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Cadmium in PDB 1mwt: Structure of Penicillin G Acyl-Penicillin Binding Protein 2A From Methicillin Resistant Staphylococcus Aureus Strain 27R at 2.45 A Resolution.

Enzymatic activity of Structure of Penicillin G Acyl-Penicillin Binding Protein 2A From Methicillin Resistant Staphylococcus Aureus Strain 27R at 2.45 A Resolution.

All present enzymatic activity of Structure of Penicillin G Acyl-Penicillin Binding Protein 2A From Methicillin Resistant Staphylococcus Aureus Strain 27R at 2.45 A Resolution.:
3.4.16.4;

Protein crystallography data

The structure of Structure of Penicillin G Acyl-Penicillin Binding Protein 2A From Methicillin Resistant Staphylococcus Aureus Strain 27R at 2.45 A Resolution., PDB code: 1mwt was solved by D.C.Lim, N.C.J.Strynadka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.89 / 2.45
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 80.545, 103.272, 186.825, 90.00, 90.00, 90.00
R / Rfree (%) 23.3 / 29.5

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Structure of Penicillin G Acyl-Penicillin Binding Protein 2A From Methicillin Resistant Staphylococcus Aureus Strain 27R at 2.45 A Resolution. (pdb code 1mwt). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 9 binding sites of Cadmium where determined in the Structure of Penicillin G Acyl-Penicillin Binding Protein 2A From Methicillin Resistant Staphylococcus Aureus Strain 27R at 2.45 A Resolution., PDB code: 1mwt:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Cadmium binding site 1 out of 9 in 1mwt

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Cadmium binding site 1 out of 9 in the Structure of Penicillin G Acyl-Penicillin Binding Protein 2A From Methicillin Resistant Staphylococcus Aureus Strain 27R at 2.45 A Resolution.


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Structure of Penicillin G Acyl-Penicillin Binding Protein 2A From Methicillin Resistant Staphylococcus Aureus Strain 27R at 2.45 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1001

b:35.4
occ:1.00
OE1 A:GLU145 2.2 41.5 1.0
O A:HOH1141 2.2 30.4 1.0
ND1 A:HIS143 2.4 41.0 1.0
OE1 B:GLU145 2.4 37.0 1.0
CL A:CL1005 2.5 36.9 1.0
OE2 B:GLU145 2.5 37.2 1.0
CD B:GLU145 2.8 38.0 1.0
CD A:GLU145 3.1 45.3 1.0
CE1 A:HIS143 3.3 41.9 1.0
CG A:HIS143 3.3 40.5 1.0
CG A:GLU145 3.5 39.8 1.0
CB A:HIS143 3.6 36.7 1.0
CD B:CD701 3.7 34.3 1.0
OE2 A:GLU145 4.1 43.9 1.0
CG B:GLU145 4.3 40.2 1.0
ND1 B:HIS143 4.3 37.9 1.0
CG2 A:VAL302 4.4 42.8 1.0
NE2 A:HIS143 4.4 42.3 1.0
CD2 A:HIS143 4.5 40.5 1.0
OD1 A:ASN307 4.6 36.8 1.0
CG B:HIS143 4.8 33.6 1.0
OG1 A:THR300 4.8 45.9 1.0
CE1 B:HIS143 4.9 37.2 1.0
CB A:GLU145 5.0 38.4 1.0
CB B:HIS143 5.0 26.9 1.0

Cadmium binding site 2 out of 9 in 1mwt

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Cadmium binding site 2 out of 9 in the Structure of Penicillin G Acyl-Penicillin Binding Protein 2A From Methicillin Resistant Staphylococcus Aureus Strain 27R at 2.45 A Resolution.


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Structure of Penicillin G Acyl-Penicillin Binding Protein 2A From Methicillin Resistant Staphylococcus Aureus Strain 27R at 2.45 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1002

b:42.6
occ:1.00
O A:GLY135 2.2 38.0 1.0
NE2 A:HIS311 2.3 38.6 1.0
CL A:CL1006 2.5 38.5 1.0
OD1 B:ASP209 2.6 44.6 1.0
OD2 B:ASP209 2.6 41.3 1.0
CG B:ASP209 3.0 41.1 1.0
C A:GLY135 3.2 37.8 1.0
CD2 A:HIS311 3.2 34.3 1.0
CE1 A:HIS311 3.3 34.5 1.0
NE2 A:GLN137 3.5 55.7 1.0
CA A:GLY135 3.5 35.5 1.0
CG A:HIS311 4.4 33.7 1.0
ND1 A:HIS311 4.4 36.4 1.0
N A:MET136 4.4 38.3 1.0
CD A:GLN137 4.4 55.6 1.0
CB B:ASP209 4.5 43.2 1.0
CG A:GLN137 4.5 51.3 1.0
CB B:GLN207 4.9 56.0 1.0
N A:GLY135 4.9 38.2 1.0
CA A:MET136 4.9 38.7 1.0

Cadmium binding site 3 out of 9 in 1mwt

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Cadmium binding site 3 out of 9 in the Structure of Penicillin G Acyl-Penicillin Binding Protein 2A From Methicillin Resistant Staphylococcus Aureus Strain 27R at 2.45 A Resolution.


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Structure of Penicillin G Acyl-Penicillin Binding Protein 2A From Methicillin Resistant Staphylococcus Aureus Strain 27R at 2.45 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1003

b:67.5
occ:0.43
NE2 A:HIS232 2.2 77.2 1.0
CE1 A:HIS232 2.7 75.8 1.0
CD2 A:HIS232 3.5 77.4 1.0
ND1 A:HIS232 3.9 75.5 1.0
CG A:HIS232 4.3 75.5 1.0
O A:LYS229 4.6 71.2 1.0
O A:LYS230 4.9 73.8 1.0

Cadmium binding site 4 out of 9 in 1mwt

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Cadmium binding site 4 out of 9 in the Structure of Penicillin G Acyl-Penicillin Binding Protein 2A From Methicillin Resistant Staphylococcus Aureus Strain 27R at 2.45 A Resolution.


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Structure of Penicillin G Acyl-Penicillin Binding Protein 2A From Methicillin Resistant Staphylococcus Aureus Strain 27R at 2.45 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1004

b:61.3
occ:0.43
OD2 A:ASP320 2.2 41.5 1.0
OE2 B:GLU150 2.7 48.7 1.0
CG A:ASP320 3.3 35.2 1.0
CD B:GLU150 3.5 49.2 1.0
OE1 B:GLU150 3.6 51.6 1.0
CB A:ASP320 3.7 33.7 1.0
NZ A:LYS318 4.1 60.4 1.0
CE A:LYS318 4.3 54.3 1.0
OD1 A:ASP320 4.4 37.5 1.0
CG B:GLU150 4.8 48.5 1.0

Cadmium binding site 5 out of 9 in 1mwt

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Cadmium binding site 5 out of 9 in the Structure of Penicillin G Acyl-Penicillin Binding Protein 2A From Methicillin Resistant Staphylococcus Aureus Strain 27R at 2.45 A Resolution.


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Structure of Penicillin G Acyl-Penicillin Binding Protein 2A From Methicillin Resistant Staphylococcus Aureus Strain 27R at 2.45 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd701

b:34.3
occ:1.00
OE1 B:GLU145 2.1 37.0 1.0
ND1 B:HIS143 2.2 37.9 1.0
O A:HOH1147 2.2 18.5 1.0
OE1 A:GLU145 2.3 41.5 1.0
CL B:CL706 2.4 30.6 1.0
OE2 A:GLU145 2.4 43.9 1.0
CD A:GLU145 2.7 45.3 1.0
CD B:GLU145 3.0 38.0 1.0
CE1 B:HIS143 3.2 37.2 1.0
CG B:HIS143 3.2 33.6 1.0
CB B:HIS143 3.5 26.9 1.0
CG B:GLU145 3.5 40.2 1.0
CD A:CD1001 3.7 35.4 1.0
OE2 B:GLU145 4.0 37.2 1.0
CG A:GLU145 4.2 39.8 1.0
ND1 A:HIS143 4.3 41.0 1.0
NE2 B:HIS143 4.3 37.5 1.0
CD2 B:HIS143 4.3 37.7 1.0
OD1 B:ASN307 4.3 53.6 1.0
CG2 B:VAL302 4.4 42.0 1.0
CE1 A:HIS143 4.8 41.9 1.0
O A:ILE144 4.8 35.6 1.0
OG1 B:THR300 4.9 31.9 1.0
CG A:HIS143 4.9 40.5 1.0
NH2 B:ARG298 4.9 60.5 1.0
CB B:GLU145 5.0 36.8 1.0

Cadmium binding site 6 out of 9 in 1mwt

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Cadmium binding site 6 out of 9 in the Structure of Penicillin G Acyl-Penicillin Binding Protein 2A From Methicillin Resistant Staphylococcus Aureus Strain 27R at 2.45 A Resolution.


