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Zinc in PDB 1xb0: Structure of the Bir Domain of Iap-Like Protein 2

Protein crystallography data

The structure of Structure of the Bir Domain of Iap-Like Protein 2, PDB code: 1xb0 was solved by H.Shin, M.Renatus, B.P.Eckelman, V.A.Nunes, C.A.M.Sampaio, G.S.Salvesen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.20
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 86.400, 86.400, 226.770, 90.00, 90.00, 90.00
R / Rfree (%) 22.3 / 24.4

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Zinc atom in the Structure of the Bir Domain of Iap-Like Protein 2 (pdb code 1xb0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 24 binding sites of Zinc where determined in the Structure of the Bir Domain of Iap-Like Protein 2, PDB code: 1xb0:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 24 in 1xb0

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Zinc binding site 1 out of 24 in the Structure of the Bir Domain of Iap-Like Protein 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the Bir Domain of Iap-Like Protein 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:20.4
occ:1.00
NE2 A:HIS320 2.2 20.8 1.0
SG A:CYS300 2.3 15.5 1.0
SG A:CYS303 2.4 19.3 1.0
SG A:CYS327 2.4 24.4 1.0
CE1 A:HIS320 2.9 23.3 1.0
CB A:CYS300 3.0 18.3 1.0
CB A:CYS327 3.1 21.5 1.0
CB A:CYS303 3.3 19.3 1.0
CD2 A:HIS320 3.3 19.9 1.0
N A:CYS303 3.7 20.0 1.0
CA A:CYS303 4.1 21.1 1.0
ND1 A:HIS320 4.1 18.7 1.0
CG A:HIS320 4.3 18.8 1.0
CA A:CYS327 4.5 21.8 1.0
CA A:CYS300 4.5 17.6 1.0
CB A:HIS302 4.7 20.9 1.0
C A:HIS302 4.8 20.8 1.0
C A:CYS303 4.9 21.1 1.0
N A:GLY304 4.9 21.4 1.0
CB A:TYR324 4.9 19.3 1.0
CB A:TYR329 4.9 20.5 1.0

Zinc binding site 2 out of 24 in 1xb0

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Zinc binding site 2 out of 24 in the Structure of the Bir Domain of Iap-Like Protein 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the Bir Domain of Iap-Like Protein 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:55.6
occ:1.00
O A:HOH938 2.5 51.2 1.0
NE2 A:HIS302 2.5 23.9 1.0
OE1 A:GLU332 2.8 40.5 1.0
OE2 A:GLU332 3.0 41.2 1.0
CD2 A:HIS302 3.1 23.8 1.0
CD A:GLU332 3.2 40.6 1.0
CE1 A:HIS302 3.7 24.4 1.0
CG A:HIS302 4.3 22.8 1.0
OE1 B:GLN354 4.4 37.2 1.0
ND1 A:HIS302 4.6 23.3 1.0
CG A:GLU332 4.7 37.4 1.0
NE2 B:GLN354 4.7 38.3 1.0
O A:ASN255 4.9 57.3 1.0

Zinc binding site 3 out of 24 in 1xb0

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Zinc binding site 3 out of 24 in the Structure of the Bir Domain of Iap-Like Protein 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of the Bir Domain of Iap-Like Protein 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn400

b:47.4
occ:1.00
OE2 A:GLU333 2.2 31.5 1.0
O A:HOH944 2.5 31.9 1.0
O B:HOH543 2.7 33.2 1.0
CD A:GLU333 2.9 30.6 1.0
OE1 A:GLU333 2.9 30.0 1.0
O B:LEU352 3.8 46.5 1.0
NE2 B:GLN354 4.0 38.3 1.0
CG B:GLN354 4.3 41.8 1.0
CB B:ALA351 4.3 56.9 1.0
CG A:GLU333 4.4 27.8 1.0
CD B:GLN354 4.6 40.1 1.0
CG2 B:THR355 4.9 42.5 1.0
C B:LEU352 5.0 48.6 1.0

Zinc binding site 4 out of 24 in 1xb0

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Zinc binding site 4 out of 24 in the Structure of the Bir Domain of Iap-Like Protein 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of the Bir Domain of Iap-Like Protein 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn902

b:31.1
occ:1.00
OE2 F:GLU266 2.0 26.7 1.0
ND1 A:HIS343 2.3 26.6 1.0
O F:HOH931 2.4 40.0 1.0
O A:HOH933 2.5 41.8 1.0
CD F:GLU266 2.8 27.3 1.0
OE1 F:GLU266 3.0 27.7 1.0
CG A:HIS343 3.2 29.5 1.0
CE1 A:HIS343 3.3 25.4 1.0
CB A:HIS343 3.5 30.8 1.0
CA A:HIS343 4.1 33.4 1.0
CG F:GLU266 4.2 23.9 1.0
NE2 A:HIS343 4.4 27.1 1.0
CD2 A:HIS343 4.4 28.5 1.0
O A:HIS343 4.5 35.9 1.0
C A:HIS343 4.8 36.4 1.0
O A:HOH943 4.9 54.5 1.0
CD2 F:TYR265 5.0 25.8 1.0

Zinc binding site 5 out of 24 in 1xb0

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Zinc binding site 5 out of 24 in the Structure of the Bir Domain of Iap-Like Protein 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of the Bir Domain of Iap-Like Protein 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:25.9
occ:1.00
OE2 A:GLU266 2.2 19.6 1.0
ND1 B:HIS343 2.3 27.1 1.0
O B:HOH534 2.4 25.3 1.0
O B:THR356 2.4 37.5 1.0
C B:THR356 2.7 38.2 1.0
CD A:GLU266 3.0 21.1 1.0
OE1 A:GLU266 3.1 20.8 1.0
CG B:HIS343 3.2 28.2 1.0
CE1 B:HIS343 3.3 26.6 1.0
CB B:HIS343 3.5 26.0 1.0
O A:HOH932 3.7 41.6 1.0
CA B:HIS343 4.0 30.2 1.0
O A:HOH953 4.1 63.3 1.0
CA B:THR356 4.2 40.0 1.0
NE2 B:HIS343 4.4 28.4 1.0
CD2 B:HIS343 4.4 26.6 1.0
CG A:GLU266 4.4 18.4 1.0
O B:HIS343 4.5 33.0 1.0
OG1 B:THR356 4.5 43.1 1.0
O A:HOH928 4.5 32.1 1.0
C B:HIS343 4.8 33.4 1.0
CB B:THR356 4.8 40.3 1.0
CD2 A:TYR265 4.8 21.2 1.0
CB A:TYR265 5.0 18.5 1.0

Zinc binding site 6 out of 24 in 1xb0

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Zinc binding site 6 out of 24 in the Structure of the Bir Domain of Iap-Like Protein 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of the Bir Domain of Iap-Like Protein 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn500

b:53.4
occ:1.00
OE1 B:GLU333 2.1 30.1 1.0
CD B:GLU333 2.9 29.7 1.0
OE2 B:GLU333 3.1 32.4 1.0
CG B:GLU333 4.4 27.1 1.0
CA B:GLU333 4.9 23.6 1.0
CB B:GLU333 4.9 23.7 1.0

Zinc binding site 7 out of 24 in 1xb0

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Zinc binding site 7 out of 24 in the Structure of the Bir Domain of Iap-Like Protein 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of the Bir Domain of Iap-Like Protein 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:60.4
occ:1.00
NE2 B:HIS302 2.6 21.2 1.0
OE1 B:GLU332 2.8 43.0 1.0
OE2 B:GLU332 3.0 43.2 1.0
CD2 B:HIS302 3.2 19.6 1.0
CD B:GLU332 3.2 40.7 1.0
O B:HOH536 3.5 42.5 1.0
CE1 B:HIS302 3.8 19.0 1.0
CG B:HIS302 4.5 20.2 1.0
CG B:GLU332 4.7 36.9 1.0
ND1 B:HIS302 4.7 18.8 1.0

