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Zinc in PDB 5w8u: Crystal Structure of Mers-Cov Papain-Like Protease in Complex with the C-Terminal Domain of Human ISG15

Protein crystallography data

The structure of Crystal Structure of Mers-Cov Papain-Like Protease in Complex with the C-Terminal Domain of Human ISG15, PDB code: 5w8u was solved by C.M.Daczkowski, O.Y.Goodwin, J.D.Dzimianski, S.D.Pegan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.63 / 2.41
Space group P 43
Cell size a, b, c (Å), α, β, γ (°) 86.370, 86.370, 224.087, 90.00, 90.00, 90.00
R / Rfree (%) 21.3 / 23.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Mers-Cov Papain-Like Protease in Complex with the C-Terminal Domain of Human ISG15 (pdb code 5w8u). 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 Mers-Cov Papain-Like Protease in Complex with the C-Terminal Domain of Human ISG15, PDB code: 5w8u:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5w8u

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Zinc binding site 1 out of 6 in the Crystal Structure of Mers-Cov Papain-Like Protease in Complex with the C-Terminal Domain of Human ISG15


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 Mers-Cov Papain-Like Protease in Complex with the C-Terminal Domain of Human ISG15 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:67.7
occ:1.00
SG A:CYS191 2.2 73.3 1.0
SG A:CYS228 2.3 67.7 1.0
SG A:CYS194 2.3 73.5 1.0
SG A:CYS226 2.4 59.3 1.0
CB A:CYS226 3.2 61.3 1.0
CB A:CYS191 3.3 70.8 1.0
CB A:CYS228 3.3 68.4 1.0
CB A:CYS194 3.4 71.3 1.0
N A:CYS228 4.0 63.6 1.0
N A:CYS194 4.0 73.4 1.0
CA A:CYS228 4.3 67.0 1.0
CA A:CYS194 4.4 72.0 1.0
CA A:CYS226 4.5 62.4 1.0
N A:GLN227 4.7 58.5 1.0
CA A:CYS191 4.7 70.0 1.0
CB A:VAL193 4.7 78.4 1.0
C A:CYS226 4.8 64.2 1.0
C A:VAL193 5.0 76.0 1.0
N A:GLY230 5.0 67.7 1.0

Zinc binding site 2 out of 6 in 5w8u

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Zinc binding site 2 out of 6 in the Crystal Structure of Mers-Cov Papain-Like Protease in Complex with the C-Terminal Domain of Human ISG15


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 Mers-Cov Papain-Like Protease in Complex with the C-Terminal Domain of Human ISG15 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:60.3
occ:1.00
NE2 A:HIS81 2.0 65.2 1.0
SG A:CYS32 2.5 61.1 1.0
CE1 A:HIS81 2.8 64.5 1.0
CD2 A:HIS81 3.1 65.0 1.0
CB A:CYS32 3.2 62.6 1.0
OD2 A:ASP58 3.8 65.3 1.0
NH1 A:ARG27 4.0 58.2 1.0
ND1 A:HIS81 4.0 63.1 1.0
ZN A:ZN403 4.0 70.0 1.0
NH2 A:ARG27 4.0 58.2 1.0
CG A:HIS81 4.2 63.6 1.0
CZ A:ARG27 4.4 59.5 1.0
OG A:SER41 4.5 62.6 1.0
OD2 A:ASP39 4.5 61.3 1.0
CA A:CYS32 4.6 65.8 1.0
CG A:ASP58 4.8 68.9 1.0
CB A:SER41 5.0 64.4 1.0

Zinc binding site 3 out of 6 in 5w8u

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Zinc binding site 3 out of 6 in the Crystal Structure of Mers-Cov Papain-Like Protease in Complex with the C-Terminal Domain of Human ISG15


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 Mers-Cov Papain-Like Protease in Complex with the C-Terminal Domain of Human ISG15 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:70.0
occ:1.00
CG A:ASP58 2.0 68.9 1.0
OD2 A:ASP58 2.0 65.3 1.0
OD1 A:ASP58 2.1 69.8 1.0
SG A:CYS32 2.4 61.1 1.0
CB A:ASP58 3.0 72.2 1.0
CB A:CYS32 3.6 62.6 1.0
NH1 A:ARG27 3.8 58.2 1.0
N A:CYS32 3.9 68.0 1.0
ZN A:ZN402 4.0 60.3 1.0
CA A:CYS32 4.4 65.8 1.0
CA A:ASP58 4.4 72.0 1.0
CD2 A:HIS81 4.4 65.0 1.0
NE2 A:HIS81 4.5 65.2 1.0
C A:GLY31 4.7 67.9 1.0
N A:ASP58 4.9 69.7 1.0
OD1 A:ASN59 4.9 73.6 1.0
CZ A:ARG27 4.9 59.5 1.0
CA A:GLY31 4.9 69.7 1.0
CG A:ARG27 5.0 65.1 1.0

