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Sodium in PDB 4knl: Crystal Structure of Staphylococcus Aureus Hydrolase Amia in Complex with Its Ligand

Enzymatic activity of Crystal Structure of Staphylococcus Aureus Hydrolase Amia in Complex with Its Ligand

All present enzymatic activity of Crystal Structure of Staphylococcus Aureus Hydrolase Amia in Complex with Its Ligand:
3.2.1.96; 3.5.1.28;

Protein crystallography data

The structure of Crystal Structure of Staphylococcus Aureus Hydrolase Amia in Complex with Its Ligand, PDB code: 4knl was solved by F.M.Buettner, T.Stehle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.21 / 1.55
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 67.810, 82.830, 77.430, 90.00, 96.18, 90.00
R / Rfree (%) 17.1 / 19.8

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Staphylococcus Aureus Hydrolase Amia in Complex with Its Ligand (pdb code 4knl). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Crystal Structure of Staphylococcus Aureus Hydrolase Amia in Complex with Its Ligand, PDB code: 4knl:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 4knl

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Sodium binding site 1 out of 8 in the Crystal Structure of Staphylococcus Aureus Hydrolase Amia in Complex with Its Ligand


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 Staphylococcus Aureus Hydrolase Amia in Complex with Its Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na502

b:22.7
occ:1.00
 O A:SER358 2.3 19.4 1.0
O A:ASN364 2.3 23.2 1.0
O A:HOH709 2.5 37.2 1.0
OD2 A:ASP362 2.6 38.1 1.0
OD1 A:ASP357 2.6 30.8 1.0
OD1 A:ASP362 2.7 27.2 1.0
O A:HOH700 2.8 34.3 1.0
CG A:ASP362 3.0 32.7 1.0
C A:SER358 3.3 16.5 1.0
C A:ASN364 3.5 20.9 1.0
CG A:ASP357 3.5 26.3 1.0
OD2 A:ASP357 3.8 27.2 1.0
O A:HOH619 3.9 21.5 1.0
CA A:ALA359 4.0 16.9 1.0
N A:ALA359 4.0 16.8 1.0
N A:SER358 4.2 16.8 1.0
CA A:ASN364 4.3 21.9 1.0
CB A:ASN364 4.3 25.7 1.0
CA A:SER358 4.4 18.1 1.0
N A:GLY365 4.4 19.6 1.0
N A:ASN364 4.4 21.2 1.0
CA A:GLY365 4.4 21.4 1.0
C A:ASP357 4.5 17.7 1.0
CB A:ASP362 4.5 24.0 1.0
ND2 A:ASN364 4.6 43.0 1.0
CB A:ASP357 4.8 19.9 1.0
O A:ASP357 4.8 18.0 1.0
C A:ALA359 4.8 17.0 1.0
O A:HOH647 4.8 23.3 1.0
CG A:ASN364 5.0 38.5 1.0

Sodium binding site 2 out of 8 in 4knl

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Sodium binding site 2 out of 8 in the Crystal Structure of Staphylococcus Aureus Hydrolase Amia in Complex with Its Ligand


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 Staphylococcus Aureus Hydrolase Amia in Complex with Its Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na504

b:27.3
occ:1.00
 O A:HOH649 2.2 27.1 1.0
O A:HOH626 2.3 18.9 1.0
O A:HOH645 2.3 23.2 1.0
OG1 A:THR305 2.4 15.5 1.0
O A:HOH620 2.4 24.6 1.0
CE2 C:TYR243 3.5 17.8 1.0
CB A:THR305 3.7 16.1 1.0
O A:HOH683 3.8 26.5 1.0
CD2 C:TYR243 3.8 17.3 1.0
OE1 A:GLN348 3.8 21.7 1.0
OH A:TYR352 4.0 17.7 1.0
O C:HOH742 4.0 35.5 1.0
CG2 A:THR305 4.0 20.0 1.0
OE1 C:GLU241 4.1 26.8 1.0
N A:THR305 4.2 14.1 1.0
OE1 A:GLU301 4.3 17.6 1.0
O C:HOH624 4.3 18.0 1.0
OE2 A:GLU301 4.4 16.9 1.0
CA A:THR305 4.5 16.1 1.0
CE2 A:TYR351 4.5 17.4 1.0
O C:HOH651 4.5 31.5 1.0
CZ C:TYR243 4.6 21.8 1.0
CD A:GLN348 4.6 19.9 1.0
NE2 A:GLN348 4.6 18.7 1.0
CD2 A:TYR351 4.7 16.8 1.0
CD A:GLU301 4.8 19.6 1.0
CZ A:TYR352 4.8 17.1 1.0
CE2 A:TYR352 4.8 15.3 1.0
OH C:TYR243 4.9 19.5 1.0
CZ A:TYR351 5.0 17.6 1.0

Sodium binding site 3 out of 8 in 4knl

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Sodium binding site 3 out of 8 in the Crystal Structure of Staphylococcus Aureus Hydrolase Amia in Complex with Its Ligand


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 Staphylococcus Aureus Hydrolase Amia in Complex with Its Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na502

b:25.8
occ:1.00
 O B:SER358 2.3 19.6 1.0
O B:ASN364 2.3 22.1 1.0
OD2 B:ASP362 2.6 39.6 1.0
OD1 B:ASP357 2.6 29.7 1.0
O B:HOH690 2.6 39.5 1.0
OD1 B:ASP362 2.6 28.4 1.0
O B:HOH694 2.7 41.5 1.0
CG B:ASP362 2.9 34.7 1.0
C B:SER358 3.3 18.4 1.0
C B:ASN364 3.5 24.4 1.0
CG B:ASP357 3.6 26.2 1.0
O B:HOH631 3.9 29.5 1.0
OD2 B:ASP357 4.0 27.5 1.0
CA B:ALA359 4.0 19.6 1.0
N B:ALA359 4.1 18.3 1.0
N B:SER358 4.2 18.6 1.0
CA B:ASN364 4.3 22.3 1.0
CA B:SER358 4.4 24.4 1.0
N B:ASN364 4.4 22.4 1.0
CB B:ASN364 4.4 31.7 1.0
N B:GLY365 4.4 21.0 1.0
C B:ASP357 4.4 18.4 1.0
CB B:ASP362 4.4 26.1 1.0
CA B:GLY365 4.4 19.0 1.0
ND2 B:ASN364 4.7 49.8 1.0
O B:ASP357 4.7 19.1 1.0
O B:HOH614 4.8 23.8 1.0
C B:ALA359 4.8 19.6 1.0
CB B:ASP357 4.8 21.1 1.0

Sodium binding site 4 out of 8 in 4knl

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Sodium binding site 4 out of 8 in the Crystal Structure of Staphylococcus Aureus Hydrolase Amia in Complex with Its Ligand


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 Staphylococcus Aureus Hydrolase Amia in Complex with Its Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na504

b:33.0
occ:1.00
 O B:HOH640 2.3 31.0 1.0
O B:HOH617 2.3 28.1 1.0
O B:HOH623 2.4 23.3 1.0
OG1 B:THR305 2.4 16.6 1.0
O B:HOH626 2.7 26.2 1.0
CE2 D:TYR243 3.6 18.8 1.0
CB B:THR305 3.7 16.0 1.0
OE1 B:GLN348 3.8 24.9 1.0
CD2 D:TYR243 3.9 20.4 1.0
CG2 B:THR305 3.9 19.5 1.0
O B:HOH656 4.0 28.8 1.0
OH B:TYR352 4.0 19.4 1.0
OE1 B:GLU301 4.1 20.7 1.0
OE1 D:GLU241 4.1 29.8 1.0
O D:HOH715 4.2 37.2 1.0
N B:THR305 4.2 18.2 1.0
OE2 B:GLU301 4.3 21.0 1.0
O D:HOH665 4.4 37.9 1.0
O D:HOH629 4.5 23.5 1.0
CA B:THR305 4.5 15.8 1.0
NE2 B:GLN348 4.5 30.1 1.0
CD B:GLN348 4.6 25.3 1.0
CD B:GLU301 4.6 25.1 1.0
CZ D:TYR243 4.6 18.1 1.0
CE2 B:TYR351 4.7 20.4 1.0
CZ B:TYR352 4.8 17.9 1.0
CE2 B:TYR352 4.8 17.3 1.0
CD2 B:TYR351 4.9 17.0 1.0
OH D:TYR243 5.0 18.5 1.0
CD D:GLU241 5.0 33.5 1.0

