Zinc in PDB 3gsh: Three-Dimensional Structure of A Post Translational Modified Barley LTP1

The structure of Three-Dimensional Structure of A Post Translational Modified Barley LTP1, PDB code: 3gsh was solved by M.B.Lascombe, T.Prange, B.Bakan, D.Marion, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.56 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	28.740, 76.133, 39.402, 90.00, 104.34, 90.00
R / Rfree (%)	19.4 / 26.2

The structure of Three-Dimensional Structure of A Post Translational Modified Barley LTP1 also contains other interesting chemical elements:

Fluorine	(F)	6 atoms
Sodium	(Na)	3 atoms

The binding sites of Zinc atom in the Three-Dimensional Structure of A Post Translational Modified Barley LTP1 (pdb code 3gsh). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Three-Dimensional Structure of A Post Translational Modified Barley LTP1, PDB code: 3gsh:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Three-Dimensional Structure of A Post Translational Modified Barley LTP1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Three-Dimensional Structure of A Post Translational Modified Barley LTP1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn101 b:27.5 occ:1.00 O B:HOH448 1.8 30.2 1.0 O2 B:ASY303 2.0 28.9 1.0 NE2 A:HIS35 2.1 19.3 1.0 O A:HOH392 2.2 31.7 1.0 O1 B:ASY303 2.3 32.3 1.0 C1 B:ASY303 2.5 30.5 1.0 O B:HOH440 2.6 29.9 1.0 CD2 A:HIS35 3.0 21.2 1.0 CE1 A:HIS35 3.1 18.1 1.0 ZN B:ZN104 3.3 52.2 1.0 O A:HOH361 3.5 18.3 1.0 NA B:NA202 3.8 21.1 1.0 O A:HOH346 3.9 52.9 1.0 C2 B:ASY303 4.0 31.9 1.0 CG A:HIS35 4.2 18.8 1.0 ND1 A:HIS35 4.2 16.3 1.0 ND2 A:ASN76 4.3 13.4 1.0 CB A:ASN76 4.5 14.5 1.0 O B:HOH441 4.7 32.5 1.0 CG A:ASN76 4.9 16.2 1.0 C3 B:ASY303 4.9 31.3 1.0 O A:HOH367 4.9 32.1 1.0

Zinc binding site 2 out of 4 in the Three-Dimensional Structure of A Post Translational Modified Barley LTP1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Three-Dimensional Structure of A Post Translational Modified Barley LTP1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn102 b:27.3 occ:1.00 O2 A:ASY302 2.0 25.4 1.0 O A:HOH397 2.0 29.9 1.0 O1 A:ASY302 2.2 29.5 1.0 O A:HOH376 2.4 37.0 1.0 C1 A:ASY302 2.5 26.4 1.0 C2 A:ASY302 4.0 30.7 1.0 NH1 A:ARG56 4.1 34.4 1.0 CZ A:ARG56 4.9 33.9 1.0 C3 A:ASY302 5.0 30.5 1.0

Zinc binding site 3 out of 4 in the Three-Dimensional Structure of A Post Translational Modified Barley LTP1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Three-Dimensional Structure of A Post Translational Modified Barley LTP1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn103 b:41.6 occ:1.00 O A:HOH401 2.0 31.0 1.0 OD2 A:ASP33 2.1 28.3 1.0 OD1 A:ASN29 2.2 26.2 1.0 O A:HOH329 2.7 50.3 1.0 CG A:ASP33 3.0 24.6 1.0 CG A:ASN29 3.1 23.6 1.0 OD1 A:ASP33 3.3 26.6 1.0 ND2 A:ASN29 3.4 24.5 1.0 NZ A:LYS9 3.7 19.8 0.5 CB A:ASP33 4.3 20.6 1.0 O A:ASN29 4.4 17.4 1.0 O A:HOH305 4.4 32.0 1.0 CB A:ASN29 4.6 18.4 1.0 C A:ASN29 4.7 17.0 1.0 O A:HOH374 4.8 26.2 1.0 CE A:LYS9 4.9 19.0 0.5 O A:HOH383 4.9 37.1 1.0

Zinc binding site 4 out of 4 in the Three-Dimensional Structure of A Post Translational Modified Barley LTP1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Three-Dimensional Structure of A Post Translational Modified Barley LTP1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn104 b:52.2 occ:1.00 O B:HOH440 2.2 29.9 1.0 O A:HOH392 2.5 31.7 1.0 NA B:NA202 3.2 21.1 1.0 O B:HOH448 3.3 30.2 1.0 ZN A:ZN101 3.3 27.5 1.0 NH1 B:ARG56 3.5 17.3 1.0 CD B:ARG56 3.9 18.1 1.0 O1 B:ASY303 4.4 32.3 1.0 O2 B:ASY303 4.4 28.9 1.0 CZ B:ARG56 4.6 17.6 1.0 O A:HOH346 4.6 52.9 1.0 O B:HOH441 4.6 32.5 1.0 C1 B:ASY303 4.7 30.5 1.0 NE B:ARG56 4.7 16.2 1.0

B.Bakan, M.Hamberg, V.Larue, T.Prange, D.Marion, M.B.Lascombe. The Crystal Structure of Oxylipin-Conjugated Barley LTP1 Highlights the Unique Plasticity of the Hydrophobic Cavity of These Plant Lipid-Binding Proteins. Biochem.Biophys.Res.Commun. V. 390 780 2009.
ISSN: ISSN 0006-291X
PubMed: 19836358
DOI: 10.1016/J.BBRC.2009.10.049