Magnesium in PDB 5flg: Crystal Structure of the 6-Carboxyhexanoate-Coa Ligase (Biow)From Bacillus Subtilis in Complex with Amppnp
Enzymatic activity of Crystal Structure of the 6-Carboxyhexanoate-Coa Ligase (Biow)From Bacillus Subtilis in Complex with Amppnp
All present enzymatic activity of Crystal Structure of the 6-Carboxyhexanoate-Coa Ligase (Biow)From Bacillus Subtilis in Complex with Amppnp:
6.2.1.14;
Protein crystallography data
The structure of Crystal Structure of the 6-Carboxyhexanoate-Coa Ligase (Biow)From Bacillus Subtilis in Complex with Amppnp, PDB code: 5flg
was solved by
L.Moynie,
M.Wang,
D.J.Campopiano,
J.H.Naismith,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
41.53 /
2.04
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
49.590,
77.900,
166.000,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
20.2 /
23.2
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of the 6-Carboxyhexanoate-Coa Ligase (Biow)From Bacillus Subtilis in Complex with Amppnp
(pdb code 5flg). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
Crystal Structure of the 6-Carboxyhexanoate-Coa Ligase (Biow)From Bacillus Subtilis in Complex with Amppnp, PDB code: 5flg:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 5flg
Go back to
Magnesium Binding Sites List in 5flg
Magnesium binding site 1 out
of 4 in the Crystal Structure of the 6-Carboxyhexanoate-Coa Ligase (Biow)From Bacillus Subtilis in Complex with Amppnp
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 the 6-Carboxyhexanoate-Coa Ligase (Biow)From Bacillus Subtilis in Complex with Amppnp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg703
b:31.5
occ:1.00
|
O1B
|
A:ANP702
|
2.0
|
25.4
|
1.0
|
O
|
A:HOH2033
|
2.0
|
29.0
|
1.0
|
O2A
|
A:ANP702
|
2.0
|
32.0
|
1.0
|
O3G
|
A:ANP702
|
2.1
|
29.6
|
1.0
|
O
|
A:HOH2007
|
2.1
|
29.3
|
1.0
|
O
|
A:HOH2043
|
2.2
|
24.2
|
1.0
|
PB
|
A:ANP702
|
3.2
|
29.5
|
1.0
|
PA
|
A:ANP702
|
3.3
|
34.0
|
1.0
|
PG
|
A:ANP702
|
3.4
|
34.6
|
1.0
|
O3A
|
A:ANP702
|
3.6
|
31.4
|
1.0
|
N3B
|
A:ANP702
|
3.7
|
28.0
|
1.0
|
O
|
A:HOH2042
|
3.7
|
45.0
|
1.0
|
O
|
A:GLY29
|
3.9
|
27.7
|
1.0
|
NZ
|
A:LYS49
|
4.1
|
41.0
|
1.0
|
OE1
|
A:GLU173
|
4.1
|
41.9
|
1.0
|
N7
|
A:ANP702
|
4.1
|
34.4
|
1.0
|
O
|
A:HOH2032
|
4.2
|
30.0
|
1.0
|
O5'
|
A:ANP702
|
4.3
|
27.6
|
1.0
|
O2G
|
A:ANP702
|
4.3
|
36.2
|
1.0
|
C8
|
A:ANP702
|
4.3
|
37.2
|
1.0
|
O1A
|
A:ANP702
|
4.4
|
29.0
|
1.0
|
O
|
A:HOH2039
|
4.5
|
42.8
|
1.0
|
NH2
|
A:ARG145
|
4.5
|
36.1
|
1.0
|
O1G
|
A:ANP702
|
4.5
|
32.9
|
1.0
|
O2B
|
A:ANP702
|
4.5
|
29.4
|
1.0
|
O71
|
A:PML701
|
4.5
|
55.7
|
1.0
|
CE
|
A:LYS49
|
4.7
|
34.6
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 5flg
Go back to
