
CB D:HIS514 4.4 48.3 1.0
N D:MET515 4.5 46.8 1.0
NZ D:LYS566 4.6 68.5 1.0
CG D:MET515 4.7 45.4 1.0
N D:HIS514 4.7 45.8 1.0
CA D:MET515 4.7 47.3 1.0
CB D:ASP512 4.7 45.1 1.0
OD2 D:ASP468 4.8 57.1 1.0
CG D:ASP468 4.8 57.2 1.0
CB D:ASP469 4.9 60.0 1.0
N D:ASP469 4.9 58.1 1.0

Magnesium binding site 2 out of 3 in 3m6m

Go back to Magnesium Binding Sites List in 3m6m
Magnesium binding site 2 out of 3 in the Crystal Structure of Rpff Complexed with Rec Domain of Rpfc


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Rpff Complexed with Rec Domain of Rpfc within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg591

b:63.6
occ:1.00
OD2 E:ASP512 2.6 92.6 1.0
O E:HIS514 2.7 94.4 1.0
OD1 E:ASP512 3.4 91.3 1.0
CG E:ASP512 3.4 91.0 1.0
CB E:HIS514 3.6 96.2 1.0
NZ E:LYS566 3.6 0.6 1.0
C E:HIS514 3.7 93.3 1.0
OD1 E:ASP469 3.8 0.9 1.0
NE2 E:HIS470 3.9 0.4 1.0
CA E:HIS514 4.0 93.4 1.0
CD2 E:HIS470 4.1 0.7 1.0
N E:HIS514 4.2 91.2 1.0
OD2 E:ASP469 4.5 0.7 1.0
CG E:ASP469 4.6 0.1 1.0
CE E:LYS566 4.8 0.7 1.0
CG E:HIS514 4.8 96.8 1.0
N E:MET515 4.8 91.9 1.0
CB E:ASP512 4.9 88.7 1.0
CD E:LYS566 4.9 0.9 1.0
ND1 E:HIS514 5.0 96.2 1.0

Magnesium binding site 3 out of 3 in 3m6m

Go back to Magnesium Binding Sites List in 3m6m
Magnesium binding site 3 out of 3 in the Crystal Structure of Rpff Complexed with Rec Domain of Rpfc


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Rpff Complexed with Rec Domain of Rpfc within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg3

b:76.9
occ:1.00
OD2 F:ASP512 2.3 82.7 1.0
O F:HIS514 2.8 87.3 1.0
OD1 F:ASP469 3.0 0.8 1.0
CG F:ASP512 3.4 79.6 1.0
CD2 F:HIS470 3.7 0.5 1.0
OD1 F:ASP512 3.9 79.8 1.0
CG F:ASP469 3.9 0.6 1.0
C F:HIS514 4.0 86.3 1.0
OD2 F:ASP469 4.0 0.5 1.0
NZ F:LYS566 4.1 98.2 1.0
NE2 F:HIS470 4.3 0.4 1.0
OD1 F:ASP468 4.4 0.5 1.0
CB F:HIS514 4.7 90.2 1.0
CB F:ASP512 4.7 76.4 1.0
CA F:HIS514 4.7 86.2 1.0
OD2 F:ASP468 4.9 0.3 1.0
CG F:HIS470 4.9 0.7 1.0
N F:HIS514 5.0 82.9 1.0

Reference:

Z.Cheng, Y.W.He, S.C.Lim, R.Qamra, M.A.Walsh, L.H.Zhang, H.Song. Structural Basis of the Sensor-Synthase Interaction in Autoinduction of the Quorum Sensing Signal Dsf Biosynthesis Structure V. 18 1199 2010.
ISSN: ISSN 0969-2126
PubMed: 20826346
DOI: 10.1016/J.STR.2010.06.011
Page generated: Mon Dec 14 08:25:37 2020

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