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Sodium in PDB 5gs8: Crystal Structure of Tla-3 Extended-Spectrum Beta-Lactamase

Enzymatic activity of Crystal Structure of Tla-3 Extended-Spectrum Beta-Lactamase

All present enzymatic activity of Crystal Structure of Tla-3 Extended-Spectrum Beta-Lactamase:
3.5.2.6;

Protein crystallography data

The structure of Crystal Structure of Tla-3 Extended-Spectrum Beta-Lactamase, PDB code: 5gs8 was solved by J.Wachino, W.Jin, Y.Arakawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 55.18 / 1.59
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 94.850, 67.930, 45.060, 90.00, 94.17, 90.00
R / Rfree (%) 13.5 / 16

Other elements in 5gs8:

The structure of Crystal Structure of Tla-3 Extended-Spectrum Beta-Lactamase also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Sodium atom in the Crystal Structure of Tla-3 Extended-Spectrum Beta-Lactamase (pdb code 5gs8). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 15 binding sites of Sodium where determined in the Crystal Structure of Tla-3 Extended-Spectrum Beta-Lactamase, PDB code: 5gs8:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 15 in 5gs8

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Sodium binding site 1 out of 15 in the Crystal Structure of Tla-3 Extended-Spectrum Beta-Lactamase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Tla-3 Extended-Spectrum Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na306

b:17.2
occ:1.00
 O A:TRP163 2.8 12.8 1.0
O A:MET159 2.8 11.5 1.0
O A:HOH574 2.8 13.3 1.0
O A:ALA162 2.9 14.5 1.0
N A:GLN166 3.0 9.2 1.0
CB A:GLN166 3.3 10.9 1.0
C A:TRP163 3.4 13.0 1.0
CG A:GLN166 3.6 10.4 1.0
O A:HOH610 3.6 16.0 1.0
N A:VAL165 3.6 10.6 1.0
CA A:GLN166 3.7 9.5 1.0
C A:MET159 3.7 9.8 1.0
NE2 A:GLN166 3.8 11.4 1.0
CA A:TRP163 3.8 12.6 1.0
CA A:MET159 3.8 8.3 1.0
C A:ALA162 3.9 13.1 1.0
C A:VAL165 3.9 9.5 1.0
CD A:GLN166 3.9 11.8 1.0
CB A:MET159 3.9 9.4 1.0
CA A:VAL165 4.0 10.8 1.0
CB A:VAL165 4.1 10.7 1.0
N A:ASN164 4.3 12.7 1.0
N A:TRP163 4.3 14.8 1.0
C A:ASN164 4.4 12.0 1.0
CG A:MET159 4.4 9.5 1.0
O A:HOH650 4.6 15.7 1.0
OE1 A:GLN166 4.7 11.0 1.0
CA A:ASN164 4.8 12.2 1.0
NE2 A:GLN55 4.8 13.3 1.0
O A:HOH581 4.8 14.1 1.0
CG1 A:VAL165 4.9 12.5 1.0
N A:HIS160 4.9 10.4 1.0
O A:VAL165 5.0 9.9 1.0

Sodium binding site 2 out of 15 in 5gs8

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Sodium binding site 2 out of 15 in the Crystal Structure of Tla-3 Extended-Spectrum Beta-Lactamase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Tla-3 Extended-Spectrum Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na307

