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Zinc 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
Sodium (Na) 3 atoms

Zinc Binding Sites:

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 3gsh

Go back to Zinc Binding Sites List in 3gsh
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 3gsh

Go back to Zinc Binding Sites List in 3gsh
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 3gsh

Go back to Zinc Binding Sites List in 3gsh
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 3gsh

Go back to Zinc Binding Sites List in 3gsh
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

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: Thu Oct 24 13:53:55 2024

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