Magnesium Binding Sites List in 5flg
Magnesium binding site 2 out
of 4 in the Crystal Structure of the 6-Carboxyhexanoate-Coa Ligase (Biow)From Bacillus Subtilis in Complex with Amppnp
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 the 6-Carboxyhexanoate-Coa Ligase (Biow)From Bacillus Subtilis in Complex with Amppnp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg704
b:45.3
occ:1.00
|
OD1
|
A:ASP196
|
2.2
|
41.4
|
1.0
|
OD1
|
A:ASP195
|
2.2
|
46.5
|
1.0
|
O2G
|
A:ANP702
|
2.3
|
36.2
|
1.0
|
O
|
A:HOH2006
|
2.5
|
36.5
|
1.0
|
O1A
|
A:ANP702
|
2.6
|
29.0
|
1.0
|
O
|
A:HOH2039
|
2.7
|
42.8
|
1.0
|
O3A
|
A:ANP702
|
2.7
|
31.4
|
1.0
|
PA
|
A:ANP702
|
3.1
|
34.0
|
1.0
|
CG
|
A:ASP195
|
3.3
|
42.6
|
1.0
|
CG
|
A:ASP196
|
3.3
|
39.8
|
1.0
|
PG
|
A:ANP702
|
3.5
|
34.6
|
1.0
|
N3B
|
A:ANP702
|
3.5
|
28.0
|
1.0
|
OD2
|
A:ASP195
|
3.7
|
47.5
|
1.0
|
OD2
|
A:ASP196
|
3.8
|
48.3
|
1.0
|
PB
|
A:ANP702
|
3.8
|
29.5
|
1.0
|
NE2
|
A:HIS53
|
3.8
|
35.7
|
1.0
|
CE1
|
A:HIS53
|
4.0
|
39.4
|
1.0
|
OG
|
A:SER194
|
4.0
|
35.5
|
1.0
|
N
|
A:ASP196
|
4.1
|
26.8
|
1.0
|
O2A
|
A:ANP702
|
4.2
|
32.0
|
1.0
|
O3G
|
A:ANP702
|
4.3
|
29.6
|
1.0
|
N
|
A:ASP195
|
4.3
|
26.9
|
1.0
|
CD
|
A:ARG55
|
4.3
|
33.7
|
1.0
|
C
|
A:ASP195
|
4.3
|
27.6
|
1.0
|
O5'
|
A:ANP702
|
4.3
|
27.6
|
1.0
|
C5'
|
A:ANP702
|
4.5
|
29.6
|
1.0
|
O2B
|
A:ANP702
|
4.5
|
29.4
|
1.0
|
O
|
A:HOH2042
|
4.5
|
45.0
|
1.0
|
CB
|
A:ASP195
|
4.5
|
34.0
|
1.0
|
CB
|
A:ASP196
|
4.5
|
33.6
|
1.0
|
O1G
|
A:ANP702
|
4.6
|
32.9
|
1.0
|
CA
|
A:ASP195
|
4.6
|
30.6
|
1.0
|
CA
|
A:ASP196
|
4.7
|
33.4
|
1.0
|
O
|
A:ILE27
|
4.8
|
35.2
|
1.0
|
O72
|
A:PML701
|
4.8
|
48.8
|
1.0
|
O1B
|
A:ANP702
|
4.8
|
25.4
|
1.0
|
O
|
A:ASP195
|
5.0
|
30.2
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 5flg
Go back to
Magnesium Binding Sites List in 5flg
Magnesium binding site 3 out
of 4 in the Crystal Structure of the 6-Carboxyhexanoate-Coa Ligase (Biow)From Bacillus Subtilis in Complex with Amppnp
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 the 6-Carboxyhexanoate-Coa Ligase (Biow)From Bacillus Subtilis in Complex with Amppnp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg703
b:20.4
occ:1.00
|
O2A
|
B:ANP702
|
1.9
|
28.1
|
1.0
|
O
|
B:HOH2029
|
1.9
|
27.8
|
1.0
|
O2G
|
B:ANP702
|
1.9
|
26.5
|
1.0
|
O
|
B:HOH2006
|
1.9
|
22.4
|
1.0
|
O1B
|
B:ANP702
|
2.1
|
23.4
|
1.0
|
O
|
B:HOH2019
|
2.2
|
22.6
|
1.0
|
PB
|
B:ANP702
|
3.0
|
28.4
|
1.0
|
PA
|
B:ANP702
|
3.2
|
32.2
|
1.0
|
PG
|
B:ANP702
|
3.4
|
27.6
|
1.0
|
O3A
|
B:ANP702
|
3.5
|
29.7
|
1.0
|
N3B
|
B:ANP702
|
3.6
|
26.3
|
1.0
|
O
|
B:HOH2028
|
3.7
|
46.3
|
1.0
|
O
|
B:GLY29
|
3.9
|
31.5
|
1.0
|
O
|
B:HOH2027
|
4.0
|
36.8
|
1.0
|
OE1
|
B:GLU173
|
4.1
|
48.0
|
1.0
|
NZ
|
B:LYS49
|
