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Cadmium in PDB 1vqq: Structure of Penicillin Binding Protein 2A From Methicillin Resistant Staphylococcus Aureus Strain 27R at 1.80 A Resolution.

Protein crystallography data

The structure of Structure of Penicillin Binding Protein 2A From Methicillin Resistant Staphylococcus Aureus Strain 27R at 1.80 A Resolution., PDB code: 1vqq was solved by D.Lim, N.C.J.Strynadka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.92 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 80.869, 100.608, 186.235, 90.00, 90.00, 90.00
R / Rfree (%) 23.7 / 27.4

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Structure of Penicillin Binding Protein 2A From Methicillin Resistant Staphylococcus Aureus Strain 27R at 1.80 A Resolution. (pdb code 1vqq). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 7 binding sites of Cadmium where determined in the Structure of Penicillin Binding Protein 2A From Methicillin Resistant Staphylococcus Aureus Strain 27R at 1.80 A Resolution., PDB code: 1vqq:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7;

Cadmium binding site 1 out of 7 in 1vqq

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Cadmium binding site 1 out of 7 in the Structure of Penicillin Binding Protein 2A From Methicillin Resistant Staphylococcus Aureus Strain 27R at 1.80 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 Binding Protein 2A From Methicillin Resistant Staphylococcus Aureus Strain 27R at 1.80 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1004

b:50.0
occ:1.00
NE2 A:HIS232 2.5 40.0 1.0
CD2 A:HIS232 3.2 39.9 1.0
CE1 A:HIS232 3.7 41.8 1.0
O A:LYS230 4.2 50.9 1.0
O A:LYS229 4.4 52.7 1.0
CG A:HIS232 4.5 43.0 1.0
ND1 A:HIS232 4.7 40.6 1.0

Cadmium binding site 2 out of 7 in 1vqq

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Cadmium binding site 2 out of 7 in the Structure of Penicillin Binding Protein 2A From Methicillin Resistant Staphylococcus Aureus Strain 27R at 1.80 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 Binding Protein 2A From Methicillin Resistant Staphylococcus Aureus Strain 27R at 1.80 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1005

b:27.1
occ:1.00
NE2 A:HIS311 2.3 26.1 1.0
OD1 B:ASP209 2.4 31.2 1.0
O A:GLY135 2.4 27.0 1.0
O A:HOH1132 2.4 26.8 1.0
OD2 B:ASP209 2.5 26.4 1.0
CL B:CL1011 2.5 27.5 1.0
CG B:ASP209 2.8 29.4 1.0
CD2 A:HIS311 3.3 21.8 1.0
CE1 A:HIS311 3.3 20.9 1.0
C A:GLY135 3.4 25.1 1.0
CA A:GLY135 3.7 26.4 1.0
O B:HOH1270 4.2 36.9 1.0
NE2 A:GLN137 4.2 36.2 1.0
O B:HOH1103 4.2 28.0 1.0
CB B:ASP209 4.3 30.7 1.0
CG A:GLN137 4.4 38.1 1.0
CG A:HIS311 4.4 26.0 1.0
ND1 A:HIS311 4.4 26.4 1.0
N A:MET136 4.6 24.4 1.0
CD A:GLN137 4.7 38.6 1.0
CB B:GLN207 4.7 27.2 1.0
NH2 A:ARG110 4.8 44.4 1.0
CG B:GLN207 4.9 30.8 1.0

Cadmium binding site 3 out of 7 in 1vqq

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Cadmium binding site 3 out of 7 in the Structure of Penicillin Binding Protein 2A From Methicillin Resistant Staphylococcus Aureus Strain 27R at 1.80 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 Binding Protein 2A From Methicillin Resistant Staphylococcus Aureus Strain 27R at 1.80 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1001

b:25.3
occ:1.00
O A:HOH1133 2.3 20.0 1.0
OE1 A:GLU145 2.3 24.5 1.0
ND1 A:HIS143 2.4 26.4 1.0
CL A:CL1009 2.5 27.6 1.0
OE1 B:GLU145 2.5 20.1 1.0
OE2 B:GLU145 2.5 23.2 1.0
CD B:GLU145 2.9 24.6 1.0
CD A:GLU145 3.1 26.1 1.0
CE1 A:HIS143 3.3 23.8 1.0
CG A:HIS143 3.4 24.9 1.0
CB A:HIS143 3.7 23.4 1.0
CG A:GLU145 3.7 28.1 1.0
CD B:CD1002 3.8 24.2 1.0
OE2 A:GLU145 3.9 25.8 1.0
CG2 A:VAL302 4.3 25.6 1.0
CG B:GLU145 4.4 25.4 1.0
ND1 B:HIS143 4.4 25.4 1.0
NE2 A:HIS143 4.4 27.6 1.0
CD2 A:HIS143 4.5 24.5 1.0
OD1 A:ASN307 4.6 26.4 1.0
OG1 A:THR300 4.7 21.4 1.0
O B:ILE144 4.7 27.7 1.0
CG B:HIS143 4.9 23.5 1.0
CE1 B:HIS143 5.0 20.9 1.0
O B:HOH1147 5.0 29.7 1.0

