Zinc in PDB 7uaj: Crystal Structure of Apo HPV16 E6

Protein crystallography data

The structure of Crystal Structure of Apo HPV16 E6, PDB code: 7uaj was solved by Q.Shen, P.G.Leonard, J.B.Cross, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 52.39 / 3.25
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 84.11, 88.68, 109.61, 106.61, 90.16, 102.76
R / Rfree (%) 25.6 / 28.2

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Apo HPV16 E6 (pdb code 7uaj). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of Apo HPV16 E6, PDB code: 7uaj:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 7uaj

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Zinc binding site 1 out of 8 in the Crystal Structure of Apo HPV16 E6


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 Apo HPV16 E6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn600

b:73.8
occ:1.00
SG A:CYS411 2.3 84.3 1.0
SG A:CYS408 2.3 96.3 1.0
SG A:CYS441 2.3 78.3 1.0
SG A:CYS444 2.3 102.5 1.0
CB A:CYS408 3.1 75.9 1.0
CB A:CYS444 3.2 84.3 1.0
CB A:CYS411 3.4 72.3 1.0
CB A:CYS441 3.4 69.1 1.0
N A:CYS411 3.8 84.7 1.0
N A:CYS441 3.9 74.2 1.0
CA A:CYS411 4.1 82.5 1.0
CA A:CYS441 4.2 77.8 1.0
N A:CYS444 4.3 84.3 1.0
CA A:CYS444 4.3 83.6 1.0
CA A:CYS408 4.5 73.3 1.0
CB A:TYR410 4.6 90.1 1.0
O A:CYS441 4.6 95.5 1.0
C A:CYS441 4.7 91.7 1.0
C A:TYR410 4.8 86.7 1.0
N A:TYR410 4.9 85.2 1.0
C A:CYS411 4.9 84.7 1.0
C A:CYS408 4.9 81.5 1.0
CA A:TYR410 5.0 88.3 1.0

Zinc binding site 2 out of 8 in 7uaj

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Zinc binding site 2 out of 8 in the Crystal Structure of Apo HPV16 E6


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 Apo HPV16 E6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn601

b:141.4
occ:1.00
SG A:CYS517 2.3 149.8 1.0
SG A:CYS514 2.4 156.7 1.0
SG A:CYS484 2.4 208.7 1.0
SG A:CYS481 2.4 176.5 1.0
CB A:CYS484 2.7 153.9 1.0
N A:CYS484 3.4 158.5 1.0
CB A:CYS514 3.5 158.7 1.0
CB A:CYS517 3.5 144.7 1.0
CA A:CYS484 3.6 150.5 1.0
CB A:CYS481 3.7 160.9 1.0
N A:CYS514 4.3 161.8 1.0
N A:CYS517 4.3 157.8 1.0
CA A:CYS514 4.5 161.0 1.0
CA A:CYS517 4.5 149.7 1.0
C A:ASN483 4.6 163.2 1.0
C A:CYS484 4.7 158.0 1.0
CB A:ASN483 4.8 167.9 1.0
N A:ASN483 4.9 169.0 1.0
N A:GLN485 4.9 162.1 1.0

Zinc binding site 3 out of 8 in 7uaj

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Zinc binding site 3 out of 8 in the Crystal Structure of Apo HPV16 E6


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 Apo HPV16 E6 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn600

b:74.1
occ:1.00
SG B:CYS411 2.3 87.5 1.0
SG B:CYS444 2.3 74.8 1.0
SG B:CYS408 2.3 83.3 1.0
SG B:CYS441 2.3 86.1 1.0
CB B:CYS408 3.0 71.5 1.0
CB B:CYS444 3.1 82.3 1.0
CB B:CYS441 3.4 71.4 1.0
CB B:CYS411 3.5 78.6 1.0
N B:CYS441 3.8 76.0 1.0
N B:CYS411 3.9 74.8 1.0
CA B:CYS441 4.1 83.6 1.0
N B:CYS444 4.2 75.1 1.0
CA B:CYS444 4.2 80.2 1.0
CA B:CYS411 4.3 84.4 1.0
CA B:CYS408 4.5 71.3 1.0
O B:CYS441 4.6 72.6 1.0
C B:CYS441 4.7 76.7 1.0
CB B:TYR410 4.8 90.0 1.0
C B:VAL440 4.9 72.6 1.0
N B:TYR410 5.0 82.9 1.0
C B:TYR410 5.0 75.1 1.0

Zinc binding site 4 out of 8 in 7uaj

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Zinc binding site 4 out of 8 in the Crystal Structure of Apo HPV16 E6


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 Apo HPV16 E6 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn601

b:127.0
occ:1.00
SG B:CYS484 2.3 149.6 1.0
SG B:CYS517 2.3 129.3 1.0
SG B:CYS514 2.3 148.6 1.0
SG B:CYS481 2.4 162.5 1.0
CB B:CYS517 3.3 140.2 1.0
CB B:CYS484 3.4 129.4 1.0
CB B:CYS514 3.4 148.8 1.0
CB B:CYS481 3.7 142.1 1.0
N B:CYS484 3.8 146.9 1.0
N B:CYS514 4.0 148.4 1.0
CA B:CYS484 4.1 138.4 1.0
N B:CYS517 4.2 144.8 1.0
CA B:CYS514 4.3 148.4 1.0
CA B:CYS517 4.4 142.3 1.0
CB B:ASN483 4.5 143.0 1.0
NH2 B:ARG513 4.6 146.5 1.0
C B:ASN483 4.7 153.8 1.0
C B:CYS514 4.9 151.4 1.0

