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Zinc in PDB 4n9f: Crystal Structure of the Vif-Cbfbeta-CUL5-Elob-Eloc Pentameric Complex

Protein crystallography data

The structure of Crystal Structure of the Vif-Cbfbeta-CUL5-Elob-Eloc Pentameric Complex, PDB code: 4n9f was solved by Y.Y.Guo, L.Y.Dong, Z.W.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.53 / 3.30
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 103.925, 204.002, 247.866, 65.51, 90.28, 90.50
R / Rfree (%) 26.2 / 32.4

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of the Vif-Cbfbeta-CUL5-Elob-Eloc Pentameric Complex (pdb code 4n9f). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the Crystal Structure of the Vif-Cbfbeta-CUL5-Elob-Eloc Pentameric Complex, PDB code: 4n9f:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in 4n9f

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Zinc binding site 1 out of 12 in the Crystal Structure of the Vif-Cbfbeta-CUL5-Elob-Eloc Pentameric 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 the Vif-Cbfbeta-CUL5-Elob-Eloc Pentameric Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
b:Zn201

b:33.7
occ:1.00
 SG b:CYS114 2.1 53.2 1.0
NE2 b:HIS139 2.5 24.8 1.0
NE2 b:HIS108 2.5 46.7 1.0
SG b:CYS133 2.5 33.5 1.0
CE1 b:HIS139 3.1 24.2 1.0
CB b:CYS133 3.1 50.4 1.0
CD2 b:HIS108 3.4 47.2 1.0
O b:GLU134 3.5 89.2 1.0
CE1 b:HIS108 3.5 48.9 1.0
CD2 b:HIS139 3.6 24.8 1.0
CB b:CYS114 3.7 70.9 1.0
CA b:CYS133 3.9 47.0 1.0
O b:TYR135 4.3 26.8 1.0
ND1 b:HIS139 4.3 24.0 1.0
CA b:CYS114 4.3 75.8 1.0
O b:ASP113 4.3 27.3 1.0
CG b:HIS139 4.5 24.0 1.0
ND1 b:HIS108 4.5 62.0 1.0
CG b:HIS108 4.6 49.4 1.0
C b:CYS133 4.6 45.2 1.0
N b:GLU134 4.7 81.5 1.0
C b:GLU134 4.7 89.2 1.0
C b:TYR135 5.0 28.5 1.0

Zinc binding site 2 out of 12 in 4n9f

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Zinc binding site 2 out of 12 in the Crystal Structure of the Vif-Cbfbeta-CUL5-Elob-Eloc Pentameric Complex


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 the Vif-Cbfbeta-CUL5-Elob-Eloc Pentameric Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn201

b:47.2
occ:1.00
 SG G:CYS133 2.0 28.3 1.0
SG G:CYS114 2.1 28.4 1.0
NE2 G:HIS139 2.2 22.6 1.0
NE2 G:HIS108 2.4 57.2 1.0
CB G:CYS133 2.8 54.3 1.0
CE1 G:HIS139 3.0 27.6 1.0
CD2 G:HIS139 3.3 29.6 1.0
CD2 G:HIS108 3.3 58.0 1.0
O G:GLU134 3.3 61.8 1.0
CE1 G:HIS108 3.4 59.2 1.0
CB G:CYS114 3.5 43.2 1.0
CA G:CYS133 3.8 50.7 1.0
O G:TYR135 4.0 23.8 1.0
CA G:CYS114 4.1 47.9 1.0
ND1 G:HIS139 4.2 27.0 1.0
CG G:HIS139 4.3 27.7 1.0
C G:CYS133 4.4 49.0 1.0
ND1 G:HIS108 4.5 72.4 1.0
CG G:HIS108 4.5 60.2 1.0
C G:GLU134 4.5 61.8 1.0
O G:ASP113 4.6 47.4 1.0
N G:GLU134 4.6 53.6 1.0
C G:TYR135 4.7 23.9 1.0
N G:CYS114 4.9 49.8 1.0

Zinc binding site 3 out of 12 in 4n9f

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Zinc binding site 3 out of 12 in the Crystal Structure of the Vif-Cbfbeta-CUL5-Elob-Eloc Pentameric Complex


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 the Vif-Cbfbeta-CUL5-Elob-Eloc Pentameric Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn201

b:25.9
occ:1.00
 NE2 M:HIS139 2.0 37.0 1.0
SG M:CYS114 2.2 37.5 1.0
SG M:CYS133 2.2 31.8 1.0
NE2 M:HIS108 2.5 40.2 1.0
CD2 M:HIS139 2.8 43.9 1.0
CD2 M:HIS108 3.0 40.4 1.0
CE1 M:HIS139 3.1 42.0 1.0
CB M:CYS133 3.4 39.9 1.0
CE1 M:HIS108 3.7 42.0 1.0
CB M:CYS114 3.8 46.3 1.0
O M:GLU134 3.8 86.5 1.0
CG M:HIS139 4.0 41.7 1.0
ND1 M:HIS139 4.1 41.1 1.0
O M:TYR135 4.1 33.8 1.0
CG M:HIS108 4.3 42.0 1.0
CA M:CYS114 4.4 51.4 1.0
CA M:CYS133 4.5 38.4 1.0
ND1 M:HIS108 4.6 54.5 1.0
OH M:TYR147 4.7 47.2 1.0
C M:TYR135 4.8 34.6 1.0
O M:ASP113 4.8 70.8 1.0
CE1 M:TYR147 4.9 54.3 1.0
C M:GLU134 5.0 86.5 1.0

Zinc binding site 4 out of 12 in 4n9f

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Zinc binding site 4 out of 12 in the Crystal Structure of the Vif-Cbfbeta-CUL5-Elob-Eloc Pentameric Complex


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 the Vif-Cbfbeta-CUL5-Elob-Eloc Pentameric Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Zn201

b:32.7
occ:1.00
 SG S:CYS114 2.1 25.8 1.0
NE2 S:HIS108 2.1 24.4 1.0
SG S:CYS133 2.4 25.2 1.0
NE2 S:HIS139 2.6 30.1 1.0
CD2 S:HIS108 2.8 24.2 1.0
CE1 S:HIS108 2.9 24.0 1.0
CB S:CYS133 3.5 38.1 1.0
CE1 S:HIS139 3.5 35.5 1.0
CD2 S:HIS139 3.6 37.7 1.0
CB S:CYS114 3.6 26.7 1.0
O S:GLU134 3.7 98.1 1.0
CG S:HIS108 3.7 23.6 1.0
ND1 S:HIS108 3.7 27.7 1.0
O S:TYR135 3.8 24.7 1.0
CA S:CYS114 4.4 27.1 1.0
CA S:CYS133 4.5 35.2 1.0
ND1 S:HIS139 4.7 34.5 1.0
O S:ASP113 4.7 36.1 1.0
CG S:HIS139 4.7 34.8 1.0
CB R:ARG151 4.7 40.1 1.0
C S:TYR135 4.8 25.3 1.0
C S:GLU134 4.9 98.5 1.0

Zinc binding site 5 out of 12 in 4n9f

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Zinc binding site 5 out of 12 in the Crystal Structure of the Vif-Cbfbeta-CUL5-Elob-Eloc Pentameric 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 the Vif-Cbfbeta-CUL5-Elob-Eloc Pentameric Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
d:Zn201

b:25.1
occ:1.00
 SG d:CYS114 2.2 29.4 1.0
NE2 d:HIS108 2.2 29.9 1.0
NE2 d:HIS139 2.3 33.0 1.0
CE1 d:HIS108 2.5 29.5 1.0
SG d:CYS133 2.6 31.6 1.0
CE1 d:HIS139 2.9 44.3 1.0
CB d:CYS114 3.1 37.4 1.0
CD2 d:HIS108 3.3 29.2 1.0
CD2 d:HIS139 3.5 48.4 1.0
CB d:CYS133 3.5 59.3 1.0
ND1 d:HIS108 3.5 39.3 1.0
CA d:CYS114 3.9 43.2 1.0
O d:GLU134 3.9 0.6 1.0
CG d:HIS108 4.0 28.4 1.0
ND1 d:HIS139 4.1 42.1 1.0
O d:TYR135 4.2 28.1 1.0
CG c:ARG151 4.3 34.0 1.0
CG d:HIS139 4.4 43.5 1.0
O d:ASP113 4.5 27.1 1.0
CA d:CYS133 4.6 56.4 1.0
N d:CYS114 4.6 44.9 1.0
CB c:ARG151 4.8 38.9 1.0
C d:ASP113 4.9 28.5 1.0

Zinc binding site 6 out of 12 in 4n9f

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Zinc binding site 6 out of 12 in the Crystal Structure of the Vif-Cbfbeta-CUL5-Elob-Eloc Pentameric 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 the Vif-Cbfbeta-CUL5-Elob-Eloc Pentameric Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
j:Zn201

b:24.9
occ:1.00
 SG j:CYS114 2.0 29.7 1.0
SG j:CYS133 2.4 66.2 1.0
CB j:CYS133 2.5 93.7 1.0
NE2 j:HIS108 2.6 33.4 1.0
CE1 j:HIS139 2.6 33.8 1.0
NE2 j:HIS139 3.3 26.8 1.0
CD2 j:HIS108 3.3 32.8 1.0
CA j:CYS133 3.5 90.8 1.0
CB j:CYS114 3.5 38.1 1.0
O j:GLU134 3.6 97.1 1.0
CE1 j:HIS108 3.7 34.2 1.0
ND1 j:HIS139 3.8 31.9 1.0
CA j:CYS114 4.0 41.0 1.0
C j:CYS133 4.2 89.0 1.0
N j:GLU134 4.5 90.8 1.0
CG j:HIS108 4.6 33.0 1.0
O j:ASP113 4.6 51.7 1.0
N j:CYS133 4.6 0.8 1.0
CD2 j:HIS139 4.6 36.9 1.0
O j:TYR135 4.6 52.4 1.0
ND1 j:HIS108 4.7 39.0 1.0
C j:GLU134 4.8 97.5 1.0
OH j:TYR147 4.8 36.2 1.0
CG j:HIS139 4.8 32.7 1.0
N j:CYS114 4.9 42.1 1.0

Zinc binding site 7 out of 12 in 4n9f

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Zinc binding site 7 out of 12 in the Crystal Structure of the Vif-Cbfbeta-CUL5-Elob-Eloc Pentameric Complex


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 the Vif-Cbfbeta-CUL5-Elob-Eloc Pentameric Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
p:Zn201

b:19.5
occ:1.00
 SG p:CYS114 2.2 29.6 1.0
NE2 p:HIS108 2.2 27.9 1.0
NE2 p:HIS139 2.5 32.3 1.0
CE1 p:HIS139 2.9 43.3 1.0
CD2 p:HIS108 2.9 27.2 1.0
SG p:CYS133 2.9 33.1 1.0
CB p:CYS114 3.1 32.6 1.0
CE1 p:HIS108 3.2 28.7 1.0
CD2 p:HIS139 3.8 48.1 1.0
CB p:CYS133 4.0 58.9 1.0
O p:GLU134 4.1 57.7 1.0
CG p:HIS108 4.1 27.4 1.0
ND1 p:HIS139 4.2 41.3 1.0
CA p:CYS114 4.2 35.4 1.0
ND1 p:HIS108 4.2 33.4 1.0
O p:TYR135 4.5 33.2 1.0
CD o:ARG151 4.5 32.6 1.0
CB o:ARG151 4.6 34.0 1.0
CG p:HIS139 4.6 43.1 1.0
O p:ASP113 4.6 31.8 1.0
CA p:CYS133 4.7 55.6 1.0
NE o:ARG151 4.7 32.4 1.0
CG o:GLU152 4.9 38.2 1.0
N p:CYS114 5.0 35.7 1.0

Zinc binding site 8 out of 12 in 4n9f

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Zinc binding site 8 out of 12 in the Crystal Structure of the Vif-Cbfbeta-CUL5-Elob-Eloc Pentameric Complex


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 the Vif-Cbfbeta-CUL5-Elob-Eloc Pentameric Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
v:Zn201

b:24.2
occ:1.00
 NE2 v:HIS139 2.1 21.1 1.0
SG v:CYS114 2.1 23.4 1.0
NE2 v:HIS108 2.3 44.8 1.0
CE1 v:HIS139 2.8 21.0 1.0
CD2 v:HIS108 2.9 44.5 1.0
SG v:CYS133 3.0 24.6 1.0
CD2 v:HIS139 3.2 22.0 1.0
CE1 v:HIS108 3.4 46.9 1.0
CB v:CYS114 3.5 24.8 1.0
CB v:CYS133 3.7 52.2 1.0
O v:GLU134 3.8 30.6 1.0
O v:TYR135 3.9 23.1 1.0
ND1 v:HIS139 4.0 20.3 1.0
CG v:HIS108 4.1 46.1 1.0
CG v:HIS139 4.2 20.1 1.0
ND1 v:HIS108 4.3 59.1 1.0
CA v:CYS114 4.3 25.6 1.0
CB u:ARG151 4.6 37.1 1.0
CA v:CYS133 4.6 49.3 1.0
O v:ASP113 4.7 69.9 1.0
C v:TYR135 4.9 24.6 1.0
C v:GLU134 5.0 31.0 1.0

Zinc binding site 9 out of 12 in 4n9f

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Zinc binding site 9 out of 12 in the Crystal Structure of the Vif-Cbfbeta-CUL5-Elob-Eloc Pentameric Complex


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 the Vif-Cbfbeta-CUL5-Elob-Eloc Pentameric Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Zn201

b:65.5
occ:1.00
 NE2 1:HIS108 2.1 93.0 1.0
NE2 1:HIS139 2.2 60.1 1.0
SG 1:CYS133 2.3 0.8 1.0
SG 1:CYS114 2.4 78.0 1.0
CE1 1:HIS139 2.8 66.6 1.0
CD2 1:HIS108 2.9 92.6 1.0
O 1:GLU134 3.1 0.6 1.0
CB 1:CYS114 3.1 95.5 1.0
CB 1:CYS133 3.2 0.8 1.0
CE1 1:HIS108 3.3 94.4 1.0
CD2 1:HIS139 3.5 70.9 1.0
CA 1:CYS114 3.8 0.3 1.0
CA 1:CYS133 4.0 0.5 1.0
ND1 1:HIS139 4.1 65.6 1.0
CG 1:HIS108 4.1 93.4 1.0
O 1:TYR135 4.2 68.8 1.0
N 1:GLU134 4.2 0.8 1.0
C 1:GLU134 4.2 0.8 1.0
ND1 1:HIS108 4.3 0.1 1.0
O 1:ASP113 4.3 65.5 1.0
C 1:CYS133 4.3 0.2 1.0
CG 1:HIS139 4.4 66.1 1.0
N 1:CYS114 4.7 0.3 1.0
CB 0:ARG151 4.7 46.6 1.0
C 1:ASP113 4.8 68.1 1.0
CD 0:ARG151 4.9 44.5 1.0
CA 1:GLU134 5.0 0.8 1.0
NE 0:ARG151 5.0 44.1 1.0
C 1:TYR135 5.0 70.8 1.0
N 1:PHE115 5.0 60.8 1.0

Zinc binding site 10 out of 12 in 4n9f

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Zinc binding site 10 out of 12 in the Crystal Structure of the Vif-Cbfbeta-CUL5-Elob-Eloc Pentameric Complex


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 the Vif-Cbfbeta-CUL5-Elob-Eloc Pentameric Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
7:Zn201

b:51.4
occ:1.00
 SG 7:CYS114 2.1 34.5 1.0
NE2 7:HIS108 2.5 49.2 1.0
CB 7:CYS133 2.6 0.9 1.0
O 7:GLU134 2.9 0.8 1.0
NE2 7:HIS139 2.9 45.7 1.0
CE1 7:HIS108 3.1 50.0 1.0
CA 7:CYS133 3.2 0.3 1.0
CB 7:CYS114 3.4 38.0 1.0
SG 7:CYS133 3.4 0.1 1.0
CE1 7:HIS139 3.6 53.7 1.0
CA 7:CYS114 3.6 41.3 1.0
CD2 7:HIS108 3.7 48.3 1.0
O 7:ASP113 3.8 62.5 1.0
N 7:GLU134 3.8 0.8 1.0
C 7:CYS133 3.8 0.9 1.0
CD2 7:HIS139 4.0 58.6 1.0
C 7:GLU134 4.0 0.5 1.0
O 7:TYR135 4.3 51.7 1.0
ND1 7:HIS108 4.4 62.2 1.0
C 7:ASP113 4.4 65.1 1.0
N 7:CYS114 4.4 43.3 1.0
N 7:CYS133 4.5 0.4 1.0
CA 7:GLU134 4.7 0.5 1.0
CG 7:HIS108 4.7 49.0 1.0
O 7:CYS133 4.8 0.0 1.0
ND1 7:HIS139 4.8 51.3 1.0
C 7:TYR135 4.9 54.1 1.0
C 7:CYS114 4.9 45.5 1.0

Reference:

Y.Y.Guo, L.Y.Dong, X.L.Qiu, Y.S.Wang, B.L.Zhang, H.N.Liu, Y.Yu, Y.Zang, M.J.Yang, Z.W.Huang. Structural Basis For Hijacking Cbf-B and CUL5 E3 Ligase Complex By Hiv-1 Vif Nature V. 505 229 2014.
ISSN: ISSN 0028-0836
Page generated: Sun Oct 27 03:02:59 2024

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