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Chlorine in PDB 6ogo: Crystal Structure of Ndm-9 Metallo-Beta-Lactamase

Protein crystallography data

The structure of Crystal Structure of Ndm-9 Metallo-Beta-Lactamase, PDB code: 6ogo was solved by J.E.Raczynska, B.Imiolczyk, M.Jaskolski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 61.46 / 1.43
Space group P 31
Cell size a, b, c (Å), α, β, γ (°) 122.929, 122.929, 38.501, 90.00, 90.00, 120.00
R / Rfree (%) 7.4 / 11.6

Other elements in 6ogo:

The structure of Crystal Structure of Ndm-9 Metallo-Beta-Lactamase also contains other interesting chemical elements:

Zinc (Zn) 6 atoms

Chlorine Binding Sites:

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

Chlorine binding site 1 out of 9 in 6ogo

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Chlorine binding site 1 out of 9 in the Crystal Structure of Ndm-9 Metallo-Beta-Lactamase


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 Ndm-9 Metallo-Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl303

b:13.8
occ:1.00
 ZN A:ZN302 2.4 12.7 1.0
NZ A:LYS211 3.1 15.9 1.0
O1 A:PO4306 3.4 12.7 1.0
CE1 A:HIS189 3.4 10.0 1.0
N A:ASN220 3.4 13.7 1.0
NE2 A:HIS250 3.4 10.9 1.0
CD2 A:HIS250 3.6 12.3 1.0
ND1 A:HIS189 3.6 10.2 1.0
CB A:CYS208 3.8 10.9 1.0
O A:HOH443 4.0 13.8 1.0
O A:HOH585 4.0 17.6 1.0
SG A:CYS208 4.0 11.4 1.0
CA A:GLY219 4.1 15.1 1.0
CB A:ASN220 4.1 12.8 1.0
O A:CYS208 4.1 12.8 1.0
CA A:ASN220 4.2 12.6 1.0
C A:GLY219 4.3 18.0 1.0
O A:ASN220 4.3 11.6 1.0
O A:LEU218 4.3 18.4 1.0
NE2 A:HIS189 4.3 9.3 1.0
O A:HOH488 4.4 17.8 1.0
O A:HOH643 4.4 37.3 1.0
CA A:CYS208 4.4 10.2 1.0
CE A:LYS211 4.5 15.5 1.0
P A:PO4306 4.5 11.8 1.0
O3 A:PO4306 4.6 11.5 1.0
CG A:HIS189 4.7 9.8 1.0
C A:ASN220 4.7 11.1 1.0
CE1 A:HIS250 4.7 11.7 1.0
C A:CYS208 4.8 10.3 1.0
CG A:HIS250 4.9 10.4 1.0

Chlorine binding site 2 out of 9 in 6ogo

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Chlorine binding site 2 out of 9 in the Crystal Structure of Ndm-9 Metallo-Beta-Lactamase


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 Ndm-9 Metallo-Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl304

b:27.9
occ:1.00
 O A:HOH649 2.7 47.0 1.0
O2 A:EDO308 3.0 28.6 1.0
N A:LYS242 3.1 16.9 1.0
C A:PHE240 3.3 13.6 1.0
CA A:PHE240 3.4 11.7 1.0
C2 A:EDO308 3.4 43.2 1.0
N A:PRO241 3.5 15.6 1.0
CB A:LYS242 3.6 22.6 1.0
CD A:PRO241 3.6 19.0 1.0
O A:HOH483 3.6 27.2 1.0
CA A:LYS242 3.8 23.6 1.0
O A:PHE240 3.8 14.9 1.0
N A:ALA243 3.8 16.2 1.0
CB A:PHE240 3.9 13.4 1.0
C A:LYS242 4.1 22.8 1.0
C A:PRO241 4.2 19.4 1.0
CG A:PRO241 4.3 19.4 1.0
CD A:LYS242 4.3 78.5 1.0
O1 A:EDO308 4.3 49.6 1.0
CA A:PRO241 4.4 18.0 1.0
CG A:LYS242 4.4 28.3 1.0
O A:HOH404 4.4 44.1 1.0
C1 A:EDO308 4.5 37.5 1.0
O A:ALA239 4.6 15.3 1.0
CD1 A:PHE240 4.6 14.1 1.0
N A:PHE240 4.6 14.1 1.0
CG A:PHE240 4.8 12.9 1.0
CA A:ALA243 4.9 16.6 1.0
O A:HOH402 4.9 36.0 1.0
CB A:ALA243 5.0 17.3 1.0

Chlorine binding site 3 out of 9 in 6ogo

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Chlorine binding site 3 out of 9 in the Crystal Structure of Ndm-9 Metallo-Beta-Lactamase


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 Ndm-9 Metallo-Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl305

b:17.2
occ:0.70
 O A:HOH487 2.9 28.2 1.0
O A:HOH488 3.0 17.8 1.0
OG A:SER251 3.2 32.0 1.0
N A:HIS250 3.2 12.0 1.0
O A:HOH585 3.3 17.6 1.0
C A:HIS250 3.5 14.0 1.0
CB A:HIS250 3.5 11.3 1.0
N A:SER251 3.5 12.1 1.0
CA A:HIS250 3.5 11.7 1.0
CB A:SER251 3.8 19.4 1.0
CG A:MET248 3.9 20.5 1.0
O A:HIS250 4.0 16.0 1.0
O A:ILE210 4.1 12.8 1.0
CD2 A:HIS250 4.1 12.3 1.0
CD A:LYS211 4.1 16.0 1.0
CG A:HIS250 4.1 10.4 1.0
CA A:SER251 4.3 13.5 1.0
O A:HOH530 4.3 37.2 1.0
CA A:LYS211 4.4 13.8 1.0
SD A:MET248 4.4 24.4 1.0
C A:SER249 4.5 9.5 1.0
O A:HOH537 4.5 28.0 1.0
N A:SER249 4.5 11.0 1.0
CB A:MET248 4.6 19.2 1.0
NZ A:LYS211 4.7 15.9 1.0
N A:ASP212 4.8 13.8 1.0
CB A:LYS211 4.9 13.3 1.0
CA A:SER249 4.9 9.3 1.0
CE A:LYS211 5.0 15.5 1.0
C A:MET248 5.0 10.4 1.0

Chlorine binding site 4 out of 9 in 6ogo

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Chlorine binding site 4 out of 9 in the Crystal Structure of Ndm-9 Metallo-Beta-Lactamase


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 Ndm-9 Metallo-Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl303

b:18.0
occ:1.00
 ZN B:ZN302 2.4 16.2 1.0
NZ B:LYS211 3.0 20.9 1.0
O1 B:PO4306 3.4 13.4 1.0
NE2 B:HIS250 3.4 13.5 1.0
N B:ASN220 3.4 16.7 1.0
CE1 B:HIS189 3.5 11.4 1.0
CD2 B:HIS250 3.5 13.3 1.0
ND1 B:HIS189 3.7 13.0 1.0
CB B:CYS208 3.8 10.7 1.0
O B:HOH582 3.8 22.0 1.0
SG B:CYS208 3.9 14.6 1.0
CA B:GLY219 4.0 25.9 1.0
O B:HOH433 4.0 17.0 1.0
O B:CYS208 4.1 14.5 1.0
CB B:ASN220 4.2 17.7 1.0
C B:GLY219 4.2 23.3 1.0
O B:LEU218 4.2 24.6 1.0
CA B:ASN220 4.3 15.5 1.0
O B:HOH463 4.4 21.2 1.0
CA B:CYS208 4.4 11.6 1.0
O B:HOH645 4.4 39.8 1.0
O B:ASN220 4.4 16.4 1.0
NE2 B:HIS189 4.4 12.9 1.0
CE B:LYS211 4.5 21.9 1.0
P B:PO4306 4.5 15.2 1.0
O4 B:PO4306 4.6 16.8 1.0
CE1 B:HIS250 4.7 16.3 1.0
CG B:HIS189 4.7 12.6 1.0
C B:CYS208 4.8 13.7 1.0
C B:ASN220 4.8 18.5 1.0
CG B:HIS250 4.8 15.9 1.0
N B:GLY219 5.0 18.8 1.0

Chlorine binding site 5 out of 9 in 6ogo

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Chlorine binding site 5 out of 9 in the Crystal Structure of Ndm-9 Metallo-Beta-Lactamase


