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Bismuth in PDB 5xp9: Crystal Structure of Bismuth Bound Ndm-1

Enzymatic activity of Crystal Structure of Bismuth Bound Ndm-1

All present enzymatic activity of Crystal Structure of Bismuth Bound Ndm-1:
3.5.2.6;

Protein crystallography data

The structure of Crystal Structure of Bismuth Bound Ndm-1, PDB code: 5xp9 was solved by H.Zhang, G.Ma, T.P.Lai, H.Sun, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.29 / 1.55
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 41.595, 60.185, 41.796, 90.00, 98.95, 90.00
R / Rfree (%) 16.3 / 19.4

Bismuth Binding Sites:

The binding sites of Bismuth atom in the Crystal Structure of Bismuth Bound Ndm-1 (pdb code 5xp9). This binding sites where shown within 5.0 Angstroms radius around Bismuth atom.
In total 2 binding sites of Bismuth where determined in the Crystal Structure of Bismuth Bound Ndm-1, PDB code: 5xp9:
Jump to Bismuth binding site number: 1; 2;

Bismuth binding site 1 out of 2 in 5xp9

Go back to Bismuth Binding Sites List in 5xp9
Bismuth binding site 1 out of 2 in the Crystal Structure of Bismuth Bound Ndm-1


Mono view


Stereo pair view

A full contact list of Bismuth with other atoms in the Bi binding site number 1 of Crystal Structure of Bismuth Bound Ndm-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Bi301

b:14.9
occ:0.55
BI A:BS3301 0.0 14.9 0.6
BI A:BS3301 2.2 18.4 0.1
O A:HOH565 2.6 35.1 1.0
NE2 A:HIS120 2.7 15.6 1.0
OD2 A:ASP124 2.7 16.7 1.0
SG A:CYS208 2.7 14.3 0.8
NE2 A:HIS189 2.9 20.7 1.0
OD1 A:ASP124 3.0 16.8 1.0
CE1 A:HIS120 3.3 15.2 1.0
CG A:ASP124 3.3 14.7 1.0
ND1 A:HIS122 3.3 18.4 1.0
CB A:CYS208 3.6 14.5 1.0
CD2 A:HIS189 3.7 20.0 1.0
CE1 A:HIS189 3.8 20.6 1.0
CD2 A:HIS120 3.9 15.1 1.0
CB A:HIS122 4.0 14.4 1.0
CG A:HIS122 4.1 16.5 1.0
NE2 A:HIS250 4.2 17.7 1.0
CE1 A:HIS122 4.4 18.5 1.0
ND1 A:HIS120 4.5 15.1 1.0
O A:HOH554 4.6 33.0 1.0
CG A:LYS125 4.7 11.3 1.0
CB A:ASP124 4.8 13.3 1.0
CG A:HIS189 4.8 19.8 1.0
ND1 A:HIS189 4.8 20.9 1.0
CG A:HIS120 4.8 14.5 1.0

Bismuth binding site 2 out of 2 in 5xp9

Go back to Bismuth Binding Sites List in 5xp9
Bismuth binding site 2 out of 2 in the Crystal Structure of Bismuth Bound Ndm-1


Mono view


Stereo pair view

A full contact list of Bismuth with other atoms in the Bi binding site number 2 of Crystal Structure of Bismuth Bound Ndm-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Bi301

b:18.4
occ:0.10
BI A:BS3301 0.0 18.4 0.1
O A:HOH565 2.0 35.1 1.0
BI A:BS3301 2.2 14.9 0.6
NE2 A:HIS250 2.2 17.7 1.0
OD2 A:ASP124 2.5 16.7 1.0
SG A:CYS208 2.7 14.3 0.8
CD2 A:HIS250 3.0 17.5 1.0
CE1 A:HIS250 3.4 17.6 1.0
NE2 A:HIS189 3.6 20.7 1.0
CG A:ASP124 3.6 14.7 1.0
CB A:CYS208 3.7 14.5 1.0
O A:HOH543 3.8 28.4 1.0
CE1 A:HIS189 3.8 20.6 1.0
OD1 A:ASP124 4.1 16.8 1.0
CG A:HIS250 4.2 17.4 1.0
ND1 A:HIS250 4.4 17.8 1.0
CD2 A:HIS189 4.6 20.0 1.0
CB A:ASP124 4.7 13.3 1.0
NE2 A:HIS120 4.7 15.6 1.0
CB A:SER249 4.8 12.7 1.0
ND1 A:HIS189 4.9 20.9 1.0
CA A:CYS208 4.9 14.4 1.0
CE1 A:HIS120 5.0 15.2 1.0

Reference:

R.Wang, T.P.Lai, P.Gao, H.Zhang, P.L.Ho, P.C.Woo, G.Ma, R.Y.Kao, H.Li, H.Sun. Bismuth Antimicrobial Drugs Serve As Broad-Spectrum Metallo-Beta-Lactamase Inhibitors Nat Commun V. 9 439 2018.
ISSN: ESSN 2041-1723
PubMed: 29382822
DOI: 10.1038/S41467-018-02828-6
Page generated: Sat Dec 12 01:59:23 2020

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