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Cadmium in PDB 7ok9: Crystal Structure of Penicillin-Binding Protein 1 (PBP1) From Staphylococcus Aureus in Complex with Pentaglycine

Protein crystallography data

The structure of Crystal Structure of Penicillin-Binding Protein 1 (PBP1) From Staphylococcus Aureus in Complex with Pentaglycine, PDB code: 7ok9 was solved by S.Martinez Caballero, J.A.Hermoso, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.32 / 3.36
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 313.993, 198.186, 220.903, 90, 90, 90
R / Rfree (%) 23 / 26.7

Other elements in 7ok9:

The structure of Crystal Structure of Penicillin-Binding Protein 1 (PBP1) From Staphylococcus Aureus in Complex with Pentaglycine also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of Penicillin-Binding Protein 1 (PBP1) From Staphylococcus Aureus in Complex with Pentaglycine (pdb code 7ok9). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 10 binding sites of Cadmium where determined in the Crystal Structure of Penicillin-Binding Protein 1 (PBP1) From Staphylococcus Aureus in Complex with Pentaglycine, PDB code: 7ok9:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 10 in 7ok9

Go back to Cadmium Binding Sites List in 7ok9
Cadmium binding site 1 out of 10 in the Crystal Structure of Penicillin-Binding Protein 1 (PBP1) From Staphylococcus Aureus in Complex with Pentaglycine


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of Penicillin-Binding Protein 1 (PBP1) From Staphylococcus Aureus in Complex with Pentaglycine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd801

b:139.8
occ:1.00
 NE2 A:HIS340 2.4 98.9 1.0
OD2 A:ASP342 2.6 143.9 1.0
CD2 A:HIS340 2.9 95.0 1.0
OD1 A:ASP342 3.1 127.7 1.0
CG A:ASP342 3.2 124.2 1.0
CE1 A:HIS340 3.5 97.1 1.0
CG A:HIS340 4.2 92.4 1.0
ND1 A:HIS340 4.4 100.0 1.0
CB A:ASP342 4.6 116.0 1.0
CG A:ARG347 4.8 124.0 1.0
CD A:ARG347 4.9 123.6 1.0

Cadmium binding site 2 out of 10 in 7ok9

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Cadmium binding site 2 out of 10 in the Crystal Structure of Penicillin-Binding Protein 1 (PBP1) From Staphylococcus Aureus in Complex with Pentaglycine


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of Penicillin-Binding Protein 1 (PBP1) From Staphylococcus Aureus in Complex with Pentaglycine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd801

b:243.9
occ:1.00
 OD2 B:ASP342 2.4 116.6 1.0
NE2 B:HIS340 2.5 108.9 1.0
CD2 B:HIS340 3.3 106.5 1.0
CG B:ASP342 3.4 122.5 1.0
CE1 B:HIS340 3.7 114.6 1.0
NH1 B:ARG347 3.9 151.4 1.0
OD1 B:ASP342 4.0 131.8 1.0
CB B:ASP342 4.5 121.4 1.0
CG B:HIS340 4.6 104.1 1.0
NH2 B:ARG347 4.6 177.8 1.0
CZ B:ARG347 4.7 164.2 1.0
ND1 B:HIS340 4.7 114.5 1.0

Cadmium binding site 3 out of 10 in 7ok9

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Cadmium binding site 3 out of 10 in the Crystal Structure of Penicillin-Binding Protein 1 (PBP1) From Staphylococcus Aureus in Complex with Pentaglycine


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of Penicillin-Binding Protein 1 (PBP1) From Staphylococcus Aureus in Complex with Pentaglycine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd801

b:72.8
occ:1.00
 NE2 C:HIS340 2.5 70.2 1.0
OD2 C:ASP342 2.9 110.4 1.0
OD2 A:ASP383 3.2 175.4 1.0
CD2 C:HIS340 3.5 79.5 1.0
CE1 C:HIS340 3.5 82.2 1.0
CG C:ASP342 3.9 105.6 1.0
CG A:ASP383 4.1 137.9 1.0
NH2 C:ARG347 4.4 61.3 1.0
OD1 C:ASP342 4.5 97.5 1.0
OD1 A:ASP383 4.6 138.7 1.0
ND1 C:HIS340 4.6 87.0 1.0
CG C:HIS340 4.7 83.3 1.0
NH1 C:ARG347 4.7 71.6 1.0
CB A:ALA382 4.9 76.4 1.0
CB C:ASP342 4.9 112.7 1.0

