Zinc in PDB 7mc9: X-Ray Structure of Pedv Papain-Like Protease 2 Bound to Ub-Pa

Enzymatic activity of X-Ray Structure of Pedv Papain-Like Protease 2 Bound to Ub-Pa

All present enzymatic activity of X-Ray Structure of Pedv Papain-Like Protease 2 Bound to Ub-Pa:
3.4.19.12; 3.6.4.12; 3.6.4.13;

Protein crystallography data

The structure of X-Ray Structure of Pedv Papain-Like Protease 2 Bound to Ub-Pa, PDB code: 7mc9 was solved by I.A.Durie, J.V.Dzimianski, C.M.Daczkowski, S.D.Pegan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.07 / 3.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 98.138, 136.873, 193.348, 90, 90, 90
R / Rfree (%) 20 / 25.7

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Zinc atom in the X-Ray Structure of Pedv Papain-Like Protease 2 Bound to Ub-Pa (pdb code 7mc9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 14 binding sites of Zinc where determined in the X-Ray Structure of Pedv Papain-Like Protease 2 Bound to Ub-Pa, PDB code: 7mc9:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 14 in 7mc9

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Zinc binding site 1 out of 14 in the X-Ray Structure of Pedv Papain-Like Protease 2 Bound to Ub-Pa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of X-Ray Structure of Pedv Papain-Like Protease 2 Bound to Ub-Pa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3701

b:52.7
occ:1.00
 SG A:CYS3495 2.3 81.2 1.0
ND1 A:HIS3523 2.4 66.1 1.0
SG A:CYS3496 2.4 46.1 1.0
SG A:CYS3521 2.5 45.5 1.0
CB A:CYS3495 3.1 50.7 1.0
CG A:HIS3523 3.2 53.3 1.0
CB A:CYS3521 3.2 49.7 1.0
CE1 A:HIS3523 3.4 68.6 1.0
CB A:HIS3523 3.4 48.4 1.0
C A:CYS3495 3.6 70.4 1.0
CB A:CYS3496 3.6 57.0 1.0
N A:CYS3496 3.7 59.9 1.0
O A:CYS3495 3.9 70.7 1.0
CA A:CYS3495 3.9 65.2 1.0
N A:HIS3523 4.0 49.6 1.0
CA A:CYS3496 4.3 50.8 1.0
CA A:HIS3523 4.3 48.5 1.0
CD2 A:HIS3523 4.3 53.9 1.0
NE2 A:HIS3523 4.4 61.5 1.0
CD A:PRO3522 4.4 57.2 1.0
N A:PRO3522 4.5 55.5 1.0
CA A:CYS3521 4.5 45.5 1.0
CG A:PRO3522 4.6 58.9 1.0
C A:CYS3521 4.6 52.2 1.0
CG2 A:THR3491 4.6 51.7 1.0
OG1 A:THR3491 4.8 60.4 1.0
N A:CYS3495 4.9 60.4 1.0
C A:PRO3522 4.9 49.1 1.0

Zinc binding site 2 out of 14 in 7mc9

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Zinc binding site 2 out of 14 in the X-Ray Structure of Pedv Papain-Like Protease 2 Bound to Ub-Pa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of X-Ray Structure of Pedv Papain-Like Protease 2 Bound to Ub-Pa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3702

b:53.0
occ:1.00
 O O:CYS1812 2.0 48.0 1.0
ND1 A:HIS3377 2.1 35.5 1.0
SG O:CYS1812 2.2 40.4 1.0
NE2 A:HIS3373 2.3 58.5 1.0
C O:CYS1812 2.8 47.0 1.0
CE1 A:HIS3377 2.9 38.0 1.0
N O:CYS1812 3.1 62.6 1.0
CG A:HIS3377 3.2 36.5 1.0
CD2 A:HIS3373 3.2 58.4 1.0
CA O:CYS1812 3.2 52.7 1.0
CB O:CYS1812 3.2 44.1 1.0
CE1 A:HIS3373 3.3 67.0 1.0
CB A:HIS3377 3.6 43.5 1.0
NE2 A:HIS3377 4.0 37.2 1.0
N O:SER1813 4.0 53.0 1.0
CD2 A:HIS3377 4.2 34.9 1.0
C O:CYS1811 4.2 60.5 1.0
CG A:HIS3373 4.4 69.9 1.0
ND1 A:HIS3373 4.4 75.0 1.0
CA O:SER1813 4.6 46.6 1.0
CA A:HIS3377 4.6 45.6 1.0
CA O:CYS1811 4.8 63.7 1.0

Zinc binding site 3 out of 14 in 7mc9

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Zinc binding site 3 out of 14 in the X-Ray Structure of Pedv Papain-Like Protease 2 Bound to Ub-Pa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of X-Ray Structure of Pedv Papain-Like Protease 2 Bound to Ub-Pa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3703

b:140.3
occ:1.00
 SG C:CYS1812 2.3 83.3 1.0
SG A:CYS3497 2.4 93.3 1.0
OE2 A:GLU3488 2.4 91.6 1.0
OE2 C:GLU1803 2.4 88.3 1.0
CD A:GLU3488 3.5 71.2 1.0
CD C:GLU1803 3.5 75.8 1.0
CB C:CYS1812 3.7 63.4 1.0
CB A:CYS3497 3.8 67.9 1.0
CG A:GLU3488 3.9 61.5 1.0
CG C:GLU1803 4.0 61.5 1.0
CE C:LYS1814 4.4 67.7 1.0
OE1 A:GLU3488 4.5 77.1 1.0
OE1 C:GLU1803 4.5 78.9 1.0
CG2 A:VAL3490 4.8 63.7 1.0
CG2 C:VAL1805 4.8 53.3 1.0

Zinc binding site 4 out of 14 in 7mc9

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Zinc binding site 4 out of 14 in the X-Ray Structure of Pedv Papain-Like Protease 2 Bound to Ub-Pa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of X-Ray Structure of Pedv Papain-Like Protease 2 Bound to Ub-Pa within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn2001

b:36.2
occ:1.00
 SG C:CYS1810 2.4 60.6 1.0
SG C:CYS1811 2.6 55.1 1.0
ND1 C:HIS1838 2.8 55.4 1.0
CB C:CYS1836 2.8 52.8 1.0
SG C:CYS1836 3.1 119.6 1.0
CB C:CYS1810 3.4 60.8 1.0
CB C:CYS1811 3.5 64.8 1.0
CG C:HIS1838 3.6 40.3 1.0
CB C:HIS1838 3.7 48.7 1.0
C C:CYS1810 3.7 75.5 1.0
CE1 C:HIS1838 3.7 58.6 1.0
N C:HIS1838 3.8 55.9 1.0
N C:CYS1811 3.9 66.2 1.0
O C:CYS1810 3.9 79.2 1.0
CD C:PRO1837 4.1 61.5 1.0
CA C:CYS1836 4.1 61.3 1.0
N C:PRO1837 4.2 57.4 1.0
CA C:CYS1810 4.2 61.8 1.0
CA C:CYS1811 4.3 57.8 1.0
CA C:HIS1838 4.4 53.7 1.0
C C:CYS1836 4.4 60.9 1.0
CD2 C:HIS1838 4.7 50.0 1.0
C C:PRO1837 4.7 58.2 1.0
NE2 C:HIS1838 4.8 57.7 1.0
CA C:PRO1837 4.9 55.1 1.0

Zinc binding site 5 out of 14 in 7mc9

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Zinc binding site 5 out of 14 in the X-Ray Structure of Pedv Papain-Like Protease 2 Bound to Ub-Pa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of X-Ray Structure of Pedv Papain-Like Protease 2 Bound to Ub-Pa within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn2001

b:68.3
occ:1.00
 SG E:CYS1836 1.8 49.4 1.0
ND1 E:HIS1838 2.2 67.7 1.0
SG E:CYS1810 2.2 61.0 1.0
SG E:CYS1811 2.6 66.5 1.0
O E:CYS1810 2.9 77.8 1.0
CB E:CYS1810 2.9 61.7 1.0
CG E:HIS1838 3.0 54.3 1.0
C E:CYS1810 3.1 70.1 1.0
CE1 E:HIS1838 3.2 63.4 1.0
CB E:HIS1838 3.3 51.5 1.0
CB E:CYS1836 3.3 39.7 1.0
CB E:CYS1811 3.5 58.7 1.0
CA E:CYS1810 3.6 57.2 1.0
N E:CYS1811 3.6 54.4 1.0
N E:HIS1838 3.7 50.6 1.0
CA E:HIS1838 4.1 51.9 1.0
CA E:CYS1811 4.1 48.7 1.0
CD2 E:HIS1838 4.2 53.4 1.0
NE2 E:HIS1838 4.2 68.6 1.0
CA E:CYS1836 4.4 46.5 1.0
N E:PRO1837 4.5 55.4 1.0
N E:CYS1810 4.5 51.8 1.0
C E:CYS1836 4.6 57.9 1.0
CD E:PRO1837 4.7 45.5 1.0
C E:PRO1837 4.8 48.8 1.0
OG1 E:THR1806 4.9 44.1 1.0
CG2 E:THR1806 5.0 45.0 1.0

Zinc binding site 6 out of 14 in 7mc9

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Zinc binding site 6 out of 14 in the X-Ray Structure of Pedv Papain-Like Protease 2 Bound to Ub-Pa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of X-Ray Structure of Pedv Papain-Like Protease 2 Bound to Ub-Pa within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn2002

b:59.2
occ:1.00
 O K:CYS127 2.3 70.1 1.0
ND1 E:HIS1692 2.3 49.5 1.0
SG K:CYS127 2.5 63.1 1.0
NE2 E:HIS1688 2.5 68.0 1.0
C K:CYS127 3.0 69.7 1.0
CE1 E:HIS1688 3.0 68.5 1.0
CG E:HIS1692 3.3 52.3 1.0
CE1 E:HIS1692 3.3 55.3 1.0
CB E:HIS1692 3.5 57.0 1.0
N K:CYS127 3.5 85.2 1.0
CA K:CYS127 3.5 78.6 1.0
CB K:CYS127 3.6 64.0 1.0
CD2 E:HIS1688 3.7 71.8 1.0
N K:SER128 4.0 71.1 1.0
ND1 E:HIS1688 4.2 61.9 1.0
NE2 E:HIS1692 4.4 53.8 1.0
CD2 E:HIS1692 4.4 48.3 1.0
CA E:HIS1692 4.4 55.9 1.0
CA K:SER128 4.4 63.2 1.0
C K:CYS126 4.5 81.0 1.0
CG E:HIS1688 4.6 73.1 1.0
O E:HIS1688 4.9 67.4 1.0

Zinc binding site 7 out of 14 in 7mc9

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Zinc binding site 7 out of 14 in the X-Ray Structure of Pedv Papain-Like Protease 2 Bound to Ub-Pa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of X-Ray Structure of Pedv Papain-Like Protease 2 Bound to Ub-Pa within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn2003

b:96.2
occ:1.00
 SG G:CYS1812 2.6 85.8 1.0
OE2 E:GLU1803 2.6 65.1 1.0
OE2 G:GLU1803 2.8 66.3 1.0
SG E:CYS1812 2.9 97.3 1.0
CB E:CYS1812 3.3 55.4 1.0
CB G:CYS1812 3.5 57.6 1.0
CD E:GLU1803 3.6 65.6 1.0
CD G:GLU1803 3.9 64.8 1.0
CG E:GLU1803 4.0 50.0 1.0
NZ G:LYS1814 4.4 76.0 1.0
CG2 G:VAL1805 4.5 49.0 1.0
CG G:GLU1803 4.5 67.2 1.0
CA E:CYS1812 4.6 48.6 1.0
OE1 E:GLU1803 4.6 61.2 1.0
CG2 E:VAL1805 4.7 45.9 1.0
C E:CYS1812 4.8 50.7 1.0
NZ E:LYS1814 4.8 61.7 1.0
CB E:VAL1805 4.8 42.4 1.0
OE1 G:GLU1803 4.9 63.3 1.0
CA G:CYS1812 5.0 49.6 1.0
N E:SER1813 5.0 50.5 1.0

Zinc binding site 8 out of 14 in 7mc9

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Zinc binding site 8 out of 14 in the X-Ray Structure of Pedv Papain-Like Protease 2 Bound to Ub-Pa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of X-Ray Structure of Pedv Papain-Like Protease 2 Bound to Ub-Pa within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn2001

b:82.4
occ:1.00
 CB G:CYS1810 2.1 49.6 1.0
SG G:CYS1836 2.1 38.3 1.0
ND1 G:HIS1838 2.2 76.0 1.0
SG G:CYS1811 2.8 54.7 1.0
CE1 G:HIS1838 3.0 77.0 1.0
SG G:CYS1810 3.2 97.2 1.0
CA G:CYS1810 3.2 55.1 1.0
C G:CYS1810 3.3 64.0 1.0
CG G:HIS1838 3.4 71.0 1.0
N G:CYS1811 3.6 59.7 1.0
CB G:CYS1836 3.8 55.1 1.0
O G:CYS1810 3.8 66.5 1.0
CB G:HIS1838 3.9 62.0 1.0
CB G:CYS1811 4.0 45.1 1.0
NE2 G:HIS1838 4.2 96.3 1.0
CA G:CYS1811 4.3 38.2 1.0
N G:CYS1810 4.4 56.5 1.0
N G:HIS1838 4.4 60.4 1.0
CD2 G:HIS1838 4.4 94.1 1.0
CD G:PRO1837 4.6 60.5 1.0
CA G:HIS1838 4.8 63.5 1.0
N G:PRO1837 4.8 65.4 1.0
CA G:CYS1836 4.8 61.6 1.0

Zinc binding site 9 out of 14 in 7mc9

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Zinc binding site 9 out of 14 in the X-Ray Structure of Pedv Papain-Like Protease 2 Bound to Ub-Pa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of X-Ray Structure of Pedv Papain-Like Protease 2 Bound to Ub-Pa within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn2002

b:47.1
occ:1.00
 NE2 G:HIS1688 2.3 48.0 1.0
O I:CYS1812 2.4 42.3 1.0
CG G:HIS1692 2.6 54.7 1.0
CD2 G:HIS1692 2.6 57.4 1.0
SG I:CYS1812 2.6 60.9 1.0
CE1 G:HIS1688 2.8 47.5 1.0
CB G:HIS1692 3.1 47.7 1.0
ND1 G:HIS1692 3.1 51.9 1.0
NE2 G:HIS1692 3.1 46.8 1.0
C I:CYS1812 3.3 53.5 1.0
CE1 G:HIS1692 3.4 49.2 1.0
CD2 G:HIS1688 3.6 61.5 1.0
CB I:CYS1812 3.8 57.9 1.0
N I:CYS1812 3.9 61.1 1.0
CA I:CYS1812 3.9 48.9 1.0
ND1 G:HIS1688 4.0 46.5 1.0
CA G:HIS1692 4.3 48.6 1.0
N I:SER1813 4.4 57.8 1.0
CG G:HIS1688 4.4 57.2 1.0
CA I:SER1813 4.8 43.7 1.0
C I:CYS1811 5.0 58.1 1.0

Zinc binding site 10 out of 14 in 7mc9

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Zinc binding site 10 out of 14 in the X-Ray Structure of Pedv Papain-Like Protease 2 Bound to Ub-Pa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of X-Ray Structure of Pedv Papain-Like Protease 2 Bound to Ub-Pa within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn2001

b:55.1
occ:1.00
 SG I:CYS1810 2.3 52.8 1.0
ND1 I:HIS1838 2.4 59.4 1.0
SG I:CYS1811 2.4 77.9 1.0
SG I:CYS1836 2.5 48.4 1.0
CB I:CYS1810 3.1 52.6 1.0
CB I:CYS1836 3.4 54.8 1.0
CE1 I:HIS1838 3.4 57.6 1.0
CG I:HIS1838 3.4 56.5 1.0
CB I:CYS1811 3.6 52.8 1.0
CB I:HIS1838 3.6 46.7 1.0
C I:CYS1810 3.7 61.7 1.0
N I:CYS1811 3.8 51.7 1.0
N I:HIS1838 3.8 47.0 1.0
O I:CYS1810 4.0 63.5 1.0
CA I:CYS1810 4.0 55.4 1.0
CD I:PRO1837 4.2 52.2 1.0
N I:PRO1837 4.3 53.0 1.0
CA I:CYS1811 4.3 49.3 1.0
CA I:HIS1838 4.3 46.0 1.0
NE2 I:HIS1838 4.5 51.5 1.0
CD2 I:HIS1838 4.5 58.2 1.0
CA I:CYS1836 4.5 48.2 1.0
C I:CYS1836 4.6 54.8 1.0
C I:PRO1837 4.8 52.5 1.0
N I:CYS1810 4.9 52.1 1.0
CG2 I:THR1806 4.9 52.5 1.0
OG1 I:THR1806 4.9 59.2 1.0
CA I:PRO1837 4.9 57.7 1.0

Reference:

I.A.Durie, J.V.Dzimianski, C.M.Daczkowski, J.Mcguire, K.Faaberg, S.D.Pegan. Structural Insights Into the Interaction of Papain-Like Protease 2 From the Alphacoronavirus Porcine Epidemic Diarrhea Virus and Ubiquitin Acta Cryst. D V. 77 943 2021.
DOI: 10.1107/S205979832100509X
Page generated: Mon Jul 12 17:23:38 2021

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