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Chlorine in PDB 6twt: Crystal Structure of N-Terminally Truncated Ndm-1 Metallo-Beta- Lactamase

Protein crystallography data

The structure of Crystal Structure of N-Terminally Truncated Ndm-1 Metallo-Beta- Lactamase, PDB code: 6twt was solved by B.Imiolczyk, J.Czyrko-Horczak, K.Brzezinski, M.Jaskolski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 53.58 / 0.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 70.482, 73.980, 77.715, 90.00, 90.00, 90.00
R / Rfree (%) 10.5 / 12

Other elements in 6twt:

The structure of Crystal Structure of N-Terminally Truncated Ndm-1 Metallo-Beta- Lactamase also contains other interesting chemical elements:

Calcium (Ca) 5 atoms
Zinc (Zn) 4 atoms

Chlorine Binding Sites:

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

Chlorine binding site 1 out of 6 in 6twt

Go back to Chlorine Binding Sites List in 6twt
Chlorine binding site 1 out of 6 in the Crystal Structure of N-Terminally Truncated Ndm-1 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 N-Terminally Truncated Ndm-1 Metallo-Beta- Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl305

b:18.8
occ:0.50
 CL A:CL305 0.0 18.8 0.5
CL A:CL305 0.3 37.5 0.5
O A:HOH657 2.9 27.7 0.5
O A:HOH649 3.0 30.1 0.5
N A:LYS242 3.2 13.6 1.0
O A:HOH594 3.2 37.7 1.0
C A:PHE240 3.2 10.0 1.0
CA A:PHE240 3.4 9.4 1.0
N A:PRO241 3.4 10.8 1.0
CD A:PRO241 3.6 11.5 1.0
N A:ALA243 3.6 12.4 1.0
O A:PHE240 3.7 11.1 1.0
CB A:LYS242 3.7 18.2 1.0
CA A:LYS242 3.8 15.6 1.0
CB A:PHE240 3.9 9.8 1.0
C A:LYS242 4.0 15.5 1.0
O A:HOH484 4.1 25.3 1.0
C A:PRO241 4.2 14.2 1.0
O A:HOH642 4.2 33.5 0.5
CG A:PRO241 4.3 12.7 1.0
CA A:PRO241 4.3 12.9 1.0
CG A:LYS242 4.4 21.6 1.0
CA A:ALA243 4.6 12.5 1.0
CB A:ALA243 4.6 13.6 1.0
O A:HOH502 4.7 28.2 1.0
CD1 A:PHE240 4.7 9.7 1.0
N A:PHE240 4.7 9.2 1.0
O A:ALA239 4.8 9.9 1.0
CG A:PHE240 4.8 9.1 1.0
O A:HOH642 4.9 23.6 0.5
O A:LYS242 4.9 18.9 1.0
CD A:LYS242 5.0 21.6 0.5

Chlorine binding site 2 out of 6 in 6twt

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Chlorine binding site 2 out of 6 in the Crystal Structure of N-Terminally Truncated Ndm-1 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 N-Terminally Truncated Ndm-1 Metallo-Beta- Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl305

b:37.5
occ:0.50
 CL A:CL305 0.0 37.5 0.5
CL A:CL305 0.3 18.8 0.5
O A:HOH657 2.6 27.7 0.5
O A:HOH649 3.1 30.1 0.5
N A:LYS242 3.2 13.6 1.0
O A:HOH594 3.3 37.7 1.0
C A:PHE240 3.4 10.0 1.0
N A:PRO241 3.5 10.8 1.0
CA A:PHE240 3.6 9.4 1.0
CD A:PRO241 3.6 11.5 1.0
CB A:LYS242 3.7 18.2 1.0
CA A:LYS242 3.8 15.6 1.0
N A:ALA243 3.8 12.4 1.0
O A:HOH484 3.9 25.3 1.0
O A:PHE240 4.0 11.1 1.0
C A:LYS242 4.1 15.5 1.0
CB A:PHE240 4.2 9.8 1.0
O A:HOH642 4.2 33.5 0.5
CG A:PRO241 4.2 12.7 1.0
CG A:LYS242 4.2 21.6 1.0
C A:PRO241 4.3 14.2 1.0
CA A:PRO241 4.4 12.9 1.0
O A:ALA239 4.8 9.9 1.0
CD A:LYS242 4.8 21.6 0.5
CD1 A:PHE240 4.8 9.7 1.0
N A:PHE240 4.8 9.2 1.0
O A:HOH502 4.8 28.2 1.0
CA A:ALA243 4.8 12.5 1.0
CB A:ALA243 4.9 13.6 1.0
O A:HOH642 4.9 23.6 0.5

Chlorine binding site 3 out of 6 in 6twt

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Chlorine binding site 3 out of 6 in the Crystal Structure of N-Terminally Truncated Ndm-1 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 N-Terminally Truncated Ndm-1 Metallo-Beta- Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl306

b:21.7
occ:0.80
 O A:HOH589 2.8 27.6 0.5
O A:HOH627 3.0 19.1 1.0
N A:ASN57 3.2 13.6 1.0
CD A:PRO56 3.6 16.1 1.0
CB A:ASN57 3.6 14.2 1.0
CB A:ALA55 3.6 14.8 1.0
N A:PRO56 3.7 14.2 1.0
ND2 A:ASN57 3.8 20.7 1.0
CA A:ASN57 3.8 13.1 1.0
CG2 A:THR201 3.9 16.2 1.0
O A:HOH529 4.0 31.2 0.5
CB A:PRO56 4.0 16.7 1.0
C A:PRO56 4.1 14.4 1.0
CG A:ASN57 4.1 16.5 1.0
CA A:PRO56 4.1 15.1 1.0
C A:ALA55 4.2 13.2 1.0
CG A:PRO56 4.3 17.0 1.0
C A:ASN57 4.3 11.5 1.0
CG2 A:VAL58 4.3 11.9 1.0
N A:VAL58 4.5 11.1 1.0
CA A:ALA55 4.5 13.8 1.0
O A:HOH589 4.7 27.2 0.5
O A:ALA55 4.8 13.5 1.0
CB A:THR201 5.0 14.4 1.0

Chlorine binding site 4 out of 6 in 6twt

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Chlorine binding site 4 out of 6 in the Crystal Structure of N-Terminally Truncated Ndm-1 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 N-Terminally Truncated Ndm-1 Metallo-Beta- Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl307

b:16.0
occ:0.70
 O B:HOH409 2.8 17.4 0.5
O B:HOH409 2.9 21.7 0.5
O B:HOH430 2.9 34.1 1.0
N B:SER160 3.1 7.7 1.0
O B:HOH481 3.6 14.6 1.0
CA B:HIS159 3.8 8.2 1.0
O A:HOH573 3.8 14.3 1.0
CB B:SER160 3.8 8.5 1.0
O B:SER160 3.9 8.7 1.0
CA B:SER160 3.9 7.6 1.0
C B:HIS159 3.9 7.4 1.0
O B:HOH413 4.2 11.4 1.0
CB B:HIS159 4.3 8.6 1.0
OG B:SER160 4.3 8.9 1.0
C B:SER160 4.4 7.5 1.0
O B:HOH618 4.5 12.9 1.0
ND1 B:HIS159 4.5 11.6 1.0
O B:GLN158 4.7 11.5 0.5
O B:GLN158 4.9 10.3 0.5
CG B:HIS159 4.9 9.5 1.0
O A:HOH401 5.0 18.7 0.5

Chlorine binding site 5 out of 6 in 6twt

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Chlorine binding site 5 out of 6 in the Crystal Structure of N-Terminally Truncated Ndm-1 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 N-Terminally Truncated Ndm-1 Metallo-Beta- Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl308

b:12.4
occ:0.50
 CL B:CL308 0.0 12.4 0.5
CL B:CL308 0.9 25.0 0.5
O B:HOH421 3.0 17.4 1.0
C B:PHE240 3.1 11.1 1.0
O B:HOH634 3.1 11.0 0.5
N B:LYS242 3.2 11.7 0.4
N B:LYS242 3.2 11.6 0.4
O B:HOH675 3.2 30.4 0.5
N B:PRO241 3.3 12.2 1.0
CA B:PHE240 3.3 9.7 1.0
CG B:LYS242 3.4 17.5 0.4
CG B:LYS242 3.4 14.2 0.4
N B:ALA243 3.4 13.2 1.0
CD B:LYS242 3.5 12.6 0.4
O B:PHE240 3.5 13.4 1.0
CD B:PRO241 3.5 11.6 1.0
CD B:LYS242 3.7 18.5 0.4
CE B:LYS242 3.7 14.2 0.4
CB B:PHE240 3.8 10.0 1.0
CA B:LYS242 3.9 13.6 0.4
CA B:LYS242 3.9 13.3 0.4
C B:LYS242 3.9 12.9 0.4
C B:LYS242 3.9 13.0 0.4
CB B:LYS242 4.1 15.8 0.4
C B:PRO241 4.2 15.1 1.0
CB B:LYS242 4.2 14.7 0.4
CE B:LYS242 4.2 19.9 0.4
O B:HOH429 4.2 15.8 1.0
CA B:PRO241 4.3 14.5 1.0
CG B:PRO241 4.3 14.1 1.0
NZ B:LYS242 4.4 12.1 0.4
CA B:ALA243 4.4 11.8 1.0
CB B:ALA243 4.5 12.2 1.0
CD1 B:PHE240 4.6 9.2 1.0
N B:PHE240 4.6 9.2 1.0
NZ B:LYS242 4.6 21.1 0.4
O B:HOH511 4.7 13.0 0.3
CG B:PHE240 4.7 8.6 1.0
O B:ALA239 4.8 9.8 1.0
O B:HOH511 4.9 11.0 0.7
O B:LYS242 4.9 14.5 0.4
O B:LYS242 4.9 14.3 0.4
CB B:PRO241 5.0 15.7 1.0

Chlorine binding site 6 out of 6 in 6twt

Go back to Chlorine Binding Sites List in 6twt
Chlorine binding site 6 out of 6 in the Crystal Structure of N-Terminally Truncated Ndm-1 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 N-Terminally Truncated Ndm-1 Metallo-Beta- Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl308

b:25.0
occ:0.50
 CL B:CL308 0.0 25.0 0.5
CL B:CL308 0.9 12.4 0.5
O B:HOH634 2.3 11.0 0.5
O B:HOH675 2.7 30.4 0.5
O B:HOH421 3.3 17.4 1.0
CA B:PHE240 3.5 9.7 1.0
O B:HOH429 3.5 15.8 1.0
C B:PHE240 3.6 11.1 1.0
CE B:LYS242 3.6 14.2 0.4
CD B:PRO241 3.7 11.6 1.0
CD B:LYS242 3.7 18.5 0.4
N B:PRO241 3.7 12.2 1.0
CG B:LYS242 3.7 14.2 0.4
CD B:LYS242 3.7 12.6 0.4
CG B:LYS242 3.7 17.5 0.4
N B:LYS242 3.9 11.6 0.4
N B:LYS242 3.9 11.7 0.4
CE B:LYS242 4.0 19.9 0.4
CB B:PHE240 4.1 10.0 1.0
NZ B:LYS242 4.2 21.1 0.4
O B:PHE240 4.2 13.4 1.0
N B:ALA243 4.3 13.2 1.0
NZ B:LYS242 4.3 12.1 0.4
O B:HOH453 4.4 49.8 1.0
CD1 B:PHE240 4.4 9.2 1.0
CG B:PRO241 4.4 14.1 1.0
O B:ALA239 4.5 9.8 1.0
O B:HOH506 4.6 13.9 1.0
CA B:LYS242 4.6 13.3 0.4
CA B:LYS242 4.6 13.6 0.4
CB B:LYS242 4.6 15.8 0.4
C B:LYS242 4.7 12.9 0.4
CB B:LYS242 4.7 14.7 0.4
C B:LYS242 4.7 13.0 0.4
N B:PHE240 4.7 9.2 1.0
CG B:PHE240 4.7 8.6 1.0
O B:HOH511 4.8 11.0 0.7
CA B:PRO241 4.8 14.5 1.0
O B:HOH511 4.8 13.0 0.3
C B:PRO241 4.9 15.1 1.0

Reference:

J.E.Raczynska, B.Imiolczyk, M.Komorowska, J.Sliwiak, J.Czyrko-Horczak, K.Brzezinski, M.Jaskolski. Flexible Loops of New Delhi Metallo-Beta-Lactamase Modulate Its Activity Towards Different Substrates. Int.J.Biol.Macromol. 2020.
ISSN: ISSN 0141-8130
PubMed: 32353499
DOI: 10.1016/J.IJBIOMAC.2020.04.219
Page generated: Mon Jul 29 15:38:08 2024

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