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Zinc in PDB 1du3: Crystal Structure of Trail-SDR5

Protein crystallography data

The structure of Crystal Structure of Trail-SDR5, PDB code: 1du3 was solved by S.-S.Cha, B.-J.Sung, B.-H.Oh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 68.630, 124.810, 128.370, 90.00, 104.49, 90.00
R / Rfree (%) 29.1 / 29.1

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Trail-SDR5 (pdb code 1du3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Trail-SDR5, PDB code: 1du3:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 1du3

Go back to Zinc Binding Sites List in 1du3
Zinc binding site 1 out of 2 in the Crystal Structure of Trail-SDR5


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 Trail-SDR5 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn1

b:57.4
occ:1.00
SG E:CYS230 1.5 47.9 1.0
SG D:CYS230 1.5 43.3 1.0
SG F:CYS230 1.5 40.3 1.0
O E:HOH3113 2.3 2.0 1.0
CB F:CYS230 3.1 29.1 1.0
CB D:CYS230 3.1 27.0 1.0
CB E:CYS230 3.2 29.3 1.0
CA F:CYS230 3.6 27.2 1.0
CA E:CYS230 3.7 26.4 1.0
CA D:CYS230 3.7 26.2 1.0
N F:TRP231 3.9 26.1 1.0
N E:TRP231 4.1 25.2 1.0
N D:TRP231 4.1 27.9 1.0
C F:CYS230 4.2 26.2 1.0
C E:CYS230 4.4 23.9 1.0
C D:CYS230 4.4 27.5 1.0
N F:SER232 4.4 29.4 1.0
N D:SER232 4.6 27.5 1.0
CB F:SER232 4.7 27.1 1.0
N E:SER232 4.7 27.6 1.0
CB E:SER232 4.8 27.5 1.0
CB D:SER232 4.9 26.2 1.0
N F:CYS230 4.9 30.2 1.0
N E:CYS230 4.9 22.7 1.0
N D:CYS230 5.0 25.7 1.0

Zinc binding site 2 out of 2 in 1du3

Go back to Zinc Binding Sites List in 1du3
Zinc binding site 2 out of 2 in the Crystal Structure of Trail-SDR5


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 Trail-SDR5 within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Zn2

b:57.7
occ:1.00
SG K:CYS230 1.5 41.7 1.0
SG L:CYS230 1.5 41.2 1.0
SG J:CYS230 1.5 43.4 1.0
O K:HOH3107 2.4 7.2 1.0
CB L:CYS230 3.1 28.8 1.0
CB K:CYS230 3.1 28.9 1.0
CB J:CYS230 3.1 23.6 1.0
CA L:CYS230 3.5 29.3 1.0
CA K:CYS230 3.6 21.0 1.0
CA J:CYS230 3.7 24.1 1.0
N L:TRP231 3.9 21.0 1.0
N K:TRP231 4.1 20.6 1.0
N J:TRP231 4.1 26.0 1.0
C L:CYS230 4.2 25.4 1.0
C K:CYS230 4.4 18.4 1.0
C J:CYS230 4.4 24.4 1.0
N L:SER232 4.6 24.9 1.0
N J:SER232 4.8 29.7 1.0
N L:CYS230 4.8 28.7 1.0
CB L:SER232 4.8 26.7 1.0
N K:SER232 4.8 27.8 1.0
N K:CYS230 4.9 21.5 1.0
N J:CYS230 4.9 18.5 1.0
CB K:SER232 5.0 29.8 1.0
CB J:SER232 5.0 30.0 1.0

Reference:

S.-S.Cha, B.-J.Sung, Y.A.Kim, Y.L.Song, H.J.Kim, S.Kim, M.S.Lee, B.-H.Oh. Crystal Structure of Trail-DR5 Complex Identifies A Critical Role of the Unique Frame Insertion in Conferring Recognition Specificity J.Biol.Chem. V. 275 31171 2000.
ISSN: ISSN 0021-9258
PubMed: 10893238
DOI: 10.1074/JBC.M004414200
Page generated: Mon Jan 25 16:09:07 2021

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