Atomistry » Bismuth » PDB 4h0w-5xp9 » 5xp9
Atomistry »
  Bismuth »
    PDB 4h0w-5xp9 »
      5xp9 »

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: Mon Jul 7 02:58:47 2025

Last articles

Cl in 5G3S
Cl in 5G2P
Cl in 5G2T
Cl in 5G36
Cl in 5G2D
Cl in 5G28
Cl in 5G2C
Cl in 5G22
Cl in 5G27
Cl in 5G1Z
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy