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Potassium 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
Magnesium (Mg) 3 atoms
Aluminium (Al) 3 atoms

Potassium Binding Sites:

The binding sites of Potassium 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 Potassium atom.
In total 6 binding sites of Potassium 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 Potassium binding site number: 1; 2; 3; 4; 5; 6;

Potassium binding site 1 out of 6 in 4iru

Go back to Potassium Binding Sites List in 4iru
Potassium binding site 1 out of 6 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 Potassium with other atoms in the K 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
A:K909

b:85.3
occ:1.00
 OE1 A:GLU536 3.3 48.8 1.0
O A:ASN563 3.5 27.5 1.0
CD A:GLU536 4.1 47.7 1.0
OE2 A:GLU536 4.1 54.3 1.0
C A:ASN563 4.5 25.4 1.0
CZ A:PHE537 4.7 19.9 1.0
CA A:SER564 4.8 29.3 1.0
CE1 A:PHE537 4.9 19.9 1.0
CD A:PRO565 5.0 31.4 1.0

Potassium binding site 2 out of 6 in 4iru

Go back to Potassium Binding Sites List in 4iru
Potassium binding site 2 out of 6 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 Potassium with other atoms in the K 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
A:K910

b:0.5
occ:1.00
 O A:ASN363 3.3 44.7 1.0
OXT A:ACT902 3.3 76.9 1.0
O A:ILE365 4.2 40.1 1.0
C A:ASN363 4.5 41.7 1.0
C A:ACT902 4.5 72.3 1.0
NZ A:LYS485 4.8 42.1 1.0
C A:PRO364 4.8 38.8 1.0
O A:PRO364 4.9 40.1 1.0
C A:ILE365 4.9 38.9 1.0
CE A:LYS485 5.0 39.3 1.0

Potassium binding site 3 out of 6 in 4iru

Go back to Potassium Binding Sites List in 4iru
Potassium binding site 3 out of 6 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 Potassium with other atoms in the K 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
A:K911

b:90.6
occ:1.00
 O A:PRO565 3.5 40.3 1.0
O A:SER564 3.6 33.2 1.0
NZ A:LYS606 3.7 27.6 1.0
O A:LEU562 3.8 29.0 1.0
CD A:LYS606 4.3 22.6 1.0
CH2 A:TRP610 4.4 24.4 1.0
C A:PRO565 4.4 34.4 1.0
CE A:LYS606 4.5 24.6 1.0
O1 A:GOL905 4.5 96.8 1.0
CG A:LEU562 4.5 21.2 1.0
C A:LEU562 4.5 25.1 1.0
CA A:LEU562 4.6 23.3 1.0
CZ2 A:TRP610 4.6 24.1 1.0
CA A:PRO565 4.7 32.0 1.0
C A:SER564 4.7 31.6 1.0
CB A:LEU562 4.8 21.7 1.0

Potassium binding site 4 out of 6 in 4iru

Go back to Potassium Binding Sites List in 4iru
Potassium binding site 4 out of 6 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 Potassium with other atoms in the K binding site number 4 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
A:K912

b:86.0
occ:1.00
 OG1 A:THR384 3.6 30.9 1.0
OE2 E:GLU356 3.9 0.7 1.0
OD1 E:ASP354 4.0 0.0 1.0
OE1 E:GLU356 4.0 0.4 1.0
OD2 E:ASP354 4.1 1.0 1.0
CD E:GLU356 4.2 0.9 1.0
CA A:LEU381 4.4 28.1 1.0
CD1 A:LEU381 4.4 29.0 1.0
CG E:ASP354 4.5 0.5 1.0
O A:GLU380 4.5 36.2 1.0
CG2 A:THR384 4.6 31.6 1.0
CB A:THR384 4.6 29.5 1.0
N A:LEU381 4.6 31.6 1.0
C A:GLU380 4.7 36.0 1.0
CD1 A:LEU521 4.7 49.9 1.0

Potassium binding site 5 out of 6 in 4iru

Go back to Potassium Binding Sites List in 4iru
Potassium binding site 5 out of 6 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 Potassium with other atoms in the K binding site number 5 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:K207

b:52.9
occ:1.00
 OE2 B:GLU38 3.8 56.3 1.0
NZ B:LYS156 3.9 54.0 1.0
OE1 B:GLU38 3.9 72.6 1.0
N2 B:GDP202 3.9 47.4 1.0
N3 B:GDP202 3.9 41.8 1.0
CD B:GLU38 4.3 61.6 1.0
C2 B:GDP202 4.4 44.0 1.0
O2' B:GDP202 4.5 33.0 1.0
CE B:LYS156 4.5 51.7 1.0
OH B:TYR36 4.7 54.6 1.0
C4 B:GDP202 4.9 39.2 1.0
C1' B:GDP202 5.0 34.2 1.0

Potassium binding site 6 out of 6 in 4iru

Go back to Potassium Binding Sites List in 4iru
Potassium binding site 6 out of 6 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 Potassium with other atoms in the K binding site number 6 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
C:K708

b:72.7
occ:1.00
 OE1 C:GLU536 3.0 50.4 1.0
O C:ASN563 4.2 26.6 1.0
CD C:GLU536 4.2 46.9 1.0
CZ C:PHE537 4.6 20.9 1.0
CE1 C:PHE537 4.6 21.3 1.0
OE2 C:GLU536 4.7 51.0 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: Mon Aug 12 11:02:19 2024

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