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Zinc in PDB 1q4q: Crystal Structure of A DIAP1-Dronc Complex

Protein crystallography data

The structure of Crystal Structure of A DIAP1-Dronc Complex, PDB code: 1q4q was solved by J.Chai, N.Yan, Y.Shi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.10
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 128.900, 128.900, 183.695, 90.00, 90.00, 120.00
R / Rfree (%) 19.9 / 24.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of A DIAP1-Dronc Complex (pdb code 1q4q). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 10 binding sites of Zinc where determined in the Crystal Structure of A DIAP1-Dronc Complex, PDB code: 1q4q:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in 1q4q

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Zinc binding site 1 out of 10 in the Crystal Structure of A DIAP1-Dronc Complex


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of A DIAP1-Dronc Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn604

b:22.7
occ:1.00
 SG A:CYS263 2.2 23.3 1.0
NE2 A:HIS283 2.3 24.7 1.0
SG A:CYS266 2.4 17.6 1.0
SG A:CYS290 2.4 27.4 1.0
CE1 A:HIS283 2.9 24.0 1.0
CB A:CYS263 3.0 17.7 1.0
CB A:CYS290 3.1 20.9 1.0
CB A:CYS266 3.3 16.5 1.0
CD2 A:HIS283 3.5 24.9 1.0
N A:CYS266 3.5 15.6 1.0
CA A:CYS266 4.0 16.3 1.0
ND1 A:HIS283 4.2 24.4 1.0
CA A:CYS290 4.4 19.1 1.0
CA A:CYS263 4.4 14.5 1.0
CB A:SER265 4.4 19.7 1.0
CG A:HIS283 4.5 24.2 1.0
CD1 A:LEU287 4.6 25.3 1.0
C A:SER265 4.7 14.6 1.0
CB A:LEU287 4.7 24.3 1.0
CB A:PHE292 4.8 18.0 1.0
CG2 A:VAL293 4.8 19.9 1.0
C A:CYS266 4.8 17.1 1.0
N A:GLY267 4.9 14.8 1.0
N A:SER265 4.9 16.7 1.0
C A:CYS263 4.9 13.3 1.0
CA A:SER265 4.9 14.5 1.0
O A:HOH621 4.9 26.9 1.0

Zinc binding site 2 out of 10 in 1q4q

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Zinc binding site 2 out of 10 in the Crystal Structure of A DIAP1-Dronc Complex


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of A DIAP1-Dronc Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn601

b:18.8
occ:1.00
 NE2 B:HIS283 2.2 10.8 1.0
SG B:CYS266 2.2 19.6 1.0
SG B:CYS263 2.4 18.6 1.0
SG B:CYS290 2.5 18.0 1.0
CE1 B:HIS283 2.8 12.5 1.0
CB B:CYS263 3.0 13.7 1.0
CB B:CYS266 3.1 19.1 1.0
CB B:CYS290 3.1 19.3 1.0
CD2 B:HIS283 3.4 12.4 1.0
N B:CYS266 3.6 17.6 1.0
CA B:CYS266 3.9 17.7 1.0
ND1 B:HIS283 4.0 12.4 1.0
CG B:HIS283 4.4 12.6 1.0
CA B:CYS290 4.4 20.3 1.0
CA B:CYS263 4.4 14.8 1.0
CB B:SER265 4.5 14.5 1.0
CD1 B:LEU287 4.6 15.7 1.0
CG2 B:VAL293 4.7 15.8 1.0
C B:CYS266 4.8 19.3 1.0
C B:SER265 4.8 17.5 1.0
N B:GLY267 4.8 20.5 1.0
CB B:PHE292 4.8 20.0 1.0
CB B:LEU287 4.8 15.8 1.0
OG B:SER265 4.9 17.3 1.0
C B:CYS263 5.0 15.4 1.0

Zinc binding site 3 out of 10 in 1q4q

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Zinc binding site 3 out of 10 in the Crystal Structure of A DIAP1-Dronc Complex


