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Silicon in PDB 3wlu: Crystal Structure of Human Galectin-9 Ncrd with Selenolactose

Protein crystallography data

The structure of Crystal Structure of Human Galectin-9 Ncrd with Selenolactose, PDB code: 3wlu was solved by H.Makyio, T.Suzuki, H.Ando, Y.Yamada, H.Ishida, M.Kiso, S.Wakatsuki, R.Kato, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 1.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 35.732, 68.167, 224.156, 90.00, 90.00, 90.00
R / Rfree (%) 17.2 / 19.4

Silicon Binding Sites:

The binding sites of Silicon atom in the Crystal Structure of Human Galectin-9 Ncrd with Selenolactose (pdb code 3wlu). This binding sites where shown within 5.0 Angstroms radius around Silicon atom.
In total 4 binding sites of Silicon where determined in the Crystal Structure of Human Galectin-9 Ncrd with Selenolactose, PDB code: 3wlu:
Jump to Silicon binding site number: 1; 2; 3; 4;

Silicon binding site 1 out of 4 in 3wlu

Go back to Silicon Binding Sites List in 3wlu
Silicon binding site 1 out of 4 in the Crystal Structure of Human Galectin-9 Ncrd with Selenolactose


Mono view


Stereo pair view

A full contact list of Silicon with other atoms in the Si binding site number 1 of Crystal Structure of Human Galectin-9 Ncrd with Selenolactose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Si201

b:23.8
occ:1.00
SI A:LSE201 0.0 23.8 1.0
C17 A:LSE201 1.8 25.3 1.0
C18 A:LSE201 1.8 26.2 1.0
C16 A:LSE201 1.9 26.7 1.0
C14 A:LSE201 1.9 21.2 1.0
C13 A:LSE201 2.8 20.1 1.0
O5 A:LSE201 4.1 18.0 1.0

Silicon binding site 2 out of 4 in 3wlu

Go back to Silicon Binding Sites List in 3wlu
Silicon binding site 2 out of 4 in the Crystal Structure of Human Galectin-9 Ncrd with Selenolactose


Mono view


Stereo pair view

A full contact list of Silicon with other atoms in the Si binding site number 2 of Crystal Structure of Human Galectin-9 Ncrd with Selenolactose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Si201

b:30.0
occ:1.00
SI B:LSE201 0.0 30.0 1.0
C18 B:LSE201 1.9 31.6 1.0
C16 B:LSE201 1.9 30.0 1.0
C14 B:LSE201 1.9 26.7 1.0
C17 B:LSE201 1.9 27.9 1.0
C13 B:LSE201 2.9 20.2 1.0
O B:HOH469 3.6 27.1 1.0
O5 B:LSE201 4.1 17.2 1.0
O B:HOH426 4.9 30.9 1.0

Silicon binding site 3 out of 4 in 3wlu

Go back to Silicon Binding Sites List in 3wlu
Silicon binding site 3 out of 4 in the Crystal Structure of Human Galectin-9 Ncrd with Selenolactose


Mono view


Stereo pair view

A full contact list of Silicon with other atoms in the Si binding site number 3 of Crystal Structure of Human Galectin-9 Ncrd with Selenolactose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Si201

b:24.2
occ:1.00
SI C:LSE201 0.0 24.2 1.0
C16 C:LSE201 1.8 24.7 1.0
C18 C:LSE201 1.8 23.7 1.0
C14 C:LSE201 1.9 21.7 1.0
C17 C:LSE201 1.9 20.3 1.0
C13 C:LSE201 2.8 20.1 1.0
O5 C:LSE201 4.1 16.2 1.0

Silicon binding site 4 out of 4 in 3wlu

Go back to Silicon Binding Sites List in 3wlu
Silicon binding site 4 out of 4 in the Crystal Structure of Human Galectin-9 Ncrd with Selenolactose


Mono view


Stereo pair view

A full contact list of Silicon with other atoms in the Si binding site number 4 of Crystal Structure of Human Galectin-9 Ncrd with Selenolactose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Si201

b:25.2
occ:1.00
SI D:LSE201 0.0 25.2 1.0
C16 D:LSE201 1.8 30.2 1.0
C18 D:LSE201 1.8 26.2 1.0
C17 D:LSE201 1.8 25.9 1.0
C14 D:LSE201 1.9 23.9 1.0
C13 D:LSE201 2.8 20.9 1.0
O5 D:LSE201 4.2 17.1 1.0
O A:HOH461 4.9 27.8 1.0
C8 D:LSE201 4.9 14.7 1.0
O2 D:LSE201 4.9 14.4 1.0

Reference:

T.Suzuki, H.Makyio, H.Ando, N.Komura, M.Menjo, Y.Yamada, A.Imamura, H.Ishida, S.Wakatsuki, R.Kato, M.Kiso. Expanded Potential of Seleno-Carbohydrates As A Molecular Tool For X-Ray Structural Determination of A Carbohydrate-Protein Complex with Single/Multi-Wavelength Anomalous Dispersion Phasing Bioorg.Med.Chem. V. 22 2090 2014.
ISSN: ISSN 0968-0896
PubMed: 24631362
DOI: 10.1016/J.BMC.2014.02.023
Page generated: Wed Dec 16 02:09:33 2020

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