Chlorine in PDB 6mh0: Crystal Structure of the New Deli Metallo Beta Lactamase Variant 3 From Klebsiella Pneumoniae

Protein crystallography data

The structure of Crystal Structure of the New Deli Metallo Beta Lactamase Variant 3 From Klebsiella Pneumoniae, PDB code: 6mh0 was solved by Y.Kim, C.Tesar, R.Jedrzejczak, G.Babnigg, A.Joachimiak, Center Forstructural Genomics Of Infectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.54 / 1.65
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 39.185, 78.699, 130.790, 90.00, 90.00, 90.00
R / Rfree (%) 16.8 / 20.5

Other elements in 6mh0:

The structure of Crystal Structure of the New Deli Metallo Beta Lactamase Variant 3 From Klebsiella Pneumoniae also contains other interesting chemical elements:

Zinc (Zn) 6 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of the New Deli Metallo Beta Lactamase Variant 3 From Klebsiella Pneumoniae (pdb code 6mh0). 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 New Deli Metallo Beta Lactamase Variant 3 From Klebsiella Pneumoniae, PDB code: 6mh0:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 6mh0

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Chlorine binding site 1 out of 8 in the Crystal Structure of the New Deli Metallo Beta Lactamase Variant 3 From Klebsiella Pneumoniae


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 New Deli Metallo Beta Lactamase Variant 3 From Klebsiella Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl303

b:38.0
occ:1.00
ZN A:ZN301 2.3 26.4 0.5
NZ A:LYS211 2.8 38.0 1.0
O1 A:SO4302 3.1 35.2 1.0
N A:ASN220 3.4 29.4 1.0
CE1 A:HIS189 3.5 20.3 1.0
CD2 A:HIS250 3.6 25.4 1.0
ZN A:ZN301 3.7 25.9 0.5
ND1 A:HIS189 3.7 18.0 1.0
NE2 A:HIS250 3.8 29.5 1.0
CA A:GLY219 4.1 33.2 1.0
CB A:CYS208 4.1 18.3 1.0
O A:HOH404 4.1 22.5 1.0
CB A:ASN220 4.2 27.9 1.0
C A:GLY219 4.2 38.1 1.0
CE A:LYS211 4.2 35.2 1.0
CA A:ASN220 4.3 28.5 1.0
O A:LEU218 4.3 27.9 1.0
O A:CYS208 4.3 21.7 1.0
S A:SO4302 4.3 45.5 1.0
O A:ASN220 4.4 22.4 1.0
SG A:CYS208 4.4 22.8 1.0
NE2 A:HIS189 4.5 16.8 1.0
O3 A:SO4302 4.5 49.4 1.0
CA A:CYS208 4.8 21.9 1.0
C A:ASN220 4.8 25.2 1.0
CG A:HIS189 4.8 15.9 1.0
CG A:HIS250 4.9 29.1 1.0
O2 A:SO4302 5.0 26.1 1.0

Chlorine binding site 2 out of 8 in 6mh0

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Chlorine binding site 2 out of 8 in the Crystal Structure of the New Deli Metallo Beta Lactamase Variant 3 From Klebsiella Pneumoniae


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 New Deli Metallo Beta Lactamase Variant 3 From Klebsiella Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl304

b:25.8
occ:1.00
O A:HOH516 3.2 35.4 1.0
N A:LYS242 3.3 19.2 1.0
C A:PHE240 3.4 15.6 1.0
CA A:PHE240 3.4 13.5 1.0
N A:PRO241 3.5 16.7 1.0
CD A:PRO241 3.6 17.1 1.0
O A:HOH481 3.7 38.9 1.0
CB A:LYS242 3.8 24.4 1.0
N A:ALA243 3.8 17.1 1.0
CA A:LYS242 3.9 20.7 1.0
O A:PHE240 4.0 16.7 1.0
CB A:PHE240 4.0 14.8 1.0
O A:HOH518 4.0 46.9 1.0
C A:LYS242 4.0 18.1 1.0
C A:PRO241 4.3 19.4 1.0
CG A:PRO241 4.4 23.9 1.0
CA A:PRO241 4.5 15.0 1.0
O A:HOH452 4.5 33.2 1.0
CG A:LYS242 4.6 24.7 1.0
CD1 A:PHE240 4.6 14.7 1.0
O A:ALA239 4.7 18.9 1.0
N A:PHE240 4.7 13.2 1.0
CA A:ALA243 4.8 16.7 1.0
CB A:ALA243 4.8 18.9 1.0
CG A:PHE240 4.8 11.8 1.0
O A:LYS242 4.9 22.3 1.0

Chlorine binding site 3 out of 8 in 6mh0

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Chlorine binding site 3 out of 8 in the Crystal Structure of the New Deli Metallo Beta Lactamase Variant 3 From Klebsiella Pneumoniae


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 New Deli Metallo Beta Lactamase Variant 3 From Klebsiella Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl305

b:34.0
occ:1.00
CD A:PRO56 3.6 24.2 1.0
C A:ALA55 3.6 21.9 1.0
N A:PRO56 3.6 22.2 1.0
CA A:ALA55 3.6 25.7 1.0
N A:ALA55 4.2 24.9 1.0
O A:ALA55 4.2 24.5 1.0
CG A:PRO56 4.3 28.9 1.0
CA A:PRO56 4.3 22.9 1.0
CG A:GLN53 4.4 28.4 1.0
O A:LEU54 4.5 22.4 1.0
C A:LEU54 4.5 20.8 1.0
CD A:GLN53 4.8 35.9 1.0
NE2 A:GLN53 4.8 36.5 1.0
CB A:ALA55 5.0 26.6 1.0
O A:HOH474 5.0 33.2 1.0
CB A:PRO56 5.0 26.8 1.0

Chlorine binding site 4 out of 8 in 6mh0

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Chlorine binding site 4 out of 8 in the Crystal Structure of the New Deli Metallo Beta Lactamase Variant 3 From Klebsiella Pneumoniae


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 New Deli Metallo Beta Lactamase Variant 3 From Klebsiella Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl306

b:26.8
occ:1.00
O A:HOH532 3.1 29.5 1.0
O A:HOH484 3.3 23.5 1.0
N A:ASN166 3.5 14.3 1.0
CG A:ASN166 3.6 15.5 1.0
CB A:ALA164 3.6 19.0 1.0
OD1 A:ASN166 3.7 15.4 1.0
N A:ALA165 3.7 15.9 1.0
CB A:ASN166 3.9 14.6 1.0
ND2 A:ASN166 4.0 19.6 1.0
CB A:ALA165 4.1 16.7 1.0
CA A:ALA165 4.2 17.2 1.0
C A:ALA165 4.2 14.4 1.0
CA A:ASN166 4.3 15.4 1.0
C A:ALA164 4.4 15.9 1.0
CA A:ALA164 4.6 14.4 1.0
O A:HOH536 4.8 40.3 1.0
O B:HOH480 5.0 33.8 1.0

Chlorine binding site 5 out of 8 in 6mh0

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Chlorine binding site 5 out of 8 in the Crystal Structure of the New Deli Metallo Beta Lactamase Variant 3 From Klebsiella Pneumoniae


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 New Deli Metallo Beta Lactamase Variant 3 From Klebsiella Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl303

b:39.5
occ:1.00
ZN B:ZN301 2.3 25.7 0.5
NZ B:LYS211 2.6 31.6 1.0
O3 B:SO4302 3.2 49.0 1.0
ZN B:ZN301 3.4 22.6 0.4
CE1 B:HIS189 3.5 19.8 1.0
CD2 B:HIS250 3.5 27.5 1.0
NE2 B:HIS250 3.7 29.6 1.0
CB B:CYS208 3.8 19.0 1.0
ND1 B:HIS189 3.8 17.0 1.0
O B:CYS208 4.1 22.1 1.0
SG B:CYS208 4.1 21.4 1.0
CE B:LYS211 4.1 33.0 1.0
O B:HOH466 4.2 26.8 1.0
NE2 B:HIS189 4.3 18.3 1.0
CA B:CYS208 4.4 19.8 1.0
S B:SO4302 4.4 55.9 1.0
N B:ASN220 4.7 52.6 1.0
O4 B:SO4302 4.7 61.9 1.0
C B:CYS208 4.7 22.9 1.0
CG B:HIS189 4.7 15.0 1.0
CG B:HIS250 4.8 30.1 1.0
O2 B:SO4302 4.8 37.8 1.0
O B:HOH430 4.9 42.0 1.0
O B:LEU218 4.9 41.6 1.0
CD B:LYS211 5.0 29.9 1.0

Chlorine binding site 6 out of 8 in 6mh0

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Chlorine binding site 6 out of 8 in the Crystal Structure of the New Deli Metallo Beta Lactamase Variant 3 From Klebsiella Pneumoniae


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 New Deli Metallo Beta Lactamase Variant 3 From Klebsiella Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl304

b:30.9
occ:1.00
N B:LYS242 3.2 21.7 1.0
CA B:PHE240 3.3 16.2 1.0
C B:PHE240 3.3 20.6 1.0
CB B:LYS242 3.4 34.0 1.0
N B:PRO241 3.6 18.2 1.0
O B:HOH453 3.7 38.2 1.0
N B:ALA243 3.7 21.4 1.0
CA B:LYS242 3.7 25.1 1.0
CD B:PRO241 3.8 19.1 1.0
CB B:PHE240 3.8 17.7 1.0
O B:PHE240 3.8 20.2 1.0
O B:HOH517 3.9 38.5 1.0
NZ B:LYS181 4.0 59.5 1.0
C B:LYS242 4.1 24.4 1.0
C B:PRO241 4.3 27.8 1.0
CD1 B:PHE240 4.4 15.5 1.0
CA B:PRO241 4.5 25.5 1.0
CG B:PRO241 4.5 20.9 1.0
CG B:PHE240 4.6 14.7 1.0
N B:PHE240 4.6 17.2 1.0
CB B:ALA243 4.6 18.9 1.0
CA B:ALA243 4.7 24.7 1.0
O B:ALA239 4.7 17.8 1.0
CG B:LYS242 4.8 43.0 1.0
CE B:LYS242 5.0 56.5 1.0

Chlorine binding site 7 out of 8 in 6mh0

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Chlorine binding site 7 out of 8 in the Crystal Structure of the New Deli Metallo Beta Lactamase Variant 3 From Klebsiella Pneumoniae


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 New Deli Metallo Beta Lactamase Variant 3 From Klebsiella Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl305

b:33.5
occ:1.00
O B:HOH536 3.2 33.6 1.0
O B:HOH529 3.2 37.7 1.0
N B:ASN57 3.3 23.6 1.0
CB B:ASN57 3.6 22.1 1.0
ND2 B:ASN57 3.7 35.4 1.0
CB B:ALA55 3.7 30.4 1.0
CD B:PRO56 3.8 23.7 1.0
N B:PRO56 3.8 21.5 1.0
CG2 B:THR201 3.9 23.7 1.0
CA B:ASN57 3.9 20.3 1.0
CG B:ASN57 4.1 29.6 1.0
CB B:PRO56 4.1 30.7 1.0
C B:PRO56 4.2 30.1 1.0
CA B:PRO56 4.3 22.1 1.0
C B:ALA55 4.3 22.8 1.0
CG2 B:VAL58 4.3 20.5 1.0
CG B:PRO56 4.3 32.9 1.0
C B:ASN57 4.4 21.8 1.0
N B:VAL58 4.6 19.7 1.0
CA B:ALA55 4.6 26.6 1.0
CB B:THR201 4.9 25.7 1.0
O B:ALA55 5.0 23.8 1.0

Chlorine binding site 8 out of 8 in 6mh0

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Chlorine binding site 8 out of 8 in the Crystal Structure of the New Deli Metallo Beta Lactamase Variant 3 From Klebsiella Pneumoniae


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 New Deli Metallo Beta Lactamase Variant 3 From Klebsiella Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl306

b:37.9
occ:1.00
O B:HOH532 2.8 28.6 1.0
O B:HOH508 3.1 21.4 1.0
N B:ASN166 3.2 16.6 1.0
CG B:ASN166 3.5 19.8 1.0
N B:ALA165 3.6 15.8 1.0
CB B:ASN166 3.6 17.4 1.0
CB B:ALA164 3.7 18.0 1.0
OD1 B:ASN166 3.8 17.9 1.0
ND2 B:ASN166 3.9 24.9 1.0
CB B:ALA165 3.9 20.7 1.0
C B:ALA165 3.9 18.2 1.0
CA B:ALA165 4.0 17.7 1.0
CA B:ASN166 4.0 16.1 1.0
C B:ALA164 4.3 15.2 1.0
O B:HOH507 4.5 32.3 1.0
CA B:ALA164 4.6 16.6 1.0
O A:HOH487 4.8 35.9 1.0
O A:HOH539 4.8 23.8 1.0

Reference:

Y.Kim, C.Tesar, R.Jedrzejczak, G.Babnigg, A.Joachimiak, Center For Structural Genomics Of Infectious Diseases(Csgid). Crystal Structure of the New Deli Metallo Beta Lactamase Variant 3 From Klebsiella Pneumoniae To Be Published.
Page generated: Sat Dec 12 13:21:19 2020

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