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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

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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

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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

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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 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

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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

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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

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