Magnesium in PDB 5fll: Crystal Structure of the 6-Carboxyhexanoate-Coa Ligase (Biow) From Bacillus Subtilis in Complex with A Pimeloyl-Adenylate
Enzymatic activity of Crystal Structure of the 6-Carboxyhexanoate-Coa Ligase (Biow) From Bacillus Subtilis in Complex with A Pimeloyl-Adenylate
All present enzymatic activity of Crystal Structure of the 6-Carboxyhexanoate-Coa Ligase (Biow) From Bacillus Subtilis in Complex with A Pimeloyl-Adenylate:
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 A Pimeloyl-Adenylate, PDB code: 5fll
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)
|
35.35 /
2.34
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
50.117,
78.105,
165.818,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
19.9 /
23.4
|
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 A Pimeloyl-Adenylate
(pdb code 5fll). 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 A Pimeloyl-Adenylate, PDB code: 5fll:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 5fll
Go back to
Magnesium Binding Sites List in 5fll
Magnesium binding site 1 out
of 4 in the Crystal Structure of the 6-Carboxyhexanoate-Coa Ligase (Biow) From Bacillus Subtilis in Complex with A Pimeloyl-Adenylate
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 A Pimeloyl-Adenylate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg703
b:30.8
occ:1.00
|
O12
|
A:PPV701
|
2.0
|
27.7
|
1.0
|
O
|
A:HOH2007
|
2.1
|
25.0
|
1.0
|
O21
|
A:PPV701
|
2.1
|
28.3
|
1.0
|
O
|
A:HOH2053
|
2.1
|
21.0
|
1.0
|
OAH
|
A:WAQ700
|
2.2
|
36.7
|
1.0
|
O
|
A:HOH2065
|
2.3
|
23.4
|
1.0
|
P1
|
A:PPV701
|
3.3
|
29.2
|
1.0
|
P2
|
A:PPV701
|
3.3
|
32.6
|
1.0
|
OPP
|
A:PPV701
|
3.5
|
33.6
|
1.0
|
PBG
|
A:WAQ700
|
3.7
|
33.3
|
1.0
|
O
|
A:HOH2064
|
3.8
|
34.4
|
1.0
|
O
|
A:HOH2011
|
3.9
|
25.2
|
1.0
|
O31
|
A:PPV701
|
3.9
|
23.7
|
1.0
|
O
|
A:GLY29
|
3.9
|
24.2
|
1.0
|
NZ
|
A:LYS49
|
4.0
|
29.7
|
1.0
|
O
|
A:HOH2051
|
4.1
|
39.3
|
1.0
|
O32
|
A:PPV701
|
4.1
|
29.7
|
1.0
|
OE1
|
A:GLU173
|
4.1
|
30.5
|
1.0
|
C8
|
A:WAQ700
|
4.3
|
31.2
|
1.0
|
N7
|
A:WAQ700
|
4.3
|
31.4
|
1.0
|
O5'
|
A:WAQ700
|
4.3
|
34.3
|
1.0
|
O
|
A:HOH2050
|
4.3
|
24.4
|
1.0
|
O22
|
A:PPV701
|
4.4
|
30.9
|
1.0
|
NH2
|
A:ARG145
|
4.4
|
33.1
|
1.0
|
OAD
|
A:WAQ700
|
4.5
|
37.0
|
1.0
|
O11
|
A:PPV701
|
4.5
|
29.4
|
1.0
|
CE
|
A:LYS49
|
4.6
|
29.8
|
1.0
|
OAU
|
A:WAQ700
|
4.7
|
34.5
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 5fll
Go back to
Magnesium Binding Sites List in 5fll
Magnesium binding site 2 out
