Zinc in PDB 4ec4: Xiap-BIR3 in Complex with A Potent Divalent Smac Mimetic

Protein crystallography data

The structure of Xiap-BIR3 in Complex with A Potent Divalent Smac Mimetic, PDB code: 4ec4 was solved by E.Mastrangelo, F.Cossu, M.Bolognesi, M.Milani, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 51.41 / 3.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 65.420, 130.490, 215.730, 90.00, 90.00, 90.00
R / Rfree (%) 21 / 27.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Xiap-BIR3 in Complex with A Potent Divalent Smac Mimetic (pdb code 4ec4). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 10 binding sites of Zinc where determined in the Xiap-BIR3 in Complex with A Potent Divalent Smac Mimetic, PDB code: 4ec4:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in 4ec4

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Zinc binding site 1 out of 10 in the Xiap-BIR3 in Complex with A Potent Divalent Smac Mimetic


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Xiap-BIR3 in Complex with A Potent Divalent Smac Mimetic within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:8.7
occ:1.00
 NE2 A:HIS320 2.1 7.9 1.0
SG A:CYS327 2.3 9.8 1.0
SG A:CYS303 2.3 9.0 1.0
SG A:CYS300 2.3 8.7 1.0
CE1 A:HIS320 2.7 8.1 1.0
CB A:CYS327 3.2 9.7 1.0
CB A:CYS300 3.4 8.3 1.0
CB A:CYS303 3.4 10.3 1.0
CD2 A:HIS320 3.4 7.7 1.0
N A:CYS303 3.7 10.9 1.0
ND1 A:HIS320 4.0 8.0 1.0
CA A:CYS303 4.1 11.1 1.0
CG A:HIS320 4.3 7.8 1.0
CA A:CYS327 4.5 10.7 1.0
CB A:HIS302 4.7 12.0 1.0
C A:HIS302 4.7 12.1 1.0
CA A:CYS300 4.8 8.6 1.0
N A:HIS302 4.9 11.2 1.0
C A:CYS303 5.0 11.1 1.0
CA A:HIS302 5.0 12.1 1.0

Zinc binding site 2 out of 10 in 4ec4

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Zinc binding site 2 out of 10 in the Xiap-BIR3 in Complex with A Potent Divalent Smac Mimetic


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Xiap-BIR3 in Complex with A Potent Divalent Smac Mimetic within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:25.4
occ:1.00
 NE2 B:HIS320 2.1 23.6 1.0
CE1 B:HIS320 2.2 24.3 1.0
SG B:CYS300 2.3 27.0 1.0
SG B:CYS327 2.3 26.4 1.0
SG B:CYS303 2.4 24.8 1.0
CB B:CYS327 3.3 25.0 1.0
CB B:CYS300 3.4 26.2 1.0
CD2 B:HIS320 3.5 22.8 1.0
ND1 B:HIS320 3.5 24.0 1.0
CB B:CYS303 3.5 26.2 1.0
N B:CYS303 3.7 29.1 1.0
CG B:HIS320 4.2 23.1 1.0
CA B:CYS303 4.2 28.2 1.0
CB B:HIS302 4.4 31.9 1.0
CA B:CYS327 4.7 26.0 1.0
CD2 B:TYR329 4.7 29.1 1.0
CA B:CYS300 4.8 27.5 1.0
C B:HIS302 4.8 31.4 1.0
CB B:TYR329 4.8 31.0 1.0
N B:HIS302 4.9 31.7 1.0
CB B:LEU330 4.9 25.3 1.0
CA B:HIS302 5.0 32.4 1.0
N B:LEU330 5.0 27.9 1.0

Zinc binding site 3 out of 10 in 4ec4

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Zinc binding site 3 out of 10 in the Xiap-BIR3 in Complex with A Potent Divalent Smac Mimetic


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Xiap-BIR3 in Complex with A Potent Divalent Smac Mimetic within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:23.1
occ:1.00
 NE2 C:HIS320 2.1 23.3 1.0
SG C:CYS303 2.3 21.0 1.0
SG C:CYS300 2.3 24.7 1.0
SG C:CYS327 2.4 23.7 1.0
CE1 C:HIS320 2.6 24.8 1.0
CB C:CYS327 3.2 22.1 1.0
CB C:CYS303 3.3 20.9 1.0
CB C:CYS300 3.3 24.3 1.0
CD2 C:HIS320 3.4 23.2 1.0
N C:CYS303 3.5 23.3 1.0
ND1 C:HIS320 3.9 25.7 1.0
CA C:CYS303 4.0 21.9 1.0
CG C:HIS320 4.3 24.7 1.0
CB C:HIS302 4.4 26.7 1.0
CA C:CYS327 4.5 21.9 1.0
C C:HIS302 4.6 24.7 1.0
CA C:CYS300 4.8 25.6 1.0
CA C:HIS302 4.8 26.3 1.0
N C:HIS302 4.8 26.5 1.0
C C:CYS303 4.9 21.7 1.0
N C:GLY304 5.0 22.5 1.0
CB C:TYR329 5.0 28.8 1.0

Zinc binding site 4 out of 10 in 4ec4

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Zinc binding site 4 out of 10 in the Xiap-BIR3 in Complex with A Potent Divalent Smac Mimetic


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Xiap-BIR3 in Complex with A Potent Divalent Smac Mimetic within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn401

b:11.7
occ:1.00
 NE2 D:HIS320 2.1 10.4 1.0
SG D:CYS327 2.3 13.5 1.0
SG D:CYS303 2.3 11.8 1.0
SG D:CYS300 2.3 12.7 1.0
CE1 D:HIS320 2.8 10.9 1.0
CB D:CYS327 3.1 12.7 1.0
CB D:CYS300 3.3 11.9 1.0
CD2 D:HIS320 3.3 9.7 1.0
CB D:CYS303 3.3 13.3 1.0
N D:CYS303 3.8 15.2 1.0
ND1 D:HIS320 4.1 10.5 1.0
CA D:CYS303 4.2 14.8 1.0
CG D:HIS320 4.3 9.8 1.0
CA D:CYS327 4.5 14.0 1.0
CA D:CYS300 4.7 12.6 1.0
CB D:HIS302 4.8 17.6 1.0
CB D:TYR324 4.9 9.9 1.0
C D:HIS302 4.9 17.0 1.0
O D:TYR324 5.0 10.4 1.0

Zinc binding site 5 out of 10 in 4ec4

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Zinc binding site 5 out of 10 in the Xiap-BIR3 in Complex with A Potent Divalent Smac Mimetic


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Xiap-BIR3 in Complex with A Potent Divalent Smac Mimetic within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn401

b:13.7
occ:1.00
 NE2 E:HIS320 2.1 12.2 1.0
SG E:CYS300 2.3 15.0 1.0
SG E:CYS327 2.3 14.3 1.0
SG E:CYS303 2.3 14.2 1.0
CE1 E:HIS320 2.8 12.5 1.0
CB E:CYS300 3.3 14.5 1.0
CB E:CYS303 3.3 15.8 1.0
CB E:CYS327 3.3 13.7 1.0
CD2 E:HIS320 3.3 11.5 1.0
N E:CYS303 3.6 17.8 1.0
CA E:CYS303 4.0 17.6 1.0
ND1 E:HIS320 4.1 12.0 1.0
CG E:HIS320 4.3 11.4 1.0
CB E:HIS302 4.6 19.2 1.0
CA E:CYS327 4.6 14.8 1.0
CA E:CYS300 4.7 15.7 1.0
N E:GLY304 4.7 17.8 1.0
C E:HIS302 4.7 19.7 1.0
C E:CYS303 4.8 18.1 1.0
N E:HIS302 4.8 19.4 1.0
CA E:HIS302 4.9 20.1 1.0

Zinc binding site 6 out of 10 in 4ec4

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Zinc binding site 6 out of 10 in the Xiap-BIR3 in Complex with A Potent Divalent Smac Mimetic


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Xiap-BIR3 in Complex with A Potent Divalent Smac Mimetic within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn402

b:9.9
occ:1.00
 NE2 J:HIS320 2.1 8.8 1.0
SG J:CYS327 2.3 10.1 1.0
SG J:CYS300 2.3 10.4 1.0
SG J:CYS303 2.3 11.4 1.0
CE1 J:HIS320 3.0 8.6 1.0
CB J:CYS327 3.2 10.2 1.0
CB J:CYS300 3.2 11.3 1.0
CD2 J:HIS320 3.3 8.5 1.0
CB J:CYS303 3.3 12.8 1.0
N J:CYS303 3.6 13.4 1.0
CA J:CYS303 4.0 14.1 1.0
ND1 J:HIS320 4.1 8.3 1.0
CG J:HIS320 4.3 8.3 1.0
CA J:CYS327 4.5 11.3 1.0
CB J:HIS302 4.7 12.8 1.0
CA J:CYS300 4.7 12.2 1.0
C J:HIS302 4.7 14.4 1.0
CB J:TYR324 4.9 10.6 1.0
C J:CYS303 4.9 15.3 1.0
CA J:HIS302 5.0 13.8 1.0

Zinc binding site 7 out of 10 in 4ec4

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Zinc binding site 7 out of 10 in the Xiap-BIR3 in Complex with A Potent Divalent Smac Mimetic


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Xiap-BIR3 in Complex with A Potent Divalent Smac Mimetic within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn401

b:14.3
occ:1.00
 NE2 F:HIS320 2.1 14.2 1.0
SG F:CYS327 2.3 15.1 1.0
SG F:CYS303 2.3 13.8 1.0
SG F:CYS300 2.3 16.0 1.0
CE1 F:HIS320 2.9 15.3 1.0
CD2 F:HIS320 3.2 13.6 1.0
CB F:CYS300 3.2 15.6 1.0
CB F:CYS303 3.3 14.8 1.0
CB F:CYS327 3.3 13.9 1.0
N F:CYS303 3.8 17.1 1.0
ND1 F:HIS320 4.1 15.5 1.0
CA F:CYS303 4.1 16.3 1.0
CG F:HIS320 4.3 14.4 1.0
CA F:CYS327 4.6 14.7 1.0
CA F:CYS300 4.7 16.8 1.0
CB F:HIS302 4.9 20.1 1.0
CB F:TYR324 4.9 11.7 1.0
C F:HIS302 4.9 18.9 1.0
CB F:LEU330 5.0 16.1 1.0

Zinc binding site 8 out of 10 in 4ec4

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Zinc binding site 8 out of 10 in the Xiap-BIR3 in Complex with A Potent Divalent Smac Mimetic


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Xiap-BIR3 in Complex with A Potent Divalent Smac Mimetic within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn401

b:16.9
occ:1.00
 NE2 G:HIS320 2.2 15.3 1.0
SG G:CYS303 2.3 17.3 1.0
SG G:CYS327 2.3 16.8 1.0
SG G:CYS300 2.3 18.7 1.0
CE1 G:HIS320 2.7 16.0 1.0
CB G:CYS300 3.3 18.4 1.0
CB G:CYS303 3.3 18.8 1.0
CB G:CYS327 3.3 15.7 1.0
CD2 G:HIS320 3.4 14.6 1.0
N G:CYS303 3.5 21.3 1.0
ND1 G:HIS320 4.0 15.8 1.0
CA G:CYS303 4.0 21.0 1.0
CG G:HIS320 4.3 14.9 1.0
CB G:HIS302 4.4 23.2 1.0
CA G:CYS327 4.5 16.6 1.0
C G:HIS302 4.7 23.6 1.0
CA G:CYS300 4.7 20.0 1.0
N G:HIS302 4.8 23.8 1.0
N G:GLY304 4.8 22.0 1.0
C G:CYS303 4.8 21.9 1.0
CA G:HIS302 4.8 24.3 1.0
CB G:TYR329 5.0 21.5 1.0

Zinc binding site 9 out of 10 in 4ec4

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Zinc binding site 9 out of 10 in the Xiap-BIR3 in Complex with A Potent Divalent Smac Mimetic


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Xiap-BIR3 in Complex with A Potent Divalent Smac Mimetic within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Zn401

b:22.7
occ:1.00
 NE2 K:HIS320 2.1 21.7 1.0
SG K:CYS303 2.3 22.4 1.0
SG K:CYS300 2.3 24.8 1.0
SG K:CYS327 2.4 22.7 1.0
CE1 K:HIS320 2.8 22.7 1.0
CB K:CYS300 3.2 24.5 1.0
CB K:CYS303 3.3 23.7 1.0
CD2 K:HIS320 3.3 20.9 1.0
CB K:CYS327 3.5 21.5 1.0
N K:CYS303 3.6 26.0 1.0
ND1 K:HIS320 4.0 22.6 1.0
CA K:CYS303 4.0 25.4 1.0
CG K:HIS320 4.3 21.5 1.0
CB K:HIS302 4.5 28.2 1.0
CA K:CYS300 4.7 25.9 1.0
C K:HIS302 4.7 27.8 1.0
CA K:CYS327 4.8 22.3 1.0
C K:CYS303 4.8 25.8 1.0
CB K:TYR329 4.9 27.1 1.0
N K:HIS302 4.9 28.4 1.0
CA K:HIS302 5.0 28.7 1.0
N K:GLY304 5.0 26.4 1.0

Zinc binding site 10 out of 10 in 4ec4

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Zinc binding site 10 out of 10 in the Xiap-BIR3 in Complex with A Potent Divalent Smac Mimetic


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Xiap-BIR3 in Complex with A Potent Divalent Smac Mimetic within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn401

b:21.1
occ:1.00
 NE2 L:HIS320 2.1 20.1 1.0
CE1 L:HIS320 2.2 21.5 1.0
SG L:CYS327 2.3 21.1 1.0
SG L:CYS300 2.3 23.7 1.0
SG L:CYS303 2.3 20.1 1.0
CB L:CYS303 3.3 20.4 1.0
CB L:CYS300 3.3 23.7 1.0
CB L:CYS327 3.3 19.4 1.0
N L:CYS303 3.5 23.1 1.0
CD2 L:HIS320 3.5 19.6 1.0
ND1 L:HIS320 3.5 22.0 1.0
CA L:CYS303 3.9 22.1 1.0
CG L:HIS320 4.2 20.9 1.0
CB L:HIS302 4.5 26.4 1.0
C L:HIS302 4.6 24.9 1.0
CA L:CYS327 4.6 19.6 1.0
N L:GLY304 4.7 23.4 1.0
CA L:CYS300 4.7 25.7 1.0
N L:HIS302 4.8 26.8 1.0
CB L:TYR329 4.8 26.6 1.0
C L:CYS303 4.8 22.8 1.0
CA L:HIS302 4.8 26.4 1.0

Reference:

F.Cossu, M.Milani, P.Vachette, F.Malvezzi, S.Grassi, D.Lecis, D.Delia, C.Drago, P.Seneci, M.Bolognesi, E.Mastrangelo. Structural Insight Into Inhibitor of Apoptosis Proteins Recognition By A Potent Divalent Smac-Mimetic. Plos One V. 7 49527 2012.
ISSN: ESSN 1932-6203
PubMed: 23166698
DOI: 10.1371/JOURNAL.PONE.0049527
Page generated: Wed Dec 16 05:15:58 2020

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