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Zinc in PDB 3siq: Crystal Structure of Autoinhibited DIAP1-BIR1 Domain

Protein crystallography data

The structure of Crystal Structure of Autoinhibited DIAP1-BIR1 Domain, PDB code: 3siq was solved by X.Li, J.Wang, Y.Shi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.98 / 2.40
Space group P 31
Cell size a, b, c (Å), α, β, γ (°) 99.782, 99.782, 71.344, 90.00, 90.00, 120.00
R / Rfree (%) 14.6 / 21.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Autoinhibited DIAP1-BIR1 Domain (pdb code 3siq). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of Autoinhibited DIAP1-BIR1 Domain, PDB code: 3siq:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 3siq

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Zinc binding site 1 out of 6 in the Crystal Structure of Autoinhibited DIAP1-BIR1 Domain


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 Autoinhibited DIAP1-BIR1 Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn200

b:28.5
occ:1.00
 NE2 A:HIS100 2.0 23.2 1.0
SG A:CYS83 2.2 27.7 1.0
SG A:CYS80 2.3 17.7 1.0
SG A:CYS107 2.4 29.7 1.0
CE1 A:HIS100 2.7 17.5 1.0
CB A:CYS80 3.2 18.2 1.0
CD2 A:HIS100 3.2 19.1 1.0
CB A:CYS107 3.2 30.9 1.0
CB A:CYS83 3.4 23.1 1.0
ND1 A:HIS100 3.9 22.2 1.0
N A:CYS83 3.9 21.9 1.0
CG1 A:VAL85 4.0 20.0 1.0
CG A:HIS100 4.2 25.1 1.0
CA A:CYS83 4.2 20.8 1.0
CA A:CYS107 4.5 30.0 1.0
CA A:CYS80 4.6 16.9 1.0
CB A:PHE82 4.8 18.1 1.0
C A:PHE82 4.8 19.8 1.0
CB A:VAL85 5.0 22.5 1.0
C A:CYS83 5.0 21.3 1.0

Zinc binding site 2 out of 6 in 3siq

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Zinc binding site 2 out of 6 in the Crystal Structure of Autoinhibited DIAP1-BIR1 Domain


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 Autoinhibited DIAP1-BIR1 Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn200

b:38.8
occ:1.00
 SG B:CYS80 2.2 31.4 1.0
SG B:CYS107 2.3 37.3 1.0
SG B:CYS83 2.3 34.6 1.0
NE2 B:HIS100 2.3 25.6 1.0
CE1 B:HIS100 2.8 25.3 1.0
CB B:CYS80 3.0 30.6 1.0
CB B:CYS83 3.3 35.5 1.0
N B:CYS83 3.5 34.7 1.0
CB B:CYS107 3.6 33.6 1.0
CD2 B:HIS100 3.6 27.2 1.0
CA B:CYS83 4.0 34.5 1.0
ND1 B:HIS100 4.1 27.0 1.0
CA B:CYS80 4.4 30.9 1.0
CB B:PHE82 4.5 34.1 1.0
CG B:HIS100 4.5 27.2 1.0
C B:PHE82 4.6 35.2 1.0
C B:CYS83 4.7 33.8 1.0
N B:GLY84 4.8 32.1 1.0
CA B:CYS107 4.8 34.5 1.0
CG1 B:VAL85 4.8 27.2 1.0
CG B:LEU110 4.9 34.9 1.0
CA B:PHE82 4.9 34.0 1.0
N B:PHE82 4.9 34.3 1.0
CD1 B:LEU110 4.9 32.6 1.0
C B:CYS80 4.9 31.6 1.0

Zinc binding site 3 out of 6 in 3siq

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Zinc binding site 3 out of 6 in the Crystal Structure of Autoinhibited DIAP1-BIR1 Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Autoinhibited DIAP1-BIR1 Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn200

b:29.6
occ:1.00
 SG C:CYS80 2.1 23.8 1.0
SG C:CYS83 2.2 21.6 1.0
NE2 C:HIS100 2.2 16.8 1.0
SG C:CYS107 2.4 31.6 1.0
CE1 C:HIS100 2.9 18.9 1.0
CB C:CYS80 3.1 18.1 1.0
CD2 C:HIS100 3.4 22.5 1.0
CB C:CYS83 3.5 21.8 1.0
CB C:CYS107 3.6 32.0 1.0
N C:CYS83 3.9 21.7 1.0
ND1 C:HIS100 4.1 23.2 1.0
CA C:CYS83 4.3 21.7 1.0
CG C:HIS100 4.4 25.2 1.0
CB C:PHE82 4.6 19.1 1.0
CA C:CYS80 4.6 19.1 1.0
C C:PHE82 4.6 19.9 1.0
CA C:CYS107 4.8 31.6 1.0
OG C:SER104 4.8 33.0 1.0
CA C:PHE82 4.9 20.4 1.0
N C:PHE82 5.0 19.0 1.0
CD2 C:LEU110 5.0 25.4 1.0
O C:THR67 5.0 19.9 1.0
CB C:SER104 5.0 31.8 1.0

Zinc binding site 4 out of 6 in 3siq

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Zinc binding site 4 out of 6 in the Crystal Structure of Autoinhibited DIAP1-BIR1 Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Autoinhibited DIAP1-BIR1 Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn200

b:40.7
occ:1.00
 SG D:CYS83 2.1 32.2 1.0
SG D:CYS80 2.2 29.6 1.0
NE2 D:HIS100 2.2 23.1 1.0
SG D:CYS107 2.4 28.5 1.0
CE1 D:HIS100 2.6 24.3 1.0
CB D:CYS80 3.1 26.7 1.0
CB D:CYS107 3.1 30.9 1.0
CB D:CYS83 3.2 29.7 1.0
CD2 D:HIS100 3.5 25.4 1.0
N D:CYS83 3.8 30.8 1.0
ND1 D:HIS100 3.9 28.7 1.0
CA D:CYS83 4.1 30.0 1.0
CG1 D:VAL85 4.3 24.1 1.0
CG D:HIS100 4.3 27.2 1.0
CA D:CYS107 4.4 32.5 1.0
C D:PHE82 4.5 31.4 1.0
CB D:PHE82 4.5 30.9 1.0
CA D:CYS80 4.6 28.9 1.0
C D:CYS83 4.7 29.8 1.0
N D:PHE82 4.8 32.0 1.0
CA D:PHE82 4.9 31.6 1.0
CB D:VAL85 4.9 29.0 1.0
N D:GLY84 5.0 26.6 1.0
C D:CYS80 5.0 30.6 1.0

Zinc binding site 5 out of 6 in 3siq

Go back to Zinc Binding Sites List in 3siq
Zinc binding site 5 out of 6 in the Crystal Structure of Autoinhibited DIAP1-BIR1 Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Autoinhibited DIAP1-BIR1 Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn200

b:28.9
occ:1.00
 NE2 E:HIS100 2.0 20.3 1.0
SG E:CYS83 2.1 29.9 1.0
SG E:CYS107 2.1 35.6 1.0
CE1 E:HIS100 2.2 21.7 1.0
SG E:CYS80 2.2 24.7 1.0
CB E:CYS80 3.2 18.6 1.0
CD2 E:HIS100 3.3 16.0 1.0
CB E:CYS107 3.4 32.5 1.0
CB E:CYS83 3.5 24.1 1.0
ND1 E:HIS100 3.5 25.9 1.0
N E:CYS83 4.0 20.7 1.0
CG E:HIS100 4.1 24.6 1.0
CA E:CYS83 4.3 21.4 1.0
CB E:PHE82 4.5 17.5 1.0
CE E:MET69 4.5 15.1 1.0
CG1 E:VAL85 4.6 23.2 1.0
CA E:CYS107 4.6 32.4 1.0
C E:PHE82 4.6 21.3 1.0
CD2 E:LEU110 4.7 26.5 1.0
CA E:CYS80 4.7 19.0 1.0
N E:PHE82 4.8 19.2 1.0
CA E:PHE82 4.8 20.2 1.0

Zinc binding site 6 out of 6 in 3siq

Go back to Zinc Binding Sites List in 3siq
Zinc binding site 6 out of 6 in the Crystal Structure of Autoinhibited DIAP1-BIR1 Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Autoinhibited DIAP1-BIR1 Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn200

b:35.7
occ:1.00
 NE2 F:HIS100 2.0 31.4 1.0
SG F:CYS80 2.1 32.5 1.0
SG F:CYS83 2.2 38.9 1.0
CE1 F:HIS100 2.4 27.8 1.0
SG F:CYS107 2.6 32.7 1.0
CB F:CYS80 3.0 27.9 1.0
CB F:CYS83 3.3 33.4 1.0
CD2 F:HIS100 3.4 34.1 1.0
CB F:CYS107 3.5 33.5 1.0
N F:CYS83 3.6 33.6 1.0
ND1 F:HIS100 3.7 30.4 1.0
CA F:CYS83 4.0 33.0 1.0
CG F:HIS100 4.2 27.7 1.0
CA F:CYS80 4.5 29.6 1.0
C F:PHE82 4.5 33.4 1.0
CB F:PHE82 4.5 33.4 1.0
CG1 F:VAL85 4.6 31.1 1.0
N F:GLY84 4.6 31.9 1.0
N F:PHE82 4.7 32.1 1.0
C F:CYS83 4.7 32.8 1.0
CA F:CYS107 4.7 33.5 1.0
CA F:PHE82 4.8 32.3 1.0
C F:CYS80 4.9 30.9 1.0
OG F:SER104 5.0 36.8 1.0
O F:THR67 5.0 26.7 1.0

Reference:

X.Li, J.Wang, Y.Shi. Structural Mechanisms of DIAP1 Auto-Inhibition and DIAP1-Mediated Inhibition of Drice. Nat Commun V. 2 408 2011.
ISSN: ESSN 2041-1723
PubMed: 21811237
DOI: 10.1038/NCOMMS1418
Page generated: Sat Oct 26 15:48:08 2024

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