of 4 in the Crystal Structure of the 6-Carboxyhexanoate-Coa Ligase (Biow) From Bacillus Subtilis in Complex with A Pimeloyl-Adenylate
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 A Pimeloyl-Adenylate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg704
b:32.5
occ:1.00
|
O32
|
A:PPV701
|
2.0
|
29.7
|
1.0
|
OD1
|
A:ASP196
|
2.0
|
34.8
|
1.0
|
OD1
|
A:ASP195
|
2.1
|
32.1
|
1.0
|
O
|
A:HOH2006
|
2.2
|
29.3
|
1.0
|
OAD
|
A:WAQ700
|
2.2
|
37.0
|
1.0
|
O31
|
A:PPV701
|
2.2
|
23.7
|
1.0
|
CG
|
A:ASP196
|
3.1
|
34.1
|
1.0
|
CG
|
A:ASP195
|
3.2
|
31.5
|
1.0
|
P2
|
A:PPV701
|
3.3
|
32.6
|
1.0
|
OD2
|
A:ASP196
|
3.4
|
40.3
|
1.0
|
PBG
|
A:WAQ700
|
3.4
|
33.3
|
1.0
|
P1
|
A:PPV701
|
3.5
|
29.2
|
1.0
|
OPP
|
A:PPV701
|
3.5
|
33.6
|
1.0
|
OD2
|
A:ASP195
|
3.6
|
34.7
|
1.0
|
O5'
|
A:WAQ700
|
3.8
|
34.3
|
1.0
|
OG
|
A:SER194
|
3.8
|
27.9
|
1.0
|
NE2
|
A:HIS53
|
3.8
|
31.7
|
1.0
|
OAH
|
A:WAQ700
|
3.9
|
36.7
|
1.0
|
O
|
A:HOH2051
|
4.0
|
39.3
|
1.0
|
O12
|
A:PPV701
|
4.0
|
27.7
|
1.0
|
CE1
|
A:HIS53
|
4.1
|
33.4
|
1.0
|
N
|
A:ASP196
|
4.2
|
30.5
|
1.0
|
N
|
A:ASP195
|
4.3
|
28.6
|
1.0
|
C5'
|
A:WAQ700
|
4.3
|
32.4
|
1.0
|
O21
|
A:PPV701
|
4.4
|
28.3
|
1.0
|
O3'
|
A:WAQ700
|
4.4
|
30.5
|
1.0
|
CB
|
A:ASP196
|
4.4
|
34.4
|
1.0
|
CB
|
A:ASP195
|
4.5
|
30.6
|
1.0
|
O22
|
A:PPV701
|
4.5
|
30.9
|
1.0
|
O11
|
A:PPV701
|
4.5
|
29.4
|
1.0
|
C
|
A:ASP195
|
4.5
|
31.4
|
1.0
|
CD
|
A:ARG55
|
4.6
|
35.1
|
1.0
|
CA
|
A:ASP195
|
4.6
|
30.6
|
1.0
|
CA
|
A:ASP196
|
4.7
|
33.7
|
1.0
|
OAU
|
A:WAQ700
|
4.7
|
34.5
|
1.0
|
C3'
|
A:WAQ700
|
4.8
|
32.1
|
1.0
|
O
|
A:ILE27
|
4.8
|
31.9
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 5fll
Go back to
Magnesium Binding Sites List in 5fll
Magnesium binding site 3 out
of 4 in the Crystal Structure of the 6-Carboxyhexanoate-Coa Ligase (Biow) From Bacillus Subtilis in Complex with A Pimeloyl-Adenylate
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 A Pimeloyl-Adenylate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg703
b:30.0
occ:1.00
|
O21
|
B:PPV701
|
2.0
|
29.8
|
1.0
|
O12
|
B:PPV701
|
2.0
|
29.1
|
1.0
|
OAH
|
B:WAQ700
|
2.1
|
28.5
|
1.0
|
O
|
B:HOH2023
|
2.1
|
26.2
|
1.0
|
O
|
B:HOH2004
|
2.1
|
30.4
|
1.0
|
O
|
B:HOH2034
|
2.3
|
19.2
|
1.0
|
P1
|
B:PPV701
|
3.1
|
28.8
|
1.0
|
P2
|
B:PPV701
|
3.2
|
32.2
|
1.0
|
OPP
|
B:PPV701
|
3.3
|
26.5
|
1.0
|
PBG
|
B:WAQ700
|
3.5
|
30.4
|
1.0
|
O
|
B:HOH2021
|
3.7
|
36.6
|
1.0
|
O
|
B:GLY29
|
3.8
|
35.3
|
1.0
|
O31
|
B:PPV701
|
3.8
|
