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Cadmium in PDB 3zfz: Crystal Structure of Ceftaroline Acyl-PBP2A From Mrsa with Non-Covalently Bound Ceftaroline and Muramic Acid at Allosteric Site Obtained By Soaking

Enzymatic activity of Crystal Structure of Ceftaroline Acyl-PBP2A From Mrsa with Non-Covalently Bound Ceftaroline and Muramic Acid at Allosteric Site Obtained By Soaking

All present enzymatic activity of Crystal Structure of Ceftaroline Acyl-PBP2A From Mrsa with Non-Covalently Bound Ceftaroline and Muramic Acid at Allosteric Site Obtained By Soaking:
3.4.16.4;

Protein crystallography data

The structure of Crystal Structure of Ceftaroline Acyl-PBP2A From Mrsa with Non-Covalently Bound Ceftaroline and Muramic Acid at Allosteric Site Obtained By Soaking, PDB code: 3zfz was solved by L.H.Otero, A.Rojas-Altuve, J.A.Hermoso, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 68.76 / 2.25
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 80.520, 101.480, 187.010, 90.00, 90.00, 90.00
R / Rfree (%) 19.37 / 24.9

Other elements in 3zfz:

The structure of Crystal Structure of Ceftaroline Acyl-PBP2A From Mrsa with Non-Covalently Bound Ceftaroline and Muramic Acid at Allosteric Site Obtained By Soaking also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of Ceftaroline Acyl-PBP2A From Mrsa with Non-Covalently Bound Ceftaroline and Muramic Acid at Allosteric Site Obtained By Soaking (pdb code 3zfz). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 8 binding sites of Cadmium where determined in the Crystal Structure of Ceftaroline Acyl-PBP2A From Mrsa with Non-Covalently Bound Ceftaroline and Muramic Acid at Allosteric Site Obtained By Soaking, PDB code: 3zfz:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Cadmium binding site 1 out of 8 in 3zfz

Go back to Cadmium Binding Sites List in 3zfz
Cadmium binding site 1 out of 8 in the Crystal Structure of Ceftaroline Acyl-PBP2A From Mrsa with Non-Covalently Bound Ceftaroline and Muramic Acid at Allosteric Site Obtained By Soaking


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 Ceftaroline Acyl-PBP2A From Mrsa with Non-Covalently Bound Ceftaroline and Muramic Acid at Allosteric Site Obtained By Soaking within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1001

b:52.4
occ:1.00
 OE2 A:GLU145 2.2 55.1 1.0
OE1 B:GLU145 2.3 79.2 1.0
ND1 A:HIS143 2.4 52.9 1.0
OE2 B:GLU145 2.5 56.1 1.0
CL A:CL1010 2.5 48.5 1.0
CD B:GLU145 2.8 73.9 1.0
CD A:GLU145 3.1 68.8 1.0
CG A:HIS143 3.4 51.4 1.0
CE1 A:HIS143 3.4 52.5 1.0
CB A:HIS143 3.5 48.0 1.0
CG A:GLU145 3.8 62.2 1.0
CD B:CD1002 3.9 52.4 1.0
OE1 A:GLU145 4.0 52.7 1.0
CG2 A:VAL302 4.2 56.1 1.0
ND1 B:HIS143 4.3 51.3 1.0
CG B:GLU145 4.3 57.4 1.0
O B:HOH2068 4.3 55.6 1.0
OD1 A:ASN307 4.4 50.3 1.0
CD2 A:HIS143 4.5 53.3 1.0
NE2 A:HIS143 4.6 53.1 1.0
O B:ILE144 4.6 48.4 1.0
CE1 B:HIS143 4.7 51.4 1.0
OG1 A:THR300 4.8 51.1 1.0
CG B:HIS143 4.9 49.5 1.0
CG1 A:VAL302 5.0 57.3 1.0

Cadmium binding site 2 out of 8 in 3zfz

Go back to Cadmium Binding Sites List in 3zfz
Cadmium binding site 2 out of 8 in the Crystal Structure of Ceftaroline Acyl-PBP2A From Mrsa with Non-Covalently Bound Ceftaroline and Muramic Acid at Allosteric Site Obtained By Soaking