Zinc binding site 4 out of 6 in 5w8u

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Zinc binding site 4 out of 6 in the Crystal Structure of Mers-Cov Papain-Like Protease in Complex with the C-Terminal Domain of Human ISG15


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 Mers-Cov Papain-Like Protease in Complex with the C-Terminal Domain of Human ISG15 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:64.6
occ:1.00
SG C:CYS191 2.3 72.8 1.0
SG C:CYS228 2.3 67.8 1.0
SG C:CYS194 2.4 72.6 1.0
SG C:CYS226 2.4 59.1 1.0
CB C:CYS226 3.2 59.2 1.0
CB C:CYS228 3.3 68.7 1.0
CB C:CYS191 3.4 71.5 1.0
CB C:CYS194 3.4 71.4 1.0
N C:CYS228 4.0 63.3 1.0
N C:CYS194 4.1 73.0 1.0
CA C:CYS228 4.2 66.9 1.0
CA C:CYS194 4.4 72.3 1.0
CA C:CYS226 4.6 59.3 1.0
CB C:VAL193 4.7 77.1 1.0
N C:GLN227 4.8 57.0 1.0
CA C:CYS191 4.8 70.3 1.0
C C:CYS226 4.8 60.7 1.0
C C:VAL193 4.9 76.0 1.0
N C:GLY230 4.9 66.6 1.0
C C:CYS228 5.0 67.9 1.0

Zinc binding site 5 out of 6 in 5w8u

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Zinc binding site 5 out of 6 in the Crystal Structure of Mers-Cov Papain-Like Protease in Complex with the C-Terminal Domain of Human ISG15


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 Mers-Cov Papain-Like Protease in Complex with the C-Terminal Domain of Human ISG15 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn402

b:71.9
occ:1.00
OD1 C:ASP58 2.0 70.3 1.0
CG C:ASP58 2.1 72.2 1.0
OD2 C:ASP58 2.1 71.8 1.0
OE2 A:GLU231 2.1 69.5 1.0
OE1 A:GLU231 2.3 69.2 1.0
SG C:CYS32 2.3 66.2 1.0
CD A:GLU231 2.4 70.1 1.0
CB C:ASP58 3.3 74.3 1.0
CB C:CYS32 3.6 63.0 1.0
NH1 C:ARG27 3.8 60.8 1.0
CG A:GLU231 3.8 70.3 1.0
ZN C:ZN403 3.9 59.0 1.0
N C:CYS32 4.0 68.1 1.0
CA C:CYS32 4.4 66.0 1.0
CD2 C:HIS81 4.4 65.6 1.0
NE2 C:HIS81 4.4 64.0 1.0
CA C:ASP58 4.6 73.5 1.0
C C:GLY31 4.8 69.3 1.0
CB A:GLU231 4.8 66.9 1.0
CG C:ARG27 4.9 67.9 1.0
CZ C:ARG27 4.9 61.7 1.0
OD1 C:ASN59 5.0 76.8 1.0
CA C:GLY31 5.0 72.1 1.0

Zinc binding site 6 out of 6 in 5w8u

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Zinc binding site 6 out of 6 in the Crystal Structure of Mers-Cov Papain-Like Protease in Complex with the C-Terminal Domain of Human ISG15


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 Mers-Cov Papain-Like Protease in Complex with the C-Terminal Domain of Human ISG15 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn403

b:59.0
occ:1.00
NE2 C:HIS81 2.0 64.0 1.0
OE1 A:GLU231 2.1 69.2 1.0
SG C:CYS32 2.4 66.2 1.0
CE1 C:HIS81 2.8 62.9 1.0
CD A:GLU231 3.1 70.1 1.0
CD2 C:HIS81 3.1 65.6 1.0
CG A:GLU231 3.3 70.3 1.0
CB C:CYS32 3.3 63.0 1.0
NH1 C:ARG27 3.8 60.8 1.0
OD1 C:ASP58 3.9 70.3 1.0
ZN C:ZN402 3.9 71.9 1.0
ND1 C:HIS81 4.0 61.4 1.0
NH2 C:ARG27 4.1 59.7 1.0
CG C:HIS81 4.2 63.4 1.0
OE2 A:GLU231 4.2 69.5 1.0
CZ C:ARG27 4.4 61.7 1.0
OG C:SER41 4.5 62.0 1.0
OD2 C:ASP39 4.6 61.6 1.0
CA C:CYS32 4.7 66.0 1.0
CB A:GLU231 4.8 66.9 1.0
CG C:ASP58 5.0 72.2 1.0

Reference:

C.M.Daczkowski, O.Y.Goodwin, J.V.Dzimianski, J.J.Farhat, S.D.Pegan. Structurally Guided Removal of Deisgylase Biochemical Activity From Papain-Like Protease Originating From Middle East Respiratory Syndrome Coronavirus. J. Virol. V. 91 2017.
ISSN: ESSN 1098-5514
PubMed: 28931677
DOI: 10.1128/JVI.01067-17
Page generated: Wed Dec 16 11:15:31 2020

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