Zinc in PDB 2fad: Crystal Structure of E. Coli Heptanoyl-Acp

The structure of Crystal Structure of E. Coli Heptanoyl-Acp, PDB code: 2fad was solved by A.Roujeinikova, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 1.60
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	49.257, 106.244, 28.195, 90.00, 90.00, 90.00
R / Rfree (%)	20.9 / 25.6

The structure of Crystal Structure of E. Coli Heptanoyl-Acp also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Zinc atom in the Crystal Structure of E. Coli Heptanoyl-Acp (pdb code 2fad). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of E. Coli Heptanoyl-Acp, PDB code: 2fad:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Crystal Structure of E. Coli Heptanoyl-Acp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of E. Coli Heptanoyl-Acp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:16.0 occ:1.00 OE2 B:GLU48 2.1 19.4 1.0 OE2 A:GLU5 2.1 10.9 1.0 O B:HOH411 2.2 16.2 1.0 CD A:GLU5 2.8 14.2 1.0 OE1 A:GLU5 2.9 15.1 1.0 CD B:GLU48 2.9 28.2 1.0 OE1 B:GLU48 3.1 20.2 1.0 O A:HOH477 3.3 37.4 1.0 O B:HOH410 3.8 20.3 1.0 O A:HOH479 4.0 17.5 1.0 CG A:GLU5 4.3 17.7 1.0 CG B:GLU48 4.4 16.4 1.0 CA A:SER1 4.6 16.5 1.0 O A:HOH445 4.8 20.8 1.0

Zinc binding site 2 out of 8 in the Crystal Structure of E. Coli Heptanoyl-Acp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of E. Coli Heptanoyl-Acp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:20.4 occ:1.00 O A:HOH459 2.1 24.1 1.0 OE1 A:GLU21 2.1 27.9 1.0 O A:HOH507 2.7 33.1 1.0 CD A:GLU21 2.9 37.4 1.0 OE2 A:GLU21 3.0 43.0 1.0 O A:HOH420 4.1 21.1 1.0 CE A:LYS18 4.3 19.8 1.0 CG A:GLU21 4.3 36.4 1.0 CG A:LYS18 4.5 22.4 1.0 CD A:LYS18 4.6 18.3 1.0 O A:HOH456 4.6 33.0 1.0 CB A:VAL17 4.7 20.8 1.0 N A:LYS18 4.7 20.1 1.0 O A:HOH457 4.7 39.7 1.0 CB A:GLU21 4.8 24.6 1.0 CA A:VAL17 4.8 18.4 1.0 NZ A:LYS18 4.9 21.3 1.0

Zinc binding site 3 out of 8 in the Crystal Structure of E. Coli Heptanoyl-Acp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of E. Coli Heptanoyl-Acp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn404 b:17.4 occ:1.00 OD2 A:ASP35 1.8 12.0 1.0 O A:HOH513 2.1 21.7 1.0 O A:HOH464 2.2 19.9 1.0 CG A:ASP35 2.8 22.8 1.0 OD1 A:ASP35 3.1 19.6 1.0 O A:HOH424 3.2 13.4 1.0 O A:HOH463 4.1 17.1 1.0 CB A:ASP35 4.2 10.0 1.0 OD1 A:ASP38 4.3 20.6 1.0 OD2 A:ASP38 4.6 21.5 1.0 CG A:ASP38 4.7 15.5 1.0 CB A:LEU37 4.8 6.1 1.0

Zinc binding site 4 out of 8 in the Crystal Structure of E. Coli Heptanoyl-Acp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of E. Coli Heptanoyl-Acp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn405 b:17.7 occ:1.00 O A:HOH428 2.0 14.8 1.0 O A:HOH427 2.1 18.7 1.0 OD1 A:ASP56 2.1 28.2 1.0 CG A:ASP56 3.2 22.8 1.0 OD2 A:ASP56 3.6 19.2 1.0 O A:HOH521 3.8 38.0 1.0 OE2 A:GLU47 4.1 11.1 1.0 OE1 A:GLU47 4.2 13.8 1.0 O A:ILE54 4.2 18.4 1.0 O A:HOH426 4.2 25.4 1.0 CG1 A:VAL43 4.5 10.3 1.0 CB A:ASP56 4.5 16.1 1.0 CD A:GLU47 4.6 17.8 1.0 CA A:ASP56 4.8 17.9 1.0 N A:ASP56 4.9 15.3 1.0

