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Cadmium in PDB 6h5o: Crystal Structure of PBP2A From Mrsa in Complex with Piperacillin at Active Site.

Enzymatic activity of Crystal Structure of PBP2A From Mrsa in Complex with Piperacillin at Active Site.

All present enzymatic activity of Crystal Structure of PBP2A From Mrsa in Complex with Piperacillin at Active Site.:
3.4.16.4;

Protein crystallography data

The structure of Crystal Structure of PBP2A From Mrsa in Complex with Piperacillin at Active Site., PDB code: 6h5o was solved by M.T.Batuecas, S.Martinez-Caballero, J.A.Hermoso, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.45 / 2.82
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 80.713, 105.014, 185.624, 90.00, 90.00, 90.00
R / Rfree (%) 24.1 / 31.1

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of PBP2A From Mrsa in Complex with Piperacillin at Active Site. (pdb code 6h5o). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 9 binding sites of Cadmium where determined in the Crystal Structure of PBP2A From Mrsa in Complex with Piperacillin at Active Site., PDB code: 6h5o:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Cadmium binding site 1 out of 9 in 6h5o

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Cadmium binding site 1 out of 9 in the Crystal Structure of PBP2A From Mrsa in Complex with Piperacillin at Active Site.


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 Piperacillin at Active Site. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd702

b:0.6
occ:1.00
O A:GLY135 2.1 86.4 1.0
OD1 B:ASP209 2.2 92.1 1.0
CD A:CD703 2.2 0.9 1.0
NE2 A:HIS311 2.5 93.9 1.0
OD2 B:ASP209 2.7 0.3 1.0
CG B:ASP209 2.8 0.6 1.0
C A:GLY135 3.0 83.7 1.0
CA A:GLY135 3.2 75.9 1.0
CE1 A:HIS311 3.4 1.0 1.0
CD2 A:HIS311 3.5 88.5 1.0
N A:MET136 4.2 90.2 1.0
CB B:ASP209 4.2 0.2 1.0
CG A:GLN137 4.4 0.8 1.0
ND1 A:HIS311 4.5 100.0 1.0
N A:GLY135 4.6 79.3 1.0
CG A:HIS311 4.6 91.5 1.0
CD A:GLN137 4.7 0.3 1.0
NE2 A:GLN137 4.7 0.2 1.0
CA A:MET136 4.9 94.6 1.0
NH2 A:ARG110 5.0 84.7 1.0
C B:ASP209 5.0 97.8 1.0

Cadmium binding site 2 out of 9 in 6h5o

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Cadmium binding site 2 out of 9 in the Crystal Structure of PBP2A From Mrsa in Complex with Piperacillin at Active Site.


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 Piperacillin at Active Site. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd703

b:0.9
occ:1.00
CD A:CD702 2.2 0.6 1.0
O A:GLY135 3.2 86.4 1.0
NE2 A:HIS311 3.3 93.9 1.0
OD1 B:ASP209 3.4 92.1 1.0
CE1 A:HIS311 4.0 1.0 1.0
NE2 A:GLN140 4.0 84.6 1.0
CD A:GLN137 4.1 0.3 1.0
CD2 A:HIS311 4.1 88.5 1.0
CG A:GLN137 4.2 0.8 1.0
CG2 B:THR210 4.2 98.5 1.0
OE1 A:GLN137 4.2 0.9 1.0
CB A:ALA310 4.4 0.7 1.0
C A:GLY135 4.4 83.7 1.0
CG B:ASP209 4.5 0.6 1.0
NE2 A:GLN137 4.5 0.2 1.0
OE1 A:GLN140 4.5 73.4 1.0
CD A:GLN140 4.7 91.4 1.0
OD2 B:ASP209 4.8 0.3 1.0
CB B:GLN207 4.9 0.8 1.0
CB A:GLN137 4.9 0.2 1.0

Cadmium binding site 3 out of 9 in 6h5o

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Cadmium binding site 3 out of 9 in the Crystal Structure of PBP2A From Mrsa in Complex with Piperacillin at Active Site.


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 Piperacillin at Active Site. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd704

b:99.4
occ:1.00
CD A:CD705 1.8 0.8 1.0
OE1 B:GLU145 2.5 79.0 1.0
ND1 A:HIS143 2.5 0.1 1.0
OE1 A:GLU145 2.6 78.7 1.0
OE2 B:GLU145 2.8 88.4 1.0
CD A:GLU145 3.0 87.6 1.0
CD B:GLU145 3.0 84.9 1.0
OE2 A:GLU145 3.2 89.3 1.0
CE1 A:HIS143 3.3 98.7 1.0
CD A:CD708 3.5 95.0 1.0
CG A:HIS143 3.6 86.7 1.0
O B:HOH827 3.7 50.7 1.0
ND1 B:HIS143 3.9 94.4 1.0
O B:ILE144 3.9 92.0 1.0
CG A:GLU145 3.9 90.8 1.0
CB A:HIS143 4.0 74.9 1.0
CE1 B:HIS143 4.4 0.3 1.0
CG B:GLU145 4.5 93.2 1.0
NE2 A:HIS143 4.5 0.2 1.0
CG B:HIS143 4.5 92.0 1.0
CD2 A:HIS143 4.7 93.3 1.0
CB B:HIS143 4.7 89.2 1.0
C B:ILE144 4.9 92.3 1.0
CA B:GLU145 5.0 88.3 1.0

Cadmium binding site 4 out of 9 in 6h5o

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Cadmium binding site 4 out of 9 in the Crystal Structure of PBP2A From Mrsa in Complex with Piperacillin at Active Site.


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 Piperacillin at Active Site. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd705

b:0.8
occ:1.00
CD A:CD704 1.8 99.4 1.0
OE1 A:GLU145 2.9 78.7 1.0
ND1 A:HIS143 2.9 0.1 1.0
O B:HOH827 3.3 50.7 1.0
CD A:GLU145 3.6 87.6 1.0
CG A:HIS143 3.6 86.7 1.0
OE1 B:GLU145 3.6 79.0 1.0
CB A:HIS143 3.7 74.9 1.0
CE1 A:HIS143 3.8 98.7 1.0
CG2 A:VAL302 4.1 96.2 1.0
OG1 A:THR300 4.2 81.2 1.0
CG A:GLU145 4.3 90.8 1.0
CD1 A:ILE309 4.3 98.4 1.0
OE2 A:GLU145 4.3 89.3 1.0
CD B:GLU145 4.5 84.9 1.0
OE2 B:GLU145 4.6 88.4 1.0
CD2 A:HIS143 4.7 93.3 1.0
NE2 A:HIS143 4.8 0.2 1.0
O B:ILE144 4.8 92.0 1.0
CG1 A:VAL302 4.9 96.9 1.0

Cadmium binding site 5 out of 9 in 6h5o

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Cadmium binding site 5 out of 9 in the Crystal Structure of PBP2A From Mrsa in Complex with Piperacillin at Active Site.


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 PBP2A From Mrsa in Complex with Piperacillin at Active Site. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd706

b:0.3
occ:1.00
CD A:CD708 2.4 95.0 1.0
OE2 A:GLU145 2.6 89.3 1.0
O A:ILE144 2.9 89.0 1.0
O B:HOH812 3.1 58.3 1.0
CD A:GLU145 3.6 87.6 1.0
ND1 B:HIS143 3.9 94.4 1.0
C A:ILE144 4.0 76.8 1.0
OE1 A:GLU145 4.2 78.7 1.0
CE1 B:HIS143 4.2 0.3 1.0
CG1 B:VAL302 4.3 0.1 1.0
OE2 B:GLU145 4.3 88.4 1.0
CA A:GLU145 4.4 85.0 1.0
CG A:GLU145 4.5 90.8 1.0
N A:GLU145 4.7 74.7 1.0

Cadmium binding site 6 out of 9 in 6h5o

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Cadmium binding site 6 out of 9 in the Crystal Structure of PBP2A From Mrsa in Complex with Piperacillin at Active Site.


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 PBP2A From Mrsa in Complex with Piperacillin at Active Site. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd707

b:0.0
occ:1.00
OD2 A:ASP386 2.9 0.3 1.0
CG A:ASP386 3.8 0.4 1.0
OD1 A:ASP386 4.0 0.3 1.0
CD A:LYS388 4.2 0.5 1.0
CB A:LYS388 4.7 0.6 1.0
CG A:PRO364 4.7 1.0 1.0
CG A:LYS388 4.7 0.4 1.0

Cadmium binding site 7 out of 9 in 6h5o

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Cadmium binding site 7 out of 9 in the Crystal Structure of PBP2A From Mrsa in Complex with Piperacillin at Active Site.


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 PBP2A From Mrsa in Complex with Piperacillin at Active Site. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd708

b:95.0
occ:1.00
OE2 A:GLU145 1.8 89.3 1.0
OE2 B:GLU145 2.1 88.4 1.0
ND1 B:HIS143 2.3 94.4 1.0
O B:HOH812 2.3 58.3 1.0
CD A:CD706 2.4 0.3 1.0
CD A:GLU145 2.9 87.6 1.0
CD B:GLU145 3.0 84.9 1.0
CE1 B:HIS143 3.1 0.3 1.0
CG B:HIS143 3.3 92.0 1.0
OE1 A:GLU145 3.4 78.7 1.0
CD A:CD704 3.5 99.4 1.0
OE1 B:GLU145 3.6 79.0 1.0
CB B:HIS143 3.6 89.2 1.0
CG B:GLU145 4.1 93.2 1.0
CG A:GLU145 4.1 90.8 1.0
ND1 A:HIS143 4.3 0.1 1.0
O A:ILE144 4.3 89.0 1.0
NE2 B:HIS143 4.3 1.0 1.0
CD2 B:HIS143 4.4 97.4 1.0
CG1 B:VAL302 4.7 0.1 1.0
CG2 B:THR300 4.8 78.3 1.0
CE1 A:HIS143 4.8 98.7 1.0
CG A:HIS143 5.0 86.7 1.0

Cadmium binding site 8 out of 9 in 6h5o

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Cadmium binding site 8 out of 9 in the Crystal Structure of PBP2A From Mrsa in Complex with Piperacillin at Active Site.


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 PBP2A From Mrsa in Complex with Piperacillin at Active Site. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd709

b:92.1
occ:0.70
CD B:CD702 1.8 0.8 0.7
O B:GLY135 2.3 86.8 1.0
OD2 A:ASP209 2.6 0.8 1.0
CE1 B:HIS311 2.8 0.0 1.0
CB A:ASP209 3.1 0.6 1.0
C B:GLY135 3.2 97.5 1.0
CG A:ASP209 3.3 0.6 1.0
CA B:GLY135 3.4 91.4 1.0
ND1 B:HIS311 3.6 95.5 1.0
NE2 B:HIS311 3.8 0.9 1.0
OE1 B:GLN137 4.2 0.1 1.0
N B:MET136 4.5 99.6 1.0
OD1 A:ASP209 4.5 0.6 1.0
CD B:GLN137 4.5 0.3 1.0
CA A:ASP209 4.6 0.8 1.0
CG B:GLN137 4.6 0.6 1.0
N B:GLY135 4.8 84.3 1.0
CG B:HIS311 4.8 95.7 1.0
NE2 A:GLN207 4.9 0.7 1.0
CD2 B:HIS311 4.9 0.3 1.0

Cadmium binding site 9 out of 9 in 6h5o

Go back to Cadmium Binding Sites List in 6h5o
Cadmium binding site 9 out of 9 in the Crystal Structure of PBP2A From Mrsa in Complex with Piperacillin at Active Site.


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Crystal Structure of PBP2A From Mrsa in Complex with Piperacillin at Active Site. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd702

b:0.8
occ:0.70
CD A:CD709 1.8 92.1 0.7
O B:GLY135 3.2 86.8 1.0
CE1 B:HIS311 3.2 0.0 1.0
NE2 A:GLN207 3.5 0.7 1.0
OE1 B:GLN137 3.8 0.1 1.0
CD B:GLN137 3.9 0.3 1.0
ND1 B:HIS311 3.9 95.5 1.0
NE2 B:HIS311 4.1 0.9 1.0
CB A:ASP209 4.2 0.6 1.0
OD2 A:ASP209 4.3 0.8 1.0
NE2 B:GLN140 4.3 99.1 1.0
NE2 B:GLN137 4.4 0.7 1.0
C B:GLY135 4.4 97.5 1.0
CG B:GLN137 4.4 0.6 1.0
CB B:ALA310 4.5 92.0 1.0
OG1 A:THR210 4.6 0.5 1.0
CD A:GLN207 4.6 1.0 1.0
OE1 B:GLN140 4.7 97.6 1.0
CG A:ASP209 4.7 0.6 1.0
CB A:GLN207 4.8 0.6 1.0
CG A:GLN207 4.9 0.1 1.0
CD B:GLN140 4.9 0.5 1.0

Reference:

M.T.Batuecas, S.Martinez-Caballero, J.A.Hermoso. Crystal Structure of PBP2A From Mrsa in Complex with Piperacillin at Active Site. To Be Published.
Page generated: Sat Dec 12 08:28:32 2020

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