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Magnesium in PDB 4iru: Crystal Structure of Lepb Gap Core in A Transition State Mimetic Complex with RAB1A and ALF3

Enzymatic activity of Crystal Structure of Lepb Gap Core in A Transition State Mimetic Complex with RAB1A and ALF3

All present enzymatic activity of Crystal Structure of Lepb Gap Core in A Transition State Mimetic Complex with RAB1A and ALF3:
3.6.5.2;

Protein crystallography data

The structure of Crystal Structure of Lepb Gap Core in A Transition State Mimetic Complex with RAB1A and ALF3, PDB code: 4iru was solved by A.K.Mishra, C.M.Delcampo, R.E.Collins, C.R.Roy, D.G.Lambright, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.01 / 3.20
Space group I 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 139.404, 139.404, 384.519, 90.00, 90.00, 90.00
R / Rfree (%) 23 / 28.8

Other elements in 4iru:

The structure of Crystal Structure of Lepb Gap Core in A Transition State Mimetic Complex with RAB1A and ALF3 also contains other interesting chemical elements:

Fluorine (F) 9 atoms
Aluminium (Al) 3 atoms
Potassium (K) 6 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Lepb Gap Core in A Transition State Mimetic Complex with RAB1A and ALF3 (pdb code 4iru). 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 Lepb Gap Core in A Transition State Mimetic Complex with RAB1A and ALF3, PDB code: 4iru:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 4iru

Go back to Magnesium Binding Sites List in 4iru
Magnesium binding site 1 out of 3 in the Crystal Structure of Lepb Gap Core in A Transition State Mimetic Complex with RAB1A and ALF3


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 Lepb Gap Core in A Transition State Mimetic Complex with RAB1A and ALF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg201

b:32.8
occ:1.00
O B:HOH303 1.7 18.3 1.0
F1 B:AF3203 1.8 32.2 1.0
O B:HOH302 1.9 22.8 1.0
O3B B:GDP202 2.1 20.2 1.0
OG B:SER25 2.5 24.1 1.0
OG1 B:THR43 2.7 17.3 1.0
PB B:GDP202 3.0 19.1 1.0
AL B:AF3203 3.1 33.4 1.0
O1B B:GDP202 3.1 19.9 1.0
CB B:THR43 3.2 17.3 1.0
CB B:SER25 3.5 27.0 1.0
N B:THR43 3.6 18.2 1.0
F2 B:AF3203 3.9 33.3 1.0
O1A B:GDP202 4.0 22.9 1.0
CA B:THR43 4.0 17.4 1.0
O3A B:GDP202 4.1 21.8 1.0
O2B B:GDP202 4.1 20.4 1.0
N B:SER25 4.2 28.2 1.0
O B:HOH308 4.3 16.4 1.0
PA B:GDP202 4.3 23.1 1.0
NH2 A:ARG444 4.3 28.0 1.0
O2A B:GDP202 4.3 23.6 1.0
OD2 B:ASP66 4.3 39.0 1.0
F3 B:AF3203 4.4 31.7 1.0
CA B:SER25 4.4 28.0 1.0
CG2 B:THR43 4.4 17.5 1.0
OD1 B:ASP66 4.5 37.5 1.0
O B:THR67 4.7 29.7 1.0
O B:ILE41 4.7 22.1 1.0
C B:SER42 4.7 18.7 1.0
CG B:ASP66 4.8 35.8 1.0
CA B:SER42 4.9 18.9 1.0
CB B:LYS24 4.9 26.4 1.0
CE B:LYS24 4.9 26.4 1.0

Magnesium binding site 2 out of 3 in 4iru

Go back to Magnesium Binding Sites List in 4iru
Magnesium binding site 2 out of 3 in the Crystal Structure of Lepb Gap Core in A Transition State Mimetic Complex with RAB1A and ALF3