b:16.2
occ:1.00
 OD2 A:ASP241 2.8 7.4 1.0
O A:GLY207 2.8 10.0 1.0
N A:LYS212 2.9 8.2 1.0
CE1 A:HIS223 3.2 8.4 1.0
N A:LEU211 3.2 7.4 1.0
CG A:LYS212 3.4 11.1 0.5
ND1 A:HIS223 3.4 8.3 1.0
CB A:LYS212 3.5 9.7 0.5
CD A:LYS212 3.6 12.6 0.5
NE2 A:HIS223 3.6 8.2 1.0
CG A:LYS212 3.6 12.4 0.5
CB A:LYS212 3.7 11.8 0.5
CA A:LEU211 3.7 7.5 1.0
CB A:LEU211 3.8 7.2 1.0
C A:LEU211 3.8 8.9 1.0
C A:ARG210 3.8 7.5 1.0
CA A:LYS212 3.8 9.1 0.5
C A:GLY207 3.9 10.6 1.0
CA A:LYS212 3.9 9.8 0.5
CG A:ASP241 3.9 8.1 1.0
CG A:HIS223 4.0 8.0 1.0
CD2 A:HIS223 4.1 6.8 1.0
N A:ARG210 4.1 7.6 1.0
CB A:ARG210 4.1 6.5 1.0
CA A:ARG210 4.2 7.3 1.0
CE A:LYS212 4.3 14.3 0.5
OD1 A:ASP241 4.4 7.5 1.0
CD A:LYS212 4.4 12.7 0.5
NA A:NA311 4.5 19.5 1.0
CA A:PRO208 4.5 10.5 1.0
O A:ARG210 4.5 9.0 1.0
C A:PRO208 4.6 10.1 1.0
CG1 A:VAL221 4.7 9.8 1.0
CG A:LEU211 4.7 7.7 1.0
N A:PRO208 4.7 10.0 1.0
O A:PRO208 4.7 12.1 1.0
CA A:GLY207 4.8 11.3 1.0
O A:THR206 4.8 9.0 1.0
C A:LYS212 4.9 9.2 1.0
N A:GLY213 4.9 9.0 1.0
CE A:LYS212 4.9 16.8 0.5
O A:LEU211 5.0 9.2 1.0

Sodium binding site 3 out of 15 in 5gs8

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Sodium binding site 3 out of 15 in the Crystal Structure of Tla-3 Extended-Spectrum Beta-Lactamase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Tla-3 Extended-Spectrum Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na308

b:21.5
occ:1.00
 O A:HOH536 2.7 35.4 1.0
O A:VAL147 2.8 15.8 1.0
O A:HOH589 2.9 16.8 1.0
O A:ILE150 3.1 11.7 1.0
N A:ILE150 3.2 11.0 1.0
N A:ASN149 3.4 12.7 1.0
C A:LYS148 3.5 12.0 1.0
CA A:LYS148 3.5 14.4 1.0
O A:HOH558 3.8 22.4 1.0
C A:VAL147 3.8 15.0 1.0
CA A:ILE150 3.8 10.6 1.0
CB A:ILE150 3.8 10.1 1.0
C A:ILE150 3.9 10.6 1.0
CA A:SER143 4.1 15.1 1.0
CB A:SER143 4.1 15.3 1.0
O A:LYS148 4.1 15.3 1.0
N A:LYS148 4.1 15.5 1.0
O A:HOH605 4.2 29.1 1.0
C A:ASN149 4.2 10.9 1.0
OG A:SER143 4.3 22.9 1.0
CA A:ASN149 4.3 11.2 1.0
CG1 A:ILE150 4.5 9.7 1.0
N A:SER143 4.5 13.2 1.0
CG2 A:ILE142 4.7 12.1 1.0
CB A:LYS148 4.8 17.8 1.0
O A:HOH599 4.8 27.4 1.0

Sodium binding site 4 out of 15 in 5gs8

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Sodium binding site 4 out of 15 in the Crystal Structure of Tla-3 Extended-Spectrum Beta-Lactamase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Tla-3 Extended-Spectrum Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na309

b:25.1
occ:1.00
 OG1 A:THR172 2.7 9.7 1.0
O A:HOH529 2.9 18.2 1.0
ND2 A:ASN149 3.0 17.5 1.0
OD2 A:ASP174 3.2 22.9 1.0
OD1 A:ASP174 3.3 14.5 1.0
CG A:ASP174 3.4 15.8 1.0
NA A:NA314 3.5 23.2 1.0
CB A:ASN149 3.5 12.4 1.0
CG A:ASN149 3.7 16.7 1.0
CB A:THR172 3.8 9.4 1.0
N A:ALA175 3.9 9.6 1.0
O A:HOH601 4.0 33.3 1.0
CB A:ALA175 4.1 9.9 1.0
CG2 A:THR172 4.1 9.8 1.0
CA A:ALA175 4.3 9.5 1.0
O A:LYS148 4.3 15.3 1.0
O A:HOH671 4.5 25.6 1.0
C A:ASP174 4.6 9.5 1.0
CB A:ASP174 4.6 13.1 1.0
NE2 A:GLN178 4.7 23.3 1.0
OE1 A:GLN178 4.8 22.1 1.0
CA A:ASN149 4.9 11.2 1.0
OD1 A:ASN149 4.9 19.8 1.0
C A:LYS148 5.0 12.0 1.0

Sodium binding site 5 out of 15 in 5gs8

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Sodium binding site 5 out of 15 in the Crystal Structure of Tla-3 Extended-Spectrum Beta-Lactamase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of Tla-3 Extended-Spectrum Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na310

b:23.6
occ:1.00
 OG1 A:THR236 2.8 9.8 1.0
O A:GLU264 2.8 11.3 1.0
O A:HOH694 2.8 37.2 1.0
O A:GLY234 3.0 13.2 1.0
O A:SER262 3.0 8.9 1.0
N A:THR236 3.6 9.7 1.0
CB A:THR236 3.7 10.2 1.0
C A:SER263 3.8 11.4 1.0
C A:GLU264 3.8 11.4 1.0
C A:GLY234 3.9 10.9 1.0
O A:SER263 4.0 14.5 1.0
C A:SER262 4.0 9.4 1.0
N A:GLU264 4.0 10.4 1.0
O A:HOH592 4.0 30.5 1.0
CA A:SER263 4.1 11.6 1.0
O A:HOH573 4.1 29.1 1.0
C A:ILE235 4.2 10.8 1.0
CA A:THR236 4.3 9.3 1.0
CG2 A:THR230 4.3 16.1 1.0
N A:SER263 4.5 10.7 1.0
CA A:ILE235 4.5 11.0 1.0
CA A:GLU264 4.6 11.7 1.0
OG1 A:THR230 4.6 15.6 1.0
N A:ILE235 4.6 10.9 1.0
ND2 A:ASN269 4.7 10.6 1.0
N A:LYS265 4.7 13.7 1.0
CA A:LYS265 4.9 15.2 1.0
CA A:GLY234 4.9 13.5 1.0
OG A:SER262 5.0 9.1 1.0

Sodium binding site 6 out of 15 in 5gs8

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Sodium binding site 6 out of 15 in the Crystal Structure of Tla-3 Extended-Spectrum Beta-Lactamase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of Tla-3 Extended-Spectrum Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na311

b:19.5
occ:1.00
 O A:THR206 2.8 9.0 1.0
NE2 A:HIS223 2.8 8.2 1.0
O A:HOH666 2.9 21.1 1.0
O A:THR204 3.1 8.5 1.0
CE1 A:HIS223 3.4 8.4 1.0
CD A:LYS212 3.4 12.6 0.5
NA A:NA316 3.4 20.0 1.0
CE A:LYS212 3.5 14.3 0.5
NZ A:LYS212 3.7 14.9 0.5
CE A:LYS212 3.7 16.8 0.5
CA A:PRO208 3.8 10.5 1.0
C A:THR205 3.9 8.4 1.0
C A:THR206 3.9 8.7 1.0
C A:THR204 3.9 6.9 1.0
CD A:LYS212 3.9 12.7 0.5
N A:PRO208 3.9 10.0 1.0
O A:THR205 4.0 8.9 1.0
CA A:THR205 4.1 7.9 1.0
CD2 A:HIS223 4.1 6.8 1.0
C A:GLY207 4.1 10.6 1.0
O A:GLY207 4.2 10.0 1.0
N A:THR206 4.2 7.3 1.0
CB A:PRO208 4.3 11.8 1.0
CG2 A:THR204 4.3 7.3 1.0
N A:THR205 4.3 7.5 1.0
O A:HOH547 4.3 12.9 1.0
O A:HOH550 4.5 28.5 1.0
NA A:NA307 4.5 16.2 1.0
CD A:PRO208 4.5 11.1 1.0
CG A:LYS212 4.6 12.4 0.5
ND1 A:HIS223 4.6 8.3 1.0
CA A:THR206 4.7 8.8 1.0
N A:GLY207 4.7 10.0 1.0
CB A:THR204 4.8 6.9 1.0
CG A:LYS212 4.8 11.1 0.5
CA A:GLY207 4.9 11.3 1.0
CA A:THR204 5.0 7.2 1.0
NZ A:LYS212 5.0 17.9 0.5

