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Zinc in PDB 5n0i: Crystal Structure of Ndm-1 in Complex with Beta-Mercaptoethanol - New Refinement

Enzymatic activity of Crystal Structure of Ndm-1 in Complex with Beta-Mercaptoethanol - New Refinement

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

Protein crystallography data

The structure of Crystal Structure of Ndm-1 in Complex with Beta-Mercaptoethanol - New Refinement, PDB code: 5n0i was solved by J.E.Raczynska, I.G.Shabalin, M.Jaskolski, W.Minor, A.Wlodawer, D.T.King, N.C.J.Strynadka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.74 / 1.47
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 107.220, 107.220, 92.850, 90.00, 90.00, 90.00
R / Rfree (%) 11 / 14.7

Other elements in 5n0i:

The structure of Crystal Structure of Ndm-1 in Complex with Beta-Mercaptoethanol - 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 Beta-Mercaptoethanol - New Refinement (pdb code 5n0i). 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 Beta-Mercaptoethanol - New Refinement, PDB code: 5n0i:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5n0i

Go back to Zinc Binding Sites List in 5n0i
Zinc binding site 1 out of 4 in the Crystal Structure of Ndm-1 in Complex with Beta-Mercaptoethanol - 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 Beta-Mercaptoethanol - New Refinement within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:13.4
occ:0.80
 OD2 A:ASP124 2.0 15.7 1.0
NE2 A:HIS250 2.0 14.5 1.0
SG A:CYS208 2.3 15.9 1.0
S2 A:BME303 2.3 14.1 0.8
CG A:ASP124 3.0 13.0 1.0
CE1 A:HIS250 3.0 17.0 1.0
CD2 A:HIS250 3.0 15.5 1.0
OD1 A:ASP124 3.3 15.5 1.0
C2 A:BME303 3.4 16.6 0.8
CB A:CYS208 3.4 15.5 1.0
ZN A:ZN302 3.6 14.1 1.0
C1 A:BME303 3.8 19.9 0.8
ND1 A:HIS250 4.1 15.9 1.0
CG A:HIS250 4.2 15.6 1.0
CB A:SER249 4.3 15.2 1.0
CB A:ASP124 4.3 11.6 1.0
CE1 A:HIS120 4.4 16.0 1.0
O A:HOH529 4.4 39.4 1.0
O1 A:BME303 4.4 26.3 0.8
O A:HOH471 4.4 26.0 1.0
NE2 A:HIS189 4.4 13.3 1.0
NE2 A:HIS120 4.5 12.5 1.0
OG A:SER249 4.6 16.6 1.0
CA A:CYS208 4.7 13.1 1.0
CE1 A:HIS189 4.7 15.0 1.0
CE A:LYS125 4.8 17.6 1.0

Zinc binding site 2 out of 4 in 5n0i

Go back to Zinc Binding Sites List in 5n0i
Zinc binding site 2 out of 4 in the Crystal Structure of Ndm-1 in Complex with Beta-Mercaptoethanol - 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 Beta-Mercaptoethanol - New Refinement within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:14.1
occ:1.00
 ND1 A:HIS122 2.0 13.5 1.0
NE2 A:HIS120 2.0 12.5 1.0
NE2 A:HIS189 2.0 13.3 1.0
S2 A:BME303 2.3 14.1 0.8
CE1 A:HIS122 3.0 14.8 1.0
CE1 A:HIS120 3.0 16.0 1.0
CD2 A:HIS120 3.0 11.7 1.0
CG A:HIS122 3.0 12.7 1.0
CE1 A:HIS189 3.0 15.0 1.0
CD2 A:HIS189 3.0 12.6 1.0
C2 A:BME303 3.3 16.6 0.8
CB A:HIS122 3.4 11.5 1.0
ZN A:ZN301 3.6 13.4 0.8
OD1 A:ASP124 4.1 15.5 1.0
NE2 A:HIS122 4.1 15.6 1.0
SG A:CYS208 4.1 15.9 1.0
ND1 A:HIS120 4.1 14.9 1.0
CD2 A:HIS122 4.1 14.4 1.0
CG A:HIS120 4.1 12.3 1.0
ND1 A:HIS189 4.1 13.9 1.0
CG A:HIS189 4.2 12.8 1.0
CB A:CYS208 4.2 15.5 1.0
CG2 A:THR190 4.6 13.0 1.0
C1 A:BME303 4.7 19.9 0.8
OD2 A:ASP124 4.8 15.7 1.0
CA A:HIS122 4.9 11.2 1.0
CG A:ASP124 4.9 13.0 1.0
ND2 A:ASN220 4.9 42.2 1.0

Zinc binding site 3 out of 4 in 5n0i

Go back to Zinc Binding Sites List in 5n0i
Zinc binding site 3 out of 4 in the Crystal Structure of Ndm-1 in Complex with Beta-Mercaptoethanol - 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 Beta-Mercaptoethanol - New Refinement within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:12.1
occ:0.80
 OD2 B:ASP124 2.0 15.6 1.0
NE2 B:HIS250 2.0 12.9 1.0
SG B:CYS208 2.3 14.4 1.0
S2 B:BME303 2.3 11.9 0.8
CE1 B:HIS250 3.0 12.9 1.0
CG B:ASP124 3.0 13.2 1.0
CD2 B:HIS250 3.1 14.1 1.0
OD1 B:ASP124 3.3 14.1 1.0
C2 B:BME303 3.4 13.0 0.8
CB B:CYS208 3.4 14.0 1.0
ZN B:ZN302 3.6 12.7 1.0
C1 B:BME303 3.8 17.2 0.8
ND1 B:HIS250 4.1 13.7 1.0
CG B:HIS250 4.2 12.2 1.0
CB B:SER249 4.2 13.2 1.0
CB B:ASP124 4.3 12.7 1.0
CE1 B:HIS120 4.3 15.0 1.0
O B:HOH562 4.4 29.5 1.0
NE2 B:HIS120 4.4 11.8 1.0
O1 B:BME303 4.4 23.8 0.8
NE2 B:HIS189 4.4 12.0 1.0
O B:HOH532 4.5 42.2 1.0
OG B:SER249 4.6 15.2 1.0
CA B:CYS208 4.7 12.1 1.0
CE1 B:HIS189 4.7 14.2 1.0
CE B:LYS125 4.9 16.8 1.0

Zinc binding site 4 out of 4 in 5n0i

Go back to Zinc Binding Sites List in 5n0i
Zinc binding site 4 out of 4 in the Crystal Structure of Ndm-1 in Complex with Beta-Mercaptoethanol - 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 Beta-Mercaptoethanol - New Refinement within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:12.7
occ:1.00
 NE2 B:HIS120 2.0 11.8 1.0
ND1 B:HIS122 2.0 11.8 1.0
NE2 B:HIS189 2.0 12.0 1.0
S2 B:BME303 2.3 11.9 0.8
CE1 B:HIS120 3.0 15.0 1.0
CE1 B:HIS122 3.0 12.4 1.0
CD2 B:HIS120 3.0 11.4 1.0
CD2 B:HIS189 3.0 10.5 1.0
CE1 B:HIS189 3.0 14.2 1.0
CG B:HIS122 3.0 11.2 1.0
C2 B:BME303 3.3 13.0 0.8
CB B:HIS122 3.4 11.2 1.0
ZN B:ZN301 3.6 12.1 0.8
SG B:CYS208 4.1 14.4 1.0
ND1 B:HIS120 4.1 13.6 1.0
OD1 B:ASP124 4.1 14.1 1.0
NE2 B:HIS122 4.1 14.1 1.0
CG B:HIS120 4.1 11.1 1.0
ND1 B:HIS189 4.1 14.0 1.0
CD2 B:HIS122 4.2 13.5 1.0
CB B:CYS208 4.2 14.0 1.0
CG B:HIS189 4.2 10.5 1.0
C1 B:GOL304 4.5 36.1 1.0
CG2 B:THR190 4.6 14.7 1.0
C1 B:BME303 4.7 17.2 0.8
OD2 B:ASP124 4.7 15.6 1.0
CA B:HIS122 4.8 10.2 1.0
CG B:ASP124 4.9 13.2 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 22:26:09 2024

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