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of A DIAP1-Dronc Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn602

b:22.5
occ:1.00
 SG C:CYS266 2.1 19.4 1.0
NE2 C:HIS283 2.2 8.1 1.0
SG C:CYS290 2.3 20.9 1.0
SG C:CYS263 2.5 12.4 1.0
CE1 C:HIS283 3.0 10.9 1.0
CB C:CYS263 3.0 12.5 1.0
CB C:CYS290 3.1 19.4 1.0
CD2 C:HIS283 3.3 10.5 1.0
CB C:CYS266 3.3 15.4 1.0
N C:CYS266 3.8 13.9 1.0
CA C:CYS266 4.1 14.0 1.0
ND1 C:HIS283 4.2 11.4 1.0
CG C:HIS283 4.3 9.9 1.0
CG2 C:VAL293 4.4 21.7 1.0
CA C:CYS290 4.5 21.2 1.0
CA C:CYS263 4.6 10.5 1.0
CD1 C:LEU287 4.7 9.8 1.0
CB C:SER265 4.7 24.5 1.0
CB C:LEU287 4.8 14.1 1.0
N C:GLY267 4.9 14.4 1.0
CB C:PHE292 4.9 19.3 1.0
C C:SER265 4.9 14.1 1.0
C C:CYS266 4.9 14.8 1.0

Zinc binding site 4 out of 10 in 1q4q

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Zinc binding site 4 out of 10 in the Crystal Structure of A DIAP1-Dronc Complex


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of A DIAP1-Dronc Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn603

b:26.8
occ:1.00
 NE2 D:HIS283 2.2 10.6 1.0
SG D:CYS266 2.3 24.2 1.0
SG D:CYS263 2.3 21.5 1.0
SG D:CYS290 2.4 20.8 1.0
CE1 D:HIS283 2.9 11.9 1.0
CB D:CYS263 3.0 19.4 1.0
CB D:CYS290 3.2 24.3 1.0
CB D:CYS266 3.2 23.6 1.0
CD2 D:HIS283 3.4 10.6 1.0
N D:CYS266 3.6 20.9 1.0
CA D:CYS266 4.0 20.2 1.0
ND1 D:HIS283 4.1 10.2 1.0
CG D:HIS283 4.4 10.2 1.0
CG2 D:VAL293 4.4 19.8 1.0
CA D:CYS263 4.4 18.3 1.0
CA D:CYS290 4.5 27.0 1.0
CB D:SER265 4.6 24.7 1.0
CD1 D:LEU287 4.6 29.9 1.0
CB D:LEU287 4.7 29.6 1.0
CB D:PHE292 4.7 26.6 1.0
C D:SER265 4.8 28.2 1.0
C D:CYS266 4.8 21.2 1.0
N D:GLY267 4.9 28.9 1.0
OG D:SER265 4.9 21.1 1.0

Zinc binding site 5 out of 10 in 1q4q

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Zinc binding site 5 out of 10 in the Crystal Structure of A DIAP1-Dronc Complex


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 A DIAP1-Dronc Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn605

b:37.2
occ:1.00
 NE2 E:HIS283 2.2 43.2 1.0
SG E:CYS266 2.3 25.3 1.0
SG E:CYS263 2.4 34.4 1.0
SG E:CYS290 2.5 33.9 1.0
CB E:CYS263 3.0 37.7 1.0
CE1 E:HIS283 3.1 44.0 1.0
CB E:CYS290 3.1 40.2 1.0
CB E:CYS266 3.2 32.2 1.0
CD2 E:HIS283 3.3 44.1 1.0
N E:CYS266 4.2 35.9 1.0
CA E:CYS266 4.2 33.3 1.0
ND1 E:HIS283 4.2 43.9 1.0
CD1 E:LEU287 4.3 36.1 1.0
CG E:HIS283 4.4 44.0 1.0
CA E:CYS290 4.4 36.2 1.0
CG2 E:VAL293 4.4 32.2 1.0
CA E:CYS263 4.5 39.8 1.0
CB E:LEU287 4.6 36.9 1.0
C E:SER265 4.6 57.0 1.0
C E:CYS266 4.8 33.5 1.0
CB E:PHE292 4.8 46.2 1.0
N E:GLY268 4.9 32.7 1.0
O E:SER265 4.9 59.4 1.0
N E:GLY267 5.0 33.6 1.0