Sodium binding site 5 out of 8 in 4knl

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Sodium binding site 5 out of 8 in the Crystal Structure of Staphylococcus Aureus Hydrolase Amia in Complex with Its Ligand


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 Staphylococcus Aureus Hydrolase Amia in Complex with Its Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na502

b:24.8
occ:1.00
 O C:SER358 2.4 19.2 1.0
O C:ASN364 2.4 23.1 1.0
O C:HOH716 2.4 33.6 1.0
OD1 C:ASP357 2.5 27.1 1.0
OD2 C:ASP362 2.6 38.8 1.0
OD1 C:ASP362 2.6 30.4 1.0
O C:HOH680 2.7 40.5 1.0
CG C:ASP362 3.0 31.5 1.0
C C:SER358 3.4 19.2 1.0
CG C:ASP357 3.5 27.6 1.0
C C:ASN364 3.5 25.1 1.0
OD2 C:ASP357 3.8 32.6 1.0
O C:HOH627 4.0 21.0 1.0
CA C:ALA359 4.0 18.6 1.0
N C:ALA359 4.0 19.7 1.0
N C:SER358 4.2 18.2 1.0
CA C:GLY365 4.3 20.7 1.0
CA C:SER358 4.4 20.9 1.0
CA C:ASN364 4.4 22.1 1.0
C C:ASP357 4.4 19.1 1.0
N C:ASN364 4.4 24.2 1.0
CB C:ASN364 4.4 31.2 1.0
N C:GLY365 4.5 21.1 1.0
CB C:ASP362 4.5 29.1 1.0
ND2 C:ASN364 4.6 47.8 1.0
O C:ASP357 4.7 19.1 1.0
CB C:ASP357 4.7 18.8 1.0
O C:HOH728 4.7 29.8 1.0
C C:ALA359 4.9 19.9 1.0
CA C:ASP357 5.0 19.1 1.0

Sodium binding site 6 out of 8 in 4knl

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Sodium binding site 6 out of 8 in the Crystal Structure of Staphylococcus Aureus Hydrolase Amia in Complex with Its Ligand


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 Staphylococcus Aureus Hydrolase Amia in Complex with Its Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na505

b:19.3
occ:1.00
 O C:HOH619 2.2 19.6 1.0
OG1 C:THR305 2.2 16.1 1.0
O C:HOH616 2.3 18.3 1.0
O C:HOH614 2.3 19.5 1.0
O C:HOH612 2.4 16.6 1.0
CB C:THR305 3.5 16.6 1.0
CE2 A:TYR243 3.6 15.8 1.0
OE1 C:GLN348 3.8 19.7 1.0
CG2 C:THR305 3.9 18.6 1.0
CD2 A:TYR243 3.9 16.2 1.0
OH C:TYR352 4.0 17.3 1.0
N C:THR305 4.0 12.8 1.0
OE1 C:GLU301 4.2 15.9 1.0
CA C:THR305 4.4 15.1 1.0
OE2 C:GLU301 4.4 17.1 1.0
NE2 C:GLN348 4.5 18.4 1.0
CE2 C:TYR351 4.5 15.4 1.0
CD C:GLN348 4.6 17.4 1.0
O C:HOH624 4.6 18.0 1.0
OE1 A:GLU241 4.6 22.4 1.0
O A:HOH628 4.6 20.4 1.0
OD2 C:ASP306 4.7 22.9 1.0
CD C:GLU301 4.7 15.9 1.0
CZ C:TYR351 4.7 17.5 1.0
CZ C:TYR352 4.8 14.7 1.0
CZ A:TYR243 4.8 15.7 1.0
CE2 C:TYR352 4.9 14.4 1.0
CD2 C:TYR351 4.9 16.6 1.0
OH C:TYR351 4.9 16.5 1.0

