Atomistry » Zinc » PDB 1zfn-1zrp » 1zkj
Atomistry »
  Zinc »
    PDB 1zfn-1zrp »
      1zkj »

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

Go back to Zinc Binding Sites List in 1zkj
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

Go back to Zinc Binding Sites List in 1zkj
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

Go back to Zinc Binding Sites List in 1zkj
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

Go back to Zinc Binding Sites List in 1zkj
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

Go back to Zinc Binding Sites List in 1zkj
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

Go back to Zinc Binding Sites List in 1zkj
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

Go back to Zinc Binding Sites List in 1zkj
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

Go back to Zinc Binding Sites List in 1zkj
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 Oct 16 21:16:24 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy