Zinc in PDB 6xfr: Metallo-Beta-Lactamase From Pontibacter Korlensis

The structure of Metallo-Beta-Lactamase From Pontibacter Korlensis, PDB code: 6xfr was solved by G.Schenk, M.A.Schembri, S.Prombhul, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.25 / 2.61
Space group	P 42 21 2
Cell size a, b, c (Å), α, β, γ (°)	97.941, 97.941, 103.237, 90, 90, 90
R / Rfree (%)	17.6 / 23.6

The structure of Metallo-Beta-Lactamase From Pontibacter Korlensis also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Zinc atom in the Metallo-Beta-Lactamase From Pontibacter Korlensis (pdb code 6xfr). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 16 binding sites of Zinc where determined in the Metallo-Beta-Lactamase From Pontibacter Korlensis, PDB code: 6xfr:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 16 in the Metallo-Beta-Lactamase From Pontibacter Korlensis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Metallo-Beta-Lactamase From Pontibacter Korlensis within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn304 b:40.4 occ:1.00 OD1 A:ASP82 2.1 39.5 1.0 NE2 A:HIS202 2.2 41.1 1.0 SG A:CYS160 2.3 36.8 1.0 O A:HOH409 2.7 38.2 1.0 CG A:ASP82 2.9 34.6 1.0 CE1 A:HIS202 3.1 41.4 1.0 OD2 A:ASP82 3.2 40.1 1.0 ZN A:ZN305 3.2 34.8 1.0 CD2 A:HIS202 3.2 42.5 1.0 O A:HOH413 3.4 47.7 1.0 CB A:CYS160 3.5 29.2 1.0 H21 A:EPE302 3.6 91.0 1.0 H22 A:EPE302 3.6 91.0 1.0 H31 A:EPE302 3.8 94.0 1.0 NE2 A:HIS141 3.9 28.7 1.0 C2 A:EPE302 4.0 75.9 1.0 CE1 A:HIS78 4.2 33.1 1.0 ND1 A:HIS202 4.2 42.8 1.0 CB A:ASP82 4.3 37.0 1.0 NE2 A:HIS78 4.3 37.7 1.0 CG A:HIS202 4.3 41.0 1.0 CE1 A:HIS141 4.4 29.6 1.0 C3 A:EPE302 4.5 78.4 1.0 CB A:SER201 4.5 42.2 1.0 CE A:LYS83 4.6 43.4 1.0 H101 A:EPE302 4.6 96.5 1.0 OG A:SER201 4.7 37.7 1.0 CD2 A:HIS141 4.7 27.1 1.0 CA A:CYS160 4.7 26.2 1.0 CD A:LYS83 4.8 35.6 1.0 CG A:LYS83 4.8 35.1 1.0 H92 A:EPE302 4.9 92.7 1.0 H82 A:EPE302 4.9 107.4 1.0

Zinc binding site 2 out of 16 in the Metallo-Beta-Lactamase From Pontibacter Korlensis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Metallo-Beta-Lactamase From Pontibacter Korlensis within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn305 b:34.8 occ:1.00 NE2 A:HIS141 2.0 28.7 1.0 NE2 A:HIS78 2.1 37.7 1.0 ND1 A:HIS80 2.2 45.4 1.0 CE1 A:HIS141 2.9 29.6 1.0 CD2 A:HIS141 2.9 27.1 1.0 O A:HOH413 3.0 47.7 1.0 CE1 A:HIS78 3.0 33.1 1.0 CG A:HIS80 3.0 36.9 1.0 ZN A:ZN304 3.2 40.4 1.0 CD2 A:HIS78 3.2 36.4 1.0 CB A:HIS80 3.2 31.8 1.0 CE1 A:HIS80 3.2 44.2 1.0 OD2 A:ASP82 3.7 40.1 1.0 SG A:CYS160 3.9 36.8 1.0 H82 A:EPE302 3.9 107.4 1.0 O A:HOH409 4.0 38.2 1.0 ND1 A:HIS141 4.1 28.6 1.0 CG A:HIS141 4.1 27.1 1.0 ND1 A:HIS78 4.2 35.9 1.0 CD2 A:HIS80 4.2 41.1 1.0 CB A:CYS160 4.2 29.2 1.0 NE2 A:HIS80 4.3 37.9 1.0 CG A:HIS78 4.3 29.0 1.0 OD1 A:ASP82 4.4 39.5 1.0 CG2 A:THR142 4.4 32.3 1.0 CG A:ASP82 4.5 34.6 1.0 H21 A:EPE302 4.5 91.0 1.0 CA A:HIS80 4.6 30.6 1.0 C8 A:EPE302 5.0 89.6 1.0 N A:HIS80 5.0 28.5 1.0

Zinc binding site 3 out of 16 in the Metallo-Beta-Lactamase From Pontibacter Korlensis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Metallo-Beta-Lactamase From Pontibacter Korlensis within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn306 b:105.2 occ:1.00 CB A:PHE119 3.5 31.4 1.0 N A:SER100 4.0 23.5 1.0 CG1 A:VAL134 4.1 22.0 1.0 C A:THR99 4.1 23.6 1.0 O A:THR99 4.2 24.3 1.0 CA A:SER100 4.2 34.0 1.0 CG A:PHE119 4.2 35.9 1.0 CD2 A:PHE119 4.3 32.7 1.0 O A:THR121 4.3 38.6 1.0 O A:PHE119 4.4 40.9 1.0 CB A:VAL134 4.4 25.1 1.0 CB A:SER100 4.5 25.8 1.0 CA A:PHE119 4.6 30.0 1.0 CG2 A:THR123 4.7 48.5 1.0 C A:PHE119 4.7 31.2 1.0 N A:PHE119 4.8 38.3 1.0 CG2 A:VAL134 4.9 21.7 1.0 OG1 A:THR123 4.9 63.4 1.0 CA A:THR99 4.9 21.9 1.0

Zinc binding site 4 out of 16 in the Metallo-Beta-Lactamase From Pontibacter Korlensis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Metallo-Beta-Lactamase From Pontibacter Korlensis within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn307 b:102.0 occ:1.00 HO8 A:EPE302 2.2 111.5 1.0 O8 A:EPE302 2.5 93.0 1.0 N A:ASP81 3.2 32.7 1.0 NZ A:LYS112 3.5 37.8 1.0 CA A:HIS80 3.7 30.6 1.0 C8 A:EPE302 3.8 89.6 1.0 CB A:ASP81 3.8 52.9 1.0 CD2 A:HIS80 4.0 41.1 1.0 C A:HIS80 4.0 30.2 1.0 CE A:LYS112 4.0 35.0 1.0 CG A:ASP81 4.0 65.6 1.0 CB A:HIS80 4.1 31.8 1.0 CA A:ASP81 4.1 46.4 1.0 H72 A:EPE302 4.1 104.2 1.0 CG A:HIS80 4.2 36.9 1.0 H82 A:EPE302 4.2 107.4 1.0 H71 A:EPE302 4.3 104.2 1.0 OD1 A:ASP81 4.3 61.9 1.0 C7 A:EPE302 4.4 86.9 1.0 OD2 A:ASP81 4.5 77.2 1.0 CZ3 A:TRP79 4.5 33.8 1.0 H81 A:EPE302 4.6 107.4 1.0 O A:TRP79 4.8 28.7 1.0 CE3 A:TRP79 4.9 31.5 1.0 NE2 A:HIS80 4.9 37.9 1.0 N A:HIS80 5.0 28.5 1.0

Zinc binding site 5 out of 16 in the Metallo-Beta-Lactamase From Pontibacter Korlensis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Metallo-Beta-Lactamase From Pontibacter Korlensis within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn308 b:160.3 occ:1.00 N A:ALA143 2.9 43.4 1.0 O A:ASP175 3.3 45.9 1.0 NE1 A:TRP79 3.5 29.7 1.0 CB A:ALA143 3.5 37.5 1.0 CB A:THR142 3.5 43.6 1.0 CA A:THR142 3.7 39.9 1.0 CB A:ASP175 3.8 41.7 1.0 C A:THR142 3.8 35.2 1.0 CA A:ALA143 3.8 43.8 1.0 CG2 A:THR142 4.0 32.3 1.0 CD1 A:LEU106 4.2 29.7 1.0 C A:ASP175 4.3 45.3 1.0 CE2 A:TRP79 4.4 30.9 1.0 CA A:ASP175 4.5 44.4 1.0 CD1 A:TRP79 4.5 29.2 1.0 CZ2 A:TRP79 4.5 33.0 1.0 OD2 A:ASP144 4.6 54.2 1.0 O A:HOH401 4.6 36.5 1.0 N A:ASP144 4.7 39.6 1.0 CG A:ASP175 4.8 59.1 1.0 OG1 A:THR142 4.8 50.7 1.0 C A:ALA143 4.8 40.9 1.0 O A:THR142 5.0 31.6 1.0

Zinc binding site 6 out of 16 in the Metallo-Beta-Lactamase From Pontibacter Korlensis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Metallo-Beta-Lactamase From Pontibacter Korlensis within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn309 b:115.5 occ:1.00 CD1 A:TRP205 2.9 27.9 1.0 NE1 A:TRP205 3.4 32.1 1.0 CD1 B:TRP205 3.4 28.6 1.0 NE1 B:TRP205 3.9 31.2 1.0 CG A:TRP205 4.1 30.1 1.0 CG1 A:VAL197 4.2 19.3 1.0 CG1 B:VAL197 4.2 25.2 1.0 O A:TRP205 4.5 35.0 1.0 C A:TRP205 4.6 23.8 1.0 CG B:TRP205 4.7 34.4 1.0 CE2 A:TRP205 4.7 48.5 1.0 CG2 B:VAL197 4.7 25.8 1.0 CG2 A:VAL197 4.7 26.3 1.0 CB A:TRP205 4.7 22.0 1.0 N A:GLY206 4.8 20.6 1.0 CA A:GLY206 4.8 28.9 1.0 O B:TRP205 5.0 29.4 1.0

Zinc binding site 7 out of 16 in the Metallo-Beta-Lactamase From Pontibacter Korlensis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Metallo-Beta-Lactamase From Pontibacter Korlensis within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:45.0 occ:1.00 NE2 B:HIS141 1.9 57.2 1.0 NE2 B:HIS78 2.2 43.0 1.0 ND1 B:HIS80 2.2 42.5 1.0 CD2 B:HIS141 2.9 38.5 1.0 CE1 B:HIS141 2.9 42.9 1.0 CE1 B:HIS78 3.1 34.6 1.0 CG B:HIS80 3.1 42.3 1.0 CD2 B:HIS78 3.2 39.6 1.0 CB B:HIS80 3.3 40.0 1.0 CE1 B:HIS80 3.3 49.2 1.0 O1 B:SO4312 3.6 110.4 1.0 OD1 B:ASP82 3.7 52.5 1.0 ZN B:ZN303 3.7 58.4 1.0 SG B:CYS160 3.7 45.5 1.0 CG B:HIS141 4.0 44.3 1.0 ND1 B:HIS141 4.0 42.7 1.0 ND1 B:HIS78 4.2 35.4 1.0 CB B:CYS160 4.3 33.2 1.0 CD2 B:HIS80 4.3 47.7 1.0 CG B:HIS78 4.3 33.9 1.0 NE2 B:HIS80 4.3 50.6 1.0 CG2 B:THR142 4.4 40.4 1.0 OD2 B:ASP82 4.4 46.5 1.0 CG B:ASP82 4.4 46.8 1.0 O B:HOH405 4.5 24.5 1.0 CA B:HIS80 4.7 40.0 1.0 S B:SO4312 4.8 110.5 1.0 O3 B:SO4312 4.8 111.7 1.0

Zinc binding site 8 out of 16 in the Metallo-Beta-Lactamase From Pontibacter Korlensis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Metallo-Beta-Lactamase From Pontibacter Korlensis within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:58.4 occ:1.00 NE2 B:HIS202 2.0 54.5 1.0 OD2 B:ASP82 2.2 46.5 1.0 O B:HOH405 2.3 24.5 1.0 SG B:CYS160 2.4 45.5 1.0 CD2 B:HIS202 3.0 47.1 1.0 CE1 B:HIS202 3.0 54.3 1.0 CG B:ASP82 3.2 46.8 1.0 CB B:CYS160 3.4 33.2 1.0 O1 B:SO4312 3.4 110.4 1.0 OD1 B:ASP82 3.6 52.5 1.0 ZN B:ZN302 3.7 45.0 1.0 ND1 B:HIS202 4.1 52.8 1.0 NE2 B:HIS141 4.1 57.2 1.0 CG B:HIS202 4.1 46.8 1.0 CE1 B:HIS141 4.2 42.9 1.0 CB B:ASP82 4.5 42.8 1.0 CB B:SER201 4.6 41.5 1.0 CA B:CYS160 4.6 30.1 1.0 S B:SO4312 4.8 110.5 1.0 OG B:SER201 4.9 46.9 1.0 CE1 B:HIS78 4.9 34.6 1.0 NE2 B:HIS78 5.0 43.0 1.0

Zinc binding site 9 out of 16 in the Metallo-Beta-Lactamase From Pontibacter Korlensis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Metallo-Beta-Lactamase From Pontibacter Korlensis within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn304 b:256.0 occ:1.00 OD2 B:ASP177 3.2 64.3 1.0 O B:ALA176 3.8 63.4 1.0 CA B:ASP177 3.8 55.5 1.0 CG B:ASP177 3.9 63.1 1.0 CB B:ASP177 4.3 58.1 1.0 N B:LEU178 4.5 44.4 1.0 C B:ASP177 4.5 53.0 1.0 OD1 B:ASP177 4.7 62.1 1.0 C B:ALA176 4.7 63.8 1.0 N B:ASP177 4.8 59.6 1.0

Zinc binding site 10 out of 16 in the Metallo-Beta-Lactamase From Pontibacter Korlensis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Metallo-Beta-Lactamase From Pontibacter Korlensis within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn305 b:238.0 occ:1.00 CG2 B:ILE127 2.7 24.6 1.0 O B:GLU42 2.9 51.8 1.0 CB B:GLU42 3.1 51.4 1.0 C B:GLU42 3.6 41.6 1.0 CG B:LYS72 3.6 26.7 1.0 CE B:LYS72 4.0 34.3 1.0 CA B:GLU42 4.0 52.4 1.0 CB B:ILE127 4.1 28.4 1.0 CG B:GLU42 4.2 60.5 1.0 CD B:LYS72 4.5 29.7 1.0 CB B:LYS72 4.5 25.2 1.0 N B:GLY128 4.5 33.4 1.0 CG1 B:ILE127 4.5 34.8 1.0 N B:GLY43 4.6 35.6 1.0 CA B:ILE127 4.6 30.8 1.0 CD1 B:ILE127 4.8 37.4 1.0 OG1 B:THR40 4.9 33.6 1.0 C B:ILE127 4.9 29.0 1.0 CA B:GLY43 5.0 34.3 1.0 N B:GLU42 5.0 45.2 1.0

G.Schenk, M.A.Schembri, S.Prombhul. Metallo-Beta-Lactamase From Pontibacter Korlensis To Be Published.