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

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy