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Zinc in PDB 5xp6: Native Structure of Ndm-1 Crystallized at PH5.5

Enzymatic activity of Native Structure of Ndm-1 Crystallized at PH5.5

All present enzymatic activity of Native Structure of Ndm-1 Crystallized at PH5.5:
3.5.2.6;

Protein crystallography data

The structure of Native Structure of Ndm-1 Crystallized at PH5.5, PDB code: 5xp6 was solved by H.Zhang, G.Ma, J.Lai, H.Sun, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.71 / 0.95
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 41.425, 59.807, 42.098, 90.00, 97.78, 90.00
R / Rfree (%) 12.7 / 13.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Native Structure of Ndm-1 Crystallized at PH5.5 (pdb code 5xp6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Native Structure of Ndm-1 Crystallized at PH5.5, PDB code: 5xp6:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5xp6

Go back to Zinc Binding Sites List in 5xp6
Zinc binding site 1 out of 2 in the Native Structure of Ndm-1 Crystallized at PH5.5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Native Structure of Ndm-1 Crystallized at PH5.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:7.2
occ:0.96
O A:OH303 1.9 7.7 0.9
NE2 A:HIS189 2.0 6.4 1.0
NE2 A:HIS120 2.0 6.5 1.0
ND1 A:HIS122 2.1 7.0 1.0
CD2 A:HIS189 2.9 6.6 1.0
CE1 A:HIS120 3.0 6.7 1.0
CD2 A:HIS120 3.0 6.0 1.0
CE1 A:HIS122 3.0 8.0 1.0
CE1 A:HIS189 3.0 7.2 1.0
CG A:HIS122 3.0 6.5 1.0
CB A:HIS122 3.3 5.9 1.0
O A:HOH409 3.6 13.7 1.0
O2 A:SIN309 3.9 9.9 1.0
ZN A:ZN302 3.9 6.4 0.9
SG A:CYS208 4.0 6.0 1.0
OD1 A:ASP124 4.0 6.8 1.0
ND1 A:HIS120 4.1 6.4 1.0
CG A:HIS189 4.1 6.5 1.0
ND1 A:HIS189 4.1 7.3 1.0
NE2 A:HIS122 4.1 8.2 1.0
CG A:HIS120 4.1 5.6 1.0
CD2 A:HIS122 4.2 7.2 1.0
CB A:CYS208 4.2 6.1 1.0
CG2 A:THR190 4.3 7.1 1.0
OD2 A:ASP124 4.8 6.8 1.0
CA A:HIS122 4.8 5.3 1.0
CG A:ASP124 4.8 5.4 1.0
C1 A:SIN309 4.8 11.7 1.0

Zinc binding site 2 out of 2 in 5xp6

Go back to Zinc Binding Sites List in 5xp6
Zinc binding site 2 out of 2 in the Native Structure of Ndm-1 Crystallized at PH5.5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Native Structure of Ndm-1 Crystallized at PH5.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:6.4
occ:0.87
OD2 A:ASP124 2.0 6.8 1.0
O2 A:SIN309 2.0 9.9 1.0
NE2 A:HIS250 2.1 6.7 1.0
SG A:CYS208 2.3 6.0 1.0
O A:OH303 2.5 7.7 0.9
C1 A:SIN309 2.9 11.7 1.0
CE1 A:HIS250 3.0 6.6 1.0
CG A:ASP124 3.0 5.4 1.0
CD2 A:HIS250 3.1 7.0 1.0
C2 A:SIN309 3.3 12.2 1.0
CB A:CYS208 3.4 6.1 1.0
OD1 A:ASP124 3.4 6.8 1.0
ZN A:ZN301 3.9 7.2 1.0
O1 A:SIN309 4.0 14.5 1.0
ND1 A:HIS250 4.2 6.7 1.0
CG A:HIS250 4.2 6.8 1.0
CB A:SER249 4.3 5.8 1.0
CB A:ASP124 4.3 5.0 1.0
O A:HOH409 4.3 13.7 1.0
NE2 A:HIS189 4.4 6.4 1.0
CE1 A:HIS189 4.4 7.2 1.0
CA A:CYS208 4.5 6.2 1.0
OG A:SER249 4.6 5.8 1.0
C3 A:SIN309 4.8 13.9 1.0
CE1 A:HIS120 4.9 6.7 1.0
NE2 A:HIS120 4.9 6.5 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: Wed Dec 16 11:21:05 2020

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