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Zinc in PDB 6ey2: Crystal Structure of Xiap-BIR3 in Complex with A CIAP1-Selective Sm

Enzymatic activity of Crystal Structure of Xiap-BIR3 in Complex with A CIAP1-Selective Sm

All present enzymatic activity of Crystal Structure of Xiap-BIR3 in Complex with A CIAP1-Selective Sm:
2.3.2.27;

Protein crystallography data

The structure of Crystal Structure of Xiap-BIR3 in Complex with A CIAP1-Selective Sm, PDB code: 6ey2 was solved by F.Cossu, A.Corti, M.Milani, E.Mastrangelo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 66.50 / 2.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 57.230, 97.060, 182.600, 90.00, 90.00, 90.00
R / Rfree (%) 23.5 / 28.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Xiap-BIR3 in Complex with A CIAP1-Selective Sm (pdb code 6ey2). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of Xiap-BIR3 in Complex with A CIAP1-Selective Sm, PDB code: 6ey2:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 6ey2

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Zinc binding site 1 out of 8 in the Crystal Structure of Xiap-BIR3 in Complex with A CIAP1-Selective Sm


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 Xiap-BIR3 in Complex with A CIAP1-Selective Sm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:36.8
occ:1.00
 NE2 A:HIS320 2.0 40.1 1.0
SG A:CYS303 2.2 35.5 1.0
SG A:CYS300 2.3 50.4 1.0
SG A:CYS327 2.3 33.6 1.0
CE1 A:HIS320 2.6 41.9 1.0
CB A:CYS327 2.8 36.4 1.0
CB A:CYS303 3.1 39.2 1.0
CB A:CYS300 3.2 45.5 1.0
CD2 A:HIS320 3.3 42.0 1.0
N A:CYS303 3.6 37.5 1.0
ND1 A:HIS320 3.8 43.8 1.0
CA A:CYS303 3.9 38.7 1.0
CA A:CYS327 4.2 36.9 1.0
CG A:HIS320 4.2 42.3 1.0
CA A:CYS300 4.6 45.4 1.0
C A:HIS302 4.7 35.1 1.0
CB A:HIS302 4.7 41.0 1.0
C A:CYS303 4.8 40.2 1.0
N A:HIS302 4.9 34.0 1.0
O A:TYR324 4.9 35.4 1.0
N A:GLY304 5.0 41.4 1.0
CA A:HIS302 5.0 37.3 1.0

Zinc binding site 2 out of 8 in 6ey2

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Zinc binding site 2 out of 8 in the Crystal Structure of Xiap-BIR3 in Complex with A CIAP1-Selective Sm


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 Xiap-BIR3 in Complex with A CIAP1-Selective Sm within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:52.0
occ:1.00
 NE2 B:HIS320 2.0 54.2 1.0
SG B:CYS303 2.1 50.8 1.0
SG B:CYS300 2.3 54.5 1.0
SG B:CYS327 2.4 43.8 1.0
CE1 B:HIS320 2.6 56.5 1.0
CB B:CYS327 2.8 45.7 1.0
CB B:CYS303 3.0 47.7 1.0
CB B:CYS300 3.1 49.7 1.0
CD2 B:HIS320 3.3 48.7 1.0
N B:CYS303 3.6 54.5 1.0
CA B:CYS303 3.9 52.4 1.0
ND1 B:HIS320 3.9 54.8 1.0
CA B:CYS327 4.2 51.4 1.0
CG B:HIS320 4.2 45.5 1.0
CA B:CYS300 4.6 53.2 1.0
C B:HIS302 4.7 59.2 1.0
CB B:HIS302 4.7 61.2 1.0
C B:CYS303 4.8 53.8 1.0
N B:GLY304 4.9 53.7 1.0
N B:HIS302 5.0 68.1 1.0
O B:TYR324 5.0 37.2 1.0

Zinc binding site 3 out of 8 in 6ey2

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Zinc binding site 3 out of 8 in the Crystal Structure of Xiap-BIR3 in Complex with A CIAP1-Selective Sm


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 Xiap-BIR3 in Complex with A CIAP1-Selective Sm within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:48.0
occ:1.00
 SG C:CYS303 2.2 46.9 1.0
SG C:CYS327 2.2 42.6 1.0
NE2 C:HIS320 2.2 52.8 1.0
SG C:CYS300 2.3 53.6 1.0
CB C:CYS327 2.7 39.9 1.0
CE1 C:HIS320 2.8 57.4 1.0
CB C:CYS303 2.9 54.7 1.0
CB C:CYS300 3.3 53.6 1.0
N C:CYS303 3.4 54.6 1.0
CD2 C:HIS320 3.5 51.0 1.0
CA C:CYS303 3.7 52.9 1.0
CA C:CYS327 4.0 37.4 1.0
ND1 C:HIS320 4.1 50.7 1.0
CG C:HIS320 4.4 50.8 1.0
C C:HIS302 4.5 53.3 1.0
CB C:HIS302 4.5 51.5 1.0
CA C:CYS300 4.7 56.0 1.0
C C:CYS303 4.7 49.6 1.0
N C:HIS302 4.9 51.2 1.0
CA C:HIS302 4.9 54.3 1.0
N C:GLY304 4.9 54.8 1.0
N C:CYS327 4.9 39.8 1.0
C C:CYS327 5.0 39.2 1.0

Zinc binding site 4 out of 8 in 6ey2

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Zinc binding site 4 out of 8 in the Crystal Structure of Xiap-BIR3 in Complex with A CIAP1-Selective Sm


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 Xiap-BIR3 in Complex with A CIAP1-Selective Sm within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn401

b:43.0
occ:1.00
 NE2 D:HIS320 2.0 34.4 1.0
SG D:CYS300 2.1 45.1 1.0
SG D:CYS303 2.3 49.2 1.0
SG D:CYS327 2.4 45.8 1.0
CE1 D:HIS320 2.5 38.2 1.0
CB D:CYS327 3.0 47.0 1.0
CB D:CYS300 3.0 52.6 1.0
CB D:CYS303 3.2 55.3 1.0
CD2 D:HIS320 3.3 36.0 1.0
N D:CYS303 3.6 56.1 1.0
ND1 D:HIS320 3.8 39.3 1.0
CA D:CYS303 4.0 56.1 1.0
CG D:HIS320 4.2 37.3 1.0
CA D:CYS327 4.3 48.6 1.0
CA D:CYS300 4.5 54.4 1.0
CB D:HIS302 4.7 60.5 1.0
C D:HIS302 4.7 56.4 1.0
C D:CYS303 4.9 49.6 1.0
N D:HIS302 4.9 58.4 1.0
N D:GLY304 5.0 48.9 1.0
CA D:HIS302 5.0 59.7 1.0

Zinc binding site 5 out of 8 in 6ey2

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Zinc binding site 5 out of 8 in the Crystal Structure of Xiap-BIR3 in Complex with A CIAP1-Selective Sm


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 Xiap-BIR3 in Complex with A CIAP1-Selective Sm within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn401

b:42.2
occ:1.00
 NE2 E:HIS320 2.1 44.2 1.0
SG E:CYS327 2.2 46.9 1.0
SG E:CYS303 2.2 48.5 1.0
SG E:CYS300 2.3 49.2 1.0
CE1 E:HIS320 2.7 44.8 1.0
CB E:CYS327 2.8 41.3 1.0
CB E:CYS303 3.1 51.2 1.0
CB E:CYS300 3.2 61.5 1.0
CD2 E:HIS320 3.4 41.8 1.0
N E:CYS303 3.6 57.1 1.0
CA E:CYS303 3.9 53.8 1.0
ND1 E:HIS320 3.9 45.4 1.0
CA E:CYS327 4.1 44.1 1.0
CG E:HIS320 4.3 42.5 1.0
CB E:HIS302 4.6 49.6 1.0
CA E:CYS300 4.7 62.3 1.0
C E:HIS302 4.7 60.1 1.0
C E:CYS303 4.9 48.4 1.0
N E:HIS302 4.9 56.9 1.0
N E:CYS327 5.0 48.4 1.0
CA E:HIS302 5.0 55.5 1.0

Zinc binding site 6 out of 8 in 6ey2

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Zinc binding site 6 out of 8 in the Crystal Structure of Xiap-BIR3 in Complex with A CIAP1-Selective Sm


