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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: Wed Dec 16 04:50:06 2020

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