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Magnesium in PDB 3hyk: 2.31 Angstrom Resolution Crystal Structure of A Holo-(Acyl-Carrier- Protein) Synthase From Bacillus Anthracis Str. Ames in Complex with Coa (3',5'-Adp)

Enzymatic activity of 2.31 Angstrom Resolution Crystal Structure of A Holo-(Acyl-Carrier- Protein) Synthase From Bacillus Anthracis Str. Ames in Complex with Coa (3',5'-Adp)

All present enzymatic activity of 2.31 Angstrom Resolution Crystal Structure of A Holo-(Acyl-Carrier- Protein) Synthase From Bacillus Anthracis Str. Ames in Complex with Coa (3',5'-Adp):
2.7.8.7;

Protein crystallography data

The structure of 2.31 Angstrom Resolution Crystal Structure of A Holo-(Acyl-Carrier- Protein) Synthase From Bacillus Anthracis Str. Ames in Complex with Coa (3',5'-Adp), PDB code: 3hyk was solved by A.S.Halavaty, G.Minasov, T.Skarina, O.Onopriyenko, L.Papazisi, A.Savchenko, W.F.Anderson, Center For Structural Genomics Ofinfectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.99 / 2.31
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 77.526, 77.526, 122.965, 90.00, 90.00, 120.00
R / Rfree (%) 19 / 24.7

Other elements in 3hyk:

The structure of 2.31 Angstrom Resolution Crystal Structure of A Holo-(Acyl-Carrier- Protein) Synthase From Bacillus Anthracis Str. Ames in Complex with Coa (3',5'-Adp) also contains other interesting chemical elements:

Chlorine (Cl) 6 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the 2.31 Angstrom Resolution Crystal Structure of A Holo-(Acyl-Carrier- Protein) Synthase From Bacillus Anthracis Str. Ames in Complex with Coa (3',5'-Adp) (pdb code 3hyk). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the 2.31 Angstrom Resolution Crystal Structure of A Holo-(Acyl-Carrier- Protein) Synthase From Bacillus Anthracis Str. Ames in Complex with Coa (3',5'-Adp), PDB code: 3hyk:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 3hyk

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Magnesium binding site 1 out of 9 in the 2.31 Angstrom Resolution Crystal Structure of A Holo-(Acyl-Carrier- Protein) Synthase From Bacillus Anthracis Str. Ames in Complex with Coa (3',5'-Adp)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of 2.31 Angstrom Resolution Crystal Structure of A Holo-(Acyl-Carrier- Protein) Synthase From Bacillus Anthracis Str. Ames in Complex with Coa (3',5'-Adp) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg120

b:22.9
occ:1.00
 O5P A:A3P124 2.0 24.2 1.0
O A:HOH332 2.0 14.4 1.0
O B:HOH328 2.0 13.6 1.0
O A:HIS103 2.1 18.1 1.0
O A:HOH331 2.1 18.0 1.0
ND1 A:HIS103 2.3 18.1 1.0
CE1 A:HIS103 3.0 19.6 1.0
C A:HIS103 3.1 16.5 1.0
P2 A:A3P124 3.3 21.9 1.0
CG A:HIS103 3.4 18.2 1.0
O4P A:A3P124 3.5 16.6 1.0
N A:HIS103 3.6 17.7 1.0
CA A:HIS103 3.6 17.6 1.0
CB A:HIS103 3.9 17.4 1.0
O1P B:A3P127 4.0 27.5 1.0
O B:HOH264 4.1 24.2 1.0
OE1 A:GLU48 4.1 21.7 1.0
O A:HOH265 4.1 23.2 1.0
C5' A:A3P124 4.2 23.0 1.0
NE2 A:HIS103 4.2 18.4 1.0
O5' A:A3P124 4.2 21.8 1.0
N A:SER104 4.3 17.7 1.0
O B:HOH333 4.3 30.8 1.0
O A:HOH329 4.3 16.7 1.0
O B:HOH334 4.4 19.4 1.0
O6P A:A3P124 4.4 18.2 1.0
CD2 A:HIS103 4.4 19.1 1.0
O A:HOH338 4.5 35.8 1.0
CD A:GLU48 4.7 21.7 1.0
CA A:SER104 4.7 17.2 1.0
O B:HOH336 4.7 11.8 1.0
OE2 A:GLU48 4.7 17.1 1.0
C A:SER102 4.9 19.0 1.0
P1 B:A3P127 5.0 24.3 1.0
O A:SER104 5.0 17.3 1.0

Magnesium binding site 2 out of 9 in 3hyk

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Magnesium binding site 2 out of 9 in the 2.31 Angstrom Resolution Crystal Structure of A Holo-(Acyl-Carrier- Protein) Synthase From Bacillus Anthracis Str. Ames in Complex with Coa (3',5'-Adp)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of 2.31 Angstrom Resolution Crystal Structure of A Holo-(Acyl-Carrier- Protein) Synthase From Bacillus Anthracis Str. Ames in Complex with Coa (3',5'-Adp) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg121

b:27.2
occ:1.00
 OD1 A:ASP8 2.0 19.3 1.0
OE2 A:GLU58 2.0 22.6 1.0
O6P C:A3P126 2.0 16.3 1.0
O C:HOH303 2.3 13.5 1.0
O A:HOH322 2.3 18.6 1.0
O A:HOH293 2.3 17.6 1.0
CG A:ASP8 2.9 17.4 1.0
CD A:GLU58 2.9 20.5 1.0
P2 C:A3P126 3.1 24.3 1.0
OD2 A:ASP8 3.2 17.9 1.0
OE1 A:GLU58 3.4 20.2 1.0
OG C:SER102 3.6 14.0 1.0
O4P C:A3P126 3.6 22.3 1.0
O A:HOH296 3.9 16.0 1.0
O5P C:A3P126 3.9 22.5 1.0
O A:HOH420 4.1 28.3 1.0
NZ A:LYS62 4.1 13.7 1.0
CG A:GLU58 4.2 19.1 1.0
CB A:ASP8 4.3 19.1 1.0
O A:ILE9 4.3 20.6 1.0
O5' C:A3P126 4.4 18.7 1.0
O A:HOH282 4.5 9.8 1.0
O A:HOH281 4.6 21.5 1.0
CE A:LYS62 4.6 15.0 1.0
O A:HOH294 4.7 27.6 1.0
CB C:SER102 4.7 20.1 1.0
CA A:ASP8 4.8 17.7 1.0
N A:ILE9 4.8 16.7 1.0
O3P A:A3P125 4.8 23.1 1.0
MG A:MG123 5.0 25.7 1.0

Magnesium binding site 3 out of 9 in 3hyk

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Magnesium binding site 3 out of 9 in the 2.31 Angstrom Resolution Crystal Structure of A Holo-(Acyl-Carrier- Protein) Synthase From Bacillus Anthracis Str. Ames in Complex with Coa (3',5'-Adp)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of 2.31 Angstrom Resolution Crystal Structure of A Holo-(Acyl-Carrier- Protein) Synthase From Bacillus Anthracis Str. Ames in Complex with Coa (3',5'-Adp) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg123

b:25.7
occ:1.00
 O A:HOH301 2.0 12.3 1.0
O3P A:A3P125 2.0 23.1 1.0
O C:HOH302 2.1 18.8 1.0
O4P C:A3P126 2.1 22.3 1.0
O A:HOH321 2.1 19.3 1.0
O A:HOH296 2.2 16.0 1.0
P1 A:A3P125 3.2 25.2 1.0
O2P A:A3P125 3.5 25.7 1.0
P2 C:A3P126 3.5 24.3 1.0
O C:HOH324 3.9 19.4 1.0
O C:HOH303 3.9 13.5 1.0
O5' C:A3P126 4.0 18.7 1.0
O C:HOH385 4.0 26.3 1.0
O C:HOH392 4.1 24.3 1.0
O1P A:A3P125 4.2 21.0 1.0
O C:HOH278 4.2 22.0 1.0
C5' C:A3P126 4.3 20.8 1.0
O3' A:A3P125 4.3 22.7 1.0
O A:HOH298 4.3 10.4 1.0
OE2 A:GLU58 4.3 22.6 1.0
O6P C:A3P126 4.4 16.3 1.0
O5P C:A3P126 4.5 22.5 1.0
CL A:CL122 4.6 22.7 1.0
O A:HOH297 4.9 17.0 1.0
O4' C:A3P126 4.9 20.8 1.0
O A:HOH282 4.9 9.8 1.0
MG A:MG121 5.0 27.2 1.0

