Zinc in PDB 6twt: Crystal Structure of N-Terminally Truncated Ndm-1 Metallo-Beta- Lactamase

The structure of Crystal Structure of N-Terminally Truncated Ndm-1 Metallo-Beta- Lactamase, PDB code: 6twt was solved by B.Imiolczyk, J.Czyrko-Horczak, K.Brzezinski, M.Jaskolski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	53.58 / 0.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	70.482, 73.980, 77.715, 90.00, 90.00, 90.00
R / Rfree (%)	10.5 / 12

The structure of Crystal Structure of N-Terminally Truncated Ndm-1 Metallo-Beta- Lactamase also contains other interesting chemical elements:

Chlorine	(Cl)	6 atoms
Calcium	(Ca)	5 atoms

The binding sites of Zinc atom in the Crystal Structure of N-Terminally Truncated Ndm-1 Metallo-Beta- Lactamase (pdb code 6twt). 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 N-Terminally Truncated Ndm-1 Metallo-Beta- Lactamase, PDB code: 6twt:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of N-Terminally Truncated Ndm-1 Metallo-Beta- Lactamase


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 N-Terminally Truncated Ndm-1 Metallo-Beta- Lactamase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:13.0 occ:0.95 O A:HOH412 1.9 15.0 1.0 NE2 A:HIS189 2.0 10.3 1.0 ND1 A:HIS122 2.0 12.0 1.0 NE2 A:HIS120 2.1 10.7 1.0 O A:HOH571 3.0 32.1 1.0 CD2 A:HIS189 3.0 9.5 1.0 CE1 A:HIS120 3.0 11.0 1.0 CE1 A:HIS122 3.0 13.5 1.0 CE1 A:HIS189 3.0 10.6 1.0 CG A:HIS122 3.0 10.6 1.0 CD2 A:HIS120 3.1 9.2 1.0 CB A:HIS122 3.3 9.6 1.0 OD1 A:ASP124 4.0 13.8 1.0 O A:HOH588 4.0 19.0 0.5 O A:HOH588 4.0 8.5 0.5 ZN A:ZN302 4.1 12.4 0.8 NE2 A:HIS122 4.1 13.8 1.0 ND1 A:HIS189 4.1 10.2 1.0 ND1 A:HIS120 4.1 10.8 1.0 CG A:HIS189 4.1 9.3 1.0 CD2 A:HIS122 4.2 12.1 1.0 SG A:CYS208 4.2 10.2 1.0 CG A:HIS120 4.2 9.4 1.0 CB A:CYS208 4.3 9.6 1.0 CG2 A:THR190 4.4 9.5 1.0 O A:HOH606 4.8 33.6 1.0 OD2 A:ASP124 4.8 14.6 1.0 CA A:HIS122 4.8 8.7 1.0 CG A:ASP124 4.8 10.4 1.0 O A:HOH598 4.8 35.1 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of N-Terminally Truncated Ndm-1 Metallo-Beta- Lactamase


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 N-Terminally Truncated Ndm-1 Metallo-Beta- Lactamase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:12.4 occ:0.85 OD2 A:ASP124 2.0 14.6 1.0 NE2 A:HIS250 2.0 12.8 1.0 O A:HOH588 2.2 8.5 0.5 O A:HOH588 2.3 19.0 0.5 SG A:CYS208 2.3 10.2 1.0 O A:HOH412 2.7 15.0 1.0 CE1 A:HIS250 3.0 12.4 1.0 CD2 A:HIS250 3.1 12.9 1.0 CG A:ASP124 3.1 10.4 1.0 CB A:CYS208 3.4 9.6 1.0 OD1 A:ASP124 3.5 13.8 1.0 ZN A:ZN301 4.1 13.0 0.9 ND1 A:HIS250 4.1 12.8 1.0 CB A:SER249 4.2 10.2 1.0 CG A:HIS250 4.2 13.2 1.0 CB A:ASP124 4.4 9.9 1.0 O A:HOH511 4.5 32.4 1.0 CA A:CYS208 4.5 9.6 1.0 OG A:SER249 4.5 10.2 1.0 NE2 A:HIS189 4.5 10.3 1.0 CE1 A:HIS189 4.6 10.6 1.0 O A:HOH515 4.7 15.0 0.3 O A:HOH571 4.8 32.1 1.0 CE1 A:HIS120 4.8 11.0 1.0 NE2 A:HIS120 4.9 10.7 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of N-Terminally Truncated Ndm-1 Metallo-Beta- Lactamase


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 N-Terminally Truncated Ndm-1 Metallo-Beta- Lactamase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:14.2 occ:0.95 O B:HOH408 1.9 15.7 1.0 NE2 B:HIS189 2.0 10.3 1.0 ND1 B:HIS122 2.0 11.8 1.0 NE2 B:HIS120 2.1 10.8 1.0 O B:HOH538 2.8 16.3 0.5 CD2 B:HIS189 3.0 9.5 1.0 CE1 B:HIS120 3.0 12.1 1.0 CE1 B:HIS122 3.0 14.2 1.0 CE1 B:HIS189 3.0 10.4 1.0 CG B:HIS122 3.0 10.3 1.0 CD2 B:HIS120 3.0 8.7 1.0 CB B:HIS122 3.4 9.0 1.0 O B:HOH599 4.0 10.9 0.4 O B:HOH599 4.0 13.9 0.6 OD1 B:ASP124 4.0 12.7 1.0 ND1 B:HIS120 4.1 11.3 1.0 NE2 B:HIS122 4.1 13.9 1.0 ND1 B:HIS189 4.1 9.9 1.0 CG B:HIS189 4.1 9.0 1.0 CG B:HIS120 4.2 9.2 1.0 CD2 B:HIS122 4.2 12.2 1.0 ZN B:ZN303 4.2 12.3 0.8 SG B:CYS208 4.3 10.2 1.0 CB B:CYS208 4.4 10.0 1.0 CG2 B:THR190 4.4 9.7 1.0 O B:HOH588 4.7 26.9 1.0 O B:HOH615 4.7 38.2 1.0 O B:HOH632 4.7 23.9 0.5 OD2 B:ASP124 4.8 14.5 1.0 CA B:HIS122 4.8 8.3 1.0 CG B:ASP124 4.9 9.8 1.0 O B:HOH632 5.0 17.0 0.5

Zinc binding site 4 out of 4 in the Crystal Structure of N-Terminally Truncated Ndm-1 Metallo-Beta- Lactamase


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 N-Terminally Truncated Ndm-1 Metallo-Beta- Lactamase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:12.3 occ:0.85 OD2 B:ASP124 2.0 14.5 1.0 NE2 B:HIS250 2.0 12.2 1.0 O B:HOH599 2.2 13.9 0.6 O B:HOH599 2.2 10.9 0.4 SG B:CYS208 2.3 10.2 1.0 O B:HOH408 2.8 15.7 1.0 CE1 B:HIS250 3.0 11.7 1.0 CD2 B:HIS250 3.0 12.2 1.0 CG B:ASP124 3.1 9.8 1.0 CB B:CYS208 3.4 10.0 1.0 OD1 B:ASP124 3.5 12.7 1.0 ND1 B:HIS250 4.1 12.6 1.0 CB B:SER249 4.1 9.9 1.0 CG B:HIS250 4.2 13.1 1.0 ZN B:ZN302 4.2 14.2 0.9 CB B:ASP124 4.4 9.1 1.0 O B:HOH503 4.5 26.2 0.5 CA B:CYS208 4.5 9.7 1.0 OG B:SER249 4.5 10.1 1.0 NE2 B:HIS189 4.6 10.3 1.0 CE1 B:HIS189 4.7 10.4 1.0 CE1 B:HIS120 4.8 12.1 1.0 O B:HOH538 5.0 16.3 0.5 NE2 B:HIS120 5.0 10.8 1.0

J.E.Raczynska, B.Imiolczyk, M.Komorowska, J.Sliwiak, J.Czyrko-Horczak, K.Brzezinski, M.Jaskolski. Flexible Loops of New Delhi Metallo-Beta-Lactamase Modulate Its Activity Towards Different Substrates. Int.J.Biol.Macromol. 2020.
ISSN: ISSN 0141-8130
PubMed: 32353499
DOI: 10.1016/J.IJBIOMAC.2020.04.219