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Zinc in PDB 5o2f: Crystal Structure of Ndm-1 in Complex with Hydrolyzed Ampicillin - New Refinement

Enzymatic activity of Crystal Structure of Ndm-1 in Complex with Hydrolyzed Ampicillin - New Refinement

All present enzymatic activity of Crystal Structure of Ndm-1 in Complex with Hydrolyzed Ampicillin - New Refinement:
3.5.2.6;

Protein crystallography data

The structure of Crystal Structure of Ndm-1 in Complex with Hydrolyzed Ampicillin - New Refinement, PDB code: 5o2f was solved by J.E.Raczynska, I.G.Shabalin, M.Jaskolski, W.Minor, A.Wlodawer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.79 / 2.01
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 38.620, 77.570, 132.310, 90.00, 90.00, 90.00
R / Rfree (%) 13.2 / 18.2

Other elements in 5o2f:

The structure of Crystal Structure of Ndm-1 in Complex with Hydrolyzed Ampicillin - New Refinement also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Ndm-1 in Complex with Hydrolyzed Ampicillin - New Refinement (pdb code 5o2f). 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 Ndm-1 in Complex with Hydrolyzed Ampicillin - New Refinement, PDB code: 5o2f:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5o2f

Go back to Zinc Binding Sites List in 5o2f
Zinc binding site 1 out of 4 in the Crystal Structure of Ndm-1 in Complex with Hydrolyzed Ampicillin - New Refinement


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 Ndm-1 in Complex with Hydrolyzed Ampicillin - New Refinement within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:18.1
occ:1.00
 ND1 A:HIS122 2.0 15.5 1.0
O A:HOH443 2.0 12.1 1.0
NE2 A:HIS189 2.0 11.2 1.0
NE2 A:HIS120 2.1 12.6 1.0
OXT A:ZZ7303 2.4 16.4 1.0
CE1 A:HIS122 2.9 15.0 1.0
CD2 A:HIS189 3.0 10.9 1.0
CG A:HIS122 3.0 15.4 1.0
CE1 A:HIS120 3.1 12.7 1.0
CE1 A:HIS189 3.1 12.1 1.0
CD2 A:HIS120 3.1 12.9 1.0
C15 A:ZZ7303 3.3 19.0 1.0
CB A:HIS122 3.4 14.2 1.0
C14 A:ZZ7303 3.8 19.2 1.0
NE2 A:HIS122 4.0 15.6 1.0
N3 A:ZZ7303 4.1 20.0 1.0
CD2 A:HIS122 4.1 16.5 1.0
ND1 A:HIS189 4.2 12.1 1.0
CG A:HIS189 4.2 11.8 1.0
ND1 A:HIS120 4.2 12.3 1.0
CG A:HIS120 4.2 13.1 1.0
SG A:CYS208 4.2 14.5 1.0
O4 A:ZZ7303 4.3 18.4 1.0
OD1 A:ASP124 4.3 15.8 1.0
CG2 A:THR190 4.3 15.8 1.0
CB A:CYS208 4.3 15.5 1.0
ZN A:ZN302 4.5 18.8 1.0
C13 A:ZZ7303 4.5 19.3 1.0
CA A:HIS122 4.9 13.3 1.0
O A:HOH491 4.9 18.6 1.0
C12 A:ZZ7303 4.9 18.6 1.0
OD2 A:ASP124 4.9 16.0 1.0

Zinc binding site 2 out of 4 in 5o2f

Go back to Zinc Binding Sites List in 5o2f
Zinc binding site 2 out of 4 in the Crystal Structure of Ndm-1 in Complex with Hydrolyzed Ampicillin - New Refinement


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 Ndm-1 in Complex with Hydrolyzed Ampicillin - New Refinement within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:18.8
occ:1.00
 OD2 A:ASP124 2.1 16.0 1.0
NE2 A:HIS250 2.1 15.8 1.0
N3 A:ZZ7303 2.2 20.0 1.0
O2 A:ZZ7303 2.2 14.2 1.0
SG A:CYS208 2.3 14.5 1.0
O A:HOH443 2.8 12.1 1.0
C2 A:ZZ7303 3.0 18.9 1.0
CE1 A:HIS250 3.0 16.6 1.0
CD2 A:HIS250 3.1 16.0 1.0
C12 A:ZZ7303 3.1 18.6 1.0
CG A:ASP124 3.3 14.2 1.0
C13 A:ZZ7303 3.3 19.3 1.0
CB A:CYS208 3.4 15.5 1.0
C16 A:ZZ7303 3.7 21.2 1.0
OD1 A:ASP124 3.8 15.8 1.0
C6 A:ZZ7303 4.0 20.0 1.0
ND1 A:HIS250 4.1 16.2 1.0
CG A:HIS250 4.2 16.2 1.0
CB A:SER249 4.2 15.2 1.0
O1 A:ZZ7303 4.2 16.4 1.0
C14 A:ZZ7303 4.3 19.2 1.0
OXT A:ZZ7303 4.4 16.4 1.0
CB A:ASP124 4.4 14.9 1.0
S1 A:ZZ7303 4.5 19.9 1.0
CA A:CYS208 4.5 16.1 1.0
ZN A:ZN301 4.5 18.1 1.0
OG A:SER249 4.6 14.6 1.0
NE2 A:HIS189 4.8 11.2 1.0
C15 A:ZZ7303 4.8 19.0 1.0
CE1 A:HIS189 4.9 12.1 1.0

Zinc binding site 3 out of 4 in 5o2f

Go back to Zinc Binding Sites List in 5o2f
Zinc binding site 3 out of 4 in the Crystal Structure of Ndm-1 in Complex with Hydrolyzed Ampicillin - New Refinement


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 Ndm-1 in Complex with Hydrolyzed Ampicillin - New Refinement within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:18.4
occ:1.00
 O B:HOH423 2.0 18.0 1.0
ND1 B:HIS122 2.0 14.7 1.0
NE2 B:HIS189 2.1 15.4 1.0
NE2 B:HIS120 2.1 11.6 1.0
O4 B:ZZ7303 2.4 19.1 1.0
CE1 B:HIS122 2.9 15.4 1.0
CD2 B:HIS189 3.0 14.4 1.0
CG B:HIS122 3.1 13.6 1.0
CE1 B:HIS120 3.1 11.8 1.0
CD2 B:HIS120 3.1 11.8 1.0
CE1 B:HIS189 3.1 14.1 1.0
C15 B:ZZ7303 3.3 21.4 1.0
CB B:HIS122 3.5 12.3 1.0
C14 B:ZZ7303 3.9 21.9 1.0
NE2 B:HIS122 4.1 15.6 1.0
N3 B:ZZ7303 4.1 19.4 1.0
OXT B:ZZ7303 4.1 23.0 1.0
CD2 B:HIS122 4.1 15.3 1.0
CG B:HIS189 4.2 14.7 1.0
ND1 B:HIS189 4.2 14.2 1.0
ND1 B:HIS120 4.2 11.9 1.0
CG B:HIS120 4.2 11.8 1.0
OD1 B:ASP124 4.2 15.2 1.0
CG2 B:THR190 4.3 15.6 1.0
SG B:CYS208 4.4 11.7 1.0
CB B:CYS208 4.5 13.6 1.0
ZN B:ZN302 4.6 18.9 1.0
C13 B:ZZ7303 4.6 21.4 1.0
O B:HOH507 4.7 20.4 1.0
CA B:HIS122 4.9 12.1 1.0
C12 B:ZZ7303 4.9 18.3 1.0

Zinc binding site 4 out of 4 in 5o2f

Go back to Zinc Binding Sites List in 5o2f
Zinc binding site 4 out of 4 in the Crystal Structure of Ndm-1 in Complex with Hydrolyzed Ampicillin - New Refinement


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 Ndm-1 in Complex with Hydrolyzed Ampicillin - New Refinement within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:18.9
occ:1.00
 NE2 B:HIS250 2.0 14.7 1.0
OD2 B:ASP124 2.0 14.7 1.0
N3 B:ZZ7303 2.2 19.4 1.0
O1 B:ZZ7303 2.2 17.4 1.0
SG B:CYS208 2.3 11.7 1.0
O B:HOH423 2.8 18.0 1.0
C2 B:ZZ7303 3.0 17.6 1.0
CE1 B:HIS250 3.0 15.2 1.0
CD2 B:HIS250 3.0 14.4 1.0
C12 B:ZZ7303 3.1 18.3 1.0
CG B:ASP124 3.2 14.8 1.0
C13 B:ZZ7303 3.3 21.4 1.0
CB B:CYS208 3.4 13.6 1.0
C16 B:ZZ7303 3.7 17.5 1.0
OD1 B:ASP124 3.7 15.2 1.0
C6 B:ZZ7303 3.9 18.2 1.0
ND1 B:HIS250 4.1 14.4 1.0
CG B:HIS250 4.2 14.1 1.0
O2 B:ZZ7303 4.2 14.9 1.0
CB B:SER249 4.3 14.3 1.0
C14 B:ZZ7303 4.3 21.9 1.0
O4 B:ZZ7303 4.3 19.1 1.0
CB B:ASP124 4.4 15.2 1.0
CA B:CYS208 4.5 13.6 1.0
S1 B:ZZ7303 4.5 20.6 1.0
ZN B:ZN301 4.6 18.4 1.0
OG B:SER249 4.7 15.0 1.0
C15 B:ZZ7303 4.8 21.4 1.0
NE2 B:HIS189 4.8 15.4 1.0
CE1 B:HIS189 5.0 14.1 1.0

Reference:

J.E.Raczynska, I.G.Shabalin, W.Minor, A.Wlodawer, M.Jaskolski. A Close Look Onto Structural Models and Primary Ligands of Metallo-Beta-Lactamases. Drug Resist. Updat. V. 40 1 2018.
ISSN: ESSN 1532-2084
PubMed: 30466711
DOI: 10.1016/J.DRUP.2018.08.001
Page generated: Sun Oct 27 23:12:48 2024

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