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Cadmium in PDB 3zg5: Crystal Structure of PBP2A From Mrsa in Complex with Peptidoglycan Analogue at Allosteric

Enzymatic activity of Crystal Structure of PBP2A From Mrsa in Complex with Peptidoglycan Analogue at Allosteric

All present enzymatic activity of Crystal Structure of PBP2A From Mrsa in Complex with Peptidoglycan Analogue at Allosteric:
3.4.16.4;

Protein crystallography data

The structure of Crystal Structure of PBP2A From Mrsa in Complex with Peptidoglycan Analogue at Allosteric, PDB code: 3zg5 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) 49.126 / 2.55
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 80.540, 102.020, 185.980, 90.00, 90.00, 90.00
R / Rfree (%) 21.37 / 29.04

Other elements in 3zg5:

The structure of Crystal Structure of PBP2A From Mrsa in Complex with Peptidoglycan Analogue at Allosteric also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of PBP2A From Mrsa in Complex with Peptidoglycan Analogue at Allosteric (pdb code 3zg5). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 4 binding sites of Cadmium where determined in the Crystal Structure of PBP2A From Mrsa in Complex with Peptidoglycan Analogue at Allosteric, PDB code: 3zg5:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in 3zg5

Go back to Cadmium Binding Sites List in 3zg5
Cadmium binding site 1 out of 4 in the Crystal Structure of PBP2A From Mrsa in Complex with Peptidoglycan Analogue at Allosteric


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 PBP2A From Mrsa in Complex with Peptidoglycan Analogue at Allosteric within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1669

b:37.9
occ:1.00
CL A:CL1672 2.4 34.0 1.0
O A:GLY135 2.4 32.3 1.0
OD2 B:ASP209 2.4 38.5 1.0
NE2 A:HIS311 2.5 42.5 1.0
OD1 B:ASP209 2.5 33.7 1.0
CG B:ASP209 2.8 39.7 1.0
CD2 A:HIS311 3.2 37.6 1.0
C A:GLY135 3.3 26.2 1.0
CA A:GLY135 3.6 17.2 1.0
CE1 A:HIS311 3.6 40.4 1.0
CB B:ASP209 4.3 32.9 1.0
CG A:GLN137 4.4 34.1 1.0
CG A:HIS311 4.4 41.1 1.0
N A:MET136 4.5 25.5 1.0
NH2 A:ARG110 4.5 54.2 1.0
NE2 A:GLN137 4.6 38.3 1.0
ND1 A:HIS311 4.6 43.5 1.0
CD A:GLN137 4.9 37.3 1.0
CB B:GLN207 4.9 37.1 1.0
N A:GLY135 5.0 23.1 1.0

Cadmium binding site 2 out of 4 in 3zg5

Go back to Cadmium Binding Sites List in 3zg5
Cadmium binding site 2 out of 4 in the Crystal Structure of PBP2A From Mrsa in Complex with Peptidoglycan Analogue at Allosteric


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 PBP2A From Mrsa in Complex with Peptidoglycan Analogue at Allosteric within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1671

b:31.0
occ:1.00
OE2 A:GLU145 2.3 43.8 1.0
OE2 B:GLU145 2.3 29.2 1.0
CL A:CL1670 2.5 32.0 1.0
ND1 A:HIS143 2.6 39.5 1.0
OE1 B:GLU145 2.7 50.7 1.0
CD B:GLU145 2.9 40.9 1.0
CD A:GLU145 3.3 49.1 1.0
CG A:HIS143 3.5 38.1 1.0
CE1 A:HIS143 3.5 41.9 1.0
CB A:HIS143 3.7 31.9 1.0
CD B:CD1669 4.0 30.3 1.0
CG A:GLU145 4.0 46.2 1.0
CG2 A:VAL302 4.0 24.7 1.0
OE1 A:GLU145 4.2 51.2 1.0
OD1 A:ASN307 4.3 41.3 1.0
ND1 B:HIS143 4.4 26.1 1.0
CG B:GLU145 4.4 41.4 1.0
CD2 A:HIS143 4.6 45.6 1.0
NE2 A:HIS143 4.6 45.5 1.0
OG1 A:THR300 4.7 49.9 1.0
CG1 A:VAL302 4.8 20.4 1.0
CB A:VAL302 4.9 25.7 1.0
CG B:HIS143 5.0 25.5 1.0
O B:ILE144 5.0 22.8 1.0
CB B:HIS143 5.0 15.9 1.0

