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Zinc in PDB 4hy0: Crystal Structure of Xiap BIR3 with T3256336

Protein crystallography data

The structure of Crystal Structure of Xiap BIR3 with T3256336, PDB code: 4hy0 was solved by G.S.Snell, D.R.Dougan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 2.84
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 58.336, 100.840, 184.583, 90.00, 90.00, 90.00
R / Rfree (%) 20.8 / 26.2

Other elements in 4hy0:

The structure of Crystal Structure of Xiap BIR3 with T3256336 also contains other interesting chemical elements:

Fluorine (F) 16 atoms

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of Xiap BIR3 with T3256336 (pdb code 4hy0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 14 binding sites of Zinc where determined in the Crystal Structure of Xiap BIR3 with T3256336, PDB code: 4hy0:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 14 in 4hy0

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Zinc binding site 1 out of 14 in the Crystal Structure of Xiap BIR3 with T3256336


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 with T3256336 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:51.5
occ:1.00
 NE2 A:HIS320 2.0 46.8 1.0
SG A:CYS327 2.1 44.6 1.0
SG A:CYS303 2.2 46.7 1.0
SG A:CYS300 2.4 49.1 1.0
CE1 A:HIS320 2.7 48.8 1.0
CB A:CYS327 2.9 46.9 1.0
CD2 A:HIS320 3.2 48.1 1.0
CB A:CYS300 3.2 47.6 1.0
CB A:CYS303 3.2 47.6 1.0
N A:CYS303 3.7 46.1 1.0
ND1 A:HIS320 4.0 50.6 1.0
CA A:CYS303 4.0 47.1 1.0
CA A:CYS327 4.1 47.8 1.0
CG A:HIS320 4.2 49.7 1.0
CB A:HIS302 4.6 47.1 1.0
CA A:CYS300 4.7 48.1 1.0
C A:HIS302 4.8 46.3 1.0
C A:CYS303 4.9 49.0 1.0
N A:CYS327 5.0 49.2 1.0
N A:GLY304 5.0 50.2 1.0
N A:HIS302 5.0 45.5 1.0

Zinc binding site 2 out of 14 in 4hy0

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Zinc binding site 2 out of 14 in the Crystal Structure of Xiap BIR3 with T3256336


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 with T3256336 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:94.1
occ:1.00
 ND1 A:HIS343 2.4 59.9 1.0
CE1 B:HIS343 2.6 61.9 1.0
ND1 A:HIS346 2.8 90.1 1.0
CG A:HIS343 3.3 60.3 1.0
CE1 A:HIS343 3.4 64.2 1.0
ND1 B:HIS343 3.4 59.9 1.0
NE2 B:HIS343 3.4 60.0 1.0
CA A:HIS343 3.4 59.3 1.0
O A:LYS322 3.4 53.8 1.0
CB A:HIS343 3.5 58.8 1.0
CE1 A:HIS346 3.6 92.2 1.0
CG A:HIS346 3.8 92.7 1.0
O A:HIS343 4.0 64.1 1.0
CB A:HIS346 4.2 89.1 1.0
C A:HIS343 4.2 64.4 1.0
ZN B:ZN402 4.4 99.3 1.0
CG B:HIS343 4.4 57.0 1.0
CD2 B:HIS343 4.4 60.2 1.0
C A:LYS322 4.5 54.0 1.0
NE2 A:HIS343 4.5 65.5 1.0
CD2 A:HIS343 4.5 63.7 1.0
N A:HIS343 4.5 56.9 1.0
NE2 A:HIS346 4.7 94.5 1.0
O A:ALA321 4.9 55.4 1.0
CD2 A:HIS346 4.9 96.7 1.0
CG A:PRO325 4.9 47.7 1.0
CA A:LYS322 4.9 57.3 1.0
O A:ILE342 5.0 58.6 1.0
OG A:SER347 5.0 1.0 1.0

Zinc binding site 3 out of 14 in 4hy0

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Zinc binding site 3 out of 14 in the Crystal Structure of Xiap BIR3 with T3256336