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 Ndm-9 Metallo-Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl304

b:30.0
occ:1.00
 O B:HOH557 2.7 36.4 1.0
O B:HOH463 3.1 21.2 1.0
N B:HIS250 3.2 16.9 1.0
O B:HOH582 3.3 22.0 1.0
OG B:SER251 3.4 39.7 1.0
CB B:HIS250 3.4 19.0 1.0
C B:HIS250 3.4 22.8 1.0
N B:SER251 3.5 19.2 1.0
CA B:HIS250 3.5 15.6 1.0
CG B:MET248 3.9 26.2 1.0
CB B:SER251 4.0 31.9 1.0
O B:HIS250 4.1 22.9 1.0
CG B:HIS250 4.1 15.9 1.0
CD2 B:HIS250 4.1 13.3 1.0
O B:ILE210 4.2 14.2 1.0
CD B:LYS211 4.2 20.8 1.0
CA B:LYS211 4.3 18.3 1.0
CA B:SER251 4.3 19.9 1.0
O B:HOH559 4.4 43.3 1.0
C B:SER249 4.5 13.3 1.0
SD B:MET248 4.6 28.4 1.0
N B:SER249 4.6 13.8 1.0
CB B:MET248 4.6 23.6 1.0
NZ B:LYS211 4.8 20.9 1.0
N B:ASP212 4.8 20.4 1.0
CB B:LYS211 4.9 19.1 1.0
CE B:LYS211 5.0 21.9 1.0
CA B:SER249 5.0 12.4 1.0
C B:MET248 5.0 12.7 1.0

Chlorine binding site 6 out of 9 in 6ogo

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Chlorine binding site 6 out of 9 in the Crystal Structure of Ndm-9 Metallo-Beta-Lactamase


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 Ndm-9 Metallo-Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl305

b:33.9
occ:1.00
 N B:LYS242 3.1 22.1 1.0
C B:PHE240 3.1 17.0 1.0
CA B:PHE240 3.3 12.9 1.0
N B:PRO241 3.3 19.7 1.0
O2 B:EDO307 3.5 42.2 1.0
CB B:LYS242 3.5 27.5 1.0
CD B:PRO241 3.6 15.5 1.0
O B:PHE240 3.7 16.4 1.0
N B:ALA243 3.7 20.7 1.0
O B:HOH616 3.8 49.6 1.0
CA B:LYS242 3.8 21.7 1.0
O B:HOH503 3.8 27.2 1.0
CB B:PHE240 3.9 15.2 1.0
C1 B:EDO307 4.0 36.7 1.0
C B:LYS242 4.1 29.9 1.0
C B:PRO241 4.2 25.9 1.0
CG B:LYS242 4.3 35.8 1.0
C2 B:EDO307 4.3 27.4 1.0
CA B:PRO241 4.3 17.6 1.0
CG B:PRO241 4.3 18.5 1.0
O B:HOH412 4.5 42.1 1.0
N B:PHE240 4.6 13.3 1.0
CD1 B:PHE240 4.6 13.8 1.0
O B:ALA239 4.7 15.5 1.0
CA B:ALA243 4.7 16.0 1.0
CB B:ALA243 4.8 20.8 1.0
CG B:PHE240 4.8 13.5 1.0
O1 B:EDO307 4.9 32.9 1.0
O A:HOH655 4.9 39.1 1.0

Chlorine binding site 7 out of 9 in 6ogo

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Chlorine binding site 7 out of 9 in the Crystal Structure of Ndm-9 Metallo-Beta-Lactamase


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 Ndm-9 Metallo-Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl303

b:19.1
occ:1.00
 ZN C:ZN302 2.4 16.9 1.0
NZ C:LYS211 3.0 20.0 1.0
O4 C:PO4306 3.3 15.3 1.0
N C:ASN220 3.4 17.1 1.0
CE1 C:HIS189 3.4 15.4 1.0
NE2 C:HIS250 3.4 16.8 1.0
CD2 C:HIS250 3.5 16.9 1.0
ND1 C:HIS189 3.7 13.6 1.0
CB C:CYS208 3.8 13.0 1.0
O C:HOH462 4.0 18.6 1.0
SG C:CYS208 4.0 15.1 1.0
O C:HOH563 4.1 21.8 1.0
CB C:ASN220 4.1 17.9 1.0
O C:CYS208 4.1 16.3 1.0
O C:HOH591 4.1 46.9 1.0
CA C:GLY219 4.2 26.7 1.0
CA C:ASN220 4.2 16.2 1.0
C C:GLY219 4.3 21.7 1.0
O C:LEU218 4.3 20.4 1.0
CA C:CYS208 4.3 12.5 1.0
O C:ASN220 4.4 16.9 1.0
NE2 C:HIS189 4.4 12.8 1.0
CE C:LYS211 4.4 19.3 1.0
P C:PO4306 4.5 15.7 1.0
O C:HOH451 4.5 21.6 1.0
O1 C:PO4306 4.5 17.2 1.0
CG C:HIS189 4.7 13.8 1.0
C C:CYS208 4.7 12.1 1.0
CE1 C:HIS250 4.8 15.0 1.0
C C:ASN220 4.8 16.6 1.0
CG C:HIS250 4.8 15.9 1.0

Chlorine binding site 8 out of 9 in 6ogo

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Chlorine binding site 8 out of 9 in the Crystal Structure of Ndm-9 Metallo-Beta-Lactamase


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 Ndm-9 Metallo-Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl304

b:27.5
occ:1.00
 O1 C:PGE309 3.1 30.4 1.0
N C:LYS242 3.2 17.1 1.0
C C:PHE240 3.2 14.0 1.0
CA C:PHE240 3.3 14.7 1.0
N C:PRO241 3.4 16.6 1.0
CD C:PRO241 3.6 16.3 1.0
CB C:LYS242 3.6 24.6 1.0
O C:PHE240 3.8 15.3 1.0
CA C:LYS242 3.8 19.9 1.0
N C:ALA243 3.8 16.8 1.0
O2 C:PGE309 3.8 41.0 1.0
O C:HOH510 3.9 38.4 1.0
CB C:PHE240 4.0 11.9 1.0
CG C:LYS242 4.1 25.5 1.0
C C:LYS242 4.1 19.8 1.0
C1 C:PGE309 4.1 29.0 1.0
C C:PRO241 4.2 18.2 1.0
CG C:PRO241 4.3 18.4 1.0
CA C:PRO241 4.3 16.9 1.0
O C:HOH626 4.4 47.6 1.0
C2 C:PGE309 4.4 32.5 1.0
CD1 C:PHE240 4.5 10.6 1.0
N C:PHE240 4.6 12.6 1.0
O C:ALA239 4.6 13.8 1.0
CG C:PHE240 4.8 11.5 1.0
CA C:ALA243 4.8 16.4 1.0
CB C:ALA243 4.9 14.5 1.0

Chlorine binding site 9 out of 9 in 6ogo

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Chlorine binding site 9 out of 9 in the Crystal Structure of Ndm-9 Metallo-Beta-Lactamase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Crystal Structure of Ndm-9 Metallo-Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl305

b:30.2
occ:1.00
 O C:HOH542 2.8 41.8 1.0
O C:HOH556 2.8 30.3 1.0
N C:ASN57 3.1 16.0 1.0
CB C:ASN57 3.6 17.3 1.0
CB C:ALA55 3.6 17.9 1.0
CD C:PRO56 3.7 16.8 1.0
ND2 C:ASN57 3.7 27.1 1.0
N C:PRO56 3.7 18.5 1.0
CA C:ASN57 3.8 16.0 1.0
CG2 C:THR201 3.8 19.6 1.0
CB C:PRO56 4.0 22.1 1.0
CG C:ASN57 4.1 19.1 1.0
C C:PRO56 4.1 15.1 1.0
C C:ASN57 4.2 13.2 1.0
C C:ALA55 4.2 17.8 1.0
CA C:PRO56 4.2 16.3 1.0
CG C:PRO56 4.3 19.0 1.0
CG2 C:VAL58 4.3 15.4 1.0
O C:HOH592 4.4 54.0 1.0
N C:VAL58 4.4 14.3 1.0
O C:HOH496 4.5 43.8 1.0
CA C:ALA55 4.5 14.9 1.0
O C:GLY200 4.8 24.2 1.0
O C:ALA55 4.9 17.1 1.0
O C:ASN57 4.9 14.4 1.0
CB C:THR201 4.9 17.6 1.0

Reference:

J.E.Raczynska, B.Imiolczyk, M.Komorowska, J.Czyrko, J.Sliwiak, K.Brzezinski, M.Jaskolski. Flexible Loop of New Delhi Metallo-Beta-Lactamase Modulates Its Activity Towards Different Substrates To Be Published.
Page generated: Mon Jul 29 12:40:53 2024

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