Zinc in PDB 5cgw: Crystal Structure of Fox-4 Cephamycinase Mutant Y150F

All present enzymatic activity of Crystal Structure of Fox-4 Cephamycinase Mutant Y150F:
3.5.2.6;

The structure of Crystal Structure of Fox-4 Cephamycinase Mutant Y150F, PDB code: 5cgw was solved by V.N.Malashkevich, R.Toro, S.Lefurgy, S.C.Almo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.28 / 1.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	53.215, 56.608, 54.179, 90.00, 96.24, 90.00
R / Rfree (%)	17.2 / 20.7

The binding sites of Zinc atom in the Crystal Structure of Fox-4 Cephamycinase Mutant Y150F (pdb code 5cgw). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Crystal Structure of Fox-4 Cephamycinase Mutant Y150F, PDB code: 5cgw:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Crystal Structure of Fox-4 Cephamycinase Mutant Y150F


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 Fox-4 Cephamycinase Mutant Y150F within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:25.5 occ:1.00 O A:HOH844 2.0 26.9 1.0 O A:HOH604 2.1 22.1 1.0 NE2 A:HIS160 2.1 16.9 1.0 OXT A:ACT408 2.3 22.9 1.0 CE1 A:HIS160 3.0 18.8 1.0 C A:ACT408 3.1 34.0 1.0 CD2 A:HIS160 3.1 18.0 1.0 O A:ACT408 3.1 43.6 1.0 HE1 A:HIS160 3.2 22.6 1.0 HD2 A:HIS160 3.3 21.6 1.0 HE21 A:GLN132 3.4 24.9 1.0 HE1 A:TRP95 3.6 22.5 1.0 HZ2 A:TRP95 4.0 24.7 1.0 NE2 A:GLN132 4.0 20.8 1.0 OD1 A:ASN128 4.1 26.9 1.0 HE22 A:GLN132 4.1 24.9 1.0 HE1 A:MET131 4.1 34.6 1.0 O A:HOH821 4.2 24.2 1.0 ND1 A:HIS160 4.2 24.7 1.0 NE1 A:TRP95 4.2 18.7 1.0 CG A:HIS160 4.2 20.1 1.0 HD21 A:ASN128 4.4 34.7 1.0 O A:HOH660 4.4 29.0 1.0 CH3 A:ACT408 4.5 33.5 1.0 CZ2 A:TRP95 4.6 20.6 1.0 HD23 A:LEU161 4.6 17.0 1.0 CE2 A:TRP95 4.7 18.1 1.0 H1 A:ACT408 4.8 40.2 1.0 HD21 A:LEU161 4.9 17.0 1.0 CE A:MET131 4.9 28.8 1.0 HD1 A:HIS160 4.9 29.6 1.0 CG A:ASN128 4.9 25.4 1.0 ND2 A:ASN128 5.0 28.9 1.0 HE2 A:MET131 5.0 34.6 1.0

Zinc binding site 2 out of 5 in the Crystal Structure of Fox-4 Cephamycinase Mutant Y150F


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 Fox-4 Cephamycinase Mutant Y150F within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:14.9 occ:1.00 O A:HOH781 1.8 14.7 1.0 ND1 A:HIS39 2.0 14.4 1.0 OE1 A:GLU5 2.0 19.1 1.0 OE2 A:GLU5 2.5 20.7 1.0 CD A:GLU5 2.6 17.7 1.0 CE1 A:HIS39 2.9 14.7 1.0 HB3 A:HIS39 3.0 16.1 1.0 HE1 A:HIS39 3.0 17.6 1.0 CG A:HIS39 3.1 13.8 1.0 CB A:HIS39 3.5 13.4 1.0 O A:HOH501 3.7 33.5 1.0 HD23 A:LEU8 3.7 28.6 1.0 HA A:HIS39 3.9 15.8 1.0 CG A:GLU5 4.0 22.4 1.0 NE2 A:HIS39 4.0 14.4 1.0 HG3 A:GLU5 4.1 26.9 1.0 CD2 A:HIS39 4.1 16.4 1.0 HB2 A:HIS39 4.3 16.1 1.0 CA A:HIS39 4.3 13.2 1.0 HG2 A:GLU5 4.3 26.9 1.0 CD2 A:LEU8 4.6 23.8 1.0 HZ A:PHE41 4.7 23.2 1.0 HA A:GLU5 4.7 25.8 1.0 HD21 A:LEU8 4.7 28.6 1.0 HE2 A:HIS39 4.8 17.3 1.0 H A:TYR40 4.9 15.7 1.0 O A:ALA38 5.0 13.8 1.0 HD22 A:LEU8 5.0 28.6 1.0

Zinc binding site 3 out of 5 in the Crystal Structure of Fox-4 Cephamycinase Mutant Y150F


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 Fox-4 Cephamycinase Mutant Y150F within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:24.8 occ:1.00 OE2 A:GLU361 1.9 24.1 1.0 ND1 A:HIS1 2.1 21.6 1.0 O A:HOH767 2.1 39.6 1.0 HB3 A:HIS1 2.8 45.8 1.0 CD A:GLU361 2.8 31.0 1.0 O A:HOH823 3.0 36.9 1.0 OE1 A:GLU361 3.0 33.8 1.0 CG A:HIS1 3.0 31.0 1.0 CE1 A:HIS1 3.1 27.6 1.0 HE1 A:HIS1 3.3 33.2 1.0 CB A:HIS1 3.3 38.2 1.0 HA A:HIS1 3.5 51.6 1.0 O A:HOH614 3.9 64.6 1.0 CA A:HIS1 4.0 43.0 1.0 HB2 A:HIS1 4.2 45.8 1.0 CD2 A:HIS1 4.2 36.6 1.0 NE2 A:HIS1 4.2 32.4 1.0 CG A:GLU361 4.2 26.6 1.0 O A:HOH623 4.3 26.1 1.0 HG2 A:GLU361 4.4 31.9 1.0 HG3 A:GLU361 4.5 31.9 1.0 HA A:GLU361 4.8 29.1 1.0 O A:HIS1 4.9 46.1 1.0 C A:HIS1 4.9 47.2 1.0 HE2 A:HIS1 5.0 38.8 1.0

Zinc binding site 4 out of 5 in the Crystal Structure of Fox-4 Cephamycinase Mutant Y150F


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 Fox-4 Cephamycinase Mutant Y150F within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn404 b:19.8 occ:1.00 OXT A:ACT407 2.0 22.0 1.0 OD1 A:ASP126 2.0 21.6 1.0 OE1 A:GLU124 2.2 25.3 1.0 O A:ACT407 2.6 27.4 1.0 C A:ACT407 2.6 21.6 1.0 CG A:ASP126 2.7 17.2 1.0 OD2 A:ASP126 2.7 20.2 1.0 CD A:GLU124 3.4 53.8 1.0 HD2 A:LYS130 3.5 36.3 1.0 HE3 A:LYS130 3.6 53.2 1.0 O A:GLU124 3.9 19.6 1.0 OE2 A:GLU124 3.9 65.2 1.0 CH3 A:ACT407 4.1 32.3 1.0 CB A:ASP126 4.1 17.2 1.0 CD A:LYS130 4.2 30.2 1.0 H A:ASP126 4.3 20.8 1.0 CE A:LYS130 4.3 44.3 1.0 HD3 A:LYS130 4.4 36.3 1.0 H1 A:ACT407 4.4 38.7 1.0 HB2 A:ASP126 4.5 20.6 1.0 HB3 A:SER127 4.5 25.4 1.0 HG3 A:GLU124 4.5 81.3 1.0 O A:HOH510 4.6 25.2 1.0 HE2 A:LYS130 4.6 53.2 1.0 CG A:GLU124 4.6 67.8 1.0 H2 A:ACT407 4.7 38.7 1.0 H3 A:ACT407 4.7 38.7 1.0 HB3 A:ASP126 4.7 20.6 1.0 C A:ASP126 4.7 19.4 1.0 HA A:GLU124 4.7 27.9 1.0 CA A:ASP126 4.8 18.7 1.0 N A:ASP126 4.8 17.4 1.0 O A:ASP126 4.8 23.2 1.0 C A:GLU124 4.9 18.3 1.0

Zinc binding site 5 out of 5 in the Crystal Structure of Fox-4 Cephamycinase Mutant Y150F


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Fox-4 Cephamycinase Mutant Y150F within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn405 b:27.8 occ:1.00 O A:HOH809 2.0 38.8 1.0 ND1 A:HIS185 2.1 20.1 1.0 O A:HOH822 2.4 31.9 1.0 O A:HOH555 2.4 18.0 1.0 HA A:HIS185 2.9 16.5 1.0 CE1 A:HIS185 3.1 28.4 1.0 CG A:HIS185 3.2 22.2 1.0 HE1 A:HIS185 3.2 34.1 1.0 HB3 A:HIS185 3.2 18.2 1.0 CB A:HIS185 3.5 15.2 1.0 CA A:HIS185 3.6 13.8 1.0 O A:HOH806 3.8 23.4 1.0 HG3 A:PRO180 3.9 20.8 1.0 HA A:PRO180 4.0 18.5 1.0 NE2 A:HIS185 4.2 30.8 1.0 O A:LEU184 4.3 18.2 1.0 CD2 A:HIS185 4.3 20.1 1.0 HB3 A:PRO180 4.4 21.0 1.0 O A:HOH557 4.4 22.2 1.0 HB2 A:HIS185 4.5 18.2 1.0 N A:HIS185 4.6 15.4 1.0 O A:HIS185 4.6 18.2 1.0 C A:HIS185 4.6 15.5 1.0 O A:HOH551 4.7 21.9 1.0 C A:LEU184 4.7 15.0 1.0 CG A:PRO180 4.7 17.3 1.0 CA A:PRO180 4.8 15.4 1.0 CB A:PRO180 4.9 17.5 1.0 HE2 A:HIS185 5.0 37.0 1.0

S.T.Lefurgy, V.N.Malashkevich, J.T.Aguilan, E.Nieves, E.C.Mundorff, B.Biju, M.A.Noel, R.Toro, D.Baiwir, K.M.Papp-Wallace, S.C.Almo, J.M.Frere, G.Bou, R.A.Bonomo. Fox-4 Cephamycinase: An Analysis of Structure and Function. Antimicrob.Agents Chemother. 2015.
ISSN: ESSN 1098-6596
PubMed: 26525784
DOI: 10.1128/AAC.01887-15