Atomistry » Cadmium » PDB 3umi-3zi7 » 3zfz
Atomistry »
  Cadmium »
    PDB 3umi-3zi7 »
      3zfz »

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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy