Zinc in PDB 4xr8: Crystal Structure of the HPV16 E6/E6AP/P53 Ternary Complex at 2.25 A Resolution
Protein crystallography data
The structure of Crystal Structure of the HPV16 E6/E6AP/P53 Ternary Complex at 2.25 A Resolution, PDB code: 4xr8
was solved by
D.Martinez-Zapien,
F.X.Ruiz,
A.Mitschler,
A.Podjarny,
G.Trave,
K.Zanier,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
49.64 /
2.25
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
77.842,
128.939,
81.560,
90.00,
92.33,
90.00
|
R / Rfree (%)
|
19.4 /
24.6
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Crystal Structure of the HPV16 E6/E6AP/P53 Ternary Complex at 2.25 A Resolution
(pdb code 4xr8). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the
Crystal Structure of the HPV16 E6/E6AP/P53 Ternary Complex at 2.25 A Resolution, PDB code: 4xr8:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
Zinc binding site 1 out
of 6 in 4xr8
Go back to
Zinc Binding Sites List in 4xr8
Zinc binding site 1 out
of 6 in the Crystal Structure of the HPV16 E6/E6AP/P53 Ternary Complex at 2.25 A Resolution
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 the HPV16 E6/E6AP/P53 Ternary Complex at 2.25 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn900
b:42.2
occ:1.00
|
ND1
|
C:HIS179
|
2.0
|
42.4
|
1.0
|
SG
|
C:CYS242
|
2.2
|
42.6
|
1.0
|
SG
|
C:CYS238
|
2.3
|
43.5
|
1.0
|
SG
|
C:CYS176
|
2.5
|
42.5
|
1.0
|
CE1
|
C:HIS179
|
2.9
|
47.8
|
1.0
|
CB
|
C:CYS242
|
3.1
|
46.8
|
1.0
|
CG
|
C:HIS179
|
3.1
|
42.1
|
1.0
|
CB
|
C:CYS238
|
3.2
|
41.8
|
1.0
|
CB
|
C:CYS176
|
3.5
|
39.5
|
1.0
|
CB
|
C:HIS179
|
3.5
|
40.5
|
1.0
|
CA
|
C:CYS238
|
3.8
|
37.5
|
1.0
|
N
|
C:CYS176
|
4.1
|
42.4
|
1.0
|
NE2
|
C:HIS179
|
4.1
|
51.6
|
1.0
|
CD2
|
C:HIS179
|
4.2
|
49.6
|
1.0
|
CA
|
C:CYS176
|
4.4
|
41.9
|
1.0
|
N
|
C:ASN239
|
4.5
|
38.8
|
1.0
|
CA
|
C:CYS242
|
4.5
|
38.0
|
1.0
|
O
|
C:HOH1064
|
4.6
|
37.9
|
1.0
|
O
|
C:MET237
|
4.6
|
38.5
|
1.0
|
N
|
C:HIS179
|
4.7
|
47.2
|
1.0
|
C
|
C:CYS238
|
4.7
|
39.5
|
1.0
|
CA
|
C:HIS179
|
4.7
|
47.1
|
1.0
|
N
|
C:CYS238
|
5.0
|
38.9
|
1.0
|
O
|
C:CYS176
|
5.0
|
49.6
|
1.0
|
|
Zinc binding site 2 out
of 6 in 4xr8
Go back to
Zinc Binding Sites List in 4xr8
Zinc binding site 2 out
of 6 in the Crystal Structure of the HPV16 E6/E6AP/P53 Ternary Complex at 2.25 A Resolution
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 HPV16 E6/E6AP/P53 Ternary Complex at 2.25 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn901
b:40.5
occ:1.00
|
ND1
|
D:HIS179
|
2.1
|
41.4
|
1.0
|
SG
|
D:CYS242
|
2.2
|
38.0
|
1.0
|
SG
|
D:CYS238
|
2.3
|
40.4
|
1.0
|
SG
|
D:CYS176
|
2.4
|
37.6
|
1.0
|
CE1
|
D:HIS179
|
3.0
|
45.9
|
1.0
|
CG
|
D:HIS179
|
3.1
|
45.4
|
1.0
|
CB
|
D:CYS242
|
3.1
|
41.1
|
1.0
|
CB
|
D:CYS238
|
3.2
|
39.2
|
1.0
|
CB
|
D:CYS176
|
3.3
|
36.5
|
1.0
|
CB
|
D:HIS179
|
3.4
|
36.5
|
1.0
|
CA
|
D:CYS238
|
3.8
|
39.4
|
1.0
|
N
|
D:CYS176
|
3.9
|
44.3
|
1.0
|
NE2
|
D:HIS179
|
4.1
|
50.0
|
1.0
|
CD2
|
D:HIS179
|
4.2
|
36.5
|
1.0
|
CA
|
D:CYS176
|
4.2
|
43.9
|
1.0
|
CA
|
D:CYS242
|
4.5
|
39.9
|
1.0
|
O
|
D:HOH1029
|
4.5
|
42.4
|
1.0
|
N
|
D:ASN239
|
4.5
|
35.8
|
1.0
|
O
|
D:MET237
|
4.6
|
42.3
|
1.0
|
N
|
D:HIS179
|
4.6
|
46.7
|
1.0
|
CA
|
D:HIS179
|
4.7
|
47.0
|
1.0
|
C
|
D:CYS238
|
4.7
|
35.7
|
1.0
|
O
|
D:CYS176
|
4.8
|
46.2
|
1.0
|
C
|
D:CYS176
|
4.9
|
50.5
|
1.0
|
N
|
D:CYS238
|
5.0
|
32.5
|
1.0
|
|
Zinc binding site 3 out
of 6 in 4xr8
Go back to
Zinc Binding Sites List in 4xr8
Zinc binding site 3 out
of 6 in the Crystal Structure of the HPV16 E6/E6AP/P53 Ternary Complex at 2.25 A Resolution
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 HPV16 E6/E6AP/P53 Ternary Complex at 2.25 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Zn201
b:47.7
occ:1.00
|
SG
|
F:CYS106
|
2.1
|
45.3
|
1.0
|
SG
|
F:CYS136
|
2.2
|
48.0
|
1.0
|
SG
|
F:CYS139
|
2.4
|
59.9
|
1.0
|
SG
|
F:CYS103
|
2.4
|
42.2
|
1.0
|
CB
|
F:CYS103
|
3.1
|
35.2
|
1.0
|
CB
|
F:CYS106
|
3.2
|
48.1
|
1.0
|
CB
|
F:CYS139
|
3.3
|
65.5
|
1.0
|
CB
|
F:CYS136
|
3.5
|
45.2
|
1.0
|
N
|
F:CYS106
|
3.6
|
46.7
|
1.0
|
CA
|
F:CYS106
|
4.0
|
45.1
|
1.0
|
N
|
F:CYS136
|
4.1
|
36.7
|
1.0
|
CA
|
F:CYS136
|
4.4
|
38.6
|
1.0
|
N
|
F:CYS139
|
4.4
|
63.4
|
1.0
|
CA
|
F:CYS139
|
4.4
|
67.1
|
1.0
|
CB
|
F:ASN105
|
4.5
|
54.6
|
1.0
|
CA
|
F:CYS103
|
4.5
|
34.3
|
1.0
|
C
|
F:CYS106
|
4.6
|
47.8
|
1.0
|
C
|
F:ASN105
|
4.7
|
46.3
|
1.0
|
N
|
F:GLN107
|
4.8
|
42.7
|
1.0
|
C
|
F:CYS136
|
5.0
|
57.7
|
1.0
|
N
|
F:ASN105
|
5.0
|
47.7
|
1.0
|
|
Zinc binding site 4 out
of 6 in 4xr8
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Zinc Binding Sites List in 4xr8
Zinc binding site 4 out
of 6 in the Crystal Structure of the HPV16 E6/E6AP/P53 Ternary Complex at 2.25 A Resolution
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 HPV16 E6/E6AP/P53 Ternary Complex at 2.25 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Zn202
b:49.4
occ:1.00
|
SG
|
F:CYS63
|
2.0
|
45.2
|
1.0
|
SG
|
F:CYS66
|
2.3
|
52.8
|
1.0
|
SG
|
F:CYS30
|
2.5
|
58.2
|
1.0
|
SG
|
F:CYS33
|
2.6
|
60.3
|
1.0
|
CB
|
F:CYS66
|
3.0
|
50.4
|
1.0
|
CB
|
F:CYS30
|
3.2
|
52.5
|
1.0
|
CB
|
F:CYS63
|
3.3
|
39.9
|
1.0
|
CB
|
F:CYS33
|
3.4
|
37.2
|
1.0
|
N
|
F:CYS33
|
3.9
|
53.5
|
1.0
|
N
|
F:CYS63
|
4.0
|
40.8
|
1.0
|
CA
|
F:CYS63
|
4.1
|
45.5
|
1.0
|
N
|
F:CYS66
|
4.1
|
47.7
|
1.0
|
CA
|
F:CYS66
|
4.2
|
50.6
|
1.0
|
CA
|
F:CYS33
|
4.2
|
54.8
|
1.0
|
O
|
F:CYS63
|
4.5
|
48.1
|
1.0
|
C
|
F:CYS63
|
4.6
|
47.0
|
1.0
|
CB
|
F:TYR32
|
4.7
|
47.4
|
1.0
|
CA
|
F:CYS30
|
4.7
|
56.2
|
1.0
|
C
|
F:TYR32
|
