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Chlorine in PDB 7oft: Structure of Sars-Cov-2 Papain-Like Protease Plpro in Complex with P- Hydroxybenzaldehyde

Enzymatic activity of Structure of Sars-Cov-2 Papain-Like Protease Plpro in Complex with P- Hydroxybenzaldehyde

All present enzymatic activity of Structure of Sars-Cov-2 Papain-Like Protease Plpro in Complex with P- Hydroxybenzaldehyde:
3.4.19.12;

Protein crystallography data

The structure of Structure of Sars-Cov-2 Papain-Like Protease Plpro in Complex with P- Hydroxybenzaldehyde, PDB code: 7oft was solved by V.Srinivasan, N.Werner, S.Falke, S.Guenther, P.Reinke, H.Brognaro, N.Ullah, H.Andaleeb, M.Perbandt, B.Alves Franca, M.Schwinzer, M.Wang, W.Ewert, J.Sprenger, J.Lieske, F.Koua, H.Ginn, T.J.Lane, M.Wolf, O.Yefanov, L.Gelisio, S.Saouane, A.Tolstikova, M.Groessler, H.Fleckenstein, F.Trost, K.Lorenzen, R.Schubert, H.Han, C.Schmidt, L.Brings, M.Galchenkova, Y.Gevorkov, C.Li, A.Perk, S.Awel, A.Wahab, I.Choudary, D.Turk, W.Hinrichs, H.N.Chapman, A.Meents, C.Betzel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.79 / 1.95
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 81.613, 81.613, 134.378, 90, 90, 120
R / Rfree (%) 18.3 / 21.4

Other elements in 7oft:

The structure of Structure of Sars-Cov-2 Papain-Like Protease Plpro in Complex with P- Hydroxybenzaldehyde also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Structure of Sars-Cov-2 Papain-Like Protease Plpro in Complex with P- Hydroxybenzaldehyde (pdb code 7oft). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Structure of Sars-Cov-2 Papain-Like Protease Plpro in Complex with P- Hydroxybenzaldehyde, PDB code: 7oft:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 7oft

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Chlorine binding site 1 out of 8 in the Structure of Sars-Cov-2 Papain-Like Protease Plpro in Complex with P- Hydroxybenzaldehyde


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of Sars-Cov-2 Papain-Like Protease Plpro in Complex with P- Hydroxybenzaldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:35.5
occ:1.00
 O A:HOH582 3.0 41.1 1.0
O A:HOH744 3.1 49.4 1.0
O A:HOH544 3.1 35.5 1.0
N A:PHE127 3.3 31.1 1.0
CD2 A:PHE127 3.9 30.1 1.0
CB A:PHE127 3.9 28.3 1.0
CA A:LYS126 4.0 35.8 1.0
CG A:GLN133 4.0 33.6 1.0
CA A:GLN133 4.0 32.1 1.0
C A:LYS126 4.1 31.1 1.0
CA A:PHE127 4.1 31.2 1.0
CB A:GLN133 4.3 32.4 1.0
CD A:LYS126 4.3 61.5 1.0
CD2 A:TYR136 4.3 35.2 1.0
CG A:PHE127 4.3 31.4 1.0
O A:PHE127 4.4 33.4 1.0
O A:LEU125 4.5 37.3 1.0
CB A:LYS126 4.6 38.0 1.0
O A:GLN133 4.7 34.1 1.0
C A:PHE127 4.8 32.5 1.0
N A:GLN133 4.8 30.2 1.0
C A:GLN133 4.9 36.1 1.0
CE2 A:PHE127 4.9 31.4 1.0
CG A:LYS126 5.0 53.7 1.0

Chlorine binding site 2 out of 8 in 7oft

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Chlorine binding site 2 out of 8 in the Structure of Sars-Cov-2 Papain-Like Protease Plpro in Complex with P- Hydroxybenzaldehyde


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of Sars-Cov-2 Papain-Like Protease Plpro in Complex with P- Hydroxybenzaldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl403

b:47.4
occ:1.00
 N A:LYS306 3.1 39.3 1.0
OG1 A:THR259 3.4 39.0 1.0
CA A:PHE258 3.5 39.7 1.0
C A:PHE258 3.6 40.1 1.0
CA A:TYR305 3.7 37.2 1.0
N A:THR259 3.7 34.1 1.0
C A:TYR305 3.9 37.6 1.0
N A:PHE258 4.0 40.3 1.0
CB A:TYR305 4.1 34.3 1.0
O A:PHE258 4.1 39.9 1.0
CG A:LYS306 4.1 58.4 1.0
CA A:LYS306 4.2 41.4 1.0
CB A:LYS306 4.3 48.8 1.0
O A:HOH703 4.3 60.0 1.0
CD2 A:TYR305 4.4 39.2 1.0
C A:THR257 4.4 44.0 1.0
O A:THR257 4.4 45.0 1.0
CA A:THR259 4.5 34.6 1.0
CB A:THR259 4.5 40.0 1.0
O A:HOH518 4.5 51.4 1.0
O A:LYS306 4.6 40.2 1.0
O A:PHE304 4.7 36.6 1.0
CG A:TYR305 4.7 39.5 1.0
CB A:PHE258 4.9 38.8 1.0
C A:LYS306 4.9 38.6 1.0
N A:TYR305 4.9 35.0 1.0