Magnesium binding site 4 out of 9 in 3hyk

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Magnesium binding site 4 out of 9 in the 2.31 Angstrom Resolution Crystal Structure of A Holo-(Acyl-Carrier- Protein) Synthase From Bacillus Anthracis Str. Ames in Complex with Coa (3',5'-Adp)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of 2.31 Angstrom Resolution Crystal Structure of A Holo-(Acyl-Carrier- Protein) Synthase From Bacillus Anthracis Str. Ames in Complex with Coa (3',5'-Adp) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg120

b:24.4
occ:1.00
 O4P A:A3P124 1.9 16.6 1.0
O3P B:A3P127 1.9 25.0 1.0
O B:HOH336 2.0 11.8 1.0
O B:HOH426 2.1 27.9 1.0
O B:HOH337 2.1 23.9 1.0
O A:HOH335 2.2 12.4 1.0
P1 B:A3P127 3.0 24.3 1.0
O2P B:A3P127 3.3 22.9 1.0
P2 A:A3P124 3.3 21.9 1.0
O A:HOH329 3.4 16.7 1.0
O A:HOH331 3.8 18.0 1.0
O1P B:A3P127 3.9 27.5 1.0
O5' A:A3P124 3.9 21.8 1.0
O A:HOH263 4.0 34.3 1.0
C5' A:A3P124 4.1 23.0 1.0
O6P A:A3P124 4.2 18.2 1.0
OE2 B:GLU58 4.2 24.1 1.0
O3' B:A3P127 4.2 28.6 1.0
O A:HOH267 4.3 21.6 1.0
O5P A:A3P124 4.3 24.2 1.0
O B:HOH328 4.5 13.6 1.0
O A:HOH268 4.5 28.2 1.0
CL B:CL122 4.8 25.2 1.0
MG B:MG121 4.8 25.5 1.0
O4' A:A3P124 4.8 22.0 1.0
O B:HOH342 5.0 8.6 1.0

Magnesium binding site 5 out of 9 in 3hyk

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Magnesium binding site 5 out of 9 in the 2.31 Angstrom Resolution Crystal Structure of A Holo-(Acyl-Carrier- Protein) Synthase From Bacillus Anthracis Str. Ames in Complex with Coa (3',5'-Adp)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of 2.31 Angstrom Resolution Crystal Structure of A Holo-(Acyl-Carrier- Protein) Synthase From Bacillus Anthracis Str. Ames in Complex with Coa (3',5'-Adp) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg121

b:25.5
occ:1.00
 O B:HOH334 2.0 19.4 1.0
O A:HOH329 2.1 16.7 1.0
OD1 B:ASP8 2.1 18.9 1.0
O B:HOH330 2.1 19.5 1.0
OE2 B:GLU58 2.2 24.1 1.0
O6P A:A3P124 2.2 18.2 1.0
CD B:GLU58 3.0 24.4 1.0
CG B:ASP8 3.0 16.7 1.0
OE1 B:GLU58 3.2 28.8 1.0
OD2 B:ASP8 3.3 15.4 1.0
P2 A:A3P124 3.3 21.9 1.0
O4P A:A3P124 3.8 16.6 1.0
OG A:SER102 3.8 18.9 1.0
O B:HOH337 4.1 23.9 1.0
O5P A:A3P124 4.1 24.2 1.0
O B:ILE9 4.3 15.3 1.0
CG B:GLU58 4.3 22.4 1.0
CB B:ASP8 4.4 15.1 1.0
O B:HOH328 4.4 13.6 1.0
NZ B:LYS62 4.4 15.4 1.0
O5' A:A3P124 4.6 21.8 1.0
O B:HOH333 4.6 30.8 1.0
O B:HOH270 4.6 23.4 1.0
O B:HOH345 4.6 35.6 1.0
O3P B:A3P127 4.7 25.0 1.0
MG B:MG120 4.8 24.4 1.0
CE B:LYS62 4.9 17.0 1.0
CG1 B:ILE10 4.9 15.6 1.0
N B:ILE9 4.9 11.9 1.0
CA B:ASP8 4.9 13.5 1.0