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 Lepb Gap Core in A Transition State Mimetic Complex with RAB1A and ALF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg201

b:36.0
occ:1.00
F1 D:AF3203 1.8 29.4 1.0
O3B D:GDP202 1.9 23.5 1.0
O D:HOH302 1.9 18.5 1.0
O D:HOH303 2.0 12.9 1.0
OG D:SER25 2.4 28.8 1.0
OG1 D:THR43 2.6 21.6 1.0
PB D:GDP202 3.0 22.9 1.0
AL D:AF3203 3.1 30.5 1.0
CB D:THR43 3.1 21.4 1.0
CB D:SER25 3.4 31.2 1.0
O1B D:GDP202 3.4 23.4 1.0
N D:THR43 3.5 22.8 1.0
F2 D:AF3203 3.8 30.3 1.0
CA D:THR43 3.9 22.0 1.0
O2B D:GDP202 4.0 24.0 1.0
O3A D:GDP202 4.1 24.4 1.0
O1A D:GDP202 4.1 25.7 1.0
NH1 C:ARG444 4.1 24.4 1.0
N D:SER25 4.2 31.1 1.0
O D:HOH301 4.2 46.6 1.0
CG2 D:THR43 4.3 21.3 1.0
OD1 D:ASP66 4.4 35.5 1.0
CA D:SER25 4.4 31.7 1.0
PA D:GDP202 4.4 25.2 1.0
F3 D:AF3203 4.4 30.2 1.0
O D:THR67 4.4 31.0 1.0
O2A D:GDP202 4.5 26.4 1.0
OD2 D:ASP66 4.5 37.2 1.0
O D:ILE41 4.6 28.7 1.0
C D:SER42 4.6 24.2 1.0
CG D:ASP66 4.8 35.5 1.0
CA D:SER42 4.8 25.4 1.0
CB D:LYS24 4.9 32.2 1.0
CE D:LYS24 5.0 33.4 1.0

Magnesium binding site 3 out of 3 in 4iru

Go back to Magnesium Binding Sites List in 4iru
Magnesium binding site 3 out of 3 in the Crystal Structure of Lepb Gap Core in A Transition State Mimetic Complex with RAB1A and ALF3


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 Lepb Gap Core in A Transition State Mimetic Complex with RAB1A and ALF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg200

b:45.2
occ:1.00
O3B F:GDP201 1.6 92.9 1.0
F1 F:AF3202 2.2 60.3 1.0
PB F:GDP201 2.4 96.9 1.0
O1B F:GDP201 2.7 98.4 1.0
N F:SER25 2.8 61.2 1.0
OD1 F:ASP66 3.1 0.9 1.0
AL F:AF3202 3.1 61.7 1.0
F2 F:AF3202 3.1 66.3 1.0
OG F:SER25 3.2 57.5 1.0
O2B F:GDP201 3.2 90.8 1.0
CB F:LYS24 3.3 80.3 1.0
CB F:SER25 3.3 57.5 1.0
CA F:SER25 3.6 57.5 1.0
OG1 F:THR43 3.7 61.1 1.0
C F:LYS24 3.8 65.3 1.0
O3A F:GDP201 3.8 94.8 1.0
CA F:LYS24 3.9 73.3 1.0
O F:THR67 3.9 99.3 1.0
CG F:ASP66 4.0 0.3 1.0
N F:LYS24 4.2 72.8 1.0
CG F:LYS24 4.3 85.3 1.0
CB F:THR43 4.3 79.0 1.0
PA F:GDP201 4.5 85.0 1.0
O2A F:GDP201 4.5 84.3 1.0
O1A F:GDP201 4.5 1.0 1.0
OD2 F:ASP66 4.5 0.3 1.0
CE F:LYS24 4.7 88.2 1.0
CD F:LYS24 4.8 87.2 1.0
C F:SER25 4.8 58.8 1.0
CB F:ASP66 4.8 0.4 1.0
F3 F:AF3202 4.9 56.4 1.0
C F:GLY23 4.9 71.1 1.0
N F:CYS26 4.9 57.3 1.0
O F:LYS24 4.9 60.7 1.0
N F:THR43 5.0 0.7 1.0

Reference:

A.K.Mishra, C.M.Del Campo, R.E.Collins, C.R.Roy, D.G.Lambright. The Legionella Pneumophila Gtpase Activating Protein Lepb Accelerates RAB1 Deactivation By A Non-Canonical Hydrolytic Mechanism. J.Biol.Chem. V. 288 24000 2013.
ISSN: ISSN 0021-9258
PubMed: 23821544
DOI: 10.1074/JBC.M113.470625
Page generated: Fri Aug 16 17:01:24 2024

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