Chlorine binding site 3 out of 8 in 7oft

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Chlorine binding site 3 out of 8 in the Structure of Sars-Cov-2 Papain-Like Protease Plpro in Complex with P- Hydroxybenzaldehyde


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structure of Sars-Cov-2 Papain-Like Protease Plpro in Complex with P- Hydroxybenzaldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl404

b:57.4
occ:1.00
 N A:ALA145 3.4 34.5 1.0
CA A:GLU143 3.4 44.6 1.0
CB A:ALA145 3.4 39.2 1.0
C A:GLU143 3.5 40.4 1.0
N A:ALA144 3.5 37.7 1.0
CB A:GLU143 3.6 48.1 1.0
CA A:ALA145 4.0 37.5 1.0
O A:GLU143 4.1 38.6 1.0
CG A:GLU143 4.1 56.4 1.0
CE2 A:TYR95 4.2 36.8 1.0
CD2 A:TYR95 4.3 38.3 1.0
C A:ALA144 4.4 35.2 1.0
O A:HOH532 4.5 54.6 1.0
CA A:ALA144 4.6 34.5 1.0
O A:GLY142 4.7 43.9 1.0
N A:GLU143 4.8 40.7 1.0

Chlorine binding site 4 out of 8 in 7oft

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Chlorine binding site 4 out of 8 in the Structure of Sars-Cov-2 Papain-Like Protease Plpro in Complex with P- Hydroxybenzaldehyde


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Structure of Sars-Cov-2 Papain-Like Protease Plpro in Complex with P- Hydroxybenzaldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl405

b:44.8
occ:1.00
 O A:HOH653 3.2 36.2 1.0
N A:VAL202 3.2 33.1 1.0
O A:HOH625 3.3 41.2 1.0
CA A:GLY201 3.5 35.4 1.0
CG2 A:VAL202 3.6 37.9 1.0
O A:HOH724 3.6 46.9 1.0
O A:HOH581 3.9 44.5 1.0
C A:GLY201 3.9 35.3 1.0
CB A:VAL202 4.1 37.9 1.0
CA A:VAL202 4.3 36.3 1.0
O A:HOH510 4.3 37.6 1.0
O A:HOH558 4.6 28.8 1.0
O A:LYS200 4.6 37.5 1.0
OE2 A:GLU203 4.6 40.7 1.0
N A:GLY201 4.7 36.9 1.0

Chlorine binding site 5 out of 8 in 7oft

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Chlorine binding site 5 out of 8 in the Structure of Sars-Cov-2 Papain-Like Protease Plpro in Complex with P- Hydroxybenzaldehyde


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Structure of Sars-Cov-2 Papain-Like Protease Plpro in Complex with P- Hydroxybenzaldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl406

b:36.1
occ:1.00
 O A:HOH649 3.1 33.9 1.0
N A:ASP164 3.1 34.9 1.0
O A:HOH706 3.3 41.0 1.0
NZ A:LYS157 3.4 43.7 1.0
CA A:GLY163 3.6 38.8 1.0
CE A:LYS157 3.7 43.3 1.0
CG A:GLU167 3.7 30.9 1.0
CB A:GLU167 3.8 30.7 1.0
C A:GLY163 3.9 36.2 1.0
CB A:ASP164 3.9 32.6 1.0
CA A:ASP164 4.0 32.7 1.0
CD A:LYS157 4.0 41.0 1.0
O A:ASP164 4.0 33.8 1.0
C A:ASP164 4.5 34.9 1.0
OG1 A:THR168 4.6 32.2 1.0
O A:HOH501 4.8 43.7 1.0
CG A:LYS157 4.8 36.3 1.0
N A:GLY163 5.0 40.2 1.0

Chlorine binding site 6 out of 8 in 7oft

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Chlorine binding site 6 out of 8 in the Structure of Sars-Cov-2 Papain-Like Protease Plpro in Complex with P- Hydroxybenzaldehyde


