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Chlorine in PDB 5odz: Crystal Structure of the Beta-Lactamase Oxa-163

Enzymatic activity of Crystal Structure of the Beta-Lactamase Oxa-163

All present enzymatic activity of Crystal Structure of the Beta-Lactamase Oxa-163:
3.5.2.6;

Protein crystallography data

The structure of Crystal Structure of the Beta-Lactamase Oxa-163, PDB code: 5odz was solved by B.A.Lund, T.J.O.Carlsen, H.K.S.Leiros, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.49 / 2.07
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 121.920, 121.920, 160.426, 90.00, 90.00, 120.00
R / Rfree (%) 14.5 / 18.7

Other elements in 5odz:

The structure of Crystal Structure of the Beta-Lactamase Oxa-163 also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of the Beta-Lactamase Oxa-163 (pdb code 5odz). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of the Beta-Lactamase Oxa-163, PDB code: 5odz:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 5odz

Go back to Chlorine Binding Sites List in 5odz
Chlorine binding site 1 out of 4 in the Crystal Structure of the Beta-Lactamase Oxa-163


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 Beta-Lactamase Oxa-163 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl301

b:21.6
occ:1.00
 HH12 B:ARG206 2.3 20.2 1.0
HH22 D:ARG206 2.4 27.1 1.0
HH12 D:ARG206 2.4 21.1 1.0
HH22 B:ARG206 2.4 25.7 1.0
NH1 B:ARG206 3.1 16.8 1.0
NH2 D:ARG206 3.2 22.6 1.0
NH1 D:ARG206 3.2 17.6 1.0
NH2 B:ARG206 3.2 21.4 1.0
O D:HOH512 3.2 47.0 1.0
HA B:GLN193 3.3 19.8 1.0
HA D:GLN193 3.3 23.1 1.0
HG3 B:GLN193 3.4 24.5 1.0
HD22 D:LEU196 3.5 22.4 1.0
HD22 B:LEU196 3.6 27.1 1.0
HG3 D:GLN193 3.6 21.1 1.0
CZ B:ARG206 3.6 20.1 1.0
CZ D:ARG206 3.6 19.2 1.0
HH11 B:ARG206 3.8 20.2 1.0
HH21 D:ARG206 3.9 27.1 1.0
HH11 D:ARG206 3.9 21.1 1.0
HH21 B:ARG206 3.9 25.7 1.0
HB2 D:GLN193 4.0 17.0 1.0
HB2 B:GLN193 4.0 20.6 1.0
HB2 B:LEU196 4.2 17.0 1.0
CA B:GLN193 4.2 16.5 1.0
CA D:GLN193 4.2 19.3 1.0
HB2 D:LEU196 4.2 16.9 1.0
CG B:GLN193 4.3 20.4 1.0
CB B:GLN193 4.4 17.1 1.0
CB D:GLN193 4.4 14.2 1.0
CG D:GLN193 4.4 17.6 1.0
CD2 D:LEU196 4.5 18.6 1.0
CD2 B:LEU196 4.5 22.6 1.0
O B:HOH492 4.6 36.8 1.0
HD13 B:LEU196 4.6 19.1 1.0
O D:HOH483 4.6 47.5 1.0
HD13 D:LEU196 4.6 21.5 1.0
HD23 D:LEU196 4.8 22.4 1.0
HD23 B:LEU196 4.8 27.1 1.0
HG2 B:GLN193 4.8 24.5 1.0
O B:GLN193 4.9 17.0 1.0
NE B:ARG206 4.9 18.0 1.0
NE D:ARG206 4.9 16.8 1.0
HD21 D:LEU196 4.9 22.4 1.0
O D:GLN193 5.0 16.8 1.0
HG2 D:GLN193 5.0 21.1 1.0

Chlorine binding site 2 out of 4 in 5odz

Go back to Chlorine Binding Sites List in 5odz
Chlorine binding site 2 out of 4 in the Crystal Structure of the Beta-Lactamase Oxa-163