5.0
|
52.6
|
1.0
|
|
Zinc binding site 5 out
of 6 in 4xr8
Go back to
Zinc Binding Sites List in 4xr8
Zinc binding site 5 out
of 6 in the Crystal Structure of the HPV16 E6/E6AP/P53 Ternary Complex at 2.25 A Resolution
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 HPV16 E6/E6AP/P53 Ternary Complex at 2.25 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Zn201
b:42.3
occ:1.00
|
SG
|
H:CYS136
|
2.1
|
46.5
|
1.0
|
SG
|
H:CYS106
|
2.3
|
37.2
|
1.0
|
SG
|
H:CYS103
|
2.4
|
39.2
|
1.0
|
SG
|
H:CYS139
|
2.4
|
45.6
|
1.0
|
CB
|
H:CYS103
|
3.2
|
36.3
|
1.0
|
CB
|
H:CYS139
|
3.2
|
42.6
|
1.0
|
CB
|
H:CYS106
|
3.4
|
41.2
|
1.0
|
CB
|
H:CYS136
|
3.4
|
39.5
|
1.0
|
N
|
H:CYS106
|
3.8
|
41.4
|
1.0
|
N
|
H:CYS136
|
4.0
|
32.5
|
1.0
|
N
|
H:CYS139
|
4.1
|
54.5
|
1.0
|
CA
|
H:CYS106
|
4.2
|
41.9
|
1.0
|
CA
|
H:CYS136
|
4.3
|
42.5
|
1.0
|
CA
|
H:CYS139
|
4.3
|
53.1
|
1.0
|
CB
|
H:ASN105
|
4.4
|
47.4
|
1.0
|
CA
|
H:CYS103
|
4.7
|
35.7
|
1.0
|
C
|
H:CYS136
|
4.8
|
43.4
|
1.0
|
C
|
H:SER138
|
4.9
|
52.9
|
1.0
|
C
|
H:ASN105
|
4.9
|
46.9
|
1.0
|
CB
|
H:SER138
|
4.9
|
39.6
|
1.0
|
ND2
|
H:ASN105
|
4.9
|
44.1
|
1.0
|
C
|
H:CYS106
|
4.9
|
44.2
|
1.0
|
CB
|
H:LYS108
|
5.0
|
35.9
|
1.0
|
CA
|
H:ASN105
|
5.0
|
48.2
|
1.0
|
|
Zinc binding site 6 out
of 6 in 4xr8
Go back to
Zinc Binding Sites List in 4xr8
Zinc binding site 6 out
of 6 in the Crystal Structure of the HPV16 E6/E6AP/P53 Ternary Complex at 2.25 A Resolution
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 HPV16 E6/E6AP/P53 Ternary Complex at 2.25 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Zn202
b:58.3
occ:1.00
|
SG
|
H:CYS30
|
2.2
|
60.1
|
1.0
|
SG
|
H:CYS66
|
2.3
|
54.4
|
1.0
|
SG
|
H:CYS63
|
2.4
|
55.0
|
1.0
|
SG
|
H:CYS33
|
2.5
|
70.5
|
1.0
|
CB
|
H:CYS30
|
2.9
|
64.5
|
1.0
|
CB
|
H:CYS66
|
3.0
|
59.4
|
1.0
|
CB
|
H:CYS33
|
3.5
|
65.0
|
1.0
|
CB
|
H:CYS63
|
3.6
|
50.3
|
1.0
|
N
|
H:CYS33
|
3.9
|
71.2
|
1.0
|
N
|
H:CYS63
|
3.9
|
55.2
|
1.0
|
CA
|
H:CYS66
|
4.2
|
55.5
|
1.0
|
N
|
H:CYS66
|
4.2
|
51.6
|
1.0
|
CA
|
H:CYS63
|
4.3
|
61.8
|
1.0
|
CA
|
H:CYS33
|
4.3
|
71.6
|
1.0
|
CA
|
H:CYS30
|
4.4
|
65.6
|
1.0
|
CB
|
H:TYR32
|
4.5
|
64.6
|
1.0
|
O
|
H:CYS63
|
4.6
|
50.9
|
1.0
|
C
|
H:CYS63
|
4.8
|
55.6
|
1.0
|
N
|
H:TYR32
|
4.9
|
62.1
|
1.0
|
C
|
H:TYR32
|
5.0
|
73.5
|
1.0
|
N
|
H:LYS34
|
5.0
|
75.7
|
1.0
|
C
|
H:CYS30
|
5.0
|
67.0
|
1.0
|
C
|
H:CYS33
|
5.0
|
73.7
|
1.0
|
|
Reference:
D.Martinez-Zapien,
F.X.Ruiz,
J.Poirson,
A.Mitschler,
J.Ramirez,
A.Forster,
A.Cousido-Siah,
M.Masson,
S.V.Pol,
A.Podjarny,
G.Trave,
K.Zanier.
Structure of the E6/E6AP/P53 Complex Required For Hpv-Mediated Degradation of P53. Nature V. 529 541 2016.
ISSN: ESSN 1476-4687
PubMed: 26789255
DOI: 10.1038/NATURE16481
Page generated: Sun Oct 27 10:43:50 2024
|