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

Protein crystallography data

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

Other elements in 3gsh:

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

Fluorine (F) 6 atoms
Zinc (Zn) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 3 binding sites of Sodium where determined in the Three-Dimensional Structure of A Post Translational Modified Barley LTP1, PDB code: 3gsh:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 3gsh

Go back to Sodium Binding Sites List in 3gsh
Sodium binding site 1 out of 3 in the Three-Dimensional Structure of A Post Translational Modified Barley LTP1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na201

b:24.7
occ:1.00
O A:HOH320 2.7 29.3 1.0
O A:ILE81 2.7 16.9 1.0
O A:LEU63 2.7 16.1 1.0
C A:LEU63 3.5 16.4 1.0
CB A:SER82 3.5 17.1 1.0
CA A:LEU63 3.5 16.4 1.0
CA A:SER82 3.6 17.2 1.0
CD2 A:LEU63 3.6 18.6 1.0
N A:ALA67 3.7 13.6 1.0
C A:ILE81 3.7 16.7 1.0
CB A:ALA67 3.7 14.1 1.0
CB A:LEU63 3.8 17.5 1.0
CB A:ALA66 3.9 14.5 1.0
CA A:ALA67 4.1 13.2 1.0
N A:SER82 4.1 17.3 1.0
CG A:LEU63 4.3 15.3 1.0
C A:ALA66 4.4 13.9 1.0
CA A:ALA66 4.7 14.5 1.0
CD A:PRO83 4.7 19.8 1.0
N A:ASN64 4.7 16.0 1.0
N A:LEU63 4.9 17.0 1.0
OG A:SER82 4.9 17.1 1.0
C A:SER82 4.9 18.0 1.0

Sodium binding site 2 out of 3 in 3gsh

Go back to Sodium Binding Sites List in 3gsh
Sodium binding site 2 out of 3 in the Three-Dimensional Structure of A Post Translational Modified Barley LTP1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na203

b:42.1
occ:1.00
OD2 A:ASP86 2.7 23.3 1.0
CG A:ASP86 3.5 20.0 1.0
CB A:ASP86 3.6 19.6 1.0
CB A:ARG89 3.8 29.2 1.0
CD A:ARG89 3.8 32.1 1.0
CG A:ARG89 4.2 30.6 1.0
O A:ASP86 4.5 19.4 1.0
OD1 A:ASP86 4.6 24.3 1.0
NE A:ARG89 4.8 35.2 1.0
CA A:ARG89 4.9 29.3 1.0
O A:HOH400 4.9 29.2 1.0
CA A:ASP86 4.9 18.8 1.0

Sodium binding site 3 out of 3 in 3gsh

Go back to Sodium Binding Sites List in 3gsh
Sodium binding site 3 out of 3 in the Three-Dimensional Structure of A Post Translational Modified Barley LTP1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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
B:Na202

b:21.1
occ:1.00
O B:HOH441 2.0 32.5 1.0
O B:HOH440 2.2 29.9 1.0
O B:HOH448 2.3 30.2 1.0
ZN B:ZN104 3.2 52.2 1.0
NH1 B:ARG56 3.4 17.3 1.0
ZN A:ZN101 3.8 27.5 1.0
O A:HOH361 3.8 18.3 1.0
CE B:LYS52 4.1 24.9 1.0
CZ B:ARG56 4.1 17.6 1.0
ND2 A:ASN76 4.2 13.4 1.0
O2 B:ASY303 4.3 28.9 1.0
O A:HOH392 4.5 31.7 1.0
CD B:ARG56 4.6 18.1 1.0
NE B:ARG56 4.6 16.2 1.0
CA B:GLY53 4.6 18.7 1.0
NH2 B:ARG56 4.8 23.0 1.0
NZ B:LYS52 4.9 27.2 1.0
O A:HOH346 4.9 52.9 1.0
N B:GLY53 5.0 17.5 1.0

Reference:

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
Page generated: Tue Dec 15 06:12:43 2020

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