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Sodium in PDB 1f7t: Holo-(Acyl Carrier Protein) Synthase at 1.8A

Enzymatic activity of Holo-(Acyl Carrier Protein) Synthase at 1.8A

All present enzymatic activity of Holo-(Acyl Carrier Protein) Synthase at 1.8A:
2.7.8.7;

Protein crystallography data

The structure of Holo-(Acyl Carrier Protein) Synthase at 1.8A, PDB code: 1f7t was solved by K.D.Parris, L.Lin, A.Tam, R.Mathew, J.Hixon, M.Stahl, C.C.Fritz, J.Seehra, W.S.Somers, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 76.262, 76.160, 85.693, 90.00, 93.32, 90.00
R / Rfree (%) 19.6 / 21.9

Other elements in 1f7t:

The structure of Holo-(Acyl Carrier Protein) Synthase at 1.8A also contains other interesting chemical elements:

Chlorine (Cl) 19 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Holo-(Acyl Carrier Protein) Synthase at 1.8A (pdb code 1f7t). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Holo-(Acyl Carrier Protein) Synthase at 1.8A, PDB code: 1f7t:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 1f7t

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Sodium binding site 1 out of 8 in the Holo-(Acyl Carrier Protein) Synthase at 1.8A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Holo-(Acyl Carrier Protein) Synthase at 1.8A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na472

b:26.2
occ:1.00
 O A:HOH536 2.3 34.7 1.0
O A:HIS105 2.3 23.9 1.0
O B:ILE9 2.4 20.5 1.0
O B:HOH528 2.4 30.8 1.0
CL B:CL490 2.9 27.8 1.0
C A:HIS105 3.5 24.7 1.0
C B:ILE9 3.5 20.4 1.0
CG2 A:THR106 3.9 24.5 1.0
O A:HOH518 4.0 27.0 1.0
CA B:THR10 4.1 22.1 1.0
OD2 B:ASP8 4.1 28.1 1.0
OG1 A:THR104 4.1 21.8 1.0
CA A:THR106 4.2 24.5 1.0
O B:HOH569 4.2 63.1 1.0
N A:THR106 4.3 24.2 1.0
N B:THR10 4.3 20.8 1.0
OG1 B:THR10 4.4 25.0 1.0
O B:HOH538 4.4 39.5 1.0
NH2 B:ARG14 4.4 39.8 1.0
N A:HIS105 4.5 22.1 1.0
N B:ILE9 4.5 19.6 1.0
CB A:THR106 4.6 25.8 1.0
CA A:HIS105 4.6 24.8 1.0
CA B:ILE9 4.7 20.2 1.0
CG B:ASP8 4.7 25.1 1.0
OD1 B:ASP8 4.7 25.8 1.0
CB B:THR10 4.8 23.0 1.0

Sodium binding site 2 out of 8 in 1f7t

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Sodium binding site 2 out of 8 in the Holo-(Acyl Carrier Protein) Synthase at 1.8A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Holo-(Acyl Carrier Protein) Synthase at 1.8A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na480

b:38.1
occ:1.00
 O A:HOH520 2.3 29.1 1.0
O A:GLU27 2.3 27.4 1.0
O A:HOH557 2.5 48.6 1.0
O A:HOH565 2.5 38.7 1.0
OE1 A:GLN75 3.3 34.3 1.0
C A:GLU27 3.4 26.6 1.0
CD A:GLN75 3.8 32.5 1.0
O A:LEU30 3.9 23.9 1.0
NE2 A:GLN75 4.1 30.6 1.0
CA A:GLU27 4.2 25.7 1.0
CB A:GLU27 4.2 26.0 1.0
O A:HOH564 4.3 42.1 1.0
N A:ARG28 4.4 26.8 1.0
CA A:ARG28 4.5 28.4 1.0
CD1 A:LEU35 4.6 24.7 1.0
CG A:GLN75 4.8 31.7 1.0
O A:HOH577 4.9 41.2 1.0

Sodium binding site 3 out of 8 in 1f7t

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Sodium binding site 3 out of 8 in the Holo-(Acyl Carrier Protein) Synthase at 1.8A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Holo-(Acyl Carrier Protein) Synthase at 1.8A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na473

b:24.8
occ:1.00
 O C:HOH543 2.2 29.7 1.0
O B:HOH529 2.3 30.1 1.0
O B:VAL101 2.3 20.4 1.0
CL C:CL491 2.8 26.4 1.0
CL B:CL484 2.9 30.1 1.0
C B:VAL101 3.5 19.2 1.0
O C:HOH568 3.7 39.5 1.0
N B:VAL101 4.0 20.1 1.0
O B:PRO87 4.1 23.4 1.0
O C:ILE5 4.3 16.5 1.0
CA B:VAL101 4.4 18.6 1.0
O B:HOH517 4.4 22.4 1.0
CG1 B:VAL101 4.4 19.5 1.0
O B:HOH510 4.4 43.1 1.0
N B:SER102 4.5 18.4 1.0
O B:HOH516 4.5 53.8 1.0
CA B:SER102 4.6 18.7 1.0
O C:LYS62 5.0 23.2 1.0
CB B:SER102 5.0 18.5 1.0

Sodium binding site 4 out of 8 in 1f7t

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Sodium binding site 4 out of 8 in the Holo-(Acyl Carrier Protein) Synthase at 1.8A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Holo-(Acyl Carrier Protein) Synthase at 1.8A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na479

b:28.6
occ:1.00
 O C:HOH551 2.3 32.8 1.0
O C:ILE9 2.4 21.2 1.0
O B:HIS105 2.4 23.8 1.0
O B:HOH544 2.4 38.4 1.0
CL C:CL483 2.9 28.3 1.0
C C:ILE9 3.6 20.1 1.0
C B:HIS105 3.6 23.9 1.0
CG2 B:THR106 4.0 24.9 1.0
OD2 C:ASP8 4.1 24.6 1.0
O B:HOH537 4.1 36.1 1.0
CA C:THR10 4.1 22.2 1.0
OG1 B:THR104 4.2 22.1 1.0
O C:HOH560 4.2 39.6 1.0
OG1 C:THR10 4.2 22.7 1.0
CA B:THR106 4.3 24.8 1.0
N C:THR10 4.3 20.8 1.0
N B:THR106 4.4 23.9 1.0
NH2 C:ARG14 4.4 40.0 1.0
N C:ILE9 4.6 18.6 1.0
N B:HIS105 4.6 20.5 1.0
CB B:THR106 4.7 24.1 1.0
CG C:ASP8 4.7 22.4 1.0
OD1 C:ASP8 4.7 23.3 1.0
CA B:HIS105 4.7 24.1 1.0
CA C:ILE9 4.7 20.1 1.0
CB C:THR10 4.8 23.8 1.0

Sodium binding site 5 out of 8 in 1f7t

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Sodium binding site 5 out of 8 in the Holo-(Acyl Carrier Protein) Synthase at 1.8A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Holo-(Acyl Carrier Protein) Synthase at 1.8A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na474

b:31.3
occ:1.00
 O C:HIS105 2.3 22.8 1.0
O C:HOH564 2.3 42.2 1.0
O A:ILE9 2.4 18.6 1.0
O A:HOH526 2.5 33.8 1.0
CL A:CL494 2.9 29.3 1.0
C C:HIS105 3.5 22.7 1.0
C A:ILE9 3.7 20.6 1.0
CG2 C:THR106 4.0 24.6 1.0
OG1 C:THR104 4.1 21.8 1.0
NH2 A:ARG14 4.1 44.5 1.0
OD2 A:ASP8 4.1 25.9 1.0
CA C:THR106 4.1 25.1 1.0
O A:HOH516 4.1 28.2 1.0
CA A:THR10 4.1 22.8 1.0
N C:THR106 4.2 24.3 1.0
OG1 A:THR10 4.3 26.5 1.0
N A:THR10 4.4 20.9 1.0
O A:HOH543 4.4 43.3 1.0
N C:HIS105 4.5 21.2 1.0
CA C:HIS105 4.6 23.8 1.0
N A:ILE9 4.6 19.0 1.0
CB C:THR106 4.6 25.6 1.0
CA A:ILE9 4.8 19.3 1.0
CG A:ASP8 4.8 21.9 1.0
CB A:THR10 4.8 25.3 1.0
OD1 A:ASP8 4.8 24.5 1.0

Sodium binding site 6 out of 8 in 1f7t

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Sodium binding site 6 out of 8 in the Holo-(Acyl Carrier Protein) Synthase at 1.8A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Holo-(Acyl Carrier Protein) Synthase at 1.8A within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na475