Zinc binding site 6 out of 10 in 1q4q

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Zinc binding site 6 out of 10 in the Crystal Structure of A DIAP1-Dronc Complex


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 A DIAP1-Dronc Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn606

b:17.9
occ:1.00
 NE2 F:HIS283 2.1 7.2 1.0
SG F:CYS266 2.2 25.7 1.0
SG F:CYS263 2.2 20.4 1.0
SG F:CYS290 2.4 20.1 1.0
CE1 F:HIS283 2.9 7.0 1.0
CB F:CYS263 2.9 19.0 1.0
CD2 F:HIS283 3.2 9.0 1.0
CB F:CYS290 3.2 20.1 1.0
CB F:CYS266 3.3 24.4 1.0
N F:CYS266 3.7 26.4 1.0
ND1 F:HIS283 4.0 9.3 1.0
CA F:CYS266 4.1 27.1 1.0
CG F:HIS283 4.2 8.2 1.0
CG2 F:VAL293 4.3 33.0 1.0
CA F:CYS263 4.4 21.0 1.0
CD1 F:LEU287 4.4 17.3 1.0
CA F:CYS290 4.5 26.6 1.0
CB F:SER265 4.6 19.7 1.0
C F:SER265 4.8 28.6 1.0
CB F:LEU287 4.9 19.9 1.0
C F:CYS266 4.9 27.8 1.0
CB F:PHE292 4.9 22.5 1.0

Zinc binding site 7 out of 10 in 1q4q

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Zinc binding site 7 out of 10 in the Crystal Structure of A DIAP1-Dronc Complex


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of A DIAP1-Dronc Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn607

b:19.2
occ:1.00
 NE2 G:HIS283 2.2 22.4 1.0
SG G:CYS290 2.3 19.0 1.0
SG G:CYS263 2.3 16.2 1.0
SG G:CYS266 2.5 14.2 1.0
CE1 G:HIS283 2.8 22.1 1.0
CB G:CYS263 3.0 14.8 1.0
CB G:CYS290 3.1 20.9 1.0
CD2 G:HIS283 3.4 22.8 1.0
CB G:CYS266 3.5 16.8 1.0
N G:CYS266 3.8 21.4 1.0
ND1 G:HIS283 4.1 21.4 1.0
CA G:CYS266 4.2 21.4 1.0
CG G:HIS283 4.4 20.8 1.0
CG2 G:VAL293 4.4 12.7 1.0
CA G:CYS290 4.4 19.7 1.0
CA G:CYS263 4.5 14.2 1.0
CD1 G:LEU287 4.5 21.7 1.0
CB G:PHE292 4.7 15.4 1.0
CB G:SER265 4.8 10.3 1.0
CB G:LEU287 4.8 24.3 1.0
C G:SER265 4.9 20.1 1.0
C G:CYS266 4.9 22.9 1.0

Zinc binding site 8 out of 10 in 1q4q

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Zinc binding site 8 out of 10 in the Crystal Structure of A DIAP1-Dronc Complex


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of A DIAP1-Dronc Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn608

b:17.3
occ:1.00
 NE2 H:HIS283 2.1 24.4 1.0
SG H:CYS263 2.2 19.2 1.0
SG H:CYS266 2.3 8.1 1.0
SG H:CYS290 2.4 17.7 1.0
CE1 H:HIS283 2.8 24.8 1.0
CB H:CYS263 2.9 18.4 1.0
CB H:CYS290 3.2 20.2 1.0
CB H:CYS266 3.2 8.2 1.0
CD2 H:HIS283 3.3 23.5 1.0
N H:CYS266 3.6 16.0 1.0
CA H:CYS266 4.0 14.7 1.0
ND1 H:HIS283 4.0 23.9 1.0
CG H:HIS283 4.3 23.7 1.0
CA H:CYS263 4.4 22.3 1.0
CA H:CYS290 4.4 20.4 1.0
CB H:SER265 4.5 15.5 1.0
C H:SER265 4.7 21.4 1.0
CG2 H:VAL293 4.7 17.5 1.0
CD1 H:LEU287 4.7 16.8 1.0
C H:CYS266 4.7 16.4 1.0
CB H:PHE292 4.8 19.3 1.0
CB H:LEU287 4.9 20.6 1.0
N H:GLY267 4.9 19.8 1.0
C H:CYS263 4.9 21.9 1.0
N H:SER265 4.9 23.1 1.0
CA H:SER265 4.9 21.0 1.0

Zinc binding site 9 out of 10 in 1q4q

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Zinc binding site 9 out of 10 in the Crystal Structure of A DIAP1-Dronc Complex


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of A DIAP1-Dronc Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn609

b:22.4
occ:1.00
 SG I:CYS263 2.2 18.8 1.0
NE2 I:HIS283 2.2 31.6 1.0
SG I:CYS266 2.3 27.8 1.0
SG I:CYS290 2.4 30.8 1.0
CB I:CYS263 2.9 17.3 1.0
CE1 I:HIS283 2.9 31.7 1.0
CB I:CYS290 3.1 29.6 1.0
CD2 I:HIS283 3.4 29.6 1.0
CB I:CYS266 3.5 28.1 1.0
N I:CYS266 3.7 31.5 1.0
ND1 I:HIS283 4.2 30.0 1.0
CA I:CYS266 4.2 31.5 1.0
CB I:SER265 4.3 32.0 1.0
CA I:CYS263 4.4 24.3 1.0
CG2 I:VAL293 4.4 23.4 1.0
CG I:HIS283 4.4 28.9 1.0
CA I:CYS290 4.5 21.6 1.0
C I:SER265 4.8 31.5 1.0
CD1 I:LEU287 4.8 17.1 1.0
C I:CYS266 4.8 31.6 1.0
C I:CYS263 4.8 24.5 1.0
CB I:PHE292 4.9 18.3 1.0
CA I:SER265 4.9 31.5 1.0
N I:SER265 4.9 31.2 1.0
CB I:LEU287 4.9 21.3 1.0
N I:GLY267 4.9 27.2 1.0

Zinc binding site 10 out of 10 in 1q4q

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Zinc binding site 10 out of 10 in the Crystal Structure of A DIAP1-Dronc Complex


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of A DIAP1-Dronc Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn610

b:29.9
occ:1.00
 NE2 J:HIS283 2.1 41.0 1.0
SG J:CYS263 2.3 34.6 1.0
SG J:CYS290 2.4 27.1 1.0
SG J:CYS266 2.6 29.3 1.0
CE1 J:HIS283 2.8 42.5 1.0
CB J:CYS263 3.0 30.5 1.0
CB J:CYS290 3.1 32.6 1.0
CD2 J:HIS283 3.2 41.6 1.0
CB J:CYS266 3.4 26.1 1.0
N J:CYS266 3.6 24.8 1.0
CD1 J:LEU287 3.7 5.9 1.0
ND1 J:HIS283 4.0 40.7 1.0
CA J:CYS266 4.1 24.7 1.0
CB J:LEU287 4.1 21.8 1.0
CG J:HIS283 4.3 40.9 1.0
CG2 J:VAL293 4.3 26.1 1.0
CA J:CYS263 4.5 26.8 1.0
CA J:CYS290 4.5 31.3 1.0
CB J:SER265 4.6 34.2 1.0
CG J:LEU287 4.6 21.7 1.0
O J:LEU287 4.6 36.0 1.0
C J:SER265 4.7 31.7 1.0
N J:GLY267 4.9 25.3 1.0
CB J:PHE292 4.9 45.4 1.0
N J:SER265 4.9 32.6 1.0
C J:CYS266 5.0 24.4 1.0
CA J:SER265 5.0 31.9 1.0
C J:CYS263 5.0 26.1 1.0

Reference:

J.Chai, N.Yan, J.R.Huh, J.-W.Wu, W.Li, B.A.Hay, Y.Shi. Molecular Mechanism of Reaper-Grim-Hid-Mediated Suppression of DIAP1-Dependent Dronc Ubiquitination Nat.Struct.Biol. V. 10 892 2003.
ISSN: ISSN 1072-8368
PubMed: 14517550
DOI: 10.1038/NSB989
Page generated: Wed Oct 16 18:03:10 2024

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