Sodium binding site 7 out of 15 in 5gs8

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Sodium binding site 7 out of 15 in the Crystal Structure of Tla-3 Extended-Spectrum Beta-Lactamase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of Tla-3 Extended-Spectrum Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na312

b:23.2
occ:1.00
 O A:HOH453 2.7 10.5 1.0
O A:GLU106 2.8 10.1 1.0
NZ A:LYS80 3.2 20.1 1.0
O A:HOH616 3.2 28.4 1.0
O A:HOH531 3.4 27.5 1.0
CE A:LYS80 3.7 16.1 1.0
C A:GLU106 3.8 10.3 1.0
CD A:LYS80 3.9 12.3 1.0
CA A:LEU107 4.0 9.0 1.0
O A:HOH457 4.0 37.1 1.0
CD2 A:LEU107 4.0 11.5 1.0
O A:HOH478 4.1 34.5 1.0
OE1 A:GLU111 4.2 13.8 1.0
N A:LEU107 4.4 8.2 1.0
N A:SER108 4.5 8.6 1.0
C A:LEU107 4.7 8.8 1.0
CB A:LEU107 4.9 9.2 1.0
CG A:LYS80 4.9 10.6 1.0
CG A:LEU107 5.0 9.8 1.0

Sodium binding site 8 out of 15 in 5gs8

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Sodium binding site 8 out of 15 in the Crystal Structure of Tla-3 Extended-Spectrum Beta-Lactamase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of Tla-3 Extended-Spectrum Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na313

b:24.0
occ:1.00
 O A:HOH409 2.6 40.6 1.0
O A:HIS252 2.9 11.8 1.0
N A:ASP40 3.2 21.4 1.0
OE1 A:GLU39 3.2 16.0 1.0
N A:GLU39 3.3 14.9 1.0
N A:ILE38 3.5 11.8 1.0
OD1 A:ASP40 3.5 27.4 0.5
CG A:ASP40 3.6 28.0 0.5
CB A:ASP40 3.8 23.1 0.5
CB A:ASP40 3.8 26.4 0.5
CA A:GLY37 4.0 11.5 1.0
CA A:GLU39 4.0 17.1 1.0
C A:HIS252 4.0 11.3 1.0
CA A:ASP40 4.0 22.4 0.5
OD2 A:ASP40 4.0 31.2 0.5
CA A:ASP40 4.0 23.9 0.5
N A:HIS252 4.0 10.8 1.0
CG A:ASP40 4.0 21.1 0.5
C A:GLU39 4.0 18.4 1.0
CB A:GLU39 4.1 17.1 1.0
CB A:LYS251 4.1 16.9 1.0
C A:GLY37 4.1 11.6 1.0
OD2 A:ASP40 4.2 25.6 0.5
C A:ILE38 4.2 14.3 1.0
CD A:GLU39 4.3 18.4 1.0
CA A:ILE38 4.3 12.5 1.0
O A:ASP40 4.5 30.0 1.0
C A:ASP40 4.6 28.2 1.0
CA A:HIS252 4.6 10.1 1.0
OD1 A:ASP40 4.6 21.8 0.5
CD A:LYS251 4.7 31.6 1.0
CG A:LYS251 4.8 24.1 1.0
CB A:ILE38 4.8 14.2 1.0
CG A:GLU39 4.8 16.4 1.0
C A:LYS251 4.9 11.0 1.0
CA A:LYS251 5.0 13.9 1.0