27.3
|
1.0
|
NZ
|
B:LYS49
|
3.9
|
31.4
|
1.0
|
OE1
|
B:GLU173
|
4.0
|
38.8
|
1.0
|
O
|
B:HOH2032
|
4.0
|
29.6
|
1.0
|
O
|
B:HOH2007
|
4.0
|
27.0
|
1.0
|
O32
|
B:PPV701
|
4.1
|
26.1
|
1.0
|
O5'
|
B:WAQ700
|
4.2
|
29.6
|
1.0
|
O22
|
B:PPV701
|
4.2
|
25.5
|
1.0
|
C8
|
B:WAQ700
|
4.3
|
34.2
|
1.0
|
O
|
B:HOH2020
|
4.3
|
31.9
|
1.0
|
NH2
|
B:ARG145
|
4.3
|
37.3
|
1.0
|
O11
|
B:PPV701
|
4.3
|
28.9
|
1.0
|
N7
|
B:WAQ700
|
4.3
|
29.4
|
1.0
|
OAD
|
B:WAQ700
|
4.4
|
30.8
|
1.0
|
CE
|
B:LYS49
|
4.6
|
32.9
|
1.0
|
OAU
|
B:WAQ700
|
4.6
|
39.0
|
1.0
|
C
|
B:GLY29
|
4.9
|
32.2
|
1.0
|
MG
|
B:MG704
|
4.9
|
29.4
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 5fll
Go back to
Magnesium Binding Sites List in 5fll
Magnesium binding site 4 out
of 4 in the Crystal Structure of the 6-Carboxyhexanoate-Coa Ligase (Biow) From Bacillus Subtilis in Complex with A Pimeloyl-Adenylate
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 A Pimeloyl-Adenylate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg704
b:29.4
occ:1.00
|
O32
|
B:PPV701
|
2.0
|
26.1
|
1.0
|
OD1
|
B:ASP195
|
2.0
|
33.7
|
1.0
|
O31
|
B:PPV701
|
2.1
|
27.3
|
1.0
|
OD1
|
B:ASP196
|
2.1
|
36.2
|
1.0
|
OAD
|
B:WAQ700
|
2.2
|
30.8
|
1.0
|
O
|
B:HOH2003
|
2.2
|
24.5
|
1.0
|
CG
|
B:ASP195
|
3.0
|
37.2
|
1.0
|
CG
|
B:ASP196
|
3.1
|
37.0
|
1.0
|
P2
|
B:PPV701
|
3.3
|
32.2
|
1.0
|
PBG
|
B:WAQ700
|
3.4
|
30.4
|
1.0
|
P1
|
B:PPV701
|
3.4
|
28.8
|
1.0
|
OD2
|
B:ASP195
|
3.5
|
39.2
|
1.0
|
OD2
|
B:ASP196
|
3.5
|
38.8
|
1.0
|
OPP
|
B:PPV701
|
3.5
|
26.5
|
1.0
|
O5'
|
B:WAQ700
|
3.7
|
29.6
|
1.0
|
C5'
|
B:WAQ700
|
3.8
|
32.6
|
1.0
|
OG
|
B:SER194
|
3.9
|
34.6
|
1.0
|
OAH
|
B:WAQ700
|
3.9
|
28.5
|
1.0
|
NE2
|
B:HIS53
|
3.9
|
32.6
|
1.0
|
O
|
B:HOH2021
|
4.0
|
36.6
|
1.0
|
O12
|
B:PPV701
|
4.1
|
29.1
|
1.0
|
N
|
B:ASP196
|
4.2
|
35.0
|
1.0
|
CE1
|
B:HIS53
|
4.2
|
33.8
|
1.0
|
O3'
|
B:WAQ700
|
4.3
|
32.5
|
1.0
|
N
|
B:ASP195
|
4.3
|
34.9
|
1.0
|
O21
|
B:PPV701
|
4.4
|
29.8
|
1.0
|
CB
|
B:ASP195
|
4.4
|
37.8
|
1.0
|
O11
|
B:PPV701
|
4.5
|
28.9
|
1.0
|
O22
|
B:PPV701
|
4.5
|
25.5
|
1.0
|
CB
|
B:ASP196
|
4.5
|
38.7
|
1.0
|
C
|
B:ASP195
|
4.5
|
37.2
|
1.0
|
C3'
|
B:WAQ700
|
4.6
|
29.3
|
1.0
|
CA
|
B:ASP195
|
4.6
|
36.0
|
1.0
|
CD
|
B:ARG55
|
4.7
|
33.3
|
1.0
|
OAU
|
B:WAQ700
|
4.7
|
39.0
|
1.0
|
O
|
B:ILE27
|
4.8
|
34.4
|
1.0
|
CA
|
B:ASP196
|
4.8
|
37.6
|
1.0
|
C4'
|
B:WAQ700
|
4.9
|
29.0
|
1.0
|
MG
|
B:MG703
|
4.9
|
30.0
|
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 04:20:05 2024
|