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:
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
|