4.1
|
44.4
|
1.0
|
N7
|
B:ANP702
|
4.2
|
28.6
|
1.0
|
O5'
|
B:ANP702
|
4.3
|
30.4
|
1.0
|
C8
|
B:ANP702
|
4.3
|
31.3
|
1.0
|
O1G
|
B:ANP702
|
4.3
|
26.2
|
1.0
|
O1A
|
B:ANP702
|
4.3
|
29.5
|
1.0
|
O
|
B:HOH2008
|
4.3
|
33.6
|
1.0
|
NH2
|
B:ARG145
|
4.4
|
36.1
|
1.0
|
O2B
|
B:ANP702
|
4.4
|
23.5
|
1.0
|
O
|
B:HOH2018
|
4.4
|
30.0
|
1.0
|
O3G
|
B:ANP702
|
4.4
|
25.8
|
1.0
|
O
|
B:HOH2025
|
4.5
|
39.2
|
1.0
|
O72
|
B:PML701
|
4.6
|
55.0
|
1.0
|
CE
|
B:LYS49
|
4.7
|
43.5
|
1.0
|
O
|
B:HOH2007
|
4.8
|
37.6
|
1.0
|
CD
|
B:GLU173
|
4.9
|
52.8
|
1.0
|
C
|
B:GLY29
|
5.0
|
30.8
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 5flg
Go back to
Magnesium Binding Sites List in 5flg
Magnesium binding site 4 out
of 4 in the Crystal Structure of the 6-Carboxyhexanoate-Coa Ligase (Biow)From Bacillus Subtilis in Complex with Amppnp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Crystal Structure of the 6-Carboxyhexanoate-Coa Ligase (Biow)From Bacillus Subtilis in Complex with Amppnp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg704
b:39.8
occ:1.00
|
OD1
|
B:ASP195
|
2.3
|
42.7
|
1.0
|
OD1
|
B:ASP196
|
2.3
|
44.1
|
1.0
|
O1G
|
B:ANP702
|
2.3
|
26.2
|
1.0
|
O1A
|
B:ANP702
|
2.5
|
29.5
|
1.0
|
O
|
B:HOH2005
|
2.5
|
32.6
|
1.0
|
O
|
B:HOH2025
|
2.8
|
39.2
|
1.0
|
O3A
|
B:ANP702
|
2.9
|
29.7
|
1.0
|
PA
|
B:ANP702
|
3.2
|
32.2
|
1.0
|
CG
|
B:ASP195
|
3.3
|
40.1
|
1.0
|
CG
|
B:ASP196
|
3.3
|
45.9
|
1.0
|
N3B
|
B:ANP702
|
3.4
|
26.3
|
1.0
|
PG
|
B:ANP702
|
3.4
|
27.6
|
1.0
|
OD2
|
B:ASP195
|
3.7
|
39.8
|
1.0
|
PB
|
B:ANP702
|
3.7
|
28.4
|
1.0
|
NE2
|
B:HIS53
|
3.8
|
30.1
|
1.0
|
OD2
|
B:ASP196
|
3.8
|
39.9
|
1.0
|
CE1
|
B:HIS53
|
4.0
|
30.6
|
1.0
|
OG
|
B:SER194
|
4.1
|
38.7
|
1.0
|
N
|
B:ASP196
|
4.2
|
33.1
|
1.0
|
O2G
|
B:ANP702
|
4.2
|
26.5
|
1.0
|
O2A
|
B:ANP702
|
4.3
|
28.1
|
1.0
|
N
|
B:ASP195
|
4.3
|
29.8
|
1.0
|
O5'
|
B:ANP702
|
4.3
|
30.4
|
1.0
|
CD
|
B:ARG55
|
4.4
|
35.1
|
1.0
|
C5'
|
B:ANP702
|
4.4
|
33.2
|
1.0
|
O2B
|
B:ANP702
|
4.5
|
23.5
|
1.0
|
C
|
B:ASP195
|
4.5
|
36.8
|
1.0
|
CB
|
B:ASP195
|
4.5
|
37.2
|
1.0
|
O71
|
B:PML701
|
4.5
|
58.2
|
1.0
|
O3G
|
B:ANP702
|
4.6
|
25.8
|
1.0
|
CB
|
B:ASP196
|
4.6
|
44.2
|
1.0
|
CA
|
B:ASP195
|
4.7
|
37.4
|
1.0
|
O
|
B:ILE27
|
4.7
|
38.5
|
1.0
|
CA
|
B:ASP196
|
4.7
|
39.1
|
1.0
|
O
|
B:HOH2028
|
4.7
|
46.3
|
1.0
|
O3'
|
B:ANP702
|
4.8
|
32.6
|
1.0
|
O1B
|
B:ANP702
|
5.0
|
23.4
|
1.0
|
|
Reference:
M.Wang,
L.Moynie,
P.J.Harrison,
V.Kelly,
A.Piper,
J.H.Naismith,
D.J.Campopiano.
Using the Pimeloyl-Coa Synthetase Adenylation Fold to Synthesize Fatty Acid Thioesters. Nat. Chem. Biol. V. 13 660 2017.
ISSN: ESSN 1552-4469
PubMed: 28414710
DOI: 10.1038/NCHEMBIO.2361
Page generated: Sun Sep 29 04:19:42 2024
|