Zinc in PDB 6nc5: Cronobacter Sakazakii (Enterobacter Sakazakii) Metallo-Beta-Lactamse Harldq Motif

The structure of Cronobacter Sakazakii (Enterobacter Sakazakii) Metallo-Beta-Lactamse Harldq Motif, PDB code: 6nc5 was solved by M.Monteiro Pedroso, D.Waite, M.Natasa, R.Mcgeary, L.Guddat, P.Hugenholtz, G.Schenk, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.05 / 2.07
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	53.468, 74.946, 76.095, 90.00, 90.00, 90.00
R / Rfree (%)	19 / 22.4

The binding sites of Zinc atom in the Cronobacter Sakazakii (Enterobacter Sakazakii) Metallo-Beta-Lactamse Harldq Motif (pdb code 6nc5). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Cronobacter Sakazakii (Enterobacter Sakazakii) Metallo-Beta-Lactamse Harldq Motif, PDB code: 6nc5:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Cronobacter Sakazakii (Enterobacter Sakazakii) Metallo-Beta-Lactamse Harldq Motif


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cronobacter Sakazakii (Enterobacter Sakazakii) Metallo-Beta-Lactamse Harldq Motif within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:26.5 occ:1.00 OD2 A:ASP91 2.0 31.8 1.0 NE2 A:HIS92 2.0 32.0 1.0 NE2 A:HIS225 2.0 26.9 1.0 O A:HOH493 2.1 32.9 1.0 CE1 A:HIS92 2.9 29.4 1.0 CG A:ASP91 2.9 33.2 1.0 CE1 A:HIS225 3.0 32.0 1.0 CD2 A:HIS92 3.0 25.3 1.0 CD2 A:HIS225 3.1 28.0 1.0 HE1 A:HIS225 3.1 38.5 1.0 HE1 A:HIS92 3.1 35.4 1.0 HD2 A:HIS92 3.2 30.5 1.0 HD2 A:HIS225 3.3 33.7 1.0 HE1 A:HIS87 3.3 29.7 1.0 OD1 A:ASP91 3.4 31.7 1.0 ZN A:ZN302 3.4 30.1 1.0 O A:HOH504 3.5 41.6 1.0 CE1 A:HIS87 3.9 24.7 1.0 ND1 A:HIS92 4.0 29.5 1.0 HB2 A:ASP91 4.0 31.7 1.0 O A:HOH466 4.0 29.9 1.0 NE2 A:HIS87 4.0 21.7 1.0 ND1 A:HIS225 4.1 38.6 1.0 CG A:HIS92 4.1 29.5 1.0 CB A:ASP91 4.1 26.4 1.0 CG A:HIS225 4.2 29.5 1.0 O A:HOH485 4.4 36.3 1.0 HD22 A:LEU41 4.4 45.0 1.0 HZ3 A:TRP20 4.4 60.0 1.0 HD21 A:ASN224 4.7 40.6 1.0 HB3 A:ASP91 4.7 31.7 1.0 ZN A:ZN303 4.7 36.3 1.0 HD21 A:LEU41 4.7 45.0 1.0 HB2 A:SER185 4.7 36.7 1.0 HD1 A:HIS92 4.8 35.5 1.0 ND2 A:ASN224 4.8 33.8 1.0 HD23 A:LEU41 4.8 45.0 1.0 HD1 A:HIS225 4.8 46.4 1.0 CD2 A:LEU41 4.8 37.4 1.0 CG A:ASN224 5.0 29.8 1.0 OD1 A:ASN224 5.0 29.5 1.0 CZ3 A:TRP20 5.0 49.9 1.0

Zinc binding site 2 out of 6 in the Cronobacter Sakazakii (Enterobacter Sakazakii) Metallo-Beta-Lactamse Harldq Motif


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cronobacter Sakazakii (Enterobacter Sakazakii) Metallo-Beta-Lactamse Harldq Motif within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:30.1 occ:1.00 O A:HOH485 1.9 36.3 1.0 NE2 A:HIS163 2.1 35.5 1.0 O A:HOH493 2.1 32.9 1.0 NE2 A:HIS87 2.2 21.7 1.0 HE1 A:HIS87 2.7 29.7 1.0 CE1 A:HIS87 2.7 24.7 1.0 CD2 A:HIS163 3.0 28.4 1.0 CE1 A:HIS163 3.1 28.1 1.0 HD2 A:HIS163 3.2 34.2 1.0 HD2 A:ARG89 3.2 43.8 1.0 HH11 A:ARG89 3.2 35.5 1.0 HE1 A:HIS163 3.3 33.8 1.0 CD2 A:HIS87 3.3 29.4 1.0 ZN A:ZN303 3.4 36.3 1.0 ZN A:ZN301 3.4 26.5 1.0 HD2 A:HIS87 3.7 35.4 1.0 O A:HOH504 3.8 41.6 1.0 HD2 A:HIS92 3.9 30.5 1.0 ND1 A:HIS87 3.9 27.2 1.0 HB2 A:ARG89 3.9 39.7 1.0 O A:HOH466 4.0 29.9 1.0 NH1 A:ARG89 4.0 29.5 1.0 CD A:ARG89 4.0 36.4 1.0 HB3 A:SER185 4.0 36.7 1.0 HD3 A:ARG89 4.1 43.8 1.0 ND1 A:HIS163 4.2 30.6 1.0 CG A:HIS163 4.2 24.6 1.0 OD2 A:ASP91 4.2 31.8 1.0 CG A:HIS87 4.2 31.4 1.0 OD1 A:ASP91 4.2 31.7 1.0 NE2 A:HIS92 4.3 32.0 1.0 HH12 A:ARG89 4.4 35.5 1.0 CD2 A:HIS92 4.4 25.3 1.0 O A:HOH516 4.5 35.3 1.0 HD1 A:HIS87 4.6 32.8 1.0 CB A:ARG89 4.7 33.0 1.0 CG A:ASP91 4.7 33.2 1.0 HB3 A:ARG89 4.7 39.7 1.0 CB A:SER185 4.7 30.5 1.0 HG A:SER185 4.7 38.9 1.0 HB2 A:SER185 4.7 36.7 1.0 OG A:SER185 4.8 32.4 1.0 CG A:ARG89 4.9 32.4 1.0 CH3 A:ACT307 4.9 34.7 1.0 HD1 A:HIS163 4.9 36.8 1.0 CZ A:ARG89 4.9 31.0 1.0 NE A:ARG89 5.0 26.4 1.0

Zinc binding site 3 out of 6 in the Cronobacter Sakazakii (Enterobacter Sakazakii) Metallo-Beta-Lactamse Harldq Motif


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cronobacter Sakazakii (Enterobacter Sakazakii) Metallo-Beta-Lactamse Harldq Motif within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:36.3 occ:1.00 O A:HOH485 1.9 36.3 1.0 O A:HOH516 2.0 35.3 1.0 O A:HOH504 2.1 41.6 1.0 O A:ACT307 2.8 35.9 1.0 C A:ACT307 3.3 31.7 1.0 HH11 A:ARG89 3.4 35.5 1.0 HD3 A:ARG89 3.4 43.8 1.0 ZN A:ZN302 3.4 30.1 1.0 CH3 A:ACT307 3.9 34.7 1.0 HD2 A:ARG89 4.0 43.8 1.0 OXT A:ACT307 4.0 38.4 1.0 NH1 A:ARG89 4.1 29.5 1.0 CD A:ARG89 4.1 36.4 1.0 HE1 A:HIS163 4.2 33.8 1.0 OD2 A:ASP91 4.2 31.8 1.0 O A:HOH493 4.2 32.9 1.0 HD11 A:LEU127 4.3 47.5 1.0 OD1 A:ASP91 4.4 31.7 1.0 HH12 A:ARG89 4.4 35.5 1.0 NE2 A:HIS163 4.5 35.5 1.0 HB3 A:ARG89 4.5 39.7 1.0 CG A:ASP91 4.5 33.2 1.0 CE1 A:HIS163 4.7 28.1 1.0 ZN A:ZN301 4.7 26.5 1.0 HZ3 A:TRP20 4.8 60.0 1.0 CZ A:ARG89 4.9 31.0 1.0 NE A:ARG89 4.9 26.4 1.0 HB2 A:ARG89 4.9 39.7 1.0 O A:HOH466 5.0 29.9 1.0

Zinc binding site 4 out of 6 in the Cronobacter Sakazakii (Enterobacter Sakazakii) Metallo-Beta-Lactamse Harldq Motif


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Cronobacter Sakazakii (Enterobacter Sakazakii) Metallo-Beta-Lactamse Harldq Motif within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn304 b:59.9 occ:1.00 OE2 A:GLU115 1.9 64.2 1.0 O4 A:PO4308 1.9 56.5 1.0 O A:HOH508 2.7 46.7 1.0 CD A:GLU115 3.0 57.4 1.0 O A:HOH519 3.1 54.7 1.0 P A:PO4308 3.3 22.3 1.0 HE1 A:HIS111 3.4 28.6 1.0 O3 A:PO4308 3.6 39.7 1.0 OE1 A:GLU115 3.7 70.6 1.0 HG2 A:GLU115 3.8 46.5 1.0 CG A:GLU115 4.0 38.7 1.0 O1 A:PO4308 4.2 48.5 1.0 O2 A:PO4308 4.2 28.7 1.0 CE1 A:HIS111 4.3 23.7 1.0 HG3 A:GLU115 4.4 46.5 1.0 HD1 A:HIS111 4.9 36.7 1.0 HA A:GLU115 4.9 37.7 1.0

Zinc binding site 5 out of 6 in the Cronobacter Sakazakii (Enterobacter Sakazakii) Metallo-Beta-Lactamse Harldq Motif


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Cronobacter Sakazakii (Enterobacter Sakazakii) Metallo-Beta-Lactamse Harldq Motif within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn305 b:29.9 occ:1.00 O2 A:PO4308 1.9 28.7 1.0 OE2 A:GLU141 1.9 30.5 1.0 HD1 A:HIS111 2.2 36.7 1.0 ND1 A:HIS111 2.4 30.5 1.0 CD A:GLU141 2.6 36.4 1.0 OE1 A:GLU141 2.8 40.1 1.0 CG A:HIS111 2.9 28.4 1.0 CE1 A:HIS111 3.0 23.7 1.0 HB2 A:HIS111 3.0 30.4 1.0 P A:PO4308 3.2 22.3 1.0 HE1 A:HIS111 3.3 28.6 1.0 CB A:HIS111 3.4 25.3 1.0 O3 A:PO4308 3.5 39.7 1.0 HA A:HIS111 3.6 33.1 1.0 CD2 A:HIS111 3.7 26.5 1.0 NE2 A:HIS111 3.7 33.5 1.0 CG A:GLU141 4.0 37.7 1.0 CA A:HIS111 4.1 27.5 1.0 O4 A:PO4308 4.1 56.5 1.0 HG2 A:GLU141 4.2 45.3 1.0 O1 A:PO4308 4.2 48.5 1.0 HB3 A:HIS111 4.3 30.4 1.0 HG3 A:GLU141 4.3 45.3 1.0 HD2 A:HIS111 4.4 31.9 1.0 O A:HOH407 4.9 40.5 1.0 C A:HIS111 4.9 29.1 1.0 O A:HIS111 5.0 25.2 1.0

Zinc binding site 6 out of 6 in the Cronobacter Sakazakii (Enterobacter Sakazakii) Metallo-Beta-Lactamse Harldq Motif


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Cronobacter Sakazakii (Enterobacter Sakazakii) Metallo-Beta-Lactamse Harldq Motif within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn306 b:70.1 occ:1.00 OD2 A:ASP129 2.0 56.5 1.0 OE1 A:GLU123 2.4 77.7 1.0 OE2 A:GLU123 2.5 71.8 1.0 CD A:GLU123 2.7 69.5 1.0 CG A:ASP129 2.8 42.0 1.0 OD1 A:ASP129 2.9 40.0 1.0 HB3 A:LYS122 3.8 44.4 1.0 HE2 A:LYS122 4.0 65.9 1.0 HE3 A:LYS122 4.0 65.9 1.0 CG A:GLU123 4.2 53.2 1.0 CB A:ASP129 4.2 36.1 1.0 H A:GLU123 4.2 36.1 1.0 CE A:LYS122 4.5 54.9 1.0 HB3 A:ASP129 4.5 43.4 1.0 HG2 A:GLU123 4.5 63.9 1.0 HB2 A:ASP129 4.5 43.4 1.0 HG3 A:GLU123 4.5 63.9 1.0 CB A:LYS122 4.8 37.0 1.0 N A:GLU123 4.8 30.0 1.0 HG2 A:LYS122 4.9 43.8 1.0 HA A:GLU123 4.9 41.4 1.0

M.Monteiro Pedroso, D.Waite, M.Natasa, R.Mcgeary, L.Guddat, P.Hugenholtz, G.Schenk. Evolution and Diversity of B3-Type Metallo-Beta-Lactamases, Emerging Contributors to the Spread of Antibiotic Resistance. To Be Published.