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 Beta-Lactamase Oxa-163 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl302

b:60.6
occ:1.00
 HG1 B:THR209 2.7 25.6 1.0
HH22 B:ARG250 2.8 47.2 1.0
HG B:SER118 2.8 26.6 0.6
HA2 B:GLY210 3.3 23.2 1.0
OG1 B:THR209 3.3 21.4 1.0
HH12 B:ARG250 3.4 42.9 1.0
HB B:THR209 3.6 24.9 1.0
NH2 B:ARG250 3.6 39.3 1.0
O B:HOH483 3.6 79.7 1.0
OG B:SER118 3.6 22.2 0.6
HB2 B:SER70 3.8 34.5 1.0
HB3 B:TYR211 3.9 36.6 1.0
CA B:GLY210 4.0 19.3 1.0
HB2 B:SER118 4.0 24.1 0.4
CB B:THR209 4.0 20.8 1.0
OG B:SER118 4.0 17.3 0.4
O B:HOH414 4.0 22.9 1.0
HB3 B:SER118 4.1 25.8 0.6
C B:THR209 4.1 22.6 1.0
HB3 B:SER118 4.1 24.1 0.4
O B:THR209 4.1 18.1 1.0
N B:GLY210 4.1 17.7 1.0
HB2 B:TYR211 4.1 36.6 1.0
HH21 B:ARG250 4.1 47.2 1.0
NH1 B:ARG250 4.2 35.7 1.0
HB2 B:SER118 4.2 25.8 0.6
C B:GLY210 4.2 24.9 1.0
CB B:SER118 4.2 21.5 0.6
H B:TYR211 4.2 28.0 1.0
CB B:SER118 4.3 20.0 0.4
O B:HOH545 4.3 56.5 1.0
N B:TYR211 4.3 23.3 1.0
HZ1 B:LYS208 4.3 30.8 1.0
CZ B:ARG250 4.3 35.1 1.0
CB B:TYR211 4.5 30.5 1.0
HZ2 B:LYS208 4.5 30.8 1.0
HG B:SER118 4.5 20.8 0.4
CB B:SER70 4.5 28.7 1.0
H B:GLY210 4.6 21.3 1.0
OG B:SER70 4.7 29.0 1.0
HZ3 B:LYS208 4.7 30.8 1.0
O B:HOH463 4.7 46.9 1.0
NZ B:LYS208 4.7 25.7 1.0
HB3 B:SER70 4.7 34.5 1.0
CA B:THR209 4.7 22.0 1.0
HA3 B:GLY210 4.8 23.2 1.0
O B:GLY210 4.9 23.6 1.0
HH11 B:ARG250 4.9 42.9 1.0

Chlorine binding site 3 out of 4 in 5odz

Go back to Chlorine Binding Sites List in 5odz
Chlorine binding site 3 out of 4 in the Crystal Structure of the Beta-Lactamase Oxa-163


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 Beta-Lactamase Oxa-163 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl302

b:47.7
occ:1.00
 O D:HOH511 2.5 28.1 1.0
O D:ALA207 2.9 18.8 1.0
O D:HOH499 2.9 27.0 1.0
HD2 D:LYS208 3.0 24.0 1.0
HA D:LYS208 3.3 22.8 1.0
HG2 D:MET115 3.3 27.7 0.6
HA D:MET195 3.4 18.3 1.0
HB3 D:MET115 3.7 23.1 0.4
HD3 D:LYS208 3.7 24.0 1.0
CD D:LYS208 3.8 20.0 1.0
HA D:LYS116 3.8 25.2 1.0
O D:HOH447 3.9 21.0 1.0
HG1 D:THR197 3.9 29.6 1.0
C D:ALA207 4.0 19.8 1.0
OG1 D:THR197 4.0 24.7 1.0
CG D:MET115 4.1 23.1 0.6
O D:MET115 4.1 17.5 0.6
O D:ALA194 4.1 17.3 1.0
CA D:LYS208 4.1 19.0 1.0
HB2 D:LYS208 4.1 17.9 1.0
O D:MET195 4.2 22.1 1.0
SD D:MET115 4.2 21.1 0.6
O D:HOH548 4.2 57.9 1.0
O D:HOH468 4.3 58.7 1.0
CA D:MET195 4.3 15.3 1.0
HZ3 D:LYS208 4.3 21.4 1.0
O D:MET115 4.4 17.8 0.4
HB3 D:MET115 4.4 21.6 0.6
C D:MET115 4.4 16.0 0.6
C D:MET195 4.4 16.1 1.0
N D:LYS208 4.5 18.8 1.0
HE2 D:LYS208 4.5 21.4 1.0
C D:MET115 4.5 17.5 0.4
CB D:LYS208 4.5 14.9 1.0
H D:THR209 4.6 22.3 1.0
CB D:MET115 4.6 19.2 0.4
H D:ALA207 4.6 20.2 1.0
CE D:LYS208 4.6 17.9 1.0
O D:HOH414 4.6 21.7 1.0
CA D:LYS116 4.7 21.0 1.0
N D:LYS116 4.7 19.6 1.0
CB D:MET115 4.7 18.0 0.6
CG D:LYS208 4.8 18.2 1.0
HG3 D:MET115 4.8 27.7 0.6
HG2 D:MET195 4.9 20.3 1.0
SD D:MET115 4.9 41.8 0.4
HB2 D:MET115 4.9 23.1 0.4
NZ D:LYS208 4.9 17.8 1.0

Chlorine binding site 4 out of 4 in 5odz

Go back to Chlorine Binding Sites List in 5odz
Chlorine binding site 4 out of 4 in the Crystal Structure of the Beta-Lactamase Oxa-163


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 Beta-Lactamase Oxa-163 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl303

b:59.2
occ:1.00
 O D:HOH566 2.1 48.0 1.0
HD21 D:ASN48 2.4 36.1 1.0
HE3 D:LYS51 2.7 71.4 1.0
O D:HOH465 3.0 54.2 1.0
ND2 D:ASN48 3.2 30.1 1.0
HD22 D:ASN231 3.3 38.0 1.0
HZ2 D:LYS51 3.3 84.3 0.6
HD2 D:LYS51 3.3 62.8 0.5
O D:HOH491 3.4 37.2 1.0
CE D:LYS51 3.4 59.5 1.0
HG3 D:LYS51 3.6 55.9 1.0
HD21 D:ASN231 3.6 38.0 1.0
HD22 D:ASN48 3.6 36.1 1.0
ND2 D:ASN231 3.7 31.7 1.0
NZ D:LYS51 3.8 70.3 0.6
CD D:LYS51 3.8 52.3 0.5
HZ1 D:LYS51 4.0 84.3 0.6
HZ2 D:TRP233 4.0 42.8 1.0
CG D:ASN48 4.2 38.1 1.0
CG D:LYS51 4.2 46.6 1.0
OD1 D:ASN48 4.2 28.6 1.0
HE2 D:LYS51 4.3 71.4 1.0
O D:HOH467 4.3 46.7 1.0
HB2 D:ASN50 4.4 43.4 1.0
HD22 D:ASN50 4.5 71.5 1.0
HZ3 D:LYS51 4.6 84.3 0.6
HD3 D:LYS51 4.7 62.8 0.5
HG2 D:LYS51 4.7 55.9 1.0
CZ2 D:TRP233 4.8 35.7 1.0
HE1 D:TRP233 4.9 33.1 1.0
CG D:ASN231 5.0 30.6 1.0

Reference:

B.A.Lund, A.M.Thomassen, T.J.O.Carlsen, H.K.S.Leiros. Structure, Activity and Thermostability Investigations of Oxa-163, Oxa-181 and Oxa-245 Using Biochemical Analysis, Crystal Structures and Differential Scanning Calorimetry Analysis. Acta Crystallogr F Struct V. 73 579 2017BIOL Commun.
ISSN: ESSN 2053-230X
PubMed: 28994407
DOI: 10.1107/S2053230X17013838
Page generated: Fri Jul 26 14:25:25 2024

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