Chlorine in PDB 7thh: Sud-C and UBL2 Domains of Sars Cov-2 NSP3 Protein

Enzymatic activity of Sud-C and UBL2 Domains of Sars Cov-2 NSP3 Protein

All present enzymatic activity of Sud-C and UBL2 Domains of Sars Cov-2 NSP3 Protein:
3.4.19.12;

Protein crystallography data

The structure of Sud-C and UBL2 Domains of Sars Cov-2 NSP3 Protein, PDB code: 7thh was solved by J.Osipiuk, R.Jedrzejczak, M.Endres, P.Wydorski, L.Joachimiak, A.Joachimiak, Center For Structural Genomics Of Infectious Diseases(Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.39 / 1.32
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 30.173, 113.693, 109.688, 90, 93.02, 90
R / Rfree (%) 14.5 / 19.1

Other elements in 7thh:

The structure of Sud-C and UBL2 Domains of Sars Cov-2 NSP3 Protein also contains other interesting chemical elements:

Iodine (I) 3 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Sud-C and UBL2 Domains of Sars Cov-2 NSP3 Protein (pdb code 7thh). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Sud-C and UBL2 Domains of Sars Cov-2 NSP3 Protein, PDB code: 7thh:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 7thh

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Chlorine binding site 1 out of 6 in the Sud-C and UBL2 Domains of Sars Cov-2 NSP3 Protein


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Sud-C and UBL2 Domains of Sars Cov-2 NSP3 Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl901

b:31.2
occ:1.00
 N A:GLY730 3.3 27.5 1.0
O A:HOH1048 3.4 25.0 1.0
CA A:GLY730 3.7 28.9 1.0
CD1 A:TYR718 3.9 20.1 1.0
CB A:HIS727 4.0 20.6 1.0
N A:ASP729 4.1 24.7 1.0
O A:HOH1013 4.1 38.5 1.0
CE1 A:TYR718 4.2 20.6 1.0
CD1 A:LEU705 4.3 35.5 1.0
CD2 A:LEU705 4.4 32.6 1.0
C A:ASP729 4.4 28.5 1.0
C A:LEU728 4.4 20.9 1.0
C A:HIS727 4.4 19.1 1.0
N A:LEU728 4.5 19.1 1.0
CA A:LEU728 4.6 19.4 1.0
CA A:ASP729 4.6 28.8 1.0
O A:HIS727 4.7 18.6 1.0
O A:HOH1023 4.7 34.8 1.0
C A:GLY730 4.7 25.8 1.0
CG A:LEU705 4.8 30.4 1.0
CB A:LEU705 4.8 25.1 1.0
CG A:TYR718 4.8 17.2 1.0
CA A:HIS727 4.8 19.2 1.0
N A:GLU731 4.9 24.4 1.0

Chlorine binding site 2 out of 6 in 7thh

Go back to Chlorine Binding Sites List in 7thh
Chlorine binding site 2 out of 6 in the Sud-C and UBL2 Domains of Sars Cov-2 NSP3 Protein


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Sud-C and UBL2 Domains of Sars Cov-2 NSP3 Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl904

b:44.0
occ:1.00
 O A:HOH1154 2.6 39.5 1.0
N A:LYS790 3.1 21.6 1.0
CB A:LYS790 3.8 27.9 1.0
CA A:ILE789 3.9 18.5 1.0
CE1 A:HIS792 3.9 29.1 1.0
CA A:LYS790 4.0 22.4 1.0
C A:ILE789 4.0 18.6 1.0
CG A:LYS790 4.0 31.9 1.0
CG2 A:ILE789 4.2 26.2 1.0
O A:LYS790 4.2 21.4 1.0
CD1 A:ILE789 4.3 30.0 1.0
CB A:ILE789 4.5 20.5 1.0
C A:LYS790 4.6 20.7 1.0
ND1 A:HIS792 4.8 25.9 1.0
O A:LYS788 4.8 24.2 1.0
NE2 A:HIS792 4.9 28.2 1.0

Chlorine binding site 3 out of 6 in 7thh

Go back to Chlorine Binding Sites List in 7thh
Chlorine binding site 3 out of 6 in the Sud-C and UBL2 Domains of Sars Cov-2 NSP3 Protein


