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Zinc in PDB 5o2e: Crystal Structure of Ndm-1 in Complex with Hydrolyzed Cefuroxime - New Refinement

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

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

Protein crystallography data

The structure of Crystal Structure of Ndm-1 in Complex with Hydrolyzed Cefuroxime - New Refinement, PDB code: 5o2e 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) 29.36 / 1.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 39.180, 78.890, 133.060, 90.00, 90.00, 90.00
R / Rfree (%) 10.1 / 13.3

Other elements in 5o2e:

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

Chlorine (Cl) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Ndm-1 in Complex with Hydrolyzed Cefuroxime - New Refinement (pdb code 5o2e). 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 Cefuroxime - New Refinement, PDB code: 5o2e:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5o2e

Go back to Zinc Binding Sites List in 5o2e
Zinc binding site 1 out of 4 in the Crystal Structure of Ndm-1 in Complex with Hydrolyzed Cefuroxime - 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 Cefuroxime - New Refinement within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:11.0
occ:1.00
 O A:HOH438 2.0 13.1 1.0
ND1 A:HIS122 2.0 9.0 1.0
NE2 A:HIS189 2.0 8.2 1.0
NE2 A:HIS120 2.1 8.7 1.0
O A:3S0304 2.8 16.7 0.9
CE1 A:HIS122 3.0 9.7 1.0
CD2 A:HIS189 3.0 6.5 1.0
CG A:HIS122 3.0 8.0 1.0
CE1 A:HIS120 3.0 10.1 1.0
CE1 A:HIS189 3.0 7.9 1.0
CD2 A:HIS120 3.1 7.8 1.0
CB A:HIS122 3.4 7.4 1.0
C A:3S0304 3.7 16.2 0.9
ZN A:ZN302 3.8 11.5 0.9
CA A:3S0304 3.9 16.4 0.9
NE2 A:HIS122 4.1 9.9 1.0
OD1 A:ASP124 4.1 9.0 1.0
OAX A:3S0304 4.1 10.5 0.9
ND1 A:HIS189 4.1 7.4 1.0
CD2 A:HIS122 4.1 8.8 1.0
ND1 A:HIS120 4.2 8.6 1.0
CG A:HIS189 4.2 6.4 1.0
SG A:CYS208 4.2 8.7 1.0
NAR A:3S0304 4.2 11.8 0.9
CG A:HIS120 4.2 6.4 1.0
CB A:CYS208 4.3 7.9 1.0
CG2 A:THR190 4.5 7.4 1.0
OD2 A:ASP124 4.7 9.8 1.0
CAW A:3S0304 4.7 10.7 0.9
CB A:3S0304 4.8 14.4 0.9
O A:HOH605 4.8 35.8 1.0
OXT A:3S0304 4.8 25.1 0.9
CG A:ASP124 4.8 8.7 1.0
CA A:HIS122 4.9 7.0 1.0
CAS A:3S0304 4.9 11.6 0.9

Zinc binding site 2 out of 4 in 5o2e

Go back to Zinc Binding Sites List in 5o2e
Zinc binding site 2 out of 4 in the Crystal Structure of Ndm-1 in Complex with Hydrolyzed Cefuroxime - 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 Cefuroxime - New Refinement within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:11.5
occ:0.90
 OD2 A:ASP124 2.0 9.8 1.0
O A:HOH438 2.1 13.1 1.0
OAX A:3S0304 2.1 10.5 0.9
NE2 A:HIS250 2.1 9.7 1.0
SG A:CYS208 2.3 8.7 1.0
NAR A:3S0304 2.4 11.8 0.9
CAW A:3S0304 3.0 10.7 0.9
CAS A:3S0304 3.1 11.6 0.9
CE1 A:HIS250 3.1 9.7 1.0
CG A:ASP124 3.1 8.7 1.0
CD2 A:HIS250 3.2 9.6 1.0
CB A:CYS208 3.4 7.9 1.0
CB A:3S0304 3.4 14.4 0.9
OD1 A:ASP124 3.5 9.0 1.0
ZN A:ZN301 3.8 11.0 1.0
CA A:3S0304 4.0 16.4 0.9
O A:3S0304 4.2 16.7 0.9
OAY A:3S0304 4.2 11.8 0.9
ND1 A:HIS250 4.2 11.6 1.0
CG A:HIS250 4.3 10.8 1.0
CB A:SER249 4.4 8.3 1.0
NE2 A:HIS189 4.4 8.2 1.0
CB A:ASP124 4.4 8.3 1.0
CAT A:3S0304 4.5 14.5 0.9
CE1 A:HIS189 4.6 7.9 1.0
C A:3S0304 4.6 16.2 0.9
CA A:CYS208 4.6 7.9 1.0
CE1 A:HIS120 4.6 10.1 1.0
OG A:SER249 4.7 8.5 1.0
NE2 A:HIS120 4.7 8.7 1.0
CAZ A:3S0304 4.8 16.3 0.9
SAV A:3S0304 4.9 14.9 0.9

Zinc binding site 3 out of 4 in 5o2e

Go back to Zinc Binding Sites List in 5o2e
Zinc binding site 3 out of 4 in the Crystal Structure of Ndm-1 in Complex with Hydrolyzed Cefuroxime - 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 Cefuroxime - New Refinement within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:10.3
occ:1.00
 NE2 B:HIS189 2.0 7.0 1.0
O B:HOH459 2.0 12.4 1.0
ND1 B:HIS122 2.0 9.0 1.0
NE2 B:HIS120 2.1 7.8 1.0
OXT B:3S0304 2.9 16.2 0.9
CE1 B:HIS122 3.0 9.9 1.0
CD2 B:HIS189 3.0 6.3 1.0
CE1 B:HIS120 3.0 8.5 1.0
CE1 B:HIS189 3.0 7.5 1.0
CG B:HIS122 3.0 8.2 1.0
CD2 B:HIS120 3.1 7.0 1.0
CB B:HIS122 3.4 7.5 1.0
C B:3S0304 3.7 19.0 0.9
ZN B:ZN303 3.8 10.0 0.9
NE2 B:HIS122 4.1 10.2 1.0
OD1 B:ASP124 4.1 9.1 1.0
CA B:3S0304 4.1 18.7 0.9
ND1 B:HIS120 4.1 7.2 1.0
ND1 B:HIS189 4.1 6.3 1.0
CD2 B:HIS122 4.1 8.7 1.0
CG B:HIS189 4.1 5.4 1.0
SG B:CYS208 4.2 7.7 1.0
OAY B:3S0304 4.2 10.4 0.9
CG B:HIS120 4.2 5.8 1.0
CB B:CYS208 4.3 7.3 1.0
NAR B:3S0304 4.3 10.0 0.9
CG2 B:THR190 4.5 7.5 1.0
O B:HOH599 4.5 14.9 0.5
OD2 B:ASP124 4.7 9.3 1.0
CAW B:3S0304 4.8 10.2 0.9
CG B:ASP124 4.8 8.1 1.0
CA B:HIS122 4.8 6.6 1.0
CB B:3S0304 4.9 13.5 0.9
O B:3S0304 5.0 24.9 0.9
CAS B:3S0304 5.0 10.5 0.9

Zinc binding site 4 out of 4 in 5o2e

Go back to Zinc Binding Sites List in 5o2e
Zinc binding site 4 out of 4 in the Crystal Structure of Ndm-1 in Complex with Hydrolyzed Cefuroxime - 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 Cefuroxime - New Refinement within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn303

b:10.0
occ:0.90
 OD2 B:ASP124 2.0 9.3 1.0
NE2 B:HIS250 2.1 8.0 1.0
O B:HOH459 2.1 12.4 1.0
OAY B:3S0304 2.1 10.4 0.9
SG B:CYS208 2.3 7.7 1.0
NAR B:3S0304 2.3 10.0 0.9
CAW B:3S0304 3.0 10.2 0.9
CAS B:3S0304 3.1 10.5 0.9
CE1 B:HIS250 3.1 8.1 1.0
CG B:ASP124 3.1 8.1 1.0
CD2 B:HIS250 3.2 8.2 1.0
CB B:3S0304 3.3 13.5 0.9
CB B:CYS208 3.3 7.3 1.0
OD1 B:ASP124 3.5 9.1 1.0
ZN B:ZN302 3.8 10.3 1.0
CA B:3S0304 4.0 18.7 0.9
ND1 B:HIS250 4.2 7.6 1.0
OAX B:3S0304 4.2 10.7 0.9
OXT B:3S0304 4.2 16.2 0.9
CG B:HIS250 4.3 8.2 1.0
NE2 B:HIS189 4.3 7.0 1.0
CB B:SER249 4.4 6.5 1.0
CB B:ASP124 4.4 7.3 1.0
C B:3S0304 4.5 19.0 0.9
CAT B:3S0304 4.5 13.9 0.9
CE1 B:HIS189 4.6 7.5 1.0
CA B:CYS208 4.6 7.3 1.0
CE1 B:HIS120 4.6 8.5 1.0
OG B:SER249 4.7 7.2 1.0
NE2 B:HIS120 4.7 7.8 1.0
CAZ B:3S0304 4.8 14.2 0.9
SAV B:3S0304 4.9 15.2 0.9

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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