Magnesium in PDB 7qtm: Transition State Analogue of Small G Protein in Complex with Relevant Gap
Enzymatic activity of Transition State Analogue of Small G Protein in Complex with Relevant Gap
All present enzymatic activity of Transition State Analogue of Small G Protein in Complex with Relevant Gap:
3.6.5.2;
Protein crystallography data
The structure of Transition State Analogue of Small G Protein in Complex with Relevant Gap, PDB code: 7qtm
was solved by
P.Baumann,
Y.Jin,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
55.31 /
2.25
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
73.632,
66.604,
76.463,
90,
95.02,
90
|
R / Rfree (%)
|
22 /
30.4
|
Other elements in 7qtm:
The structure of Transition State Analogue of Small G Protein in Complex with Relevant Gap also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Transition State Analogue of Small G Protein in Complex with Relevant Gap
(pdb code 7qtm). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
Transition State Analogue of Small G Protein in Complex with Relevant Gap, PDB code: 7qtm:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 7qtm
Go back to
Magnesium Binding Sites List in 7qtm
Magnesium binding site 1 out
of 4 in the Transition State Analogue of Small G Protein in Complex with Relevant Gap
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Transition State Analogue of Small G Protein in Complex with Relevant Gap within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg202
b:25.8
occ:1.00
|
MG
|
B:MGF202
|
0.0
|
25.8
|
1.0
|
F3
|
B:MGF202
|
1.8
|
22.1
|
1.0
|
F1
|
B:MGF202
|
1.8
|
27.3
|
1.0
|
F2
|
B:MGF202
|
1.8
|
23.1
|
1.0
|
O
|
B:HOH305
|
1.9
|
27.1
|
1.0
|
O3B
|
B:GDP201
|
2.2
|
32.9
|
1.0
|
PB
|
B:GDP201
|
3.4
|
33.1
|
1.0
|
MG
|
B:MG203
|
3.6
|
32.1
|
1.0
|
F1
|
B:F2Y34
|
3.7
|
36.4
|
1.0
|
O2B
|
B:GDP201
|
3.7
|
26.6
|
1.0
|
NE2
|
B:GLN63
|
3.8
|
30.9
|
1.0
|
OE1
|
B:GLN63
|
3.8
|
28.8
|
1.0
|
N
|
B:THR37
|
4.0
|
28.8
|
1.0
|
N
|
B:ALA15
|
4.0
|
31.4
|
1.0
|
O
|
B:HOH309
|
4.1
|
25.2
|
1.0
|
NZ
|
B:LYS18
|
4.1
|
35.8
|
1.0
|
OH
|
B:F2Y34
|
4.2
|
39.7
|
1.0
|
CA
|
B:PRO36
|
4.2
|
31.7
|
1.0
|
N
|
B:GLY62
|
4.3
|
29.8
|
1.0
|
CD
|
B:GLN63
|
4.3
|
29.6
|
1.0
|
O1B
|
B:GDP201
|
4.3
|
34.7
|
1.0
|
CA
|
B:GLY14
|
4.4
|
31.2
|
1.0
|
O
|
B:HOH301
|
4.4
|
22.6
|
1.0
|
O
|
B:THR37
|
4.5
|
31.3
|
1.0
|
CB
|
B:PRO36
|
4.5
|
31.1
|
1.0
|
CE
|
B:LYS18
|
4.6
|
39.1
|
1.0
|
C
|
B:PRO36
|
4.6
|
29.3
|
1.0
|
CB
|
B:THR37
|
4.6
|
28.4
|
1.0
|
O3A
|
B:GDP201
|
4.7
|
33.8
|
1.0
|
C
|
B:GLY14
|
4.7
|
32.2
|
1.0
|
CE1
|
B:F2Y34
|
4.8
|
39.7
|
1.0
|
CA
|
B:THR37
|
4.8
|
28.7
|
1.0
|
OG1
|
B:THR37
|
4.9
|
28.7
|
1.0
|
CA
|
B:ALA61
|
4.9
|
29.9
|
