Zinc in PDB 4rl2: Structural and Mechanistic Insights Into Ndm-1 Catalyzed Hydrolysis of Cephalosporins

All present enzymatic activity of Structural and Mechanistic Insights Into Ndm-1 Catalyzed Hydrolysis of Cephalosporins:
3.5.2.6;

The structure of Structural and Mechanistic Insights Into Ndm-1 Catalyzed Hydrolysis of Cephalosporins, PDB code: 4rl2 was solved by H.Feng, J.Ding, D.Zhu, X.Liu, X.Xu, Y.Zhang, S.Zang, D.-C.Wang, W.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.78 / 2.01
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	38.620, 77.570, 132.310, 90.00, 90.00, 90.00
R / Rfree (%)	14.6 / 19.3

The binding sites of Zinc atom in the Structural and Mechanistic Insights Into Ndm-1 Catalyzed Hydrolysis of Cephalosporins (pdb code 4rl2). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structural and Mechanistic Insights Into Ndm-1 Catalyzed Hydrolysis of Cephalosporins, PDB code: 4rl2:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structural and Mechanistic Insights Into Ndm-1 Catalyzed Hydrolysis of Cephalosporins


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structural and Mechanistic Insights Into Ndm-1 Catalyzed Hydrolysis of Cephalosporins within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:14.4 occ:1.00 O A:HOH561 1.8 8.8 1.0 ND1 A:HIS122 2.0 11.1 1.0 NE2 A:HIS189 2.1 9.9 1.0 NE2 A:HIS120 2.1 9.8 1.0 O A:3S3303 2.5 11.6 1.0 CD2 A:HIS189 2.9 6.7 1.0 CE1 A:HIS122 2.9 13.3 1.0 CG A:HIS122 3.0 12.1 1.0 CE1 A:HIS120 3.0 9.0 1.0 CE1 A:HIS189 3.1 11.0 1.0 CD2 A:HIS120 3.2 9.5 1.0 HA A:3S3303 3.3 19.3 1.0 C A:3S3303 3.3 15.9 1.0 CB A:HIS122 3.4 8.1 1.0 CA A:3S3303 3.8 16.1 1.0 NE2 A:HIS122 4.1 13.9 1.0 NAQ A:3S3303 4.1 19.8 1.0 CD2 A:HIS122 4.1 15.4 1.0 CG A:HIS189 4.1 8.0 1.0 ND1 A:HIS120 4.2 9.5 1.0 ND1 A:HIS189 4.2 8.2 1.0 SG A:CYS208 4.2 9.9 1.0 CG2 A:THR190 4.3 11.4 1.0 OXT A:3S3303 4.3 16.9 1.0 CG A:HIS120 4.3 8.9 1.0 OD1 A:ASP124 4.3 10.7 1.0 CB A:CYS208 4.3 10.3 1.0 ZN A:ZN302 4.5 14.7 1.0 CB A:3S3303 4.5 15.9 1.0 CA A:HIS122 4.8 9.8 1.0 HB A:3S3303 4.9 19.1 1.0 OD2 A:ASP124 4.9 10.5 1.0 O A:HOH550 4.9 17.1 1.0

Zinc binding site 2 out of 4 in the Structural and Mechanistic Insights Into Ndm-1 Catalyzed Hydrolysis of Cephalosporins


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structural and Mechanistic Insights Into Ndm-1 Catalyzed Hydrolysis of Cephalosporins within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:14.7 occ:1.00 NE2 A:HIS250 2.1 8.1 1.0 OD2 A:ASP124 2.2 10.5 1.0 OAW A:3S3303 2.3 8.7 1.0 SG A:CYS208 2.3 9.9 1.0 NAQ A:3S3303 2.4 19.8 1.0 CAR A:3S3303 2.8 19.1 1.0 HB A:3S3303 2.9 19.1 1.0 CAV A:3S3303 2.9 14.3 1.0 O A:HOH561 3.0 8.8 1.0 CD2 A:HIS250 3.1 10.1 1.0 CE1 A:HIS250 3.1 11.7 1.0 CB A:3S3303 3.2 15.9 1.0 CB A:CYS208 3.4 10.3 1.0 CG A:ASP124 3.4 11.2 1.0 HAT A:3S3303 3.5 21.5 1.0 CAS A:3S3303 3.8 19.3 1.0 OD1 A:ASP124 3.9 10.7 1.0 HAS A:3S3303 4.0 23.2 1.0 HA A:3S3303 4.0 19.3 1.0 CAT A:3S3303 4.1 17.9 1.0 OAX A:3S3303 4.2 12.7 1.0 CA A:3S3303 4.2 16.1 1.0 CB A:SER249 4.2 9.8 1.0 CG A:HIS250 4.2 13.6 1.0 ND1 A:HIS250 4.2 9.6 1.0 O A:3S3303 4.3 11.6 1.0 ZN A:ZN301 4.5 14.4 1.0 CA A:CYS208 4.5 10.8 1.0 SAU A:3S3303 4.5 17.3 1.0 OG A:SER249 4.6 9.2 1.0 CB A:ASP124 4.6 11.6 1.0 NE2 A:HIS189 4.7 9.9 1.0 C A:3S3303 4.8 15.9 1.0 CE1 A:HIS189 4.8 11.0 1.0 NZ A:LYS211 5.0 16.5 1.0

Zinc binding site 3 out of 4 in the Structural and Mechanistic Insights Into Ndm-1 Catalyzed Hydrolysis of Cephalosporins


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structural and Mechanistic Insights Into Ndm-1 Catalyzed Hydrolysis of Cephalosporins within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:14.8 occ:1.00 ND1 B:HIS122 2.0 11.0 1.0 O B:HOH599 2.0 12.7 1.0 NE2 B:HIS189 2.1 12.9 1.0 NE2 B:HIS120 2.2 8.0 1.0 O B:3S3303 2.4 13.6 1.0 CE1 B:HIS122 2.9 15.6 1.0 CD2 B:HIS189 3.0 10.2 1.0 CG B:HIS122 3.0 10.5 1.0 CD2 B:HIS120 3.1 9.1 1.0 CE1 B:HIS120 3.2 8.6 1.0 CE1 B:HIS189 3.2 11.4 1.0 C B:3S3303 3.2 13.7 1.0 HA B:3S3303 3.4 19.1 1.0 CB B:HIS122 3.4 7.5 1.0 CA B:3S3303 3.8 15.9 1.0 NE2 B:HIS122 4.0 15.4 1.0 NAQ B:3S3303 4.1 17.0 1.0 OXT B:3S3303 4.1 20.4 1.0 CD2 B:HIS122 4.1 12.1 1.0 CG B:HIS189 4.2 10.1 1.0 CG2 B:THR190 4.2 9.1 1.0 ND1 B:HIS189 4.2 8.8 1.0 ND1 B:HIS120 4.2 7.2 1.0 CG B:HIS120 4.3 7.8 1.0 OD1 B:ASP124 4.3 11.4 1.0 SG B:CYS208 4.4 7.4 1.0 CB B:CYS208 4.5 11.5 1.0 CB B:3S3303 4.5 18.6 1.0 ZN B:ZN302 4.5 14.8 1.0 CA B:HIS122 4.8 7.0 1.0 O B:HOH564 4.9 15.1 1.0 HB B:3S3303 4.9 22.3 1.0

Zinc binding site 4 out of 4 in the Structural and Mechanistic Insights Into Ndm-1 Catalyzed Hydrolysis of Cephalosporins


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structural and Mechanistic Insights Into Ndm-1 Catalyzed Hydrolysis of Cephalosporins within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:14.8 occ:1.00 NE2 B:HIS250 2.0 8.9 1.0 OD2 B:ASP124 2.2 11.1 1.0 OAW B:3S3303 2.3 15.1 1.0 NAQ B:3S3303 2.4 17.0 1.0 SG B:CYS208 2.4 7.4 1.0 CAR B:3S3303 2.7 22.0 1.0 O B:HOH599 2.8 12.7 1.0 CAV B:3S3303 2.9 13.8 1.0 CE1 B:HIS250 3.0 9.4 1.0 HB B:3S3303 3.0 22.3 1.0 CD2 B:HIS250 3.0 7.6 1.0 CB B:3S3303 3.2 18.6 1.0 CG B:ASP124 3.3 10.7 1.0 CB B:CYS208 3.4 11.5 1.0 HAT B:3S3303 3.5 23.6 1.0 CAS B:3S3303 3.8 19.2 1.0 OD1 B:ASP124 3.9 11.4 1.0 HAS B:3S3303 3.9 23.0 1.0 CAT B:3S3303 4.0 19.6 1.0 ND1 B:HIS250 4.1 9.8 1.0 HA B:3S3303 4.1 19.1 1.0 OAX B:3S3303 4.1 11.3 1.0 CG B:HIS250 4.1 10.7 1.0 CA B:3S3303 4.2 15.9 1.0 O B:3S3303 4.3 13.6 1.0 CB B:SER249 4.3 8.2 1.0 CA B:CYS208 4.5 10.9 1.0 CB B:ASP124 4.5 11.3 1.0 SAU B:3S3303 4.5 18.6 1.0 ZN B:ZN301 4.5 14.8 1.0 OG B:SER249 4.6 11.9 1.0 C B:3S3303 4.8 13.7 1.0 NE2 B:HIS189 4.8 12.9 1.0

H.Feng, J.Ding, D.Zhu, X.Liu, X.Xu, Y.Zhang, S.Zang, D.C.Wang, W.Liu. Structural and Mechanistic Insights Into Ndm-1 Catalyzed Hydrolysis of Cephalosporins. J.Am.Chem.Soc. V. 136 14694 2014.
ISSN: ISSN 0002-7863
PubMed: 25268575
DOI: 10.1021/JA508388E