Magnesium binding site 6 out of 9 in 3hyk

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Magnesium binding site 6 out of 9 in the 2.31 Angstrom Resolution Crystal Structure of A Holo-(Acyl-Carrier- Protein) Synthase From Bacillus Anthracis Str. Ames in Complex with Coa (3',5'-Adp)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of 2.31 Angstrom Resolution Crystal Structure of A Holo-(Acyl-Carrier- Protein) Synthase From Bacillus Anthracis Str. Ames in Complex with Coa (3',5'-Adp) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg123

b:25.9
occ:1.00
 O C:HOH339 1.9 9.0 1.0
O B:HOH340 2.0 19.2 1.0
O B:HIS103 2.0 19.2 1.0
O5P B:A3P126 2.1 23.4 1.0
O B:HOH341 2.1 19.9 1.0
ND1 B:HIS103 2.6 17.0 1.0
C B:HIS103 3.1 17.3 1.0
CE1 B:HIS103 3.3 16.5 1.0
P2 B:A3P126 3.4 23.3 1.0
CG B:HIS103 3.6 17.6 1.0
CA B:HIS103 3.8 17.8 1.0
N B:HIS103 3.8 17.5 1.0
O C:HOH291 3.8 19.3 1.0
O4P B:A3P126 3.8 25.3 1.0
O1P C:A3P125 3.9 24.5 1.0
CB B:HIS103 4.0 17.7 1.0
OE1 B:GLU48 4.1 24.2 1.0
N B:SER104 4.2 18.1 1.0
O5' B:A3P126 4.4 19.2 1.0
O B:HOH312 4.4 20.2 1.0
O C:HOH398 4.4 17.6 1.0
C5' B:A3P126 4.4 23.7 1.0
O6P B:A3P126 4.4 20.0 1.0
O C:HOH313 4.5 19.3 1.0
NE2 B:HIS103 4.5 14.7 1.0
CA B:SER104 4.5 18.1 1.0
O B:HOH364 4.6 31.8 1.0
CD2 B:HIS103 4.7 16.9 1.0
CD B:GLU48 4.7 25.3 1.0
OE2 B:GLU48 4.7 24.8 1.0
O C:HOH311 4.8 14.9 1.0
P1 C:A3P125 4.8 26.8 1.0
O B:HOH362 4.8 15.8 0.5
O B:SER104 4.9 19.1 1.0
O3P C:A3P125 4.9 19.4 1.0

Magnesium binding site 7 out of 9 in 3hyk

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Magnesium binding site 7 out of 9 in the 2.31 Angstrom Resolution Crystal Structure of A Holo-(Acyl-Carrier- Protein) Synthase From Bacillus Anthracis Str. Ames in Complex with Coa (3',5'-Adp)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of 2.31 Angstrom Resolution Crystal Structure of A Holo-(Acyl-Carrier- Protein) Synthase From Bacillus Anthracis Str. Ames in Complex with Coa (3',5'-Adp) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg120

b:27.1
occ:1.00
 O6P B:A3P126 2.0 20.0 1.0
O C:HOH313 2.0 19.3 1.0
O B:HOH312 2.2 20.2 1.0
OD1 C:ASP8 2.2 19.6 1.0
OE2 C:GLU58 2.2 27.7 1.0
O C:HOH290 2.3 18.1 1.0
CD C:GLU58 3.0 26.0 1.0
P2 B:A3P126 3.2 23.3 1.0
CG C:ASP8 3.2 17.9 1.0
OE1 C:GLU58 3.3 24.5 1.0
OD2 C:ASP8 3.5 19.8 1.0
O4P B:A3P126 3.6 25.3 1.0
OG B:SER102 3.6 20.1 1.0
O5P B:A3P126 3.9 23.4 1.0
O B:HOH310 4.1 17.5 1.0
O C:ILE9 4.2 17.2 1.0
NZ C:LYS62 4.2 15.8 1.0
O C:HOH339 4.2 9.0 1.0
CG C:GLU58 4.3 22.6 1.0
O5' B:A3P126 4.4 19.2 1.0
O C:HOH399 4.4 17.9 1.0
CB C:ASP8 4.6 18.1 1.0
O C:HOH397 4.6 28.3 1.0
CE C:LYS62 4.8 18.9 1.0
O C:HOH398 4.8 17.6 1.0
N C:ILE9 4.8 15.5 1.0
CB B:SER102 4.8 20.4 1.0
O3P C:A3P125 4.8 19.4 1.0
CG1 C:ILE10 4.9 12.1 0.5
CA C:ASP8 5.0 16.6 1.0