1.0
|
CZ
|
B:F2Y34
|
5.0
|
41.8
|
1.0
|
CA
|
B:GLY62
|
5.0
|
32.4
|
1.0
|
CA
|
B:ALA15
|
5.0
|
32.7
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 7qtm
Go back to
Magnesium Binding Sites List in 7qtm
Magnesium binding site 2 out
of 4 in the Transition State Analogue of Small G Protein in Complex with Relevant Gap
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Transition State Analogue of Small G Protein in Complex with Relevant Gap within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg203
b:32.1
occ:1.00
|
F1
|
B:MGF202
|
1.9
|
27.3
|
1.0
|
OG1
|
B:THR19
|
2.0
|
35.2
|
1.0
|
O2B
|
B:GDP201
|
2.1
|
26.6
|
1.0
|
O
|
B:HOH309
|
2.2
|
25.2
|
1.0
|
O
|
B:HOH301
|
2.2
|
22.6
|
1.0
|
OG1
|
B:THR37
|
2.3
|
28.7
|
1.0
|
CB
|
B:THR37
|
3.0
|
28.4
|
1.0
|
CB
|
B:THR19
|
3.1
|
33.6
|
1.0
|
PB
|
B:GDP201
|
3.3
|
33.1
|
1.0
|
MG
|
B:MGF202
|
3.6
|
25.8
|
1.0
|
O3B
|
B:GDP201
|
3.7
|
32.9
|
1.0
|
OD2
|
B:ASP59
|
3.8
|
32.9
|
1.0
|
N
|
B:THR37
|
3.8
|
28.8
|
1.0
|
O2A
|
B:GDP201
|
3.9
|
34.9
|
1.0
|
N
|
B:THR19
|
4.0
|
34.0
|
1.0
|
CA
|
B:THR37
|
4.1
|
28.7
|
1.0
|
CA
|
B:THR19
|
4.1
|
36.8
|
1.0
|
CG2
|
B:THR37
|
4.1
|
27.0
|
1.0
|
OD1
|
B:ASP59
|
4.1
|
28.8
|
1.0
|
CG2
|
B:THR19
|
4.2
|
34.5
|
1.0
|
CG
|
B:ASP59
|
4.3
|
30.6
|
1.0
|
O1B
|
B:GDP201
|
4.3
|
34.7
|
1.0
|
O
|
B:HOH304
|
4.3
|
20.0
|
1.0
|
F1
|
B:F2Y34
|
4.3
|
36.4
|
1.0
|
O3A
|
B:GDP201
|
4.5
|
33.8
|
1.0
|
PA
|
B:GDP201
|
4.6
|
32.4
|
1.0
|
F2
|
B:MGF202
|
4.6
|
23.1
|
1.0
|
O
|
B:HOH305
|
4.7
|
27.1
|
1.0
|
O
|
B:VAL35
|
4.7
|
34.0
|
1.0
|
O
|
B:THR60
|
4.7
|
24.0
|
1.0
|
O1A
|
B:GDP201
|
4.8
|
30.7
|
1.0
|
F3
|
B:MGF202
|
4.9
|
22.1
|
1.0
|
CE
|
B:LYS18
|
4.9
|
39.1
|
1.0
|
C
|
B:PRO36
|
4.9
|
29.3
|
1.0
|
O
|
B:HOH303
|
5.0
|
26.2
|
1.0
|
CB
|
B:LYS18
|
5.0
|
38.9
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 7qtm
Go back to
Magnesium Binding Sites List in 7qtm
Magnesium binding site 3 out
of 4 in the Transition State Analogue of Small G Protein in Complex with Relevant Gap
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Transition State Analogue of Small G Protein in Complex with Relevant Gap within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Mg202
b:26.1
occ:1.00
|
MG
|
I:MGF202
|
0.0
|
26.1
|
1.0
|
F1
|
I:MGF202
|
1.9
|
29.5
|
1.0
|
F2
|
I:MGF202
|
1.9
|
21.0
|
1.0
|
F3
|
I:MGF202
|
1.9
|
22.9
|
1.0
|
O
|
I:HOH320
|
2.0
|
33.2
|
1.0
|
O3B
|
I:GDP201
|
2.3
|
26.8
|
1.0
|
MG
|
I:MG203
|
3.4
|
30.6
|
1.0
|
F1
|
I:F2Y34
|
3.5
|
45.4
|
1.0
|
PB
|
I:GDP201
|
3.5
|
25.5
|
1.0
|
NE2
|
I:GLN63
|
3.6
|
33.3
|
1.0
|
O
|
I:HOH309
|
3.7
|
27.4
|
1.0
|
O1B
|
I:GDP201
|
3.7
|
23.3
|
1.0
|
NZ
|
I:LYS18
|
3.9
|
30.1
|
1.0
|
N
|
I:THR37
|
4.0
|
32.1
|
1.0
|
N
|
I:GLY62
|
4.0
|
26.3
|
1.0
|
OE1
|
I:GLN63
|
4.1
|
35.4
|
1.0
|
OH
|
I:F2Y34
|
4.2
|
44.7
|
1.0
|
O
|
I:HOH302
|
4.2
|
19.0
|
1.0
|
N
|
I:ALA15
|
4.2
|
30.4
|
1.0
|
CD
|
I:GLN63
|
4.2
|
31.0
|
1.0
|
CA
|
I:PRO36
|
4.3
|
31.0
|
1.0
|
O2B
|
I:GDP201
|
4.4
|
29.1
|
1.0
|
O
|
I:THR37
|
4.4
|
28.7
|
1.0
|
CA
|
I:GLY14
|
4.4
|
28.5
|
1.0
|
CE
|
I:LYS18
|
4.6
|
33.0
|
1.0
|
CB
|
I:PRO36
|
4.6
|
30.6
|
1.0
|
C
|
I:PRO36
|
4.6
|
31.0
|
1.0
|
CE1
|
I:F2Y34
|
4.6
|
43.7
|
1.0
|
CB
|
I:THR37
|
4.7
|
35.1
|
1.0
|
CA
|
I:GLY62
|
4.8
|
28.5
|
1.0
|
CA
|
I:ALA61
|
4.8
|
26.8
|
1.0
|
CA
|
I:THR37
|
4.8
|
31.4
|
1.0
|
OG1
|
I:THR37
|
4.8
|
34.0
|
1.0
|
O3A
|
I:GDP201
|
4.8
|
28.1
|
1.0
|
C
|
I:GLY14
|
4.9
|
28.9
|
1.0
|
O
|
I:THR60
|
4.9
|
26.2
|
1.0
|
CZ
|
I:F2Y34
|
4.9
|
44.6
|
1.0
|
C
|
I:ALA61
|
4.9
|
26.0
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 7qtm
Go back to
Magnesium Binding Sites List in 7qtm
Magnesium binding site 4 out
of 4 in the Transition State Analogue of Small G Protein in Complex with Relevant Gap
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Transition State Analogue of Small G Protein in Complex with Relevant Gap within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Mg203
b:30.6
occ:1.00
|
F1
|
I:MGF202
|
1.8
|
29.5
|
1.0
|
O
|
I:HOH309
|
2.0
|
27.4
|
1.0
|
O1B
|
I:GDP201
|
2.1
|
23.3
|
1.0
|
OG1
|
I:THR19
|
2.1
|
35.1
|
1.0
|
O
|
I:HOH302
|
2.2
|
19.0
|
1.0
|
OG1
|
I:THR37
|
2.4
|
34.0
|
1.0
|
CB
|
I:THR37
|
3.1
|
35.1
|
1.0
|
CB
|
I:THR19
|
3.2
|
34.7
|
1.0
|
PB
|
I:GDP201
|
3.3
|
25.5
|
1.0
|
MG
|
I:MGF202
|
3.4
|
26.1
|
1.0
|
O3B
|
I:GDP201
|
3.6
|
26.8
|
1.0
|
O2A
|
I:GDP201
|
3.8
|
27.5
|
1.0
|
N
|
I:THR37
|
3.8
|
32.1
|
1.0
|
OD1
|
I:ASP59
|
3.8
|
29.4
|
1.0
|
N
|
I:THR19
|
4.0
|
35.0
|
1.0
|
OD2
|
I:ASP59
|
4.0
|
31.3
|
1.0
|
CA
|
I:THR37
|
4.1
|
31.4
|
1.0
|
F1
|
I:F2Y34
|
4.1
|
45.4
|
1.0
|
CA
|
I:THR19
|
4.1
|
37.1
|
1.0
|
CG2
|
I:THR37
|
4.1
|
34.9
|
1.0
|
CG2
|
I:THR19
|
4.2
|
34.2
|
1.0
|
CG
|
I:ASP59
|
4.3
|
30.2
|
1.0
|
O2B
|
I:GDP201
|
4.3
|
29.1
|
1.0
|
O
|
I:HOH320
|
4.4
|
33.2
|
1.0
|
F2
|
I:MGF202
|
4.4
|
21.0
|
1.0
|
O
|
I:HOH303
|
4.5
|
29.5
|
1.0
|
O3A
|
I:GDP201
|
4.5
|
28.1
|
1.0
|
O
|
I:THR60
|
4.5
|
26.2
|
1.0
|
PA
|
I:GDP201
|
4.6
|
26.0
|
1.0
|
F3
|
I:MGF202
|
4.7
|
22.9
|
1.0
|
NZ
|
I:LYS18
|
4.8
|
30.1
|
1.0
|
CB
|
I:LYS18
|
4.8
|
34.3
|
1.0
|
O
|
I:VAL35
|
4.9
|
32.7
|
1.0
|
CE
|
I:LYS18
|
4.9
|
33.0
|
1.0
|
C
|
I:PRO36
|
4.9
|
31.0
|
1.0
|
O1A
|
I:GDP201
|
5.0
|
26.3
|
1.0
|
|
Reference:
P.Baumann,
Y.Jin.
Transition State Analogue of Small G Protein in Complex with Relevant Gap To Be Published.
Page generated: Thu Oct 3 07:01:18 2024
|