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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

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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 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

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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 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

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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 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

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