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 Xiap-BIR3 in Complex with A CIAP1-Selective Sm within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn401

b:49.1
occ:1.00
 NE2 F:HIS320 2.1 47.2 1.0
SG F:CYS303 2.2 53.9 1.0
SG F:CYS327 2.2 40.7 1.0
SG F:CYS300 2.3 54.7 1.0
CE1 F:HIS320 2.7 42.3 1.0
CB F:CYS327 2.8 43.6 1.0
CB F:CYS303 3.0 56.1 1.0
CB F:CYS300 3.2 51.1 1.0
CD2 F:HIS320 3.4 43.3 1.0
N F:CYS303 3.5 53.0 1.0
CA F:CYS303 3.8 55.7 1.0
ND1 F:HIS320 4.0 38.2 1.0
CA F:CYS327 4.1 37.3 1.0
CG F:HIS320 4.3 38.7 1.0
CB F:HIS302 4.6 53.8 1.0
C F:HIS302 4.6 53.6 1.0
CA F:CYS300 4.7 54.3 1.0
C F:CYS303 4.8 56.2 1.0
N F:HIS302 4.9 63.0 1.0
O F:TYR324 5.0 37.7 1.0
CA F:HIS302 5.0 56.4 1.0
N F:CYS327 5.0 40.6 1.0
N F:GLY304 5.0 48.6 1.0

Zinc binding site 7 out of 8 in 6ey2

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Zinc binding site 7 out of 8 in the Crystal Structure of Xiap-BIR3 in Complex with A CIAP1-Selective Sm


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Xiap-BIR3 in Complex with A CIAP1-Selective Sm within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn401

b:50.3
occ:1.00
 SG G:CYS303 2.1 55.7 1.0
NE2 G:HIS320 2.1 59.3 1.0
SG G:CYS327 2.3 53.6 1.0
SG G:CYS300 2.4 63.5 1.0
CB G:CYS327 2.7 50.7 1.0
CE1 G:HIS320 2.8 50.7 1.0
CB G:CYS303 2.9 51.4 1.0
CB G:CYS300 3.2 55.9 1.0
CD2 G:HIS320 3.4 47.1 1.0
N G:CYS303 3.5 61.3 1.0
CA G:CYS303 3.8 51.2 1.0
ND1 G:HIS320 4.0 45.7 1.0
CA G:CYS327 4.1 46.4 1.0
CG G:HIS320 4.3 48.2 1.0
CA G:CYS300 4.7 62.4 1.0
C G:HIS302 4.7 62.8 1.0
C G:CYS303 4.7 48.0 1.0
CB G:HIS302 4.8 52.5 1.0
O G:TYR324 4.9 39.2 1.0
N G:CYS327 4.9 41.5 1.0
N G:GLY304 4.9 45.5 1.0
CB G:TYR324 5.0 56.8 1.0

Zinc binding site 8 out of 8 in 6ey2

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Zinc binding site 8 out of 8 in the Crystal Structure of Xiap-BIR3 in Complex with A CIAP1-Selective Sm


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Xiap-BIR3 in Complex with A CIAP1-Selective Sm within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn401

b:46.3
occ:1.00
 NE2 H:HIS320 2.1 54.2 1.0
SG H:CYS327 2.2 50.4 1.0
SG H:CYS303 2.3 58.7 1.0
SG H:CYS300 2.3 54.7 1.0
CE1 H:HIS320 2.7 55.9 1.0
CB H:CYS327 2.7 50.2 1.0
CB H:CYS303 3.0 53.1 1.0
CB H:CYS300 3.2 55.2 1.0
CD2 H:HIS320 3.4 52.9 1.0
N H:CYS303 3.5 58.0 1.0
CA H:CYS303 3.9 55.7 1.0
ND1 H:HIS320 3.9 46.8 1.0
CA H:CYS327 4.1 48.1 1.0
CG H:HIS320 4.3 48.3 1.0
CB H:HIS302 4.6 49.8 1.0
C H:HIS302 4.6 56.5 1.0
CA H:CYS300 4.7 57.2 1.0
C H:CYS303 4.8 56.5 1.0
N H:HIS302 4.9 54.1 1.0
CA H:HIS302 4.9 54.3 1.0
N H:CYS327 5.0 46.3 1.0
N H:GLY304 5.0 55.1 1.0

Reference:

A.Corti, M.Milani, D.Lecis, P.Seneci, M.De Rosa, E.Mastrangelo, F.Cossu. Structure-Based Design and Molecular Profiling of Smac-Mimetics Selective For Cellular Iaps. Febs J. V. 285 3286 2018.
ISSN: ISSN 1742-4658
PubMed: 30055105
DOI: 10.1111/FEBS.14616
Page generated: Thu Aug 21 13:57:57 2025

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