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Cadmium in PDB 4dki: Structural Insights Into the Anti- Methicillin-Resistant Staphylococcus Aureus (Mrsa) Activity of Ceftobiprole

Enzymatic activity of Structural Insights Into the Anti- Methicillin-Resistant Staphylococcus Aureus (Mrsa) Activity of Ceftobiprole

All present enzymatic activity of Structural Insights Into the Anti- Methicillin-Resistant Staphylococcus Aureus (Mrsa) Activity of Ceftobiprole:
3.4.16.4;

Protein crystallography data

The structure of Structural Insights Into the Anti- Methicillin-Resistant Staphylococcus Aureus (Mrsa) Activity of Ceftobiprole, PDB code: 4dki was solved by A.L.Lovering, M.C.Gretes, N.C.J.Strynadka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 53.29 / 2.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 80.847, 103.471, 186.500, 90.00, 90.00, 90.00
R / Rfree (%) 17.3 / 23.6

Other elements in 4dki:

The structure of Structural Insights Into the Anti- Methicillin-Resistant Staphylococcus Aureus (Mrsa) Activity of Ceftobiprole also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Structural Insights Into the Anti- Methicillin-Resistant Staphylococcus Aureus (Mrsa) Activity of Ceftobiprole (pdb code 4dki). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 7 binding sites of Cadmium where determined in the Structural Insights Into the Anti- Methicillin-Resistant Staphylococcus Aureus (Mrsa) Activity of Ceftobiprole, PDB code: 4dki:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7;

Cadmium binding site 1 out of 7 in 4dki

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Cadmium binding site 1 out of 7 in the Structural Insights Into the Anti- Methicillin-Resistant Staphylococcus Aureus (Mrsa) Activity of Ceftobiprole


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Structural Insights Into the Anti- Methicillin-Resistant Staphylococcus Aureus (Mrsa) Activity of Ceftobiprole within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd705

b:43.5
occ:1.00
 OE1 A:GLU145 2.2 25.6 1.0
ND1 A:HIS143 2.4 45.4 1.0
OE2 B:GLU145 2.4 41.1 1.0
CL A:CL708 2.5 41.3 1.0
OE1 B:GLU145 2.7 31.6 1.0
CD B:GLU145 2.9 51.5 1.0
CD A:GLU145 3.1 52.5 1.0
CE1 A:HIS143 3.2 44.7 1.0
CG A:HIS143 3.5 43.7 1.0
CG A:GLU145 3.8 42.0 1.0
CB A:HIS143 3.8 40.9 1.0
OE2 A:GLU145 3.8 26.2 1.0
CD B:CD703 3.9 41.0 1.0
OD1 A:ASN307 4.1 55.3 1.0
O B:ILE144 4.3 38.4 1.0
ND1 B:HIS143 4.4 40.6 1.0
CG2 A:VAL302 4.4 42.9 1.0
CG B:GLU145 4.4 43.6 1.0
NE2 A:HIS143 4.4 45.1 1.0
CD2 A:HIS143 4.6 45.1 1.0
CG B:HIS143 4.9 38.6 1.0
CE1 B:HIS143 4.9 40.0 1.0
OG1 A:THR300 5.0 50.4 1.0

Cadmium binding site 2 out of 7 in 4dki

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Cadmium binding site 2 out of 7 in the Structural Insights Into the Anti- Methicillin-Resistant Staphylococcus Aureus (Mrsa) Activity of Ceftobiprole


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Structural Insights Into the Anti- Methicillin-Resistant Staphylococcus Aureus (Mrsa) Activity of Ceftobiprole within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd706

b:0.8
occ:1.00
 NE2 A:HIS232 2.8 0.4 1.0
CD2 A:HIS232 3.6 0.5 1.0
CE1 A:HIS232 3.9 0.5 1.0
NZ A:LYS229 4.4 0.8 1.0
O A:LYS229 4.7 93.2 1.0
CG A:HIS232 4.8 0.9 1.0
ND1 A:HIS232 4.9 0.4 1.0

Cadmium binding site 3 out of 7 in 4dki

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Cadmium binding site 3 out of 7 in the Structural Insights Into the Anti- Methicillin-Resistant Staphylococcus Aureus (Mrsa) Activity of Ceftobiprole


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Structural Insights Into the Anti- Methicillin-Resistant Staphylococcus Aureus (Mrsa) Activity of Ceftobiprole within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd707

b:60.3
occ:1.00
 OD2 B:ASP209 2.2 77.5 1.0
OD1 B:ASP209 2.2 71.7 1.0
O A:GLY135 2.4 49.5 1.0
NE2 A:HIS311 2.4 53.6 1.0
CL A:CL709 2.4 47.6 1.0
CG B:ASP209 2.5 71.1 1.0
CD2 A:HIS311 3.3 52.6 1.0
C A:GLY135 3.4 49.4 1.0
CE1 A:HIS311 3.4 53.8 1.0
CA A:GLY135 3.7 47.1 1.0
CB B:ASP209 4.0 59.8 1.0
NE2 A:GLN137 4.3 52.4 1.0
CG A:HIS311 4.4 50.5 1.0
ND1 A:HIS311 4.5 53.4 1.0
CG A:GLN137 4.6 50.8 1.0
N A:MET136 4.6 44.2 1.0
CD A:GLN137 4.7 64.9 1.0
CA B:ASP209 4.9 58.4 1.0
CB B:GLN207 4.9 66.2 1.0
OG1 B:THR210 4.9 70.2 1.0
C B:ASP209 5.0 60.2 1.0