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 Ceftaroline Acyl-PBP2A From Mrsa with Non-Covalently Bound Ceftaroline and Muramic Acid at Allosteric Site Obtained By Soaking within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1003

b:62.9
occ:1.00
 OD2 A:ASP209 2.2 65.7 1.0
O B:GLY135 2.3 52.7 1.0
OD1 A:ASP209 2.4 67.6 1.0
NE2 B:HIS311 2.4 56.2 1.0
CL B:CL1012 2.4 57.0 1.0
CG A:ASP209 2.6 66.1 1.0
CD2 B:HIS311 3.2 55.7 1.0
C B:GLY135 3.3 54.2 1.0
CE1 B:HIS311 3.5 56.2 1.0
CA B:GLY135 3.6 54.0 1.0
O A:HOH2110 3.7 55.6 1.0
CB A:ASP209 4.1 60.3 1.0
CG B:GLN137 4.3 53.7 1.0
NE2 B:GLN137 4.4 64.8 1.0
CG B:HIS311 4.4 54.8 1.0
N B:MET136 4.5 50.2 1.0
ND1 B:HIS311 4.6 57.0 1.0
CD B:GLN137 4.6 77.9 1.0
CB A:GLN207 4.8 60.5 1.0
NH2 B:ARG110 4.9 89.4 1.0

Cadmium binding site 3 out of 8 in 3zfz

Go back to Cadmium Binding Sites List in 3zfz
Cadmium binding site 3 out of 8 in the Crystal Structure of Ceftaroline Acyl-PBP2A From Mrsa with Non-Covalently Bound Ceftaroline and Muramic Acid at Allosteric Site Obtained By Soaking


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 Ceftaroline Acyl-PBP2A From Mrsa with Non-Covalently Bound Ceftaroline and Muramic Acid at Allosteric Site Obtained By Soaking within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1004

b:0.5
occ:1.00
 NE2 A:HIS232 3.1 93.0 1.0
O A:HOH2120 3.4 55.6 1.0
CD2 A:HIS232 3.6 91.0 1.0
O A:LYS229 4.1 99.9 1.0
CE1 A:HIS232 4.2 92.8 1.0
O A:LYS230 4.8 95.2 1.0
CG A:HIS232 4.9 87.5 1.0

Cadmium binding site 4 out of 8 in 3zfz

Go back to Cadmium Binding Sites List in 3zfz
Cadmium binding site 4 out of 8 in the Crystal Structure of Ceftaroline Acyl-PBP2A From Mrsa with Non-Covalently Bound Ceftaroline and Muramic Acid at Allosteric Site Obtained By Soaking


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 Ceftaroline Acyl-PBP2A From Mrsa with Non-Covalently Bound Ceftaroline and Muramic Acid at Allosteric Site Obtained By Soaking within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1005

b:57.5
occ:1.00
 NE2 A:HIS311 2.3 54.3 1.0
OD1 B:ASP209 2.3 57.0 1.0
OD2 B:ASP209 2.4 61.9 1.0
CL A:CL1011 2.4 50.4 1.0
O A:GLY135 2.4 53.7 1.0
CG B:ASP209 2.7 59.0 1.0
O A:HOH2051 2.8 55.6 1.0
CD2 A:HIS311 3.2 54.2 1.0
CE1 A:HIS311 3.3 54.2 1.0
C A:GLY135 3.4 54.0 1.0
CA A:GLY135 3.7 52.5 1.0
NE2 A:GLN137 4.0 57.9 1.0
CB B:ASP209 4.2 59.2 1.0
CG A:HIS311 4.4 52.8 1.0
ND1 A:HIS311 4.4 54.9 1.0
CG A:GLN137 4.6 52.0 1.0
CD A:GLN137 4.6 63.9 1.0
O B:HOH2110 4.6 55.6 1.0
N A:MET136 4.6 49.5 1.0
CB B:GLN207 4.8 68.6 1.0
CG B:GLN207 4.9 72.4 1.0
NH2 A:ARG110 5.0 74.3 1.0

Cadmium binding site 5 out of 8 in 3zfz

Go back to Cadmium Binding Sites List in 3zfz
Cadmium binding site 5 out of 8 in the Crystal Structure of Ceftaroline Acyl-PBP2A From Mrsa with Non-Covalently Bound Ceftaroline and Muramic Acid at Allosteric Site Obtained By Soaking


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 Ceftaroline Acyl-PBP2A From Mrsa with Non-Covalently Bound Ceftaroline and Muramic Acid at Allosteric Site Obtained By Soaking within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1008

b:0.5
occ:1.00
 OE1 B:GLU150 3.0 0.1 1.0
O A:HOH2171 3.2 55.6 1.0
OD2 A:ASP320 3.5 73.3 1.0
CD B:GLU150 3.9 0.5 1.0
O B:HOH2080 4.0 55.6 1.0
CG A:ASP320 4.3 66.5 1.0
CG B:GLU150 4.4 72.8 1.0
CE A:LYS318 4.5 0.5 1.0
CB A:ASP320 4.5 57.1 1.0
OE2 B:GLU150 4.7 0.9 1.0
NZ A:LYS318 4.8 0.7 1.0

Cadmium binding site 6 out of 8 in 3zfz

Go back to Cadmium Binding Sites List in 3zfz
Cadmium binding site 6 out of 8 in the Crystal Structure of Ceftaroline Acyl-PBP2A From Mrsa with Non-Covalently Bound Ceftaroline and Muramic Acid at Allosteric Site Obtained By Soaking


