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Iodine in PDB 7m1y: The Crystal Structure of Papain-Like Protease of Sars Cov-2, C111S Mutant, in Complex with Ebselen

Protein crystallography data

The structure of The Crystal Structure of Papain-Like Protease of Sars Cov-2, C111S Mutant, in Complex with Ebselen, PDB code: 7m1y was solved by J.Osipiuk, C.Tesar, M.Endres, N.Maltseva, A.Joachimiak, Center Forstructural Genomics Of Infectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.80 / 2.02
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 114.887, 114.887, 252.82, 90, 90, 120
R / Rfree (%) 18.4 / 21.3

Other elements in 7m1y:

The structure of The Crystal Structure of Papain-Like Protease of Sars Cov-2, C111S Mutant, in Complex with Ebselen also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Zinc (Zn) 2 atoms
Sodium (Na) 2 atoms

Iodine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Iodine atom in the The Crystal Structure of Papain-Like Protease of Sars Cov-2, C111S Mutant, in Complex with Ebselen (pdb code 7m1y). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 13 binding sites of Iodine where determined in the The Crystal Structure of Papain-Like Protease of Sars Cov-2, C111S Mutant, in Complex with Ebselen, PDB code: 7m1y:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 13 in 7m1y

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Iodine binding site 1 out of 13 in the The Crystal Structure of Papain-Like Protease of Sars Cov-2, C111S Mutant, in Complex with Ebselen


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of The Crystal Structure of Papain-Like Protease of Sars Cov-2, C111S Mutant, in Complex with Ebselen within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I505

b:78.0
occ:0.70
NE2 A:GLN229 3.3 91.6 1.0
N A:PRO223 3.6 85.2 1.0
C A:ILE222 3.6 78.2 1.0
CG A:PRO223 3.9 88.3 1.0
CA A:ILE222 3.9 72.9 1.0
CG A:GLN229 4.0 92.4 1.0
CA A:PRO223 4.0 86.2 1.0
O A:ILE222 4.0 79.8 1.0
CD A:PRO223 4.1 85.0 1.0
CD A:GLN229 4.1 94.6 1.0
N A:ILE222 4.2 68.5 1.0
CB A:PRO223 4.2 88.7 1.0
C A:GLN221 4.4 70.8 1.0
O A:GLN221 4.4 72.1 1.0
CB A:GLN229 4.6 88.3 1.0
CB A:GLN221 4.8 78.2 1.0
CA A:GLN229 4.9 80.7 1.0

Iodine binding site 2 out of 13 in 7m1y

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Iodine binding site 2 out of 13 in the The Crystal Structure of Papain-Like Protease of Sars Cov-2, C111S Mutant, in Complex with Ebselen


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of The Crystal Structure of Papain-Like Protease of Sars Cov-2, C111S Mutant, in Complex with Ebselen within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I506

b:66.2
occ:0.50
N A:LYS306 3.5 51.9 1.0
OG1 A:THR259 3.6 51.1 1.0
CA A:PHE258 3.7 51.4 1.0
C A:PHE258 3.7 49.0 1.0
N A:THR259 3.9 47.5 1.0
N A:PHE258 3.9 53.4 1.0
CA A:TYR305 4.0 48.2 1.0
O A:THR257 4.2 58.5 1.0
O A:PHE258 4.2 52.0 1.0
C A:THR257 4.2 55.5 1.0
C A:TYR305 4.3 47.4 1.0
CB A:TYR305 4.3 47.0 1.0
CB A:LYS306 4.3 62.7 1.0
CA A:LYS306 4.5 56.4 1.0
CD2 A:TYR305 4.5 44.8 1.0
CG A:LYS306 4.6 73.8 1.0
O A:LYS306 4.6 53.1 1.0
CA A:THR259 4.7 47.1 1.0
CB A:THR259 4.7 49.7 1.0
CG A:TYR305 4.9 45.0 1.0

Iodine binding site 3 out of 13 in 7m1y

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Iodine binding site 3 out of 13 in the The Crystal Structure of Papain-Like Protease of Sars Cov-2, C111S Mutant, in Complex with Ebselen


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of The Crystal Structure of Papain-Like Protease of Sars Cov-2, C111S Mutant, in Complex with Ebselen within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I507

b:95.8
occ:0.50
NE2 B:HIS50 3.6 79.8 1.0
N A:LYS45 3.6 68.2 1.0
CA A:ILE44 4.2 69.4 1.0
CB A:LYS45 4.2 71.8 1.0
CE1 B:HIS50 4.2 82.8 1.0
CG A:LYS45 4.3 73.8 1.0
C A:ILE44 4.3 68.2 1.0
CD1 B:ILE44 4.4 82.1 1.0
CB B:HIS47 4.5 82.1 1.0
CD1 A:ILE44 4.5 76.8 1.0
CA A:LYS45 4.5 70.9 1.0
CG2 A:ILE44 4.6 73.3 1.0
CD2 B:HIS50 4.6 82.4 1.0
CG B:HIS47 4.7 83.0 1.0
O A:LYS43 4.8 77.2 1.0
CD A:LYS45 4.9 77.2 1.0
CB A:ILE44 4.9 71.0 1.0
O A:LYS45 4.9 71.9 1.0
OG B:SER49 4.9 79.9 1.0
ND1 B:HIS47 5.0 80.9 1.0