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 with T3256336 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:64.5
occ:1.00
 NE2 B:HIS320 1.9 62.9 1.0
SG B:CYS303 2.2 60.3 1.0
SG B:CYS327 2.2 65.8 1.0
SG B:CYS300 2.4 70.1 1.0
CE1 B:HIS320 2.7 64.6 1.0
CB B:CYS327 2.8 62.5 1.0
CB B:CYS300 3.0 72.4 1.0
CD2 B:HIS320 3.1 63.3 1.0
CB B:CYS303 3.1 61.9 1.0
N B:CYS303 3.7 68.6 1.0
ND1 B:HIS320 3.9 66.3 1.0
CA B:CYS303 4.0 66.4 1.0
CG B:HIS320 4.1 64.5 1.0
CA B:CYS327 4.2 61.8 1.0
CA B:CYS300 4.6 76.1 1.0
CB B:HIS302 4.8 73.2 1.0
C B:CYS303 4.8 69.0 1.0
C B:HIS302 4.8 72.3 1.0
N B:GLY304 4.9 70.9 1.0
O B:TYR324 5.0 55.1 1.0
N B:CYS327 5.0 60.6 1.0

Zinc binding site 4 out of 14 in 4hy0

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Zinc binding site 4 out of 14 in the Crystal Structure of Xiap BIR3 with T3256336


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 with T3256336 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:99.3
occ:1.00
 ND1 B:HIS343 2.5 59.9 1.0
CE1 A:HIS343 2.6 64.2 1.0
ND1 B:HIS346 3.0 88.9 1.0
O B:LYS322 3.1 61.2 1.0
CG B:HIS343 3.3 57.0 1.0
ND1 A:HIS343 3.4 59.9 1.0
CB B:HIS343 3.5 55.0 1.0
CA B:HIS343 3.5 55.2 1.0
NE2 A:HIS343 3.5 65.5 1.0
CE1 B:HIS343 3.5 61.9 1.0
CE1 B:HIS346 3.7 89.3 1.0
CG B:HIS346 3.8 86.9 1.0
CB B:HIS346 4.1 81.7 1.0
O B:HIS343 4.1 63.1 1.0
C B:LYS322 4.2 61.7 1.0
C B:HIS343 4.3 59.3 1.0
ZN A:ZN402 4.4 94.1 1.0
CG A:HIS343 4.5 60.3 1.0
O B:ALA321 4.5 61.0 1.0
CD2 A:HIS343 4.5 63.7 1.0
N B:HIS343 4.5 53.9 1.0
CA B:LYS322 4.6 62.7 1.0
CD2 B:HIS343 4.6 60.2 1.0
NE2 B:HIS343 4.6 60.0 1.0
NE2 B:HIS346 4.7 88.6 1.0
CD2 B:HIS346 4.7 88.8 1.0
CG B:PRO325 4.8 57.1 1.0
O B:ILE342 4.8 59.1 1.0

Zinc binding site 5 out of 14 in 4hy0

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Zinc binding site 5 out of 14 in the Crystal Structure of Xiap BIR3 with T3256336


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 with T3256336 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:48.0
occ:1.00
 NE2 C:HIS320 2.0 45.9 1.0
SG C:CYS327 2.2 44.5 1.0
SG C:CYS303 2.3 48.6 1.0
SG C:CYS300 2.3 53.2 1.0
CE1 C:HIS320 2.7 47.7 1.0
CB C:CYS327 2.9 45.5 1.0
CB C:CYS300 3.0 51.2 1.0
CD2 C:HIS320 3.2 46.0 1.0
CB C:CYS303 3.3 48.4 1.0
N C:CYS303 3.7 51.6 1.0
ND1 C:HIS320 3.9 48.1 1.0
CA C:CYS303 4.0 50.7 1.0
CA C:CYS327 4.2 46.8 1.0
CG C:HIS320 4.2 46.1 1.0
CA C:CYS300 4.5 51.6 1.0
CB C:HIS302 4.6 53.6 1.0
C C:HIS302 4.8 54.4 1.0
N C:GLY304 4.8 49.9 1.0
C C:CYS303 4.8 51.0 1.0
O C:TYR324 4.9 43.3 1.0
N C:HIS302 4.9 54.7 1.0
CB C:TYR324 5.0 48.6 1.0
CA C:HIS302 5.0 54.6 1.0
N C:GLY305 5.0 49.2 1.0

Zinc binding site 6 out of 14 in 4hy0

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Zinc binding site 6 out of 14 in the Crystal Structure of Xiap BIR3 with T3256336


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 with T3256336 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn401

b:59.4
occ:1.00
 NE2 D:HIS320 2.0 52.2 1.0
SG D:CYS300 2.1 60.6 1.0
SG D:CYS327 2.2 50.5 1.0
SG D:CYS303 2.3 60.5 1.0
CE1 D:HIS320 2.4 54.1 1.0
CB D:CYS327 3.0 52.5 1.0
CB D:CYS300 3.1 59.5 1.0
CB D:CYS303 3.2 59.8 1.0
CD2 D:HIS320 3.3 51.2 1.0
N D:CYS303 3.5 61.9 1.0
ND1 D:HIS320 3.7 52.0 1.0
CA D:CYS303 4.0 63.2 1.0
CG D:HIS320 4.2 50.5 1.0
CA D:CYS327 4.2 54.1 1.0
CB D:HIS302 4.5 62.5 1.0
CA D:CYS300 4.5 59.9 1.0
C D:HIS302 4.6 64.4 1.0
N D:HIS302 4.8 64.4 1.0
C D:CYS303 4.9 66.8 1.0
N D:GLY304 4.9 68.0 1.0
CA D:HIS302 4.9 65.0 1.0
C D:CYS300 4.9 61.6 1.0

Zinc binding site 7 out of 14 in 4hy0

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Zinc binding site 7 out of 14 in the Crystal Structure of Xiap BIR3 with T3256336


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 with T3256336 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn402

b:0.2
occ:1.00
 ND1 D:HIS343 2.6 54.9 1.0
CE1 E:HIS343 2.6 60.6 1.0
ND1 D:HIS346 3.0 0.9 1.0
O D:LYS322 3.3 59.9 1.0
NE2 E:HIS343 3.3 61.3 1.0
CE1 D:HIS346 3.4 0.8 1.0
CE1 D:HIS343 3.5 59.7 1.0
CG D:HIS343 3.5 54.3 1.0
CA D:HIS343 3.6 53.5 1.0
ND1 E:HIS343 3.6 56.6 1.0
CB D:HIS343 3.7 53.2 1.0
CG D:HIS346 4.0 0.6 1.0
C D:LYS322 4.1 56.8 1.0
O D:HIS343 4.1 63.8 1.0
O D:ALA321 4.3 47.3 1.0
CA D:LYS322 4.3 54.6 1.0
C D:HIS343 4.4 58.5 1.0
CD2 E:HIS343 4.5 58.8 1.0
NE2 D:HIS346 4.6 0.4 1.0
N D:HIS343 4.6 52.5 1.0
CG E:HIS343 4.6 54.6 1.0
CB D:HIS346 4.6 93.7 1.0
ZN E:ZN402 4.6 0.4 1.0
NE2 D:HIS343 4.7 60.2 1.0
CG D:PRO325 4.7 49.6 1.0
CD2 D:HIS343 4.7 57.1 1.0
CD2 D:HIS346 4.9 0.7 1.0
O D:ILE342 4.9 56.5 1.0

Zinc binding site 8 out of 14 in 4hy0

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Zinc binding site 8 out of 14 in the Crystal Structure of Xiap BIR3 with T3256336


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 with T3256336 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn401

b:66.2
occ:1.00
 NE2 E:HIS320 2.1 63.1 1.0
SG E:CYS303 2.1 58.4 1.0
SG E:CYS327 2.1 50.9 1.0
SG E:CYS300 2.3 73.0 1.0
CE1 E:HIS320 2.8 64.4 1.0
CB E:CYS327 2.8 51.5 1.0
CB E:CYS300 3.1 71.8 1.0
CD2 E:HIS320 3.2 62.5 1.0
CB E:CYS303 3.4 59.5 1.0
N E:CYS303 3.7 63.7 1.0
ND1 E:HIS320 4.0 64.0 1.0
CA E:CYS303 4.1 63.6 1.0
CA E:CYS327 4.2 53.2 1.0
CG E:HIS320 4.3 61.7 1.0
CB E:HIS302 4.5 66.5 1.0
CA E:CYS300 4.5 75.2 1.0
C E:HIS302 4.8 67.3 1.0
N E:HIS302 4.9 72.2 1.0
O E:TYR324 4.9 47.8 1.0
C E:CYS300 5.0 74.6 1.0
CA E:HIS302 5.0 69.6 1.0
CB E:TYR324 5.0 54.1 1.0