Cadmium binding site 4 out of 7 in 1vqq

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Cadmium binding site 4 out of 7 in the Structure of Penicillin Binding Protein 2A From Methicillin Resistant Staphylococcus Aureus Strain 27R at 1.80 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 Binding Protein 2A From Methicillin Resistant Staphylococcus Aureus Strain 27R at 1.80 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1002

b:24.2
occ:1.00
OE1 B:GLU145 2.2 20.1 1.0
O A:HOH1134 2.3 22.7 1.0
ND1 B:HIS143 2.3 25.4 1.0
OE2 A:GLU145 2.4 25.8 1.0
OE1 A:GLU145 2.5 24.5 1.0
CL B:CL1008 2.5 27.0 1.0
CD A:GLU145 2.8 26.1 1.0
CD B:GLU145 3.1 24.6 1.0
CG B:HIS143 3.3 23.5 1.0
CE1 B:HIS143 3.3 20.9 1.0
CB B:HIS143 3.5 21.0 1.0
CG B:GLU145 3.8 25.4 1.0
CD B:CD1001 3.8 25.3 1.0
OE2 B:GLU145 3.9 23.2 1.0
ND1 A:HIS143 4.2 26.4 1.0
CG A:GLU145 4.3 28.1 1.0
CG2 B:VAL302 4.4 27.0 1.0
NE2 B:HIS143 4.4 25.9 1.0
CD2 B:HIS143 4.4 24.8 1.0
OD1 B:ASN307 4.7 27.8 1.0
O A:ILE144 4.7 24.7 1.0
CE1 A:HIS143 4.8 23.8 1.0
OG1 B:THR300 4.8 21.3 1.0
CG A:HIS143 4.9 24.9 1.0

Cadmium binding site 5 out of 7 in 1vqq

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Cadmium binding site 5 out of 7 in the Structure of Penicillin Binding Protein 2A From Methicillin Resistant Staphylococcus Aureus Strain 27R at 1.80 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 Binding Protein 2A From Methicillin Resistant Staphylococcus Aureus Strain 27R at 1.80 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1003

b:27.1
occ:1.00
O B:GLY135 2.3 29.1 1.0
OD1 A:ASP209 2.3 32.9 1.0
OD2 A:ASP209 2.3 30.3 1.0
NE2 B:HIS311 2.3 30.5 1.0
CL B:CL1010 2.4 29.6 1.0
CG A:ASP209 2.7 33.2 1.0
CD2 B:HIS311 3.2 27.7 1.0
C B:GLY135 3.3 26.2 1.0
CE1 B:HIS311 3.4 25.4 1.0
CA B:GLY135 3.7 28.4 1.0
CG B:GLN137 4.1 35.9 1.0
CB A:ASP209 4.2 30.4 1.0
O A:HOH1169 4.4 29.6 1.0
NE2 B:GLN137 4.4 38.1 1.0
CG B:HIS311 4.4 28.3 1.0
ND1 B:HIS311 4.5 27.4 1.0
N B:MET136 4.5 25.8 1.0
CD B:GLN137 4.5 39.3 1.0
CB A:GLN207 4.8 32.2 1.0
CA B:MET136 5.0 26.6 1.0

Cadmium binding site 6 out of 7 in 1vqq

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Cadmium binding site 6 out of 7 in the Structure of Penicillin Binding Protein 2A From Methicillin Resistant Staphylococcus Aureus Strain 27R at 1.80 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 Binding Protein 2A From Methicillin Resistant Staphylococcus Aureus Strain 27R at 1.80 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1006

b:57.2
occ:1.00
NE2 B:HIS232 2.5 47.4 1.0
CD2 B:HIS232 3.4 44.7 1.0
CE1 B:HIS232 3.4 46.9 1.0
ND1 B:HIS232 4.6 44.3 1.0
CG B:HIS232 4.6 43.7 1.0

Cadmium binding site 7 out of 7 in 1vqq

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Cadmium binding site 7 out of 7 in the Structure of Penicillin Binding Protein 2A From Methicillin Resistant Staphylococcus Aureus Strain 27R at 1.80 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 Binding Protein 2A From Methicillin Resistant Staphylococcus Aureus Strain 27R at 1.80 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1007

b:31.1
occ:1.00
O B:HOH1171 2.5 18.6 1.0
OD2 B:ASP573 2.5 27.4 1.0
OD1 B:ASP573 2.5 26.4 1.0
OD1 B:ASN569 2.5 24.1 1.0
O B:HOH1173 2.6 26.2 1.0
O B:HOH1172 2.6 19.1 1.0
CG B:ASP573 2.8 26.1 1.0
CG B:ASN569 3.3 30.4 1.0
ND2 B:ASN569 3.5 29.3 1.0
O B:HOH1209 3.7 33.0 1.0
O B:HOH1198 4.3 28.8 1.0
CB B:ASP573 4.3 25.5 1.0
O B:HOH1271 4.5 36.4 1.0
O B:ASN569 4.5 24.5 1.0
NZ B:LYS456 4.7 31.3 1.0
CB B:ASN569 4.8 26.5 1.0

Reference:

D.Lim, N.C.J.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 12:33:56 2020
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