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Chlorine in PDB 5v6a: Crystal Structure of the Middle East Respiratory Syndrome Coronavirus Papain-Like Protease Bound to Ubiquitin Variant Me.2

Protein crystallography data

The structure of Crystal Structure of the Middle East Respiratory Syndrome Coronavirus Papain-Like Protease Bound to Ubiquitin Variant Me.2, PDB code: 5v6a was solved by B.A.Bailey-Elkin, B.L.Mark, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.97 / 2.70
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 47.071, 109.779, 183.863, 90.00, 90.00, 90.00
R / Rfree (%) 21.7 / 27.3

Other elements in 5v6a:

The structure of Crystal Structure of the Middle East Respiratory Syndrome Coronavirus Papain-Like Protease Bound to Ubiquitin Variant Me.2 also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of the Middle East Respiratory Syndrome Coronavirus Papain-Like Protease Bound to Ubiquitin Variant Me.2 (pdb code 5v6a). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of the Middle East Respiratory Syndrome Coronavirus Papain-Like Protease Bound to Ubiquitin Variant Me.2, PDB code: 5v6a:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 5v6a

Go back to Chlorine Binding Sites List in 5v6a
Chlorine binding site 1 out of 4 in the Crystal Structure of the Middle East Respiratory Syndrome Coronavirus Papain-Like Protease Bound to Ubiquitin Variant Me.2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of the Middle East Respiratory Syndrome Coronavirus Papain-Like Protease Bound to Ubiquitin Variant Me.2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1904

b:63.9
occ:1.00
OD2 A:ASP1557 3.6 48.7 1.0
N A:ASP1557 3.9 44.2 1.0
CD2 A:PHE1560 4.0 48.6 1.0
NH2 A:ARG1563 4.0 40.3 1.0
OD1 A:ASN1638 4.1 55.5 1.0
CB A:ASP1557 4.2 41.2 1.0
O A:ALA1635 4.3 47.0 1.0
CG A:ASP1557 4.4 44.9 1.0
CA A:VAL1556 4.5 42.0 1.0
O A:TYR1636 4.5 42.6 1.0
CE2 A:PHE1560 4.6 43.1 1.0
CB A:VAL1556 4.7 47.0 1.0
CA A:TYR1636 4.7 42.3 1.0
C A:VAL1556 4.7 40.9 1.0
CA A:ASP1557 4.8 43.8 1.0
CG A:PHE1560 4.8 49.4 1.0
CB A:PHE1560 4.9 40.0 1.0
CD1 A:TYR1636 4.9 42.0 1.0
CG1 A:VAL1556 5.0 40.0 1.0

Chlorine binding site 2 out of 4 in 5v6a

Go back to Chlorine Binding Sites List in 5v6a
Chlorine binding site 2 out of 4 in the Crystal Structure of the Middle East Respiratory Syndrome Coronavirus Papain-Like Protease Bound to Ubiquitin Variant Me.2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of the Middle East Respiratory Syndrome Coronavirus Papain-Like Protease Bound to Ubiquitin Variant Me.2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1905

b:79.1
occ:1.00
CG2 A:VAL1582 3.6 58.5 1.0
NH1 A:ARG1764 3.8 58.9 1.0
CA A:VAL1582 3.8 56.4 1.0
CB A:ASP1602 3.8 59.7 1.0
CB A:VAL1582 3.9 53.1 1.0
NH1 A:ARG1583 3.9 54.6 1.0
NH2 A:ARG1764 4.1 54.5 1.0
O A:LYS1581 4.1 61.6 1.0
N A:ARG1583 4.2 48.3 1.0
OD2 A:ASP1602 4.2 65.7 1.0
CG A:ASP1602 4.3 63.4 1.0
CZ A:ARG1764 4.4 53.2 1.0
C A:VAL1582 4.5 49.4 1.0
CZ A:ARG1583 4.8 60.7 1.0
N A:VAL1582 4.8 58.5 1.0
C A:LYS1581 4.9 50.6 1.0
O A:ASP1602 4.9 64.6 1.0

Chlorine binding site 3 out of 4 in 5v6a

Go back to Chlorine Binding Sites List in 5v6a
Chlorine binding site 3 out of 4 in the Crystal Structure of the Middle East Respiratory Syndrome Coronavirus Papain-Like Protease Bound to Ubiquitin Variant Me.2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of the Middle East Respiratory Syndrome Coronavirus Papain-Like Protease Bound to Ubiquitin Variant Me.2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1906

b:99.0
occ:1.00
O A:CYS1672 4.4 78.5 1.0
CG1 A:ILE1677 4.4 70.7 1.0
CD1 A:ILE1677 4.6 62.0 1.0
CA A:ASN1673 4.7 79.6 1.0
CA A:GLY1676 4.7 64.7 1.0
OD1 A:ASN1673 4.7 77.0 1.0
O A:ASN1673 4.9 74.2 1.0

Chlorine binding site 4 out of 4 in 5v6a

Go back to Chlorine Binding Sites List in 5v6a
Chlorine binding site 4 out of 4 in the Crystal Structure of the Middle East Respiratory Syndrome Coronavirus Papain-Like Protease Bound to Ubiquitin Variant Me.2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of the Middle East Respiratory Syndrome Coronavirus Papain-Like Protease Bound to Ubiquitin Variant Me.2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1907

b:75.4
occ:1.00
CG2 A:THR1627 3.6 57.6 1.0
O A:TRP1574 3.9 55.2 1.0
O A:VAL1571 4.0 62.1 1.0
C A:TRP1574 4.1 54.6 1.0
N A:THR1627 4.3 61.7 1.0
CB A:THR1627 4.3 60.2 1.0
CB A:TRP1574 4.4 55.2 1.0
N A:LYS1575 4.4 57.4 1.0
CA A:THR1627 4.4 59.2 1.0
CD1 A:ILE1630 4.4 38.0 1.0
CG1 A:VAL1571 4.5 52.2 1.0
N A:MET1576 4.5 53.4 1.0
CB A:MET1576 4.5 40.9 1.0
CA A:LYS1575 4.6 48.5 1.0
C A:LYS1575 4.7 51.4 1.0
CA A:TRP1574 4.7 56.9 1.0
C A:SER1626 4.8 54.5 1.0

Reference:

W.Zhang, B.A.Bailey-Elkin, R.C.M.Knaap, B.Khare, T.J.Dalebout, G.G.Johnson, P.B.Van Kasteren, N.J.Mcleish, J.Gu, W.He, M.Kikkert, B.L.Mark, S.S.Sidhu. Potent and Selective Inhibition of Pathogenic Viruses By Engineered Ubiquitin Variants. Plos Pathog. V. 13 06372 2017.
ISSN: ESSN 1553-7374
PubMed: 28542609
DOI: 10.1371/JOURNAL.PPAT.1006372
Page generated: Sat Dec 12 12:33:22 2020

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