Iodine binding site 4 out of 13 in 7m1y

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Iodine binding site 4 out of 13 in the The Crystal Structure of Papain-Like Protease of Sars Cov-2, C111S Mutant, in Complex with Ebselen


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of The Crystal Structure of Papain-Like Protease of Sars Cov-2, C111S Mutant, in Complex with Ebselen within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I508

b:71.6
occ:0.50
O A:HOH644 3.3 55.0 1.0
N A:VAL159 3.4 53.5 1.0
CB A:THR158 3.9 61.5 1.0
N A:ALA86 3.9 52.5 1.0
CG2 A:VAL159 3.9 52.7 1.0
CA A:ALA86 3.9 53.6 1.0
C A:SER85 3.9 57.8 1.0
CA A:THR158 4.0 55.5 1.0
CB A:VAL159 4.0 52.5 1.0
CB A:SER85 4.0 64.0 1.0
O A:SER85 4.1 62.4 1.0
CD2 A:HIS89 4.2 61.0 1.0
C A:THR158 4.2 55.1 1.0
CA A:VAL159 4.4 52.7 1.0
CB A:ALA86 4.4 52.0 1.0
CG2 A:THR158 4.4 62.6 1.0
NE2 A:HIS89 4.5 61.4 1.0
CA A:SER85 4.7 62.0 1.0
O A:HOH623 5.0 56.8 1.0

Iodine binding site 5 out of 13 in 7m1y

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Iodine binding site 5 out of 13 in the The Crystal Structure of Papain-Like Protease of Sars Cov-2, C111S Mutant, in Complex with Ebselen


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of The Crystal Structure of Papain-Like Protease of Sars Cov-2, C111S Mutant, in Complex with Ebselen within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I509

b:92.2
occ:0.50
CE1 A:HIS47 3.7 71.7 1.0
NH1 B:ARG3 3.8 100.7 1.0
CB B:SER24 4.0 91.5 1.0
CA B:SER24 4.2 92.6 1.0
CB A:SER49 4.2 71.1 1.0
N A:SER49 4.3 69.6 1.0
ND1 A:HIS47 4.3 69.3 1.0
CB A:ASN48 4.3 80.0 1.0
N B:SER24 4.6 92.2 1.0
O B:MET23 4.7 91.6 1.0
CA A:SER49 4.7 69.3 1.0
NE2 A:HIS47 4.7 74.2 1.0
C B:MET23 4.8 89.9 1.0
CZ B:ARG3 4.9 100.2 1.0
OG A:SER49 4.9 72.0 1.0
C A:ASN48 5.0 71.7 1.0

Iodine binding site 6 out of 13 in 7m1y

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Iodine binding site 6 out of 13 in the The Crystal Structure of Papain-Like Protease of Sars Cov-2, C111S Mutant, in Complex with Ebselen


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of The Crystal Structure of Papain-Like Protease of Sars Cov-2, C111S Mutant, in Complex with Ebselen within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I510

b:80.1
occ:0.55
O A:HOH714 3.4 60.5 1.0
CD A:LYS105 3.8 64.0 1.0
CB A:PRO96 3.9 56.0 1.0
CB A:LYS94 4.0 53.4 0.4
CB A:LYS94 4.1 57.1 0.6
CD A:LYS94 4.1 64.7 0.6
CG A:PRO96 4.1 54.5 1.0
CD A:PRO96 4.3 54.4 1.0
CB A:LYS105 4.4 57.2 1.0
CE A:LYS105 4.5 69.8 1.0
CG A:LYS105 4.5 58.9 1.0
CB A:ALA288 4.6 54.6 1.0
CG A:LYS94 4.6 55.1 0.4
CG A:LYS94 4.6 61.1 0.6
N A:PRO96 4.9 54.5 1.0
CA A:PRO96 4.9 55.2 1.0

Iodine binding site 7 out of 13 in 7m1y

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Iodine binding site 7 out of 13 in the The Crystal Structure of Papain-Like Protease of Sars Cov-2, C111S Mutant, in Complex with Ebselen


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of The Crystal Structure of Papain-Like Protease of Sars Cov-2, C111S Mutant, in Complex with Ebselen within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I401

b:101.3
occ:0.50
N B:LYS45 3.6 82.8 1.0
NE2 A:HIS50 3.7 64.3 1.0
CG B:LYS45 4.0 90.8 1.0
CA B:ILE44 4.0 84.9 1.0
CE1 A:HIS50 4.2 65.8 1.0
CB B:LYS45 4.2 88.3 1.0
CB B:ILE44 4.3 83.8 1.0
C B:ILE44 4.4 84.4 1.0
CA B:LYS45 4.5 85.0 1.0
CB A:HIS47 4.5 66.2 1.0
CG A:HIS47 4.6 68.2 1.0
CD2 A:HIS50 4.7 63.6 1.0
O B:LYS45 4.8 81.6 1.0
CE B:LYS45 4.9 94.6 1.0
CD B:LYS45 4.9 94.4 1.0
O B:LYS43 4.9 89.6 1.0
CD2 A:HIS47 5.0 71.0 1.0

Iodine binding site 8 out of 13 in 7m1y

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Iodine binding site 8 out of 13 in the The Crystal Structure of Papain-Like Protease of Sars Cov-2, C111S Mutant, in Complex with Ebselen


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of The Crystal Structure of Papain-Like Protease of Sars Cov-2, C111S Mutant, in Complex with Ebselen within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I402

b:95.3
occ:0.50
CE1 B:HIS47 3.7 84.6 1.0
NH1 A:ARG3 3.7 105.8 1.0
CB B:ASN48 3.9 93.4 1.0
CA A:SER24 4.0 80.5 1.0
CB A:SER24 4.2 79.7 1.0
O A:MET23 4.3 76.0 1.0
ND2 B:ASN48 4.3 100.0 1.0
ND1 B:HIS47 4.4 80.9 1.0
CB B:SER49 4.4 83.7 1.0
N B:SER49 4.5 85.0 1.0
N A:SER24 4.6 76.4 1.0
CG B:ASN48 4.7 96.3 1.0
NE2 B:HIS47 4.7 85.2 1.0
C A:MET23 4.7 78.6 1.0
CA B:SER49 4.8 83.5 1.0
OG B:SER49 4.9 79.9 1.0
O A:HOH701 5.0 62.2 1.0
CZ A:ARG3 5.0 103.1 1.0

Iodine binding site 9 out of 13 in 7m1y

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Iodine binding site 9 out of 13 in the The Crystal Structure of Papain-Like Protease of Sars Cov-2, C111S Mutant, in Complex with Ebselen


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of The Crystal Structure of Papain-Like Protease of Sars Cov-2, C111S Mutant, in Complex with Ebselen within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I407

b:71.3
occ:0.80
NE2 B:GLN229 3.5 67.2 1.0
N B:PRO223 3.8 60.7 1.0
C B:ILE222 3.8 58.2 1.0
CD B:PRO223 3.9 61.8 1.0
CG B:PRO223 3.9 64.3 1.0
CG B:GLN229 4.1 64.8 1.0
CA B:ILE222 4.2 57.5 1.0
O B:ILE222 4.2 57.7 1.0
CD B:GLN229 4.3 66.8 1.0
CB B:GLN229 4.3 64.0 1.0
N B:ILE222 4.4 55.6 1.0
CA B:PRO223 4.4 63.8 1.0
CA B:GLN229 4.5 60.2 1.0
C B:GLN221 4.5 56.5 1.0
O B:GLN221 4.6 54.2 1.0
CB B:PRO223 4.8 63.1 1.0
CB B:GLN221 5.0 63.6 1.0

Iodine binding site 10 out of 13 in 7m1y

Go back to Iodine Binding Sites List in 7m1y
Iodine binding site 10 out of 13 in the The Crystal Structure of Papain-Like Protease of Sars Cov-2, C111S Mutant, in Complex with Ebselen


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of The Crystal Structure of Papain-Like Protease of Sars Cov-2, C111S Mutant, in Complex with Ebselen within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I408

b:74.6
occ:0.45
N B:VAL159 3.4 59.9 1.0
CG2 B:VAL159 3.7 64.5 1.0
CB B:SER85 3.8 62.3 1.0
N B:ALA86 3.8 63.2 1.0
CB B:THR158 3.9 66.7 1.0
CA B:ALA86 3.9 58.1 1.0
CA B:THR158 3.9 63.0 1.0
C B:SER85 3.9 61.9 1.0
CB B:VAL159 4.0 63.6 1.0
O B:SER85 4.1 64.7 1.0
C B:THR158 4.2 63.4 1.0
CD2 B:HIS89 4.2 67.5 1.0
CG2 B:THR158 4.3 65.6 1.0
CA B:VAL159 4.3 59.6 1.0
CB B:ALA86 4.4 58.0 1.0
CA B:SER85 4.5 64.2 1.0
NE2 B:HIS89 4.6 67.2 1.0
O B:VAL159 4.9 64.3 1.0
OG B:SER85 4.9 69.7 1.0

Reference:

J.Osipiuk, C.Tesar, M.Endres, N.Maltseva, A.Joachimiak, Center For Structural Genomics Of Infectious Diseases(Csgid). The Crystal Structure of Papain-Like Protease of Sars Cov-2, C111S Mutant, in Complex with Ebselen To Be Published.
Page generated: Sat Apr 3 16:04:39 2021

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