Sodium binding site 7 out of 8 in 4knl

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Sodium binding site 7 out of 8 in the Crystal Structure of Staphylococcus Aureus Hydrolase Amia in Complex with Its Ligand


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 Staphylococcus Aureus Hydrolase Amia in Complex with Its Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na502

b:29.0
occ:1.00
 O D:ASN364 2.3 27.9 1.0
OD2 D:ASP362 2.4 43.3 1.0
O D:SER358 2.4 23.3 1.0
O D:HOH661 2.5 41.0 1.0
O D:HOH707 2.5 41.3 1.0
OD1 D:ASP362 2.7 33.6 1.0
OD1 D:ASP357 2.7 32.8 1.0
CG D:ASP362 2.9 40.0 1.0
C D:SER358 3.4 22.8 1.0
C D:ASN364 3.5 23.6 1.0
CG D:ASP357 3.5 31.7 1.0
OD2 D:ASP357 3.8 33.1 1.0
O D:HOH674 4.0 29.2 1.0
CA D:ALA359 4.0 20.9 1.0
N D:ALA359 4.1 20.7 1.0
N D:SER358 4.2 28.1 1.0
CA D:ASN364 4.3 26.7 1.0
CB D:ASP362 4.4 37.4 1.0
N D:ASN364 4.4 25.7 1.0
N D:GLY365 4.4 22.8 1.0
CB D:ASN364 4.4 31.6 1.0
CA D:GLY365 4.4 18.5 1.0
CA D:SER358 4.4 22.3 1.0
C D:ASP357 4.5 23.8 1.0
ND2 D:ASN364 4.5 57.0 1.0
O D:HOH681 4.8 30.0 1.0
C D:ALA359 4.8 21.1 1.0
CB D:ASP357 4.8 24.3 1.0
O D:ASP357 4.8 20.0 1.0
CG D:ASN364 4.9 48.3 1.0

Sodium binding site 8 out of 8 in 4knl

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Sodium binding site 8 out of 8 in the Crystal Structure of Staphylococcus Aureus Hydrolase Amia in Complex with Its Ligand


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 Staphylococcus Aureus Hydrolase Amia in Complex with Its Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na503

b:22.9
occ:1.00
 OG1 D:THR305 2.3 18.7 1.0
O D:HOH616 2.3 20.9 1.0
O D:HOH619 2.4 20.5 1.0
O D:HOH627 2.4 23.0 1.0
O D:HOH615 2.5 20.1 1.0
CB D:THR305 3.5 18.8 1.0
CE2 B:TYR243 3.6 19.8 1.0
CD2 B:TYR243 3.9 20.2 1.0
CG2 D:THR305 3.9 20.7 1.0
OE1 D:GLN348 3.9 22.3 1.0
OH D:TYR352 4.0 16.9 1.0
N D:THR305 4.1 15.3 1.0
OE1 D:GLU301 4.3 19.9 1.0
CA D:THR305 4.4 16.7 1.0
OE2 D:GLU301 4.4 20.2 1.0
O D:HOH629 4.5 23.5 1.0
NE2 D:GLN348 4.5 21.5 1.0
CE2 D:TYR351 4.6 21.0 1.0
CD D:GLN348 4.6 23.8 1.0
OD2 D:ASP306 4.6 24.2 1.0
O B:HOH651 4.6 26.7 1.0
OE1 B:GLU241 4.6 28.0 1.0
CZ D:TYR351 4.7 17.9 1.0
CD D:GLU301 4.7 19.9 1.0
CZ B:TYR243 4.8 22.6 1.0
CZ D:TYR352 4.9 17.4 1.0
CE2 D:TYR352 4.9 18.3 1.0
OH D:TYR351 4.9 17.8 1.0
CD2 D:TYR351 4.9 19.8 1.0

Reference:

F.M.Buettner, S.Zoll, F.Goetz, T.Stehle. High-Resolution Structural Analysis Reveals the Determinants of Peptidoglycan Recognition and Cleavage By Staphylococcus Aureus Amidase To Be Published.
Page generated: Sun Aug 17 20:17:40 2025

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