Sodium binding site 9 out of 15 in 5gs8

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Sodium binding site 9 out of 15 in the Crystal Structure of Tla-3 Extended-Spectrum Beta-Lactamase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Crystal Structure of Tla-3 Extended-Spectrum Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na314

b:23.2
occ:1.00
 OD1 A:ASP174 2.7 14.5 1.0
O A:GLU48 2.8 12.2 1.0
O A:HOH651 2.8 33.0 1.0
O A:HOH671 2.8 25.6 1.0
OD2 A:ASP174 3.3 22.9 1.0
CG A:ASP174 3.4 15.8 1.0
NA A:NA309 3.5 25.1 1.0
C A:GLU48 3.6 11.8 1.0
CG2 A:THR172 3.6 9.8 1.0
CB A:THR172 3.6 9.4 1.0
CG A:GLU48 3.7 12.5 1.0
OG1 A:THR172 3.9 9.7 1.0
CA A:LYS49 4.0 12.5 1.0
N A:LYS49 4.1 10.8 1.0
CB A:GLU48 4.2 10.8 1.0
CG A:LYS49 4.2 17.6 1.0
ND2 A:ASN149 4.5 17.5 1.0
CA A:GLU48 4.5 10.6 1.0
CB A:LYS49 4.7 14.5 1.0
O A:HOH414 4.7 36.2 1.0
O A:HOH459 4.7 26.2 1.0
NZ A:LYS49 4.8 35.4 1.0
CB A:ASP174 4.8 13.1 1.0
CD A:GLU48 5.0 13.7 1.0

Sodium binding site 10 out of 15 in 5gs8

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Sodium binding site 10 out of 15 in the Crystal Structure of Tla-3 Extended-Spectrum Beta-Lactamase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Crystal Structure of Tla-3 Extended-Spectrum Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na315

b:19.2
occ:1.00
 O A:HOH436 2.7 9.6 1.0
O A:HOH676 2.7 20.6 1.0
O A:HOH700 2.8 29.9 1.0
O A:HOH524 2.9 11.9 1.0
ND1 A:HIS119 3.3 13.2 1.0
CA A:SER115 3.6 7.8 1.0
N A:SER115 3.6 7.6 1.0
CE1 A:HIS119 3.8 9.1 1.0
C A:LYS114 3.8 8.2 1.0
O A:LYS114 3.9 8.5 1.0
O3 A:SO4305 4.0 23.3 0.8
CB A:LYS114 4.0 9.4 1.0
CB A:SER115 4.0 9.3 1.0
CG A:HIS119 4.2 8.9 1.0
O A:HOH465 4.3 11.5 1.0
O A:HOH594 4.3 35.1 1.0
OG A:SER115 4.4 11.4 1.0
O A:HOH688 4.5 33.4 1.0
CA A:LYS114 4.6 7.3 1.0
O A:HOH684 4.6 12.9 1.0
O A:HOH675 4.7 19.0 1.0
O A:HOH674 4.7 29.1 1.0
NE2 A:HIS119 4.7 13.7 1.0
CB A:HIS119 4.8 7.3 1.0
O A:HOH463 4.8 11.8 1.0
O A:GLU111 4.9 7.7 1.0
C A:SER115 4.9 7.4 1.0
CD2 A:HIS119 5.0 8.1 1.0

Reference:

W.Jin, J.Wachino, Y.Yamaguchi, K.Kimura, A.Kumar, M.Yamada, A.Morinaka, Y.Sakamaki, M.Yonezawa, H.Kurosaki, Y.Arakawa. Structural Insights Into the Tla-3 Extended-Spectrum Beta-Lactamase and Its Inhibition By Avibactam and OP0595. Antimicrob. Agents V. 61 2017CHEMOTHER..
ISSN: ESSN 1098-6596
PubMed: 28739781
DOI: 10.1128/AAC.00501-17
Page generated: Tue Dec 15 11:01:52 2020

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