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Structure of Sars-Cov-2 Papain-Like Protease Plpro in Complex with P- Hydroxybenzaldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl407

b:38.2
occ:1.00
 O A:HOH720 2.9 45.6 1.0
ND1 A:HIS73 3.1 34.4 1.0
CG A:PRO129 3.5 32.3 1.0
CD A:PRO129 3.5 33.5 1.0
CB A:ASN128 3.6 34.6 1.0
CD2 A:HIS175 3.6 31.0 1.0
O A:HOH586 3.7 39.2 1.0
CA A:HIS175 3.7 31.4 1.0
CB A:HIS73 3.9 34.9 1.0
CG A:HIS73 3.9 35.4 1.0
CB A:HIS175 4.1 30.1 1.0
CG A:HIS175 4.1 35.1 1.0
CE1 A:HIS73 4.2 34.4 1.0
C A:HIS175 4.2 33.7 1.0
N A:PRO129 4.2 32.9 1.0
O A:HIS175 4.2 30.6 1.0
ND2 A:ASN128 4.3 41.8 1.0
O A:GLN174 4.3 35.5 1.0
O A:HOH714 4.5 44.2 1.0
CG A:ASN128 4.6 39.5 1.0
CA A:ASN128 4.7 31.8 1.0
C A:ASN128 4.7 30.8 1.0
NE2 A:HIS175 4.7 33.5 1.0
N A:HIS175 4.8 29.5 1.0
CB A:PRO129 4.8 32.2 1.0

Chlorine binding site 7 out of 8 in 7oft

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Chlorine binding site 7 out of 8 in the Structure of Sars-Cov-2 Papain-Like Protease Plpro in Complex with P- Hydroxybenzaldehyde


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Structure of Sars-Cov-2 Papain-Like Protease Plpro in Complex with P- Hydroxybenzaldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl408

b:69.3
occ:1.00
 N A:LYS45 3.1 49.0 1.0
CB A:LYS45 3.9 51.0 1.0
CA A:ILE44 3.9 51.4 1.0
C A:ILE44 4.0 49.6 1.0
CA A:LYS45 4.0 48.3 1.0
CG2 A:ILE44 4.1 56.3 1.0
CE1 A:HIS47 4.1 63.7 0.5
O A:LYS45 4.2 55.3 1.0
CG A:LYS45 4.3 51.6 1.0
CD1 A:ILE44 4.3 56.1 1.0
CB A:ILE44 4.5 49.0 1.0
C A:LYS45 4.6 52.9 1.0
CD A:LYS45 4.6 55.4 1.0
CE1 A:HIS47 4.7 62.0 0.5
O A:LYS43 4.8 51.1 1.0
ND1 A:HIS47 4.9 61.9 0.5
CG1 A:ILE44 4.9 53.2 1.0

Chlorine binding site 8 out of 8 in 7oft

Go back to Chlorine Binding Sites List in 7oft
Chlorine binding site 8 out of 8 in the Structure of Sars-Cov-2 Papain-Like Protease Plpro in Complex with P- Hydroxybenzaldehyde


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Structure of Sars-Cov-2 Papain-Like Protease Plpro in Complex with P- Hydroxybenzaldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl409

b:59.5
occ:1.00
 N A:GLY100 3.1 38.5 1.0
O A:HOH560 3.4 48.9 1.0
CA A:GLY100 3.4 44.0 1.0
CB A:GLN97 3.8 39.1 1.0
O A:GLN97 4.1 38.3 1.0
C A:ASN99 4.2 41.4 1.0
C A:GLN97 4.3 34.1 1.0
N A:ASN99 4.3 37.1 1.0
CA A:ASN99 4.5 39.3 1.0
C A:GLY100 4.5 42.2 1.0
CA A:GLN97 4.7 41.3 1.0
CG A:GLN97 4.8 42.4 1.0
N A:VAL98 4.8 36.7 1.0
C A:VAL98 4.8 33.1 1.0
OE1 A:GLN97 5.0 45.9 1.0

Reference:

V.Srinivasan, N.Werner, S.Falke, S.Guenther, P.Reinke, W.Ewert, J.Sprenger, F.Koua, H.Brognaro, N.Ullah, H.Andaleeb, M.Perbandt, B.Alves Franca, M.Schwinzer, M.Wang, J.Lieske, H.Ginn, T.J.Lane, O.Yefanov, L.Gelisio, J.Hakanpaeae, S.Saouane, A.Tolstikova, M.Groessler, H.Fleckenstein, F.Trost, M.Wolf, K.Lorenzen, R.Schubert, H.Han, C.Schmidt, L.Brings, M.Galchenkova, Y.Gevorkov, C.Li, A.Perk, S.Awel, A.Wahab, I.Choudary, D.Turk, W.Hinrichs, H.N.Chapman, A.Meents, C.Betzel. Sars-Cov-2 Papain-Like Protease Plpro in Complex with Inhibitors To Be Published.
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