Magnesium binding site 8 out of 9 in 3hyk

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Magnesium binding site 8 out of 9 in the 2.31 Angstrom Resolution Crystal Structure of A Holo-(Acyl-Carrier- Protein) Synthase From Bacillus Anthracis Str. Ames in Complex with Coa (3',5'-Adp)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of 2.31 Angstrom Resolution Crystal Structure of A Holo-(Acyl-Carrier- Protein) Synthase From Bacillus Anthracis Str. Ames in Complex with Coa (3',5'-Adp) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg121

b:24.2
occ:1.00
 O C:HIS103 2.0 18.2 1.0
O A:HOH282 2.1 9.8 1.0
O5P C:A3P126 2.1 22.5 1.0
O C:HOH324 2.2 19.4 1.0
O C:HOH323 2.2 22.5 1.0
ND1 C:HIS103 2.3 18.4 1.0
C C:HIS103 3.0 17.7 1.0
CE1 C:HIS103 3.1 15.7 1.0
CG C:HIS103 3.4 17.7 1.0
P2 C:A3P126 3.4 24.3 1.0
CA C:HIS103 3.6 17.9 1.0
N C:HIS103 3.6 18.3 1.0
O4P C:A3P126 3.6 22.3 1.0
CB C:HIS103 3.8 18.1 1.0
O1P A:A3P125 4.0 21.0 1.0
O A:HOH279 4.1 20.1 1.0
OE1 C:GLU48 4.1 26.6 1.0
O C:HOH299 4.1 31.3 1.0
N C:SER104 4.2 18.9 1.0
C5' C:A3P126 4.2 20.8 1.0
O A:HOH322 4.2 18.6 1.0
O5' C:A3P126 4.3 18.7 1.0
NE2 C:HIS103 4.3 11.5 1.0
O C:HOH303 4.4 13.5 1.0
CD2 C:HIS103 4.4 15.1 1.0
O6P C:A3P126 4.5 16.3 1.0
O A:HOH281 4.6 21.5 1.0
CD C:GLU48 4.6 26.4 1.0
CA C:SER104 4.7 19.0 1.0
OE2 C:GLU48 4.8 23.1 1.0
C C:SER102 4.8 19.6 1.0
O A:HOH301 4.9 12.3 1.0
P1 A:A3P125 4.9 25.2 1.0
O C:SER104 5.0 20.3 1.0

Magnesium binding site 9 out of 9 in 3hyk

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Magnesium binding site 9 out of 9 in the 2.31 Angstrom Resolution Crystal Structure of A Holo-(Acyl-Carrier- Protein) Synthase From Bacillus Anthracis Str. Ames in Complex with Coa (3',5'-Adp)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of 2.31 Angstrom Resolution Crystal Structure of A Holo-(Acyl-Carrier- Protein) Synthase From Bacillus Anthracis Str. Ames in Complex with Coa (3',5'-Adp) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg123

b:21.5
occ:1.00
 O B:HOH310 2.0 17.5 1.0
O C:HOH311 2.0 14.9 1.0
O4P B:A3P126 2.1 25.3 1.0
O C:HOH318 2.1 17.1 1.0
O B:HOH381 2.3 18.2 1.0
O3P C:A3P125 2.3 19.4 1.0
P2 B:A3P126 3.5 23.3 1.0
P1 C:A3P125 3.6 26.8 1.0
O B:HOH308 3.7 18.0 1.0
O2P C:A3P125 3.8 26.2 1.0
O B:HOH312 3.9 20.2 1.0
O B:HOH341 3.9 19.9 1.0
O5' B:A3P126 3.9 19.2 1.0
C5' B:A3P126 4.0 23.7 1.0
O B:HOH382 4.3 28.3 1.0
OE2 C:GLU58 4.3 27.7 1.0
O C:HOH304 4.3 14.7 1.0
O6P B:A3P126 4.4 20.0 1.0
O5P B:A3P126 4.5 23.4 1.0
CL C:CL122 4.5 25.8 1.0
O1P C:A3P125 4.6 24.5 1.0
O4' B:A3P126 4.6 22.0 1.0
O3' C:A3P125 4.6 24.3 1.0
O C:HOH339 4.9 9.0 1.0
O C:HOH287 4.9 22.0 1.0
C4' B:A3P126 4.9 21.4 1.0

Reference:

A.S.Halavaty, Y.Kim, G.Minasov, L.Shuvalova, I.Dubrovska, J.Winsor, M.Zhou, O.Onopriyenko, T.Skarina, L.Papazisi, K.Kwon, S.N.Peterson, A.Joachimiak, A.Savchenko, W.F.Anderson. Structural Characterization and Comparison of Three Acyl-Carrier-Protein Synthases From Pathogenic Bacteria. Acta Crystallogr.,Sect.D V. 68 1359 2012.
ISSN: ISSN 0907-4449
PubMed: 22993090
DOI: 10.1107/S0907444912029101
Page generated: Wed Aug 14 15:30:20 2024

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