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Sodium in PDB 8r37: Klebsiella Pneumoniae Fosfomycin-Resistance Protein (Fosakp)

Protein crystallography data

The structure of Klebsiella Pneumoniae Fosfomycin-Resistance Protein (Fosakp), PDB code: 8r37 was solved by A.C.Papageorgiou, C.Varotsou, N.E.Labrou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.85 / 1.48
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 40.62, 47.03, 149.2, 90, 90, 90
R / Rfree (%) 17.3 / 20.6

Other elements in 8r37:

The structure of Klebsiella Pneumoniae Fosfomycin-Resistance Protein (Fosakp) also contains other interesting chemical elements:

Manganese (Mn) 2 atoms
Potassium (K) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Klebsiella Pneumoniae Fosfomycin-Resistance Protein (Fosakp) (pdb code 8r37). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 10 binding sites of Sodium where determined in the Klebsiella Pneumoniae Fosfomycin-Resistance Protein (Fosakp), PDB code: 8r37:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 10 in 8r37

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Sodium binding site 1 out of 10 in the Klebsiella Pneumoniae Fosfomycin-Resistance Protein (Fosakp)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Klebsiella Pneumoniae Fosfomycin-Resistance Protein (Fosakp) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na203

b:40.9
occ:1.00
 O B:HOH416 2.8 35.8 1.0
O A:HOH416 2.9 25.1 1.0
O B:HOH350 2.9 23.2 1.0
OD1 B:ASP64 3.1 22.9 1.0
O B:HOH443 3.5 39.6 1.0
CG B:ASP64 3.7 25.8 1.0
OD2 B:ASP64 3.8 23.9 1.0
CB B:THR66 3.8 21.0 1.0
O B:HOH407 3.8 23.4 1.0
OG1 B:THR66 4.0 19.7 1.0
N B:ASP64 4.4 23.5 1.0
O B:HOH409 4.4 26.0 1.0
NH1 A:ARG55 4.4 22.1 1.0
O B:HOH344 4.5 21.1 1.0
CG2 B:THR66 4.5 22.3 1.0
CB B:SER63 4.6 28.4 1.0
O B:ASP64 4.7 22.3 1.0
O B:HOH384 4.7 32.2 1.0
O A:HOH469 4.8 34.7 1.0
CB B:ASP64 4.9 21.2 1.0
CA B:THR66 4.9 20.4 1.0
O B:THR66 4.9 21.0 1.0
N B:THR66 4.9 20.6 1.0
CA B:ASP64 4.9 21.0 1.0
C B:ASP64 5.0 23.5 1.0

Sodium binding site 2 out of 10 in 8r37

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Sodium binding site 2 out of 10 in the Klebsiella Pneumoniae Fosfomycin-Resistance Protein (Fosakp)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Klebsiella Pneumoniae Fosfomycin-Resistance Protein (Fosakp) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na204

b:44.6
occ:1.00
 O B:LEU2 3.0 28.3 1.0
O A:HOH317 3.2 28.9 1.0
O A:HOH396 3.5 41.8 1.0
O A:GLY27 3.6 23.9 1.0
SG A:CYS42 3.7 28.9 1.0
C B:LEU2 3.9 28.1 1.0
CA A:CYS42 3.9 24.9 1.0
CB B:LEU2 4.0 22.0 1.0
CA A:MET28 4.1 20.2 1.0
C A:GLY27 4.1 23.9 1.0
CB A:CYS42 4.2 25.3 1.0
N B:LEU2 4.3 24.7 1.0
CA B:LEU2 4.3 22.8 1.0
N A:MET28 4.4 22.4 1.0
N A:GLY43 4.5 29.0 1.0
CG A:MET28 4.5 23.6 1.0
O A:LEU26 4.6 23.4 1.0
C A:CYS42 4.6 27.3 1.0
O A:SER41 4.6 24.0 1.0
CB A:MET28 4.7 26.3 1.0
CG B:MET1 4.9 37.3 1.0
O A:HOH342 4.9 43.5 1.0
N B:SER3 5.0 24.8 1.0

