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Zinc in PDB 1zkj: Structural Basis For the Extended Substrate Spectrum of Cmy- 10, A Plasmid-Encoded Class C Beta-Lactamase

Enzymatic activity of Structural Basis For the Extended Substrate Spectrum of Cmy- 10, A Plasmid-Encoded Class C Beta-Lactamase

All present enzymatic activity of Structural Basis For the Extended Substrate Spectrum of Cmy- 10, A Plasmid-Encoded Class C Beta-Lactamase:
3.5.2.6;

Protein crystallography data

The structure of Structural Basis For the Extended Substrate Spectrum of Cmy- 10, A Plasmid-Encoded Class C Beta-Lactamase, PDB code: 1zkj was solved by S.S.Cha, H.I.Jung, Y.J.An, S.H.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.55
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 49.703, 59.296, 63.856, 90.00, 103.08, 90.00
R / Rfree (%) 20.9 / 23.5

Zinc Binding Sites:

The binding sites of Zinc atom in the Structural Basis For the Extended Substrate Spectrum of Cmy- 10, A Plasmid-Encoded Class C Beta-Lactamase (pdb code 1zkj). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Structural Basis For the Extended Substrate Spectrum of Cmy- 10, A Plasmid-Encoded Class C Beta-Lactamase, PDB code: 1zkj:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 1zkj

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Zinc binding site 1 out of 8 in the Structural Basis For the Extended Substrate Spectrum of Cmy- 10, A Plasmid-Encoded Class C Beta-Lactamase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structural Basis For the Extended Substrate Spectrum of Cmy- 10, A Plasmid-Encoded Class C Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn506

b:28.2
occ:1.00
 OD2 A:ASP7 1.9 14.7 1.0
ND1 A:HIS40 2.1 11.9 1.0
CG A:ASP7 2.8 15.6 1.0
CE1 A:HIS40 2.9 13.5 1.0
CG A:HIS40 3.2 11.1 1.0
OD1 A:ASP7 3.2 14.4 1.0
CB A:HIS40 3.7 8.8 1.0
O A:HOH1600 3.9 15.8 1.0
CB A:ASP7 4.0 13.4 1.0
NZ A:LYS38 4.0 29.3 1.0
O A:HOH1539 4.1 12.4 1.0
NE2 A:HIS40 4.1 11.7 1.0
CE A:LYS38 4.1 27.0 1.0
CA A:HIS40 4.1 7.8 1.0
CD2 A:HIS40 4.2 10.9 1.0
O A:ALA39 4.7 10.9 1.0
CA A:ASP7 4.8 14.4 1.0
CD A:LYS38 5.0 24.7 1.0

Zinc binding site 2 out of 8 in 1zkj

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Zinc binding site 2 out of 8 in the Structural Basis For the Extended Substrate Spectrum of Cmy- 10, A Plasmid-Encoded Class C Beta-Lactamase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structural Basis For the Extended Substrate Spectrum of Cmy- 10, A Plasmid-Encoded Class C Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn507

b:16.6
occ:1.00
 NE2 A:HIS148 2.1 8.0 1.0
O A:HOH1566 2.2 30.5 1.0
O A:HOH1571 2.4 20.8 1.0
O A:HOH1699 2.6 34.3 1.0
CD2 A:HIS148 3.0 9.0 1.0
CE1 A:HIS148 3.1 7.7 1.0
O A:HOH1772 4.0 23.1 1.0
ND1 A:HIS148 4.2 7.1 1.0
CG A:HIS148 4.2 6.1 1.0
CE2 A:TYR143 4.6 16.4 1.0
CD2 A:TYR143 4.9 14.8 1.0
CB A:PRO297 4.9 9.3 1.0
CD A:PRO297 4.9 7.7 1.0

Zinc binding site 3 out of 8 in 1zkj

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Zinc binding site 3 out of 8 in the Structural Basis For the Extended Substrate Spectrum of Cmy- 10, A Plasmid-Encoded Class C Beta-Lactamase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structural Basis For the Extended Substrate Spectrum of Cmy- 10, A Plasmid-Encoded Class C Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn508

b:8.2
occ:1.00
 O A:ACY1404 2.0 9.8 1.0
NE2 A:HIS161 2.0 4.5 1.0
O A:ACY1403 2.0 8.9 1.0
C A:ACY1403 2.7 9.7 1.0
OXT A:ACY1403 2.8 11.8 1.0
C A:ACY1404 2.9 10.8 1.0
CD2 A:HIS161 3.0 7.0 1.0
CE1 A:HIS161 3.0 7.3 1.0
CH3 A:ACY1404 3.3 10.5 1.0
NH2 A:ARG133 4.1 7.2 1.0
ND1 A:HIS161 4.1 5.4 1.0
OXT A:ACY1404 4.1 11.3 1.0
CG A:HIS161 4.1 5.9 1.0
O A:HOH1455 4.2 7.9 1.0
CH3 A:ACY1403 4.2 10.9 1.0
NE1 A:TRP96 4.5 6.3 1.0
CZ2 A:TRP96 4.9 6.5 1.0

Zinc binding site 4 out of 8 in 1zkj

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Zinc binding site 4 out of 8 in the Structural Basis For the Extended Substrate Spectrum of Cmy- 10, A Plasmid-Encoded Class C Beta-Lactamase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structural Basis For the Extended Substrate Spectrum of Cmy- 10, A Plasmid-Encoded Class C Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn509

b:27.9
occ:1.00
 O A:HOH1641 2.6 27.4 1.0
O A:HOH1493 2.6 23.1 1.0
NE2 A:HIS187 2.8 18.6 1.0
CE1 A:HIS187 2.8 19.3 1.0
ND1 A:HIS187 4.0 17.5 1.0
CD2 A:HIS187 4.0 16.3 1.0
CB A:HIS186 4.5 5.6 1.0
CG A:HIS187 4.6 14.6 1.0
O A:HIS186 4.9 6.3 1.0

Zinc binding site 5 out of 8 in 1zkj

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Zinc binding site 5 out of 8 in the Structural Basis For the Extended Substrate Spectrum of Cmy- 10, A Plasmid-Encoded Class C Beta-Lactamase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structural Basis For the Extended Substrate Spectrum of Cmy- 10, A Plasmid-Encoded Class C Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn510

b:13.2
occ:1.00
 O A:HOH1476 2.0 13.2 1.0
O A:HOH1474 2.0 12.6 1.0
O A:HOH1595 2.0 18.2 1.0
ND2 A:ASN191 2.1 4.7 1.0
O A:HOH1444 2.1 13.6 1.0
O A:HOH1446 2.2 8.2 1.0
CG A:ASN191 3.1 6.8 1.0
OD1 A:ASN191 3.3 9.2 1.0
O A:HOH1734 4.0 21.6 1.0
OD2 A:ASP220 4.2 10.1 1.0
O A:HOH1788 4.2 25.5 1.0
OD1 A:ASP220 4.3 6.9 1.0
O A:HOH1733 4.3 27.1 1.0
CB A:ASN191 4.4 5.3 1.0
CG A:ASP220 4.6 6.6 1.0

Zinc binding site 6 out of 8 in 1zkj

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Zinc binding site 6 out of 8 in the Structural Basis For the Extended Substrate Spectrum of Cmy- 10, A Plasmid-Encoded Class C Beta-Lactamase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structural Basis For the Extended Substrate Spectrum of Cmy- 10, A Plasmid-Encoded Class C Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn511

b:8.8
occ:1.00
 OXT A:GLY359 2.8 18.4 1.0
C A:GLY359 3.2 20.9 1.0
O A:GLY359 3.3 22.5 1.0
CA A:GLY359 4.3 17.1 1.0

Zinc binding site 7 out of 8 in 1zkj

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Zinc binding site 7 out of 8 in the Structural Basis For the Extended Substrate Spectrum of Cmy- 10, A Plasmid-Encoded Class C Beta-Lactamase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structural Basis For the Extended Substrate Spectrum of Cmy- 10, A Plasmid-Encoded Class C Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn512

b:9.6
occ:1.00
 O A:ACY1401 3.3 13.2 1.0
ND1 A:HIS24 3.6 8.3 1.0
CA A:TYR341 3.6 4.9 1.0
CB A:TYR341 3.6 4.5 1.0
CD A:PRO342 3.8 6.7 1.0
CB A:HIS24 3.8 6.4 1.0
O A:HOH1551 3.9 16.4 1.0
CG A:HIS24 4.0 7.3 1.0
O A:ASN340 4.1 8.2 1.0
CG A:ARG339 4.2 13.5 1.0
O A:HIS24 4.2 7.1 1.0
CD A:ARG339 4.2 14.3 1.0
C A:ACY1401 4.4 13.1 1.0
N A:TYR341 4.4 5.5 1.0
CA A:HIS24 4.5 6.6 1.0
C A:ASN340 4.6 5.6 1.0
CE1 A:HIS24 4.6 7.6 1.0
N A:PRO342 4.7 6.2 1.0
C A:TYR341 4.7 5.4 1.0
CG A:PRO342 4.8 5.7 1.0
C A:HIS24 4.8 7.1 1.0
NE A:ARG339 4.9 13.8 1.0

Zinc binding site 8 out of 8 in 1zkj

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Zinc binding site 8 out of 8 in the Structural Basis For the Extended Substrate Spectrum of Cmy- 10, A Plasmid-Encoded Class C Beta-Lactamase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structural Basis For the Extended Substrate Spectrum of Cmy- 10, A Plasmid-Encoded Class C Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn514

b:17.8
occ:1.00
 O A:HOH1683 2.0 19.9 1.0
OD2 A:ASP14 2.1 8.1 1.0
O A:HOH1684 2.8 22.3 1.0
O A:HOH1640 3.0 26.2 1.0
CG A:ASP14 3.0 8.4 1.0
CB A:ASP14 3.2 8.0 1.0
O A:HOH1550 3.9 15.2 1.0
O A:HOH1532 3.9 17.9 1.0
NE A:ARG10 3.9 16.3 1.0
OD1 A:ASP14 4.2 7.7 1.0
CZ A:ARG10 4.3 17.7 1.0
NH2 A:ARG10 4.3 16.6 1.0
CD A:ARG10 4.6 13.8 1.0
CG A:ARG10 4.6 12.4 1.0
CA A:PRO11 4.7 7.9 1.0
O A:ARG10 4.7 7.9 1.0
CA A:ASP14 4.7 7.6 1.0

Reference:

J.Y.Kim, H.I.Jung, Y.J.An, J.H.Lee, S.J.Kim, S.H.Jeong, K.J.Lee, P.G.Suh, H.S.Lee, S.H.Lee, S.S.Cha. Structural Basis For the Extended Substrate Spectrum of Cmy-10, A Plasmid-Encoded Class C Beta-Lactamase. Mol.Microbiol. V. 60 907 2006.
ISSN: ISSN 0950-382X
PubMed: 16677302
DOI: 10.1111/J.1365-2958.2006.05146.X
Page generated: Wed Dec 16 03:15:47 2020

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