Zinc binding site 9 out of 14 in 4hy0

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Zinc binding site 9 out of 14 in the Crystal Structure of Xiap BIR3 with T3256336


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of Xiap BIR3 with T3256336 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn402

b:0.4
occ:1.00
 ND1 E:HIS343 2.4 56.6 1.0
CE1 D:HIS343 2.6 59.7 1.0
ND1 E:HIS346 3.1 0.8 1.0
O E:LYS322 3.2 59.1 1.0
CE1 E:HIS343 3.3 60.6 1.0
CG E:HIS343 3.4 54.6 1.0
NE2 D:HIS343 3.4 60.2 1.0
ND1 D:HIS343 3.5 54.9 1.0
CA E:HIS343 3.5 54.7 1.0
CE1 E:HIS346 3.6 0.6 1.0
CB E:HIS343 3.6 53.1 1.0
CG E:HIS346 3.9 0.8 1.0
O E:HIS343 4.2 55.7 1.0
C E:LYS322 4.3 57.8 1.0
C E:HIS343 4.4 57.5 1.0
O E:ALA321 4.4 57.7 1.0
CB E:HIS346 4.4 97.0 1.0
NE2 E:HIS343 4.5 61.3 1.0
CD2 D:HIS343 4.5 57.1 1.0
CD2 E:HIS343 4.5 58.8 1.0
CG D:HIS343 4.5 54.3 1.0
N E:HIS343 4.5 53.1 1.0
NE2 E:HIS346 4.5 0.2 1.0
ZN D:ZN402 4.6 0.2 1.0
CA E:LYS322 4.7 60.8 1.0
CD2 E:HIS346 4.7 0.5 1.0
CG E:PRO325 4.7 46.9 1.0
O E:ILE342 5.0 55.2 1.0

Zinc binding site 10 out of 14 in 4hy0

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Zinc binding site 10 out of 14 in the Crystal Structure of Xiap BIR3 with T3256336


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of Xiap BIR3 with T3256336 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn401

b:67.8
occ:1.00
 NE2 F:HIS320 2.1 66.2 1.0
SG F:CYS303 2.1 61.3 1.0
SG F:CYS327 2.2 59.4 1.0
SG F:CYS300 2.4 71.8 1.0
CE1 F:HIS320 2.8 66.4 1.0
CB F:CYS327 2.9 59.3 1.0
CB F:CYS303 3.2 63.6 1.0
CD2 F:HIS320 3.2 62.7 1.0
CB F:CYS300 3.4 70.8 1.0
N F:CYS303 3.5 69.1 1.0
CA F:CYS303 4.0 68.2 1.0
ND1 F:HIS320 4.1 63.9 1.0
CA F:CYS327 4.2 61.9 1.0
CG F:HIS320 4.3 61.4 1.0
CB F:HIS302 4.4 73.5 1.0
C F:HIS302 4.6 74.4 1.0
N F:HIS302 4.8 76.9 1.0
CA F:CYS300 4.8 73.4 1.0
CA F:HIS302 4.8 76.6 1.0
C F:CYS303 5.0 70.3 1.0
CB F:LEU330 5.0 60.2 1.0

Reference:

K.Hashimoto, B.Saito, N.Miyamoto, Y.Oguro, D.Tomita, Z.Shiokawa, M.Asano, H.Kakei, N.Taya, M.Kawasaki, H.Sumi, M.Yabuki, K.Iwai, S.Yoshida, M.Yoshimatsu, K.Aoyama, Y.Kosugi, T.Kojima, N.Morishita, D.R.Dougan, G.P.Snell, S.Imamura, T.Ishikawa. Design and Synthesis of Potent Inhibitor of Apoptosis (Iap) Proteins Antagonists Bearing An Octahydropyrrolo[1,2-A]Pyrazine Scaffold As A Novel Proline Mimetic. J.Med.Chem. V. 56 1228 2013.
ISSN: ISSN 0022-2623
PubMed: 23298277
DOI: 10.1021/JM301674Z
Page generated: Sun Oct 27 00:20:46 2024

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