Sodium binding site 3 out of 10 in 8r37

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Sodium binding site 3 out of 10 in the Klebsiella Pneumoniae Fosfomycin-Resistance Protein (Fosakp)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Klebsiella Pneumoniae Fosfomycin-Resistance Protein (Fosakp) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na205

b:38.9
occ:1.00
 O B:HOH307 2.0 36.5 1.0
OD2 B:ASP52 3.2 28.0 1.0
N A:TYR65 3.6 19.2 1.0
O A:HOH316 3.6 41.0 1.0
O B:HOH468 3.6 38.6 1.0
C A:ASP64 3.9 19.8 1.0
CB A:TYR65 3.9 21.4 1.0
CA A:TYR65 4.0 19.1 1.0
CG B:ASP52 4.1 31.1 1.0
CA A:ASP64 4.1 19.7 1.0
O B:HOH369 4.3 35.5 1.0
O A:SER63 4.3 20.3 1.0
CD1 A:TYR65 4.3 24.6 1.0
OD1 B:ASP52 4.4 31.7 1.0
O A:ASP64 4.6 20.7 1.0
CG A:TYR65 4.6 19.9 1.0
O A:HOH451 4.6 33.8 1.0
O B:HOH314 4.8 37.5 1.0
NZ A:LYS111 4.8 18.6 1.0
O B:HOH455 4.9 46.0 1.0
CB A:ASP64 5.0 22.0 1.0

Sodium binding site 4 out of 10 in 8r37

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Sodium binding site 4 out of 10 in the Klebsiella Pneumoniae Fosfomycin-Resistance Protein (Fosakp)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Klebsiella Pneumoniae Fosfomycin-Resistance Protein (Fosakp) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na206

b:42.3
occ:1.00
 O A:HOH400 2.6 29.5 1.0
O B:HOH425 2.6 43.7 1.0
O B:ASP44 3.0 30.2 1.0
C B:ASP44 3.6 28.8 1.0
CB B:TRP46 3.7 22.2 1.0
N B:TRP46 3.7 20.8 1.0
O B:HOH309 3.8 39.5 1.0
O B:HOH337 3.9 33.2 1.0
C B:LEU45 3.9 21.4 1.0
CA B:TRP46 4.0 19.6 1.0
CB A:LEU119 4.1 22.2 1.0
O A:HOH421 4.2 29.3 1.0
O B:LEU45 4.2 21.3 1.0
CA B:ASP44 4.3 31.6 0.4
CD2 A:LEU119 4.3 24.2 1.0
CA B:ASP44 4.3 31.6 0.6
N B:LEU45 4.4 24.4 1.0
CA B:LEU45 4.6 22.0 1.0
O B:GLY43 4.7 30.1 1.0
O B:HOH411 4.7 24.7 1.0
CG B:TRP46 4.8 20.9 1.0
CG A:LEU119 4.9 22.2 1.0
N A:LEU119 4.9 23.6 1.0

Sodium binding site 5 out of 10 in 8r37

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Sodium binding site 5 out of 10 in the Klebsiella Pneumoniae Fosfomycin-Resistance Protein (Fosakp)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Klebsiella Pneumoniae Fosfomycin-Resistance Protein (Fosakp) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na207

b:56.2
occ:1.00
 O B:HOH373 2.1 28.5 1.0
NA B:NA209 3.3 49.8 1.0
O B:HOH421 3.7 36.2 1.0
N B:ALA90 3.7 21.8 1.0
CB B:ALA90 3.8 28.3 1.0
O B:HOH467 3.9 43.9 1.0
O B:GLY88 4.1 26.9 1.0
CA B:ALA90 4.4 24.7 1.0
CA B:VAL89 4.6 19.8 1.0
C B:VAL89 4.6 23.1 1.0
O B:LEU105 4.9 19.0 1.0
O B:ASP106 5.0 20.5 1.0

Sodium binding site 6 out of 10 in 8r37

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Sodium binding site 6 out of 10 in the Klebsiella Pneumoniae Fosfomycin-Resistance Protein (Fosakp)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Klebsiella Pneumoniae Fosfomycin-Resistance Protein (Fosakp) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na208

b:59.1
occ:1.00
 O B:HOH460 4.0 53.2 1.0
CZ B:TYR65 4.1 29.4 1.0
O A:HOH398 4.2 37.6 1.0
CE2 B:TYR65 4.2 27.1 1.0
OH B:TYR65 4.4 32.4 1.0
CE1 B:TYR65 4.4 28.6 1.0
OG A:SER50 4.6 26.6 1.0
CD2 B:TYR65 4.6 23.0 1.0
NZ B:LYS93 4.8 41.1 1.0
CD1 B:TYR65 4.8 24.8 1.0
O B:HOH370 4.9 40.8 1.0
CG B:TYR65 4.9 24.6 1.0

Sodium binding site 7 out of 10 in 8r37

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Sodium binding site 7 out of 10 in the Klebsiella Pneumoniae Fosfomycin-Resistance Protein (Fosakp)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Klebsiella Pneumoniae Fosfomycin-Resistance Protein (Fosakp) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na209

b:49.8
occ:1.00
 O B:HOH467 2.8 43.9 1.0
O B:HOH373 3.1 28.5 1.0
NA B:NA207 3.3 56.2 1.0
CA B:PRO107 3.8 20.0 1.0
CG B:PRO107 4.0 22.1 1.0
N B:PRO107 4.0 19.6 1.0
CB B:PRO107 4.2 21.9 1.0
C B:ASP106 4.3 20.7 1.0
O B:HOH472 4.4 36.9 1.0
CD B:PRO107 4.4 20.3 1.0
O B:ASP106 4.5 20.5 1.0
O B:HOH423 4.5 43.4 1.0
CE1 B:PHE21 4.6 20.9 1.0
O B:LEU105 4.6 19.0 1.0
CD1 B:PHE21 4.7 20.5 1.0
C B:PRO107 5.0 21.5 1.0

Sodium binding site 8 out of 10 in 8r37

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Sodium binding site 8 out of 10 in the Klebsiella Pneumoniae Fosfomycin-Resistance Protein (Fosakp)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Klebsiella Pneumoniae Fosfomycin-Resistance Protein (Fosakp) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na203

b:28.1
occ:1.00
 O A:HOH315 2.7 20.7 1.0
NA A:NA204 2.8 26.9 1.0
O A:HOH411 2.9 24.8 1.0
N A:LYS111 3.0 19.9 1.0
CA A:HIS110 3.5 18.6 1.0
O A:GLY109 3.7 21.0 1.0
O A:THR66 3.7 19.8 1.0
C A:HIS110 3.7 20.0 1.0
CB A:LYS111 3.9 19.0 1.0
CG A:LYS111 4.0 20.4 1.0
CA A:LYS111 4.0 17.9 1.0
O A:HOH437 4.2 29.8 1.0
O A:HOH416 4.2 25.1 1.0
ND1 A:HIS110 4.2 20.4 1.0
CB A:HIS110 4.3 20.9 1.0
N A:HIS110 4.4 20.2 1.0
CD A:LYS111 4.4 19.1 1.0
C A:GLY109 4.5 19.6 1.0
OG A:SER63 4.5 22.6 1.0
O A:HOH313 4.5 23.7 1.0
CG A:HIS110 4.7 18.7 1.0
CB A:SER63 4.8 19.3 1.0
C A:THR66 4.8 19.8 1.0
O A:HOH469 4.8 34.7 1.0
CE2 A:TYR68 4.8 18.6 1.0
OH A:TYR68 4.9 20.4 1.0
O A:LYS111 4.9 18.9 1.0
O A:HIS110 4.9 19.7 1.0
C A:LYS111 5.0 19.8 1.0

Sodium binding site 9 out of 10 in 8r37

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Sodium binding site 9 out of 10 in the Klebsiella Pneumoniae Fosfomycin-Resistance Protein (Fosakp)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Klebsiella Pneumoniae Fosfomycin-Resistance Protein (Fosakp) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na204

b:26.9
occ:1.00
 ND1 A:HIS110 2.7 20.4 1.0
O A:HOH416 2.7 25.1 1.0
OH A:TYR68 2.7 20.4 1.0
NA A:NA203 2.8 28.1 1.0
CE1 A:HIS110 3.4 19.1 1.0
CE2 A:TYR68 3.4 18.6 1.0
CZ A:TYR68 3.5 18.5 1.0
CG A:HIS110 3.8 18.7 1.0
O A:HOH411 4.2 24.8 1.0
CB A:HIS110 4.2 20.9 1.0
CA A:HIS110 4.3 18.6 1.0
CG2 B:THR66 4.4 22.3 1.0
O A:HOH437 4.4 29.8 1.0
NH1 A:ARG55 4.5 22.1 1.0
O A:HOH315 4.5 20.7 1.0
NE2 A:HIS110 4.6 20.1 1.0
CD2 A:TYR68 4.7 21.8 1.0
N A:LYS111 4.8 19.9 1.0
CE1 A:TYR68 4.8 18.4 1.0
OH B:TYR68 4.8 21.1 1.0
CD2 A:HIS110 4.9 19.5 1.0
OG1 B:THR66 4.9 19.7 1.0
O A:THR66 5.0 19.8 1.0

Sodium binding site 10 out of 10 in 8r37

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Sodium binding site 10 out of 10 in the Klebsiella Pneumoniae Fosfomycin-Resistance Protein (Fosakp)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Klebsiella Pneumoniae Fosfomycin-Resistance Protein (Fosakp) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na205

b:47.2
occ:1.00
 O B:HOH376 2.5 35.5 1.0
O A:HOH329 2.6 39.6 1.0
O A:LEU5 2.7 29.4 1.0
O B:HOH305 3.2 34.4 1.0
O A:HOH470 3.5 37.9 1.0
C A:LEU5 3.8 24.2 1.0
O A:HOH381 4.1 24.4 1.0
N A:LEU5 4.2 25.1 1.0
OD2 B:ASP44 4.3 38.2 0.4
O A:HOH349 4.3 29.8 1.0
OD1 B:ASP44 4.4 34.1 0.4
O A:ASP44 4.5 28.1 1.0
CA A:LEU5 4.5 22.2 1.0
O B:HOH301 4.6 40.0 1.0
O A:HOH369 4.7 47.2 1.0
CG B:ASP44 4.7 34.1 0.4
C A:GLY4 4.8 25.4 1.0
N A:ASN6 4.8 20.7 1.0
O B:HOH452 4.9 37.8 1.0
OG B:SER71 4.9 23.2 1.0
CB A:LEU5 4.9 24.0 1.0
CB A:ASP44 4.9 32.5 1.0
CA A:ASN6 5.0 21.5 1.0
CA A:GLY4 5.0 24.1 1.0

Reference:

C.Varotsou, F.Ataya, A.C.Papageorgiou, N.E.Labrou. Structural Studies of Klebsiella Pneumoniae Fosfomycin-Resistance Protein and Its Application For the Development of An Optical Biosensor For Fosfomycin Determination. Int J Mol Sci V. 25 2023.
ISSN: ESSN 1422-0067
PubMed: 38203259
DOI: 10.3390/IJMS25010085
Page generated: Wed Oct 9 13:19:20 2024

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