Zinc binding site 5 out of 8 in the Crystal Structure of E. Coli Heptanoyl-Acp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of E. Coli Heptanoyl-Acp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn406 b:19.5 occ:1.00 O B:HOH428 2.1 23.1 1.0 OE2 A:GLU48 2.2 29.1 1.0 OE2 B:GLU5 2.3 19.1 1.0 CD A:GLU48 3.0 22.5 1.0 CD B:GLU5 3.0 18.4 1.0 OE1 B:GLU5 3.1 21.5 1.0 OE1 A:GLU48 3.1 21.6 1.0 O A:HOH431 3.7 16.9 1.0 O B:HOH476 4.0 35.1 1.0 O A:HOH471 4.2 30.6 1.0 O A:HOH467 4.2 16.9 1.0 CG A:GLU48 4.4 18.7 1.0 CG B:GLU5 4.5 12.4 1.0 CA B:SER1 4.7 11.3 1.0 CB B:SER1 4.7 19.9 1.0

Zinc binding site 6 out of 8 in the Crystal Structure of E. Coli Heptanoyl-Acp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of E. Coli Heptanoyl-Acp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn407 b:15.6 occ:0.50 O A:HOH433 1.8 17.8 0.5 O A:HOH496 2.0 15.3 1.0 O A:HOH434 2.0 13.7 0.5 OXT A:ALA77 2.1 14.6 1.0 C A:ALA77 3.2 24.9 1.0 O A:ALA77 3.8 7.7 1.0 O A:HOH528 4.1 36.9 1.0 OE1 A:GLN76 4.2 12.6 1.0 OD2 A:ASP51 4.5 30.6 1.0 CA A:ALA77 4.5 19.8 1.0 CG A:GLN76 4.5 17.9 1.0 N A:ALA77 4.6 13.7 1.0 CD A:GLN76 4.7 20.4 1.0 CB A:ASP51 4.8 15.1 1.0

Zinc binding site 7 out of 8 in the Crystal Structure of E. Coli Heptanoyl-Acp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of E. Coli Heptanoyl-Acp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn408 b:46.1 occ:1.00 OE1 A:GLU60 2.2 53.6 1.0 OE2 A:GLU57 2.3 49.1 1.0 OE2 A:GLU60 2.6 68.0 1.0 CD A:GLU60 2.7 60.5 1.0 OE1 A:GLU57 2.9 47.2 1.0 CD A:GLU57 2.9 44.9 1.0 CG A:GLU60 4.2 45.7 1.0 CG A:GLU57 4.5 39.5 1.0 CB A:GLU60 4.7 39.6 1.0

Zinc binding site 8 out of 8 in the Crystal Structure of E. Coli Heptanoyl-Acp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of E. Coli Heptanoyl-Acp within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn409 b:19.7 occ:1.00 O B:HOH476 2.4 35.1 1.0 OE2 B:GLU5 4.2 19.1 1.0 CG B:GLU5 4.4 12.4 1.0 O B:HOH433 4.4 34.3 1.0 CD B:GLU5 4.6 18.4 1.0 O B:HOH416 4.8 16.7 1.0 OE2 B:GLU4 4.9 22.6 1.0

A.Roujeinikova, W.J.Simon, J.Gilroy, D.W.Rice, J.B.Rafferty, A.R.Slabas. Structural Studies of Fatty Acyl-(Acyl Carrier Protein) Thioesters Reveal A Hydrophobic Binding Cavity That Can Expand to Fit Longer Substrates. J.Mol.Biol. V. 365 135 2007.
ISSN: ISSN 0022-2836
PubMed: 17059829
DOI: 10.1016/J.JMB.2006.09.049