Cadmium binding site 4 out of 10 in 7ok9

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Cadmium binding site 4 out of 10 in the Crystal Structure of Penicillin-Binding Protein 1 (PBP1) From Staphylococcus Aureus in Complex with Pentaglycine


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Crystal Structure of Penicillin-Binding Protein 1 (PBP1) From Staphylococcus Aureus in Complex with Pentaglycine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd801

b:120.0
occ:1.00
 NE2 D:HIS340 2.3 96.7 1.0
OD2 D:ASP342 2.8 91.5 1.0
CD2 D:HIS340 3.1 95.0 1.0
CE1 D:HIS340 3.3 93.2 1.0
NH2 D:ARG347 3.4 99.8 1.0
NH1 D:ARG347 3.8 108.2 1.0
CG D:ASP342 3.8 93.4 1.0
CZ D:ARG347 4.1 108.0 1.0
OD1 D:ASP342 4.2 79.2 1.0
CG D:HIS340 4.3 97.9 1.0
ND1 D:HIS340 4.3 98.9 1.0

Cadmium binding site 5 out of 10 in 7ok9

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Cadmium binding site 5 out of 10 in the Crystal Structure of Penicillin-Binding Protein 1 (PBP1) From Staphylococcus Aureus in Complex with Pentaglycine


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Crystal Structure of Penicillin-Binding Protein 1 (PBP1) From Staphylococcus Aureus in Complex with Pentaglycine within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cd801

b:181.5
occ:1.00
 OD2 E:ASP342 2.2 111.0 1.0
NE2 E:HIS340 2.4 100.4 1.0
NH1 E:ARG347 2.9 154.4 1.0
CD2 E:HIS340 2.9 102.5 1.0
CG E:ASP342 2.9 118.7 1.0
OD1 E:ASP342 3.1 118.7 1.0
CZ E:ARG347 3.4 149.8 1.0
CE1 E:HIS340 3.5 97.4 1.0
NH2 E:ARG347 3.6 156.5 1.0
CG E:HIS340 4.1 102.6 1.0
CB E:ASP342 4.2 124.9 1.0
NE E:ARG347 4.3 133.3 1.0
ND1 E:HIS340 4.3 98.9 1.0
CG E:ARG347 4.8 117.1 1.0
CD E:ARG347 4.9 121.2 1.0

Cadmium binding site 6 out of 10 in 7ok9

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Cadmium binding site 6 out of 10 in the Crystal Structure of Penicillin-Binding Protein 1 (PBP1) From Staphylococcus Aureus in Complex with Pentaglycine


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Crystal Structure of Penicillin-Binding Protein 1 (PBP1) From Staphylococcus Aureus in Complex with Pentaglycine within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cd801

b:184.8
occ:1.00
 OD2 F:ASP342 2.3 145.2 1.0
NE2 F:HIS340 2.4 100.0 1.0
CD2 F:HIS340 3.0 105.5 1.0
CG F:ASP342 3.1 132.7 1.0
OD1 F:ASP342 3.2 131.8 1.0
CE1 F:HIS340 3.4 97.7 1.0
CG F:HIS340 4.1 104.6 1.0
NH1 F:ARG347 4.2 161.6 1.0
ND1 F:HIS340 4.3 102.4 1.0
CB F:ASP342 4.5 131.0 1.0

Cadmium binding site 7 out of 10 in 7ok9

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Cadmium binding site 7 out of 10 in the Crystal Structure of Penicillin-Binding Protein 1 (PBP1) From Staphylococcus Aureus in Complex with Pentaglycine


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Crystal Structure of Penicillin-Binding Protein 1 (PBP1) From Staphylococcus Aureus in Complex with Pentaglycine within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cd801

b:150.2
occ:1.00
 OD2 G:ASP342 2.4 132.8 1.0
OD1 G:ASP342 2.6 148.5 1.0
CG G:ASP342 2.8 132.4 1.0
NE2 G:HIS340 2.8 104.5 1.0
CD2 G:HIS340 3.3 103.3 1.0
NH1 G:ARG347 3.6 117.0 1.0
CE1 G:HIS340 3.9 105.6 1.0
CB G:ASP342 4.3 119.5 1.0
CD G:ARG347 4.5 99.5 1.0
CG G:HIS340 4.5 100.7 1.0
CZ G:ARG347 4.6 109.5 1.0
ND1 G:HIS340 4.8 103.9 1.0
CG G:ARG347 4.9 102.4 1.0