Zinc binding site 5 out of 8 in 7uaj

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Zinc binding site 5 out of 8 in the Crystal Structure of Apo HPV16 E6


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 Apo HPV16 E6 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn600

b:80.4
occ:1.00
SG C:CYS444 2.3 95.2 1.0
SG C:CYS411 2.3 94.7 1.0
SG C:CYS441 2.3 104.3 1.0
SG C:CYS408 2.4 110.9 1.0
CB C:CYS444 3.1 102.7 1.0
CB C:CYS441 3.2 95.8 1.0
CB C:CYS408 3.3 93.2 1.0
CB C:CYS411 3.3 104.5 1.0
N C:CYS441 3.8 90.0 1.0
N C:CYS411 3.9 95.6 1.0
CA C:CYS441 4.1 96.4 1.0
N C:CYS444 4.1 106.8 1.0
CA C:CYS444 4.2 104.3 1.0
CA C:CYS411 4.2 101.4 1.0
CB C:TYR410 4.6 103.8 1.0
O C:CYS441 4.6 106.0 1.0
C C:CYS441 4.6 102.3 1.0
CA C:CYS408 4.7 88.7 1.0
OH D:TYR342 4.8 117.8 1.0
C C:TYR410 4.9 100.5 1.0
N C:TYR410 5.0 101.6 1.0

Zinc binding site 6 out of 8 in 7uaj

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Zinc binding site 6 out of 8 in the Crystal Structure of Apo HPV16 E6


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 Apo HPV16 E6 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn601

b:220.6
occ:1.00
SG C:CYS517 2.3 205.4 1.0
SG C:CYS514 2.3 203.4 1.0
SG C:CYS484 2.4 235.7 1.0
SG C:CYS481 2.4 233.6 1.0
CB C:CYS484 2.6 218.2 1.0
CB C:CYS517 3.5 202.6 1.0
CB C:CYS481 3.6 208.9 1.0
N C:CYS484 3.6 217.5 1.0
N C:CYS517 3.7 199.1 1.0
CA C:CYS484 3.7 215.0 1.0
CB C:CYS514 3.7 198.3 1.0
CB C:SER516 3.9 197.4 1.0
CA C:CYS517 4.2 199.4 1.0
OG C:SER516 4.2 197.5 1.0
C C:SER516 4.4 202.4 1.0
CA C:CYS514 4.5 196.4 1.0
O C:CYS514 4.5 197.7 1.0
CA C:SER516 4.5 201.3 1.0
N C:CYS514 4.6 193.7 1.0
C C:CYS484 4.6 210.4 1.0
N C:SER516 4.6 201.4 1.0
C C:CYS514 4.7 196.9 1.0
C C:ASN483 4.8 220.1 1.0
CA C:CYS481 4.9 200.4 1.0
N C:GLN485 5.0 211.0 1.0

Zinc binding site 7 out of 8 in 7uaj

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Zinc binding site 7 out of 8 in the Crystal Structure of Apo HPV16 E6


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 Apo HPV16 E6 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn600

b:80.9
occ:1.00
SG D:CYS444 2.3 76.6 1.0
SG D:CYS411 2.3 95.0 1.0
SG D:CYS441 2.3 83.5 1.0
SG D:CYS408 2.3 86.8 1.0
CB D:CYS444 3.0 86.0 1.0
CB D:CYS408 3.1 90.0 1.0
CB D:CYS411 3.4 82.5 1.0
CB D:CYS441 3.4 78.8 1.0
N D:CYS411 3.7 86.6 1.0
N D:CYS441 3.9 82.9 1.0
CA D:CYS411 4.2 90.1 1.0
CA D:CYS441 4.2 87.2 1.0
N D:CYS444 4.2 83.5 1.0
CA D:CYS444 4.2 91.1 1.0
CB D:TYR410 4.4 94.7 1.0
CA D:CYS408 4.6 91.9 1.0
C D:TYR410 4.7 88.0 1.0
C D:CYS441 4.8 95.9 1.0
O D:CYS441 4.8 93.3 1.0
N D:TYR410 4.8 82.8 1.0
CA D:TYR410 4.9 83.6 1.0

Zinc binding site 8 out of 8 in 7uaj

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Zinc binding site 8 out of 8 in the Crystal Structure of Apo HPV16 E6


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 Apo HPV16 E6 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn601

b:218.5
occ:1.00
SG D:CYS514 2.3 199.4 1.0
SG D:CYS484 2.3 220.7 1.0
SG D:CYS517 2.3 209.0 1.0
SG D:CYS481 2.3 221.2 1.0
CB D:CYS484 3.2 206.0 1.0
CB D:CYS517 3.3 200.2 1.0
CB D:CYS514 3.4 197.5 1.0
N D:CYS484 3.6 210.4 1.0
CB D:CYS481 3.6 211.5 1.0
CA D:CYS484 4.0 205.6 1.0
N D:CYS514 4.2 205.4 1.0
N D:CYS517 4.2 195.2 1.0
CA D:CYS517 4.3 195.3 1.0
CA D:CYS514 4.4 202.0 1.0
CB D:ASN483 4.5 219.1 1.0
C D:ASN483 4.6 213.1 1.0
N D:ASN483 4.7 219.7 1.0
CA D:ASN483 4.8 218.2 1.0
CA D:CYS481 5.0 209.8 1.0
C D:CYS514 5.0 197.5 1.0

Reference:

Q.Shen, P.G.Leonard, J.B.Cross. Disorder-to-Order Transition of the Interdomain Linker of Hpv E6 Upon E6AP Binding Reshapes P53 Binding Pocket To Be Published.
Page generated: Sat Apr 8 03:59:42 2023

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