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Chlorine in PDB 5k0w: Crystal Structure of the Metallo-Beta-Lactamase Gob-18 From Elizabethkingia Meningoseptica

Protein crystallography data

The structure of Crystal Structure of the Metallo-Beta-Lactamase Gob-18 From Elizabethkingia Meningoseptica, PDB code: 5k0w was solved by A.Buschiazzo, N.Larrieux, A.J.Vila, M.N.Lisa, J.Moran-Barrio, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.33 / 2.61
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 64.000, 48.510, 88.940, 90.00, 100.10, 90.00
R / Rfree (%) 19.2 / 24.2

Other elements in 5k0w:

The structure of Crystal Structure of the Metallo-Beta-Lactamase Gob-18 From Elizabethkingia Meningoseptica also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of the Metallo-Beta-Lactamase Gob-18 From Elizabethkingia Meningoseptica (pdb code 5k0w). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Crystal Structure of the Metallo-Beta-Lactamase Gob-18 From Elizabethkingia Meningoseptica, PDB code: 5k0w:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 5k0w

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Chlorine binding site 1 out of 8 in the Crystal Structure of the Metallo-Beta-Lactamase Gob-18 From Elizabethkingia Meningoseptica


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of the Metallo-Beta-Lactamase Gob-18 From Elizabethkingia Meningoseptica within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl303

b:23.4
occ:1.00
NZ A:LYS133 3.1 36.2 1.0
CD A:LYS133 3.8 17.8 1.0
CE A:LYS133 3.9 24.0 1.0

Chlorine binding site 2 out of 8 in 5k0w

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Chlorine binding site 2 out of 8 in the Crystal Structure of the Metallo-Beta-Lactamase Gob-18 From Elizabethkingia Meningoseptica


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of the Metallo-Beta-Lactamase Gob-18 From Elizabethkingia Meningoseptica within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl304

b:53.0
occ:1.00
CD2 A:TYR224 4.3 18.3 1.0
CG A:TYR224 4.4 18.1 1.0
CE2 A:TYR224 4.4 19.4 1.0
OD1 A:ASP221 4.5 26.6 1.0
CD2 A:HIS171 4.5 22.4 1.0
CD1 A:TYR224 4.5 20.1 1.0
CZ A:TYR224 4.6 29.6 1.0
CE1 A:TYR224 4.6 21.9 1.0
O A:HOH427 4.7 14.2 1.0
NE2 A:HIS171 4.9 21.9 1.0
CB A:TYR224 5.0 15.2 1.0

Chlorine binding site 3 out of 8 in 5k0w

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Chlorine binding site 3 out of 8 in the Crystal Structure of the Metallo-Beta-Lactamase Gob-18 From Elizabethkingia Meningoseptica


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of the Metallo-Beta-Lactamase Gob-18 From Elizabethkingia Meningoseptica within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl305

b:31.4
occ:1.00
N A:VAL20 3.6 26.5 1.0
CG2 A:VAL20 4.0 27.6 1.0
CA A:GLN19 4.1 30.8 1.0
CB A:VAL20 4.2 28.0 1.0
C A:GLN19 4.4 32.9 1.0
CA A:VAL20 4.5 24.5 1.0
CB A:GLN19 4.8 32.2 1.0
O A:ALA18 5.0 32.7 1.0

Chlorine binding site 4 out of 8 in 5k0w

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Chlorine binding site 4 out of 8 in the Crystal Structure of the Metallo-Beta-Lactamase Gob-18 From Elizabethkingia Meningoseptica


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of the Metallo-Beta-Lactamase Gob-18 From Elizabethkingia Meningoseptica within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl306

b:71.8
occ:1.00
OD1 A:ASP206 3.1 61.9 1.0
N A:ASP206 3.5 32.6 1.0
CG A:LYS207 3.6 45.2 1.0
N A:LYS207 3.6 29.1 1.0
OE1 A:GLU137 3.8 52.9 1.0
CB A:ASP206 3.9 37.4 1.0
CG A:ASP206 3.9 60.4 1.0
CD A:LYS207 4.0 52.7 1.0
CB A:LYS207 4.1 30.8 1.0
CA A:ASP206 4.1 33.7 1.0
OE2 A:GLU137 4.2 60.9 1.0
CA A:VAL205 4.3 24.3 1.0
C A:ASP206 4.3 34.5 1.0
C A:VAL205 4.4 32.9 1.0
CB A:VAL205 4.4 26.7 1.0
CD A:GLU137 4.4 59.6 1.0
CA A:LYS207 4.5 28.5 1.0
CE A:LYS207 4.6 63.4 1.0
CG1 A:VAL205 4.6 26.2 1.0
NZ A:LYS140 5.0 86.5 1.0

Chlorine binding site 5 out of 8 in 5k0w

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Chlorine binding site 5 out of 8 in the Crystal Structure of the Metallo-Beta-Lactamase Gob-18 From Elizabethkingia Meningoseptica


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of the Metallo-Beta-Lactamase Gob-18 From Elizabethkingia Meningoseptica within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl307

b:52.6
occ:1.00
CE A:LYS117 4.2 59.8 1.0
NZ A:LYS117 4.3 74.3 1.0

Chlorine binding site 6 out of 8 in 5k0w

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Chlorine binding site 6 out of 8 in the Crystal Structure of the Metallo-Beta-Lactamase Gob-18 From Elizabethkingia Meningoseptica


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of the Metallo-Beta-Lactamase Gob-18 From Elizabethkingia Meningoseptica within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl308

b:41.4
occ:1.00
CA A:ASP246 3.5 22.1 1.0
N A:HIS248 3.7 32.2 1.0
C A:ASP246 3.7 28.9 1.0
OE1 A:GLU249 3.9 57.8 1.0
N A:LEU247 3.9 27.8 1.0
N A:GLU249 4.0 26.6 1.0
CA A:SER243 4.0 16.4 1.0
CB A:HIS248 4.1 32.4 1.0
CA A:HIS248 4.1 31.7 1.0
CD A:GLU249 4.2 60.5 1.0
CG A:GLU249 4.3 41.2 1.0
CB A:ASP246 4.3 23.8 1.0
CD2 A:HIS248 4.3 37.6 1.0
O A:ASP246 4.4 28.3 1.0
C A:HIS248 4.4 33.6 1.0
O A:SER243 4.4 22.7 1.0
CG A:HIS248 4.5 35.6 1.0
CB A:GLU249 4.6 26.9 1.0
OD1 A:ASP246 4.6 36.0 1.0
N A:ASP246 4.6 21.6 1.0
O A:ALA242 4.6 21.1 1.0
C A:LEU247 4.7 33.8 1.0
C A:SER243 4.7 21.4 1.0
CB A:SER243 4.7 17.6 1.0
N A:SER243 4.7 17.3 1.0
CA A:LEU247 4.8 28.6 1.0
CA A:GLU249 4.9 25.6 1.0
CG A:ASP246 5.0 35.1 1.0
C A:ALA242 5.0 21.5 1.0

Chlorine binding site 7 out of 8 in 5k0w

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Chlorine binding site 7 out of 8 in the Crystal Structure of the Metallo-Beta-Lactamase Gob-18 From Elizabethkingia Meningoseptica


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of the Metallo-Beta-Lactamase Gob-18 From Elizabethkingia Meningoseptica within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl309

b:46.5
occ:1.00
O A:HOH413 3.4 17.6 1.0
O A:SER210 3.8 28.4 1.0
O A:VAL212 3.9 27.7 1.0
CA A:THR213 4.0 23.0 1.0
CG2 A:THR213 4.1 33.8 1.0
CA A:PRO216 4.1 18.1 1.0
C A:VAL212 4.3 27.5 1.0
N A:THR213 4.4 23.4 1.0
CB A:THR213 4.4 33.7 1.0
O A:PRO216 4.4 18.9 1.0
C A:SER210 4.5 28.4 1.0
O A:PHE209 4.6 27.0 1.0
CB A:PRO216 4.7 19.6 1.0
CA A:SER210 4.8 23.5 1.0
C A:PRO216 4.8 20.4 1.0
C A:THR213 4.9 25.9 1.0
O A:TYR215 5.0 24.1 1.0
N A:PRO216 5.0 19.0 1.0

Chlorine binding site 8 out of 8 in 5k0w

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Chlorine binding site 8 out of 8 in the Crystal Structure of the Metallo-Beta-Lactamase Gob-18 From Elizabethkingia Meningoseptica


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Crystal Structure of the Metallo-Beta-Lactamase Gob-18 From Elizabethkingia Meningoseptica within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl303

b:54.8
occ:1.00
N B:HIS248 3.4 43.4 1.0
CA B:ASP246 3.6 33.6 1.0
N B:LEU247 3.6 40.0 1.0
C B:ASP246 3.6 41.4 1.0
CD2 B:HIS248 3.7 49.2 1.0
CA B:SER243 3.7 23.8 1.0
CB B:HIS248 3.8 43.5 1.0
CA B:HIS248 4.0 43.0 1.0
CG B:HIS248 4.1 46.9 1.0
O B:ALA242 4.1 28.9 1.0
N B:GLU249 4.2 42.3 1.0
N B:SER243 4.3 24.1 1.0
C B:LEU247 4.3 46.1 1.0
O B:ASP246 4.4 41.8 1.0
O B:SER243 4.4 29.2 1.0
C B:ALA242 4.4 28.6 1.0
C B:HIS248 4.4 47.5 1.0
CA B:LEU247 4.4 40.5 1.0
N B:ASP246 4.5 32.0 1.0
CB B:SER243 4.5 26.8 1.0
CB B:ASP246 4.5 35.8 1.0
C B:SER243 4.5 28.9 1.0
OE1 B:GLU249 4.5 62.8 1.0
CG B:GLU249 4.8 53.6 1.0
NE2 B:HIS248 4.9 49.1 1.0
CD B:GLU249 4.9 76.7 1.0
OD1 B:ASP246 4.9 50.4 1.0
CB B:LEU247 5.0 40.6 1.0

Reference:

J.Moran-Barrio, M.N.Lisa, N.Larrieux, S.I.Drusin, A.M.Viale, D.M.Moreno, A.Buschiazzo, A.J.Vila. Crystal Structure of the Metallo-Beta-Lactamase Gob in the Periplasmic Dizinc Form Reveals An Unusual Metal Site. Antimicrob.Agents Chemother. V. 60 6013 2016.
ISSN: ESSN 1098-6596
PubMed: 27458232
DOI: 10.1128/AAC.01067-16
Page generated: Sat Dec 12 11:55:18 2020

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