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Sud-C and UBL2 Domains of Sars Cov-2 NSP3 Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl901

b:45.6
occ:1.00
 O E:HOH1091 3.2 39.6 1.0
CB E:ARG748 4.0 42.3 1.0
CB E:MET768 4.2 36.0 1.0
CD E:ARG748 4.3 51.7 1.0
C E:MET768 4.4 31.0 1.0
CG E:ARG748 4.4 48.5 1.0
NH1 E:ARG745 4.5 36.1 1.0
N E:SER769 4.5 31.8 1.0
CD E:ARG745 4.5 46.4 1.0
CB E:SER769 4.6 37.5 1.0
O E:MET768 4.6 34.9 1.0
CA E:SER769 4.7 33.8 1.0
N E:ARG748 4.7 35.0 1.0
CA E:MET768 4.9 32.5 1.0
CA E:ARG748 5.0 36.6 1.0

Chlorine binding site 4 out of 6 in 7thh

Go back to Chlorine Binding Sites List in 7thh
Chlorine binding site 4 out of 6 in the Sud-C and UBL2 Domains of Sars Cov-2 NSP3 Protein


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Sud-C and UBL2 Domains of Sars Cov-2 NSP3 Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl902

b:35.7
occ:1.00
 O E:HOH1061 3.1 48.2 1.0
O E:HOH1103 3.1 52.9 1.0
O E:HOH1107 3.2 42.0 1.0
O E:HOH1091 3.7 39.6 1.0
CB E:SER769 4.0 37.5 1.0
OG E:SER769 4.0 41.7 1.0
CG2 E:VAL747 4.6 49.0 1.0
CA E:VAL747 4.9 33.8 1.0
CD E:ARG745 5.0 46.4 1.0
CB E:VAL747 5.0 40.6 1.0

Chlorine binding site 5 out of 6 in 7thh

Go back to Chlorine Binding Sites List in 7thh
Chlorine binding site 5 out of 6 in the Sud-C and UBL2 Domains of Sars Cov-2 NSP3 Protein


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Sud-C and UBL2 Domains of Sars Cov-2 NSP3 Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl901

b:42.8
occ:1.00
 N F:GLY730 3.3 39.3 1.0
O F:HOH1034 3.4 27.9 1.0
CA F:GLY730 3.9 41.6 1.0
N F:ASP729 3.9 36.4 1.0
CB F:HIS727 4.0 33.6 1.0
CD1 F:TYR718 4.0 28.4 1.0
C F:ASP729 4.3 36.7 1.0
CE1 F:TYR718 4.4 29.1 1.0
CA F:ASP729 4.4 35.5 1.0
C F:LEU728 4.5 38.6 1.0
C F:HIS727 4.5 28.6 1.0
N F:LEU728 4.5 30.6 1.0
CD1 F:LEU705 4.6 39.8 1.0
CA F:LEU728 4.7 32.1 1.0
O F:HIS727 4.7 31.4 1.0
CD2 F:LEU705 4.8 42.9 1.0
CA F:HIS727 4.9 30.2 1.0
C F:GLY730 4.9 49.8 1.0
CG F:HIS727 5.0 36.9 1.0
CG F:TYR718 5.0 27.9 1.0

Chlorine binding site 6 out of 6 in 7thh

Go back to Chlorine Binding Sites List in 7thh
Chlorine binding site 6 out of 6 in the Sud-C and UBL2 Domains of Sars Cov-2 NSP3 Protein


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Sud-C and UBL2 Domains of Sars Cov-2 NSP3 Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl902

b:59.5
occ:1.00
 N F:SER721 3.3 31.2 1.0
CA F:THR720 3.5 30.0 1.0
CB F:THR720 3.6 31.2 1.0
C F:THR720 3.9 33.4 1.0
CG2 F:THR720 3.9 33.6 1.0
CB F:SER721 4.3 36.7 1.0
CA F:SER721 4.4 31.7 1.0
OG F:SER721 4.6 41.0 1.0
O F:SER721 4.6 38.1 1.0
O F:TYR719 4.8 26.8 1.0
N F:THR720 4.8 27.9 1.0
CA F:GLY706 4.9 29.1 1.0
OG1 F:THR720 4.9 31.5 1.0
C F:SER721 5.0 33.8 1.0

Reference:

J.Osipiuk, R.Jedrzejczak, M.Endres, P.Wydorski, L.Joachimiak, A.Joachimiak, Center For Structural Genomics Of Infectious Diseases(Csgid). Sud-C and UBL2 Domains of Sars Cov-2 NSP3 Protein To Be Published.
Page generated: Tue Jul 30 04:35:39 2024

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