Cadmium binding site 4 out of 7 in 4dki

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Cadmium binding site 4 out of 7 in the Structural Insights Into the Anti- Methicillin-Resistant Staphylococcus Aureus (Mrsa) Activity of Ceftobiprole


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Structural Insights Into the Anti- Methicillin-Resistant Staphylococcus Aureus (Mrsa) Activity of Ceftobiprole within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd703

b:41.0
occ:1.00
 OE1 B:GLU145 2.2 31.6 1.0
OE2 A:GLU145 2.3 26.2 1.0
ND1 B:HIS143 2.3 40.6 1.0
CL B:CL707 2.4 52.0 1.0
OE1 A:GLU145 2.8 25.6 1.0
CD A:GLU145 2.9 52.5 1.0
CD B:GLU145 3.1 51.5 1.0
CE1 B:HIS143 3.2 40.0 1.0
CG B:HIS143 3.3 38.6 1.0
OD1 B:ASN307 3.4 61.2 1.0
CB B:HIS143 3.6 34.9 1.0
CG B:GLU145 3.8 43.6 1.0
CD A:CD705 3.9 43.5 1.0
OE2 B:GLU145 3.9 41.1 1.0
ND1 A:HIS143 4.1 45.4 1.0
CG A:GLU145 4.4 42.0 1.0
NE2 B:HIS143 4.4 40.3 1.0
CD2 B:HIS143 4.5 40.3 1.0
O A:ILE144 4.5 36.7 1.0
CG B:ASN307 4.6 77.6 1.0
CE1 A:HIS143 4.7 44.7 1.0
CG A:HIS143 4.8 43.7 1.0
CG2 B:VAL302 4.8 35.9 1.0
OG1 B:THR300 4.9 27.0 1.0

Cadmium binding site 5 out of 7 in 4dki

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Cadmium binding site 5 out of 7 in the Structural Insights Into the Anti- Methicillin-Resistant Staphylococcus Aureus (Mrsa) Activity of Ceftobiprole


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Structural Insights Into the Anti- Methicillin-Resistant Staphylococcus Aureus (Mrsa) Activity of Ceftobiprole within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd704

b:46.6
occ:1.00
 OD1 A:ASP209 2.2 66.8 1.0
CL B:CL708 2.3 44.7 1.0
NE2 B:HIS311 2.3 44.0 1.0
O B:GLY135 2.3 35.3 1.0
OD2 A:ASP209 2.4 68.8 1.0
CG A:ASP209 2.6 64.2 1.0
CE1 B:HIS311 3.1 44.4 1.0
C B:GLY135 3.3 37.0 1.0
CD2 B:HIS311 3.5 43.2 1.0
CA B:GLY135 3.6 36.2 1.0
NE2 B:GLN137 3.8 59.5 1.0
CB A:ASP209 4.2 51.3 1.0
ND1 B:HIS311 4.3 44.3 1.0
CG B:HIS311 4.5 41.6 1.0
N B:MET136 4.5 32.3 1.0
CD B:GLN137 4.6 59.5 1.0
CG B:GLN137 4.6 41.2 1.0
CB A:GLN207 4.7 52.7 1.0
NH2 B:ARG110 4.9 82.8 1.0
CG A:GLN207 4.9 62.3 1.0
N B:GLY135 5.0 37.7 1.0

Cadmium binding site 6 out of 7 in 4dki

Go back to Cadmium Binding Sites List in 4dki
Cadmium binding site 6 out of 7 in the Structural Insights Into the Anti- Methicillin-Resistant Staphylococcus Aureus (Mrsa) Activity of Ceftobiprole


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Structural Insights Into the Anti- Methicillin-Resistant Staphylococcus Aureus (Mrsa) Activity of Ceftobiprole within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd705

b:0.3
occ:1.00
 NE2 B:HIS232 2.5 85.3 1.0
CE1 B:HIS232 2.7 84.1 1.0
CD2 B:HIS232 3.8 83.3 1.0
ND1 B:HIS232 4.0 81.6 1.0
CG B:HIS232 4.5 78.9 1.0

Cadmium binding site 7 out of 7 in 4dki

Go back to Cadmium Binding Sites List in 4dki
Cadmium binding site 7 out of 7 in the Structural Insights Into the Anti- Methicillin-Resistant Staphylococcus Aureus (Mrsa) Activity of Ceftobiprole


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Structural Insights Into the Anti- Methicillin-Resistant Staphylococcus Aureus (Mrsa) Activity of Ceftobiprole within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd706

b:0.3
occ:1.00
 OD2 B:ASP573 2.4 90.0 1.0
OD1 B:ASP573 2.5 91.2 1.0
CG B:ASP573 2.8 89.8 1.0
OD1 B:ASN569 3.6 0.6 1.0
CB B:ASP573 4.3 81.7 1.0
CG B:ASN569 4.4 1.0 1.0
CB B:ASN569 4.5 74.0 1.0
NZ B:LYS456 4.7 97.3 1.0
O B:ASN569 4.7 75.6 1.0

Reference:

A.L.Lovering, M.C.Gretes, S.S.Safadi, F.Danel, L.De Castro, M.G.Page, N.C.Strynadka. Structural Insights Into the Anti-Methicillin-Resistant Staphylococcus Aureus (Mrsa) Activity of Ceftobiprole. J.Biol.Chem. V. 287 32096 2012.
ISSN: ISSN 0021-9258
PubMed: 22815485
DOI: 10.1074/JBC.M112.355644
Page generated: Fri Jul 19 17:12:31 2024

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