Cadmium binding site 3 out of 4 in 3zg5

Go back to Cadmium Binding Sites List in 3zg5
Cadmium binding site 3 out of 4 in the Crystal Structure of PBP2A From Mrsa in Complex with Peptidoglycan Analogue at Allosteric


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 PBP2A From Mrsa in Complex with Peptidoglycan Analogue at Allosteric within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1669

b:30.3
occ:1.00
OE2 B:GLU145 2.2 29.2 1.0
OE2 A:GLU145 2.3 43.8 1.0
ND1 B:HIS143 2.5 26.1 1.0
OE1 A:GLU145 2.5 51.2 1.0
CL B:CL1671 2.6 21.7 1.0
CD A:GLU145 2.6 49.1 1.0
CD B:GLU145 3.2 40.9 1.0
CG B:HIS143 3.4 25.5 1.0
CE1 B:HIS143 3.5 25.4 1.0
CB B:HIS143 3.5 15.9 1.0
CG B:GLU145 3.6 41.4 1.0
CD A:CD1671 4.0 31.0 1.0
CG2 B:VAL302 4.0 16.9 1.0
ND2 B:ASN307 4.0 52.4 1.0
CG A:GLU145 4.0 46.2 1.0
OE1 B:GLU145 4.3 50.7 1.0
CD2 B:HIS143 4.6 28.8 1.0
NE2 B:HIS143 4.6 31.2 1.0
OG1 B:THR300 4.6 28.7 1.0
ND1 A:HIS143 4.7 39.5 1.0
O A:ILE144 4.9 32.8 1.0
CB B:GLU145 4.9 34.4 1.0
CB A:GLU145 5.0 35.5 1.0

Cadmium binding site 4 out of 4 in 3zg5

Go back to Cadmium Binding Sites List in 3zg5
Cadmium binding site 4 out of 4 in the Crystal Structure of PBP2A From Mrsa in Complex with Peptidoglycan Analogue at Allosteric


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 PBP2A From Mrsa in Complex with Peptidoglycan Analogue at Allosteric within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1670

b:30.5
occ:1.00
NE2 B:HIS311 2.4 52.2 1.0
CL B:CL1672 2.4 23.4 1.0
OD2 A:ASP209 2.5 38.9 1.0
O B:GLY135 2.5 24.4 1.0
OD1 A:ASP209 2.5 33.5 1.0
CG A:ASP209 2.8 34.6 1.0
CE1 B:HIS311 2.9 51.4 1.0
C B:GLY135 3.5 28.4 1.0
CD2 B:HIS311 3.6 49.5 1.0
NE2 B:GLN137 3.7 37.0 1.0
CA B:GLY135 3.8 17.0 1.0
CG B:GLN137 3.9 36.6 1.0
CD B:GLN137 4.0 37.0 1.0
ND1 B:HIS311 4.1 48.7 1.0
CB A:ASP209 4.3 30.6 1.0
CG B:HIS311 4.5 44.0 1.0
NH2 B:ARG110 4.6 50.5 1.0
N B:MET136 4.7 26.5 1.0
CB A:GLN207 4.8 27.0 1.0
OG1 A:THR210 4.8 40.9 1.0
O A:HOH2039 4.9 28.9 1.0
OE1 B:GLN137 4.9 33.7 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: Sat Dec 12 08:23:50 2020

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