Zinc in PDB 3w8k: Crystal Structure of Class C Beta-Lactamase Mox-1

All present enzymatic activity of Crystal Structure of Class C Beta-Lactamase Mox-1:
3.5.2.6;

The structure of Crystal Structure of Class C Beta-Lactamase Mox-1, PDB code: 3w8k was solved by A.Shimizu-Ibuka, T.Oguri, T.Furuyama, Y.Ishii, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 1.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	49.617, 59.378, 62.685, 90.00, 102.19, 90.00
R / Rfree (%)	16.4 / 18.9

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of Class C Beta-Lactamase Mox-1 (pdb code 3w8k). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 11 binding sites of Zinc where determined in the Crystal Structure of Class C Beta-Lactamase Mox-1, PDB code: 3w8k:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 11 in the Crystal Structure of Class C Beta-Lactamase Mox-1


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 Class C Beta-Lactamase Mox-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:17.8 occ:0.90 OXT A:ACT1013 1.9 22.4 1.0 NE2 A:HIS161 2.0 15.8 1.0 O A:ACT1014 2.0 24.4 1.0 O A:HOH3176 2.1 28.7 1.0 C A:ACT1014 2.7 26.2 1.0 OXT A:ACT1014 2.8 25.4 1.0 C A:ACT1013 3.0 21.0 1.0 CD2 A:HIS161 3.0 17.0 1.0 CE1 A:HIS161 3.0 17.8 1.0 CH3 A:ACT1013 3.4 22.4 1.0 NH2 A:ARG133 4.0 18.6 1.0 O A:ACT1013 4.1 22.6 1.0 ND1 A:HIS161 4.1 16.3 1.0 CG A:HIS161 4.1 16.5 1.0 O A:HOH3033 4.2 20.0 1.0 CH3 A:ACT1014 4.2 26.1 1.0 NE1 A:TRP96 4.5 21.4 1.0

Zinc binding site 2 out of 11 in the Crystal Structure of Class C Beta-Lactamase Mox-1


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 Class C Beta-Lactamase Mox-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:16.1 occ:0.90 OXT A:ACT1012 1.6 24.7 1.0 ND1 A:HIS24 2.1 18.3 1.0 O A:HOH3004 2.3 10.0 1.0 C A:ACT1012 2.7 23.1 1.0 CE1 A:HIS24 3.0 19.0 1.0 CG A:HIS24 3.1 17.9 1.0 CH3 A:ACT1012 3.5 20.8 1.0 CB A:HIS24 3.5 17.7 1.0 O A:ACT1012 3.6 20.3 1.0 CA A:HIS24 3.8 18.6 1.0 CD A:PRO342 4.0 16.4 1.0 NE2 A:HIS24 4.1 19.4 1.0 CD2 A:HIS24 4.2 19.1 1.0 O A:HOH3131 4.3 32.2 1.0 NZ A:LYS206 4.4 36.8 1.0 CG A:PRO342 4.6 17.3 1.0 O A:GLU23 4.7 23.1 1.0 O A:HIS24 4.7 18.6 1.0 C A:HIS24 4.8 18.5 1.0 N A:HIS24 4.8 19.7 1.0 CB A:TYR341 4.8 16.3 1.0 O A:HOH3154 4.8 35.0 1.0 CA A:TYR341 5.0 15.7 1.0

Zinc binding site 3 out of 11 in the Crystal Structure of Class C Beta-Lactamase Mox-1


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 Class C Beta-Lactamase Mox-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1003 b:24.9 occ:0.90 ND1 A:HIS259 2.1 24.1 1.0 O A:HOH3041 2.2 24.1 1.0 O A:HOH3084 2.3 22.8 1.0 CE1 A:HIS259 3.0 24.0 1.0 CG A:HIS259 3.1 22.0 1.0 O A:HOH3090 3.2 21.9 1.0 CB A:HIS259 3.5 22.1 1.0 NE2 A:HIS259 4.2 23.2 1.0 CD2 A:HIS259 4.2 23.6 1.0 CA A:HIS259 4.5 21.4 1.0 O A:HOH3158 4.6 39.1 1.0 O A:HOH3256 4.6 31.5 1.0 CG2 A:THR112 4.8 18.1 1.0 O A:HOH3251 4.8 43.5 1.0 OG1 A:THR112 4.8 18.3 1.0 O A:GLY108 4.9 18.1 1.0 CA A:GLY108 4.9 18.5 1.0 C A:GLY108 4.9 18.8 1.0

Zinc binding site 4 out of 11 in the Crystal Structure of Class C Beta-Lactamase Mox-1


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 Class C Beta-Lactamase Mox-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1004 b:15.6 occ:0.60 O A:HOH3070 2.1 23.5 1.0 NE2 A:HIS351 2.2 19.0 1.0 OXT A:ACT1015 2.2 25.9 1.0 O A:VAL278 2.3 20.6 1.0 O A:ACT1015 2.4 25.6 1.0 C A:ACT1015 2.6 25.1 1.0 CE1 A:HIS351 3.1 19.0 1.0 CD2 A:HIS351 3.2 19.4 1.0 C A:VAL278 3.2 20.2 1.0 CA A:THR279 3.8 20.9 1.0 N A:THR279 3.9 21.1 1.0 N A:VAL278 4.0 22.8 1.0 CH3 A:ACT1015 4.1 24.9 1.0 ND1 A:HIS351 4.2 19.4 1.0 CA A:VAL278 4.3 22.1 1.0 O A:HOH3100 4.3 28.4 1.0 CG A:HIS351 4.3 17.8 1.0 C A:THR279 4.4 21.1 1.0 O A:HOH3036 4.4 21.9 1.0 N A:GLU280 4.5 22.1 1.0 CB A:PRO277 4.7 24.8 1.0 C A:PRO277 4.7 23.4 1.0 CG1 A:VAL278 4.9 22.4 1.0

Zinc binding site 5 out of 11 in the Crystal Structure of Class C Beta-Lactamase Mox-1


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 Class C Beta-Lactamase Mox-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1005 b:32.8 occ:1.00 O A:HOH3310 1.5 30.4 1.0 OE1 A:GLU50 2.6 36.5 1.0 OE2 A:GLU50 3.1 43.0 1.0 CD A:GLU50 3.2 35.1 1.0 CG A:GLU50 4.7 32.9 1.0

Zinc binding site 6 out of 11 in the Crystal Structure of Class C Beta-Lactamase Mox-1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Class C Beta-Lactamase Mox-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1006 b:13.6 occ:0.90 OXT A:ACT1016 2.0 19.8 1.0 O A:HOH3126 2.0 14.2 1.0 ND1 A:HIS186 2.1 17.0 1.0 C A:ACT1016 2.9 15.9 1.0 CE1 A:HIS186 3.0 16.4 1.0 CG A:HIS186 3.1 15.4 1.0 O A:ACT1016 3.1 22.4 1.0 CB A:HIS186 3.4 15.0 1.0 CA A:HIS186 4.0 15.4 1.0 NE2 A:HIS186 4.1 16.6 1.0 O A:HOH3020 4.1 15.9 1.0 O A:HIS186 4.2 15.7 1.0 CD2 A:HIS186 4.2 16.5 1.0 CH3 A:ACT1016 4.3 20.5 1.0 C A:HIS186 4.6 16.2 1.0 CB A:PRO181 4.6 18.2 1.0 CG A:PRO181 5.0 18.5 1.0

Zinc binding site 7 out of 11 in the Crystal Structure of Class C Beta-Lactamase Mox-1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Class C Beta-Lactamase Mox-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1007 b:21.8 occ:0.50 O A:HOH3173 2.1 39.9 1.0 ND1 A:HIS256 2.1 22.2 1.0 O A:HOH3260 2.1 48.6 1.0 CE1 A:HIS256 3.1 23.6 1.0 CG A:HIS256 3.1 22.5 1.0 CB A:HIS256 3.4 21.4 1.0 NE2 A:HIS256 4.2 22.4 1.0 CD2 A:HIS256 4.2 20.9 1.0 O A:HOH3259 4.6 42.4 1.0 CZ A:PHE310 4.7 19.9 1.0 CE2 A:PHE310 4.8 19.7 1.0 CA A:HIS256 5.0 21.1 1.0

Zinc binding site 8 out of 11 in the Crystal Structure of Class C Beta-Lactamase Mox-1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Class C Beta-Lactamase Mox-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1008 b:25.3 occ:0.50 O A:HOH3247 1.9 33.7 1.0 OD2 A:ASP14 2.0 24.9 1.0 O A:HOH3248 2.2 49.9 1.0 CG A:ASP14 3.0 23.2 1.0 CB A:ASP14 3.3 20.9 1.0 O A:HOH3079 3.9 27.2 1.0 NE A:ARG10 4.1 35.7 1.0 OD1 A:ASP14 4.2 24.7 1.0 CZ A:ARG10 4.2 39.7 1.0 CD A:ARG10 4.4 31.9 1.0 NH1 A:ARG10 4.5 42.6 1.0 NH2 A:ARG10 4.6 38.9 1.0 CG A:ARG10 4.7 28.7 1.0 O A:ARG10 4.8 20.1 1.0 NE2 A:GLN18 4.8 36.2 1.0 CA A:PRO11 4.8 20.1 1.0 CA A:ASP14 4.8 19.4 1.0 O A:HOH3146 5.0 36.4 1.0

Zinc binding site 9 out of 11 in the Crystal Structure of Class C Beta-Lactamase Mox-1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of Class C Beta-Lactamase Mox-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1009 b:42.3 occ:0.50 OD2 A:ASP220 2.8 25.6 1.0 OD1 A:ASP220 3.0 23.0 1.0 CG A:ASP220 3.3 21.9 1.0 ND2 A:ASN191 4.2 19.8 1.0 OD1 A:ASN191 4.6 23.2 1.0 CG2 A:VAL190 4.6 23.2 1.0 CB A:ASP220 4.7 19.1 1.0 O A:HOH3314 4.8 34.5 1.0 CG A:ASN191 4.8 19.6 1.0 O A:HOH3145 4.9 30.4 1.0

Zinc binding site 10 out of 11 in the Crystal Structure of Class C Beta-Lactamase Mox-1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of Class C Beta-Lactamase Mox-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1010 b:28.4 occ:0.50 OD1 A:ASP231 1.9 18.6 1.0 ND1 A:HIS187 2.2 29.0 1.0 O A:HOH3063 2.5 26.9 1.0 O A:HOH3092 2.7 24.2 1.0 O A:HOH3196 2.7 35.1 1.0 O A:HOH3124 2.9 35.9 1.0 CG A:ASP231 3.0 18.3 1.0 CG A:HIS187 3.1 25.4 1.0 CE1 A:HIS187 3.2 27.4 1.0 CB A:HIS187 3.4 21.3 1.0 OD2 A:ASP231 3.4 17.4 1.0 N A:HIS187 3.9 17.3 1.0 CB A:ASP231 4.2 17.1 1.0 OG A:SER228 4.2 16.5 1.0 CA A:HIS187 4.3 19.3 1.0 NE2 A:HIS187 4.3 29.9 1.0 CD2 A:HIS187 4.3 28.6 1.0 N A:HIS186 4.5 15.7 1.0 N A:ASP231 4.5 16.2 1.0 CA A:ASP231 4.6 16.6 1.0 C A:HIS186 4.7 16.2 1.0 O A:HOH3030 4.9 21.2 1.0 CB A:ALA230 4.9 16.6 1.0 CA A:HIS186 5.0 15.4 1.0

T.Oguri, T.Furuyama, T.Okuno, Y.Ishii, K.Tateda, R.A.Bonomo, A.Shimizu-Ibuka. Crystal Structure of Mox-1, A Unique Plasmid-Mediated Class C Beta-Lactamase with Hydrolytic Activity Towards Moxalactam Antimicrob.Agents Chemother. 2014.
ISSN: ESSN 1098-6596