Zinc binding site 8 out of 24 in 1xb0

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Zinc binding site 8 out of 24 in the Structure of the Bir Domain of Iap-Like Protein 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of the Bir Domain of Iap-Like Protein 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn503

b:17.6
occ:1.00
NE2 B:HIS320 2.2 16.2 1.0
SG B:CYS303 2.3 17.4 1.0
SG B:CYS300 2.4 20.0 1.0
SG B:CYS327 2.4 19.4 1.0
CE1 B:HIS320 2.9 15.7 1.0
CB B:CYS300 3.0 17.4 1.0
CB B:CYS327 3.1 16.7 1.0
CB B:CYS303 3.3 16.5 1.0
CD2 B:HIS320 3.3 14.8 1.0
N B:CYS303 3.7 19.3 1.0
CA B:CYS303 4.1 19.7 1.0
ND1 B:HIS320 4.1 14.8 1.0
CG B:HIS320 4.4 15.1 1.0
CA B:CYS327 4.4 17.4 1.0
CA B:CYS300 4.5 19.1 1.0
CB B:HIS302 4.7 20.2 1.0
C B:HIS302 4.9 19.9 1.0
C B:CYS303 4.9 19.5 1.0
CB B:TYR329 4.9 18.8 1.0
N B:GLY304 4.9 19.7 1.0
CB B:TYR324 4.9 18.7 1.0

Zinc binding site 9 out of 24 in 1xb0

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Zinc binding site 9 out of 24 in the Structure of the Bir Domain of Iap-Like Protein 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Structure of the Bir Domain of Iap-Like Protein 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn502

b:29.6
occ:1.00
OE2 B:GLU266 2.0 21.9 1.0
ND1 C:HIS343 2.2 26.3 1.0
O C:HOH636 2.3 32.0 1.0
O B:HOH557 2.5 31.1 1.0
CD B:GLU266 2.9 24.3 1.0
CG C:HIS343 3.1 28.6 1.0
OE1 B:GLU266 3.1 21.7 1.0
CE1 C:HIS343 3.2 27.2 1.0
CB C:HIS343 3.4 28.8 1.0
CA C:HIS343 4.0 32.9 1.0
CD2 C:HIS343 4.3 27.4 1.0
NE2 C:HIS343 4.3 26.2 1.0
CG B:GLU266 4.3 21.8 1.0
O C:HIS343 4.4 35.9 1.0
CD2 B:TYR265 4.7 25.1 1.0
C C:HIS343 4.7 36.2 1.0
O B:HOH524 4.8 40.7 1.0
CB B:TYR265 5.0 23.7 1.0

Zinc binding site 10 out of 24 in 1xb0

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Zinc binding site 10 out of 24 in the Structure of the Bir Domain of Iap-Like Protein 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Structure of the Bir Domain of Iap-Like Protein 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn600

b:64.1
occ:1.00
OE2 C:GLU333 2.2 34.3 1.0
O C:HOH608 2.6 32.7 1.0
OE1 C:GLU333 2.8 28.8 1.0
CD C:GLU333 2.8 30.4 1.0
CG C:GLU333 4.3 28.9 1.0

Reference:

H.Shin, M.Renatus, B.P.Eckelman, V.A.Nunes, C.A.M.Sampaio, G.S.Salvesen. The Bir Domain of Iap-Like Protein 2 Is Conformationally Unstable: Implications For Caspase Inhibition Biochem.J. V. 385 1 2005.
ISSN: ISSN 0264-6021
PubMed: 15485395
DOI: 10.1042/BJ20041107
Page generated: Wed Dec 16 03:12:08 2020

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