Atomistry » Zinc » PDB 3sci-3sjb » 3sfp
Atomistry »
  Zinc »
    PDB 3sci-3sjb »
      3sfp »

Zinc in PDB 3sfp: Crystal Structure of the Mono-Zinc-Boundform of New Delhi Metallo- Beta-Lactamase-1 From Klebsiella Pneumoniae

Enzymatic activity of Crystal Structure of the Mono-Zinc-Boundform of New Delhi Metallo- Beta-Lactamase-1 From Klebsiella Pneumoniae

All present enzymatic activity of Crystal Structure of the Mono-Zinc-Boundform of New Delhi Metallo- Beta-Lactamase-1 From Klebsiella Pneumoniae:
3.5.2.6;

Protein crystallography data

The structure of Crystal Structure of the Mono-Zinc-Boundform of New Delhi Metallo- Beta-Lactamase-1 From Klebsiella Pneumoniae, PDB code: 3sfp was solved by Y.Kim, C.Tesar, R.Jedrzejczak, J.Babnigg, T.A.Binkowski, A.Joachimiak, Midwest Center For Structural Genomics (Mcsg), Structures Of Mtbproteins Conferring Susceptibility To Known Mtb Inhibitors (Mtbi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.41 / 2.27
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 97.944, 97.944, 187.547, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 23.6

Other elements in 3sfp:

The structure of Crystal Structure of the Mono-Zinc-Boundform of New Delhi Metallo- Beta-Lactamase-1 From Klebsiella Pneumoniae also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Mono-Zinc-Boundform of New Delhi Metallo- Beta-Lactamase-1 From Klebsiella Pneumoniae (pdb code 3sfp). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of the Mono-Zinc-Boundform of New Delhi Metallo- Beta-Lactamase-1 From Klebsiella Pneumoniae, PDB code: 3sfp:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 3sfp

Go back to Zinc Binding Sites List in 3sfp
Zinc binding site 1 out of 4 in the Crystal Structure of the Mono-Zinc-Boundform of New Delhi Metallo- Beta-Lactamase-1 From Klebsiella Pneumoniae


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Mono-Zinc-Boundform of New Delhi Metallo- Beta-Lactamase-1 From Klebsiella Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn280

b:94.1
occ:1.00
NE2 A:HIS120 2.2 64.0 1.0
ND1 A:HIS122 2.5 76.8 1.0
CD2 A:HIS120 3.0 59.0 1.0
NE2 A:HIS189 3.1 35.1 1.0
CE1 A:HIS120 3.3 62.4 1.0
CE1 A:HIS122 3.4 78.0 1.0
CG A:HIS122 3.4 75.5 1.0
CD2 A:HIS189 3.6 35.8 1.0
CB A:HIS122 3.7 65.2 1.0
SG A:CYS208 3.8 26.7 0.5
CB A:CYS208 4.0 32.0 0.5
SG A:CYS208 4.0 29.8 0.5
CB A:CYS208 4.1 30.8 0.5
OD1 A:ASP124 4.1 74.6 1.0
CE1 A:HIS189 4.2 37.9 1.0
CG A:HIS120 4.2 50.6 1.0
ND1 A:HIS120 4.3 55.5 1.0
O A:HOH313 4.5 54.0 1.0
NE2 A:HIS122 4.5 80.5 1.0
CD2 A:HIS122 4.5 80.1 1.0
CG2 A:THR190 4.6 20.9 1.0
OD2 A:ASP124 4.6 76.0 1.0
CG A:ASP124 4.8 73.1 1.0
CG A:HIS189 4.8 35.0 1.0

Zinc binding site 2 out of 4 in 3sfp

Go back to Zinc Binding Sites List in 3sfp
Zinc binding site 2 out of 4 in the Crystal Structure of the Mono-Zinc-Boundform of New Delhi Metallo- Beta-Lactamase-1 From Klebsiella Pneumoniae


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Mono-Zinc-Boundform of New Delhi Metallo- Beta-Lactamase-1 From Klebsiella Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn280

b:0.6
occ:1.00
ND1 B:HIS122 2.3 58.6 1.0
NE2 B:HIS120 2.4 55.3 1.0
CE1 B:HIS122 3.1 58.9 1.0
NE2 B:HIS189 3.2 43.5 1.0
CE1 B:HIS120 3.3 55.8 1.0
CG B:HIS122 3.3 56.2 1.0
CD2 B:HIS120 3.4 52.1 1.0
SG B:CYS208 3.4 30.4 0.4
CD2 B:HIS189 3.5 37.8 1.0
O B:HOH271 3.6 46.6 1.0
CB B:HIS122 3.7 49.6 1.0
SG B:CYS208 3.8 24.1 0.6
CB B:CYS208 3.9 32.4 0.4
CB B:CYS208 4.0 31.9 0.6
OD1 B:ASP124 4.1 63.9 1.0
O B:HOH324 4.2 66.6 1.0
NE2 B:HIS122 4.3 58.9 1.0
CE1 B:HIS189 4.4 43.7 1.0
ND1 B:HIS120 4.4 54.2 1.0
CD2 B:HIS122 4.4 58.3 1.0
CG B:HIS120 4.5 49.3 1.0
OD2 B:ASP124 4.5 55.8 1.0
CG B:ASP124 4.7 58.8 1.0
CG2 B:THR190 4.7 20.2 1.0
CG B:HIS189 4.8 37.7 1.0

Zinc binding site 3 out of 4 in 3sfp

Go back to Zinc Binding Sites List in 3sfp
Zinc binding site 3 out of 4 in the Crystal Structure of the Mono-Zinc-Boundform of New Delhi Metallo- Beta-Lactamase-1 From Klebsiella Pneumoniae


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Mono-Zinc-Boundform of New Delhi Metallo- Beta-Lactamase-1 From Klebsiella Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn280

b:85.5
occ:1.00
ND1 C:HIS122 1.9 61.5 1.0
NE2 C:HIS189 2.5 44.1 1.0
NE2 C:HIS120 2.7 39.2 1.0
CE1 C:HIS122 2.8 59.3 1.0
O C:HOH320 2.8 56.4 1.0
CG C:HIS122 3.0 60.5 1.0
CD2 C:HIS120 3.3 40.7 1.0
CD2 C:HIS189 3.3 40.3 1.0
CB C:HIS122 3.4 51.5 1.0
CE1 C:HIS189 3.6 44.2 1.0
CE1 C:HIS120 3.8 43.2 1.0
NE2 C:HIS122 3.9 61.0 1.0
SG C:CYS208 3.9 40.8 1.0
CD2 C:HIS122 4.0 63.6 1.0
OD2 C:ASP124 4.1 46.4 1.0
OD1 C:ASP124 4.2 58.9 1.0
CB C:CYS208 4.3 36.2 1.0
CG C:ASP124 4.5 52.7 1.0
CG C:HIS189 4.5 41.9 1.0
CG C:HIS120 4.6 39.2 1.0
ND1 C:HIS189 4.6 44.7 1.0
ND1 C:HIS120 4.8 44.0 1.0
CG2 C:THR190 4.8 26.9 1.0
CA C:HIS122 5.0 49.0 1.0

Zinc binding site 4 out of 4 in 3sfp

Go back to Zinc Binding Sites List in 3sfp
Zinc binding site 4 out of 4 in the Crystal Structure of the Mono-Zinc-Boundform of New Delhi Metallo- Beta-Lactamase-1 From Klebsiella Pneumoniae


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the Mono-Zinc-Boundform of New Delhi Metallo- Beta-Lactamase-1 From Klebsiella Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn280

b:70.4
occ:1.00
ND1 D:HIS122 2.0 59.1 1.0
NE2 D:HIS189 2.5 38.2 1.0
NE2 D:HIS120 2.5 41.5 1.0
CE1 D:HIS122 2.8 57.8 1.0
CD2 D:HIS189 3.1 34.0 1.0
CG D:HIS122 3.1 55.2 1.0
CD2 D:HIS120 3.1 40.2 1.0
O D:HOH349 3.2 72.7 1.0
CB D:HIS122 3.6 46.0 1.0
CE1 D:HIS120 3.7 38.3 1.0
CE1 D:HIS189 3.7 39.6 1.0
SG D:CYS208 3.9 39.2 1.0
NE2 D:HIS122 4.0 57.3 1.0
OD1 D:ASP124 4.1 47.7 1.0
CD2 D:HIS122 4.1 59.9 1.0
CB D:CYS208 4.1 35.5 1.0
CG D:HIS189 4.4 34.0 1.0
OD2 D:ASP124 4.4 42.0 1.0
CG D:HIS120 4.4 35.9 1.0
CG2 D:THR190 4.5 30.7 1.0
ND1 D:HIS189 4.6 38.2 1.0
ND1 D:HIS120 4.6 34.8 1.0
CG D:ASP124 4.7 43.8 1.0

Reference:

Y.Kim, C.Tesar, J.Mire, R.Jedrzejczak, A.Binkowski, G.Babnigg, J.Sacchettini, A.Joachimiak. Structure of Apo- and Monometalated Forms of Ndm-1 A Highly Potent Carbapenem-Hydrolyzing Metallo-Beta-Lactamase Plos One V. 6 24621 2011.
ISSN: ESSN 1932-6203
PubMed: 21931780
DOI: 10.1371/JOURNAL.PONE.0024621
Page generated: Sat Oct 26 15:44:38 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy