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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

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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

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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

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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

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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

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