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Sodium in PDB 3od9: Crystal Structure of Plii-Ah, Periplasmic Lysozyme Inhibitor of I-Type Lysozyme From Aeromonas Hydrophyla

Protein crystallography data

The structure of Crystal Structure of Plii-Ah, Periplasmic Lysozyme Inhibitor of I-Type Lysozyme From Aeromonas Hydrophyla, PDB code: 3od9 was solved by S.Leysen, J.M.Van Herreweghe, L.Callewaert, M.Heirbaut, P.Buntinx, C.W.Michiels, S.V.Strelkov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.44 / 1.41
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 103.021, 60.327, 82.187, 90.00, 115.65, 90.00
R / Rfree (%) 16.1 / 19.7

Other elements in 3od9:

The structure of Crystal Structure of Plii-Ah, Periplasmic Lysozyme Inhibitor of I-Type Lysozyme From Aeromonas Hydrophyla also contains other interesting chemical elements:

Potassium (K) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Plii-Ah, Periplasmic Lysozyme Inhibitor of I-Type Lysozyme From Aeromonas Hydrophyla (pdb code 3od9). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 10 binding sites of Sodium where determined in the Crystal Structure of Plii-Ah, Periplasmic Lysozyme Inhibitor of I-Type Lysozyme From Aeromonas Hydrophyla, PDB code: 3od9:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 10 in 3od9

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Sodium binding site 1 out of 10 in the Crystal Structure of Plii-Ah, Periplasmic Lysozyme Inhibitor of I-Type Lysozyme From Aeromonas Hydrophyla


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 Plii-Ah, Periplasmic Lysozyme Inhibitor of I-Type Lysozyme From Aeromonas Hydrophyla within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na4

b:15.5
occ:0.76
 O A:GLN92 2.4 18.2 1.0
OD1 A:ASN88 2.4 19.3 1.0
OD1 A:ASP90 2.5 20.8 1.0
OD1 A:ASP86 2.5 19.5 1.0
OE2 A:GLU