Cadmium binding site 8 out of 10 in 7ok9

Go back to Cadmium Binding Sites List in 7ok9
Cadmium binding site 8 out of 10 in the Crystal Structure of Penicillin-Binding Protein 1 (PBP1) From Staphylococcus Aureus in Complex with Pentaglycine


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Crystal Structure of Penicillin-Binding Protein 1 (PBP1) From Staphylococcus Aureus in Complex with Pentaglycine within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cd801

b:76.0
occ:1.00
 OD2 H:ASP342 2.4 88.7 1.0
NE2 H:HIS340 2.5 89.3 1.0
CD2 H:HIS340 2.9 88.6 1.0
NH1 H:ARG347 3.0 68.8 1.0
OD2 G:ASP383 3.2 131.4 1.0
CG H:ASP342 3.4 86.0 1.0
CE1 H:HIS340 3.7 97.5 1.0
OD1 H:ASP342 3.7 78.4 1.0
CZ H:ARG347 4.0 79.7 1.0
CG G:ASP383 4.1 112.0 1.0
CG H:HIS340 4.2 89.1 1.0
ND1 H:HIS340 4.6 92.5 1.0
NH2 H:ARG347 4.6 82.2 1.0
NE H:ARG347 4.7 86.7 1.0
OD1 G:ASP383 4.8 115.0 1.0
CB H:ASP342 4.8 91.8 1.0
N G:ASP383 4.8 76.5 1.0
N G:ALA382 4.9 59.0 1.0
CB G:ASP383 4.9 100.7 1.0

Cadmium binding site 9 out of 10 in 7ok9

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Cadmium binding site 9 out of 10 in the Crystal Structure of Penicillin-Binding Protein 1 (PBP1) From Staphylococcus Aureus in Complex with Pentaglycine


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Crystal Structure of Penicillin-Binding Protein 1 (PBP1) From Staphylococcus Aureus in Complex with Pentaglycine within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Cd801

b:171.7
occ:1.00
 OD2 I:ASP342 2.2 116.8 1.0
NE2 I:HIS340 2.6 104.8 1.0
CG I:ASP342 3.1 124.7 1.0
CD2 I:HIS340 3.2 100.2 1.0
OD1 I:ASP342 3.6 134.5 1.0
NH2 I:ARG347 3.7 134.3 1.0
CE1 I:HIS340 3.9 105.5 1.0
CB I:ASP342 4.1 124.3 1.0
CG I:HIS340 4.5 100.9 1.0
CZ I:ARG347 4.6 141.8 1.0
NH1 I:ARG347 4.6 149.6 1.0
ND1 I:HIS340 4.8 104.8 1.0

Cadmium binding site 10 out of 10 in 7ok9

Go back to Cadmium Binding Sites List in 7ok9
Cadmium binding site 10 out of 10 in the Crystal Structure of Penicillin-Binding Protein 1 (PBP1) From Staphylococcus Aureus in Complex with Pentaglycine


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Crystal Structure of Penicillin-Binding Protein 1 (PBP1) From Staphylococcus Aureus in Complex with Pentaglycine within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Cd801

b:104.8
occ:1.00
 NE2 J:HIS340 2.4 89.0 1.0
OD2 J:ASP342 2.6 85.2 1.0
CD2 J:HIS340 3.0 90.4 1.0
CG J:ASP342 3.6 86.9 1.0
NH2 J:ARG347 3.7 76.6 1.0
CE1 J:HIS340 3.7 94.9 1.0
OD1 J:ASP342 4.0 82.2 1.0
NH1 J:ARG347 4.2 84.0 1.0
CG J:HIS340 4.3 92.6 1.0
CZ J:ARG347 4.3 81.7 1.0
ND1 J:HIS340 4.6 93.1 1.0
CB J:ASP342 4.7 92.9 1.0

Reference:

S.Martinez-Caballero, K.V.Mahasenan, C.Kim, R.Molina, R.Feltzer, M.Lee, R.Bouley, D.Hesek, J.F.Fisher, I.G.Munoz, M.Chang, S.Mobashery, J.A.Hermoso. Integrative Structural Biology of the Penicillin-Binding Protein-1 From Staphylococcus Aureus , An Essential Component of the Divisome Machinery. Comput Struct Biotechnol J V. 19 5392 2021.
ISSN: ESSN 2001-0370
PubMed: 34667534
DOI: 10.1016/J.CSBJ.2021.09.018
Page generated: Fri Jul 19 20:02:56 2024

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