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Structure of Penicillin G Acyl-Penicillin Binding Protein 2A From Methicillin Resistant Staphylococcus Aureus Strain 27R at 2.45 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd702

b:35.8
occ:1.00
NE2 B:HIS311 2.2 31.1 1.0
O B:GLY135 2.3 26.1 1.0
OD2 A:ASP209 2.4 37.6 1.0
CL B:CL707 2.5 32.2 1.0
OD1 A:ASP209 2.9 43.8 1.0
CG A:ASP209 3.0 42.5 1.0
CD2 B:HIS311 3.0 30.6 1.0
C B:GLY135 3.3 31.8 1.0
CE1 B:HIS311 3.3 29.0 1.0
CA B:GLY135 3.6 30.0 1.0
CG B:HIS311 4.3 32.1 1.0
ND1 B:HIS311 4.3 34.8 1.0
CG B:GLN137 4.4 43.2 1.0
NE2 B:GLN137 4.4 49.7 1.0
CB A:ASP209 4.5 39.9 1.0
N B:MET136 4.5 31.3 1.0
CD B:GLN137 4.5 47.2 1.0
N B:GLY135 4.9 33.8 1.0
CB A:GLN207 5.0 43.9 1.0

Cadmium binding site 7 out of 9 in 1mwt

Go back to Cadmium Binding Sites List in 1mwt
Cadmium binding site 7 out of 9 in the Structure of Penicillin G Acyl-Penicillin Binding Protein 2A From Methicillin Resistant Staphylococcus Aureus Strain 27R at 2.45 A Resolution.


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Structure of Penicillin G Acyl-Penicillin Binding Protein 2A From Methicillin Resistant Staphylococcus Aureus Strain 27R at 2.45 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd703

b:60.5
occ:0.58
OD2 B:ASP573 2.1 47.6 1.0
OD1 B:ASN569 2.6 66.3 1.0
OD1 B:ASP573 2.7 42.4 1.0
CG B:ASP573 2.8 46.5 1.0
CG B:ASN569 3.3 66.3 1.0
ND2 B:ASN569 3.4 68.2 1.0
CB B:ASP573 4.3 46.7 1.0
O B:ASN569 4.7 56.5 1.0
CB B:ASN569 4.8 61.3 1.0
NZ B:LYS456 4.9 69.0 1.0

Cadmium binding site 8 out of 9 in 1mwt

Go back to Cadmium Binding Sites List in 1mwt
Cadmium binding site 8 out of 9 in the Structure of Penicillin G Acyl-Penicillin Binding Protein 2A From Methicillin Resistant Staphylococcus Aureus Strain 27R at 2.45 A Resolution.


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Structure of Penicillin G Acyl-Penicillin Binding Protein 2A From Methicillin Resistant Staphylococcus Aureus Strain 27R at 2.45 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd704

b:57.4
occ:0.58
OD2 B:ASP586 2.1 61.7 1.0
OG B:SER643 2.6 49.0 1.0
ND1 B:HIS583 2.9 65.9 1.0
CG B:ASP586 3.4 62.8 1.0
CB B:SER643 3.5 47.4 1.0
CG B:HIS583 3.8 62.1 1.0
CA B:HIS583 3.8 57.2 1.0
CE1 B:HIS583 3.9 65.6 1.0
CB B:HIS583 3.9 59.3 1.0
O B:THR582 4.0 53.5 1.0
OD1 B:ASP586 4.0 66.4 1.0
CA B:SER643 4.3 50.0 1.0
CB B:ASP586 4.5 63.7 1.0
C B:HIS583 4.6 58.4 1.0
N B:HIS583 4.8 53.8 1.0
C B:THR582 4.8 52.9 1.0
O B:HIS583 4.9 59.0 1.0
CD2 B:HIS583 5.0 63.0 1.0
NE2 B:HIS583 5.0 63.1 1.0

Cadmium binding site 9 out of 9 in 1mwt

Go back to Cadmium Binding Sites List in 1mwt
Cadmium binding site 9 out of 9 in the Structure of Penicillin G Acyl-Penicillin Binding Protein 2A From Methicillin Resistant Staphylococcus Aureus Strain 27R at 2.45 A Resolution.


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Structure of Penicillin G Acyl-Penicillin Binding Protein 2A From Methicillin Resistant Staphylococcus Aureus Strain 27R at 2.45 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd705

b:60.6
occ:0.42
NE2 B:HIS232 2.4 74.4 1.0
CE1 B:HIS232 2.8 73.0 1.0
CD2 B:HIS232 3.7 71.3 1.0
ND1 B:HIS232 4.1 71.5 1.0
CG B:HIS232 4.5 69.9 1.0

Reference:

D.Lim, N.C.Strynadka. Structural Basis For the Beta Lactam Resistance of PBP2A From Methicillin-Resistant Staphylococcus Aureus. Nat.Struct.Biol. V. 9 870 2002.
ISSN: ISSN 1072-8368
PubMed: 12389036
Page generated: Fri Aug 28 12:14:09 2020
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