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 Ceftaroline Acyl-PBP2A From Mrsa with Non-Covalently Bound Ceftaroline and Muramic Acid at Allosteric Site Obtained By Soaking within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1002

b:52.4
occ:1.00
 ND1 B:HIS143 2.2 51.3 1.0
OE2 B:GLU145 2.3 56.1 1.0
O A:HOH2057 2.3 55.6 1.0
CL B:CL1009 2.4 50.2 1.0
OE1 A:GLU145 2.5 52.7 1.0
OE2 A:GLU145 2.8 55.1 1.0
CD A:GLU145 3.0 68.8 1.0
CE1 B:HIS143 3.1 51.4 1.0
CD B:GLU145 3.1 73.9 1.0
CG B:HIS143 3.2 49.5 1.0
CB B:HIS143 3.5 45.8 1.0
CG B:GLU145 3.6 57.4 1.0
CD A:CD1001 3.9 52.4 1.0
C19 A:1W81669 4.0 0.3 1.0
OE1 B:GLU145 4.1 79.2 1.0
NE2 B:HIS143 4.3 52.6 1.0
CG2 B:VAL302 4.3 51.0 1.0
C18 A:1W81669 4.3 0.7 1.0
ND1 A:HIS143 4.3 52.9 1.0
CD2 B:HIS143 4.4 52.7 1.0
OD1 B:ASN307 4.4 46.0 1.0
CG A:GLU145 4.5 62.2 1.0
O A:ILE144 4.7 59.2 1.0
OG1 B:THR300 4.7 57.1 1.0
CG A:HIS143 4.8 51.4 1.0
CE1 A:HIS143 4.9 52.5 1.0
CA B:HIS143 5.0 45.0 1.0
CG1 B:VAL302 5.0 52.2 1.0
N6 A:1W81669 5.0 0.2 1.0

Cadmium binding site 7 out of 8 in 3zfz

Go back to Cadmium Binding Sites List in 3zfz
Cadmium binding site 7 out of 8 in the Crystal Structure of Ceftaroline Acyl-PBP2A From Mrsa with Non-Covalently Bound Ceftaroline and Muramic Acid at Allosteric Site Obtained By Soaking


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 Ceftaroline Acyl-PBP2A From Mrsa with Non-Covalently Bound Ceftaroline and Muramic Acid at Allosteric Site Obtained By Soaking within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1006

b:0.0
occ:1.00
 NE2 B:HIS232 3.0 90.2 1.0
CE1 B:HIS232 3.1 89.3 1.0
CD2 B:HIS232 4.2 88.4 1.0
ND1 B:HIS232 4.2 87.3 1.0
O B:HOH2122 4.5 55.6 1.0
CG B:HIS232 4.8 84.2 1.0

Cadmium binding site 8 out of 8 in 3zfz

Go back to Cadmium Binding Sites List in 3zfz
Cadmium binding site 8 out of 8 in the Crystal Structure of Ceftaroline Acyl-PBP2A From Mrsa with Non-Covalently Bound Ceftaroline and Muramic Acid at Allosteric Site Obtained By Soaking


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 Ceftaroline Acyl-PBP2A From Mrsa with Non-Covalently Bound Ceftaroline and Muramic Acid at Allosteric Site Obtained By Soaking within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1007

b:93.8
occ:1.00
 OD2 B:ASP573 2.2 80.6 1.0
OD1 B:ASP573 2.5 76.3 1.0
OD1 B:ASN569 2.5 57.4 1.0
CG B:ASP573 2.7 74.7 1.0
O B:HOH2257 3.1 55.6 1.0
CG B:ASN569 3.4 76.9 1.0
ND2 B:ASN569 3.5 75.2 1.0
CB B:ASP573 4.2 63.5 1.0
NZ B:LYS456 4.4 80.2 1.0
O B:HOH2295 4.5 55.6 1.0
O B:ASN569 4.6 63.0 1.0
CB B:ASN569 4.8 59.4 1.0

Reference:

L.H.Otero, A.Rojas-Altuve, L.I.Llarrull, C.Carrasco-Lopez, M.Kumarasiri, E.Lastochkin, J.Fishovitz, M.Dawley, D.Hesek, M.Lee, J.W.Johnson, J.F.Fisher, M.Chang, S.Mobashery, J.A.Hermoso. How Allosteric Control of Staphylococcus Aureus Penicillin Binding Protein 2A Enables Methicillin Resistance and Physiological Function Proc.Natl.Acad.Sci.Usa V. 110 16808 2013.
ISSN: ISSN 0027-8424
PubMed: 24085846
DOI: 10.1073/PNAS.1300118110
Page generated: Fri Jul 19 16:47:49 2024

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