b:28.6
occ:1.00
 O D:HOH547 2.3 38.2 1.0
O D:HIS105 2.3 22.7 1.0
O E:HOH528 2.3 32.4 1.0
O E:ILE9 2.4 20.3 1.0
CL E:CL482 3.0 26.9 1.0
C D:HIS105 3.5 24.2 1.0
C E:ILE9 3.6 21.0 1.0
OD2 E:ASP8 4.0 27.0 1.0
CG2 D:THR106 4.0 24.1 1.0
OG1 D:THR104 4.1 23.2 1.0
CA E:THR10 4.1 22.5 1.0
O D:HOH528 4.1 25.2 1.0
CA D:THR106 4.2 24.5 1.0
OG1 E:THR10 4.2 24.3 1.0
N D:THR106 4.3 24.6 1.0
N E:THR10 4.3 20.9 1.0
O E:HOH534 4.3 37.6 1.0
NH1 E:ARG14 4.3 40.5 1.0
N D:HIS105 4.5 22.6 1.0
N E:ILE9 4.5 19.6 1.0
CA D:HIS105 4.6 24.0 1.0
CB D:THR106 4.6 24.8 1.0
CG E:ASP8 4.7 25.1 1.0
CA E:ILE9 4.7 19.9 1.0
OD1 E:ASP8 4.7 26.3 1.0
CB E:THR10 4.7 23.9 1.0

Sodium binding site 7 out of 8 in 1f7t

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Sodium binding site 7 out of 8 in the Holo-(Acyl Carrier Protein) Synthase at 1.8A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Holo-(Acyl Carrier Protein) Synthase at 1.8A within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na478

b:30.1
occ:1.00
 O F:HOH546 2.3 37.9 1.0
O D:ILE9 2.4 20.6 1.0
O F:HIS105 2.4 21.9 1.0
O D:HOH544 2.4 34.3 1.0
CL D:CL492 3.0 27.6 1.0
C F:HIS105 3.6 23.3 1.0
C D:ILE9 3.6 20.4 1.0
OD2 D:ASP8 4.0 24.4 1.0
CG2 F:THR106 4.0 25.8 1.0
OG1 F:THR104 4.1 20.2 1.0
NH1 D:ARG14 4.1 43.1 1.0
CA D:THR10 4.2 20.7 1.0
O D:HOH530 4.2 26.6 1.0
O D:HOH549 4.2 38.7 1.0
CA F:THR106 4.3 25.6 1.0
N D:THR10 4.3 20.0 1.0
N F:THR106 4.4 23.4 1.0
OG1 D:THR10 4.4 23.3 1.0
N D:ILE9 4.5 18.3 1.0
N F:HIS105 4.5 21.3 1.0
OD1 D:ASP8 4.6 25.7 1.0
CG D:ASP8 4.6 22.4 1.0
CA D:ILE9 4.7 19.6 1.0
CA F:HIS105 4.7 22.9 1.0
CB F:THR106 4.7 27.1 1.0
CB D:THR10 4.9 21.6 1.0

Sodium binding site 8 out of 8 in 1f7t

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Sodium binding site 8 out of 8 in the Holo-(Acyl Carrier Protein) Synthase at 1.8A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Holo-(Acyl Carrier Protein) Synthase at 1.8A within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na476

b:35.8
occ:1.00
 O F:ILE9 2.3 23.2 1.0
O E:HOH543 2.3 39.8 1.0
O F:HOH539 2.4 37.0 1.0
O E:HIS105 2.5 25.8 1.0
CL F:CL485 2.9 33.0 1.0
C F:ILE9 3.5 22.1 1.0
C E:HIS105 3.6 25.9 1.0
CG2 E:THR106 4.0 25.2 1.0
OD2 F:ASP8 4.0 27.2 1.0
CA F:THR10 4.1 25.0 1.0
O F:HOH514 4.2 47.0 1.0
OG1 E:THR104 4.2 24.6 1.0
CA E:THR106 4.3 26.6 1.0
N F:THR10 4.3 24.1 1.0
OG1 F:THR10 4.3 27.3 1.0
N E:THR106 4.4 26.0 1.0
N F:ILE9 4.5 21.0 1.0
NH1 F:ARG14 4.6 50.2 1.0
O E:HOH518 4.6 31.5 1.0
CA F:ILE9 4.6 20.9 1.0
N E:HIS105 4.6 24.2 1.0
OD1 F:ASP8 4.6 26.7 1.0
CG F:ASP8 4.7 26.2 1.0
CB E:THR106 4.7 26.9 1.0
CA E:HIS105 4.7 26.2 1.0
CB F:THR10 4.8 27.4 1.0

Reference:

K.D.Parris, L.Lin, A.Tam, R.Mathew, J.Hixon, M.Stahl, C.C.Fritz, J.Seehra, W.S.Somers. Crystal Structures of Substrate Binding to Bacillus Subtilis Holo-(Acyl Carrier Protein) Synthase Reveal A Novel Trimeric Arrangement of Molecules Resulting in Three Active Sites. Structure Fold.Des. V. 8 883 2000.
ISSN: ISSN 0969-2126
PubMed: 10997907
DOI: 10.1016/S0969-2126(00)00178-7
Page generated: Sun Oct 6 18:28:08 2024

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