Atomistry » Sodium » PDB 1evr-1gb5 » 1f7t
Atomistry »
  Sodium »
    PDB 1evr-1gb5 »
      1f7t »

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

Go back to Sodium Binding Sites List in 1f7t
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

Go back to Sodium Binding Sites List in 1f7t
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

Go back to Sodium Binding Sites List in 1f7t
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

Go back to Sodium Binding Sites List in 1f7t
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

Go back to Sodium Binding Sites List in 1f7t
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

Go back to Sodium Binding Sites List in 1f7t
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

Go back to Sodium Binding Sites List in 1f7t
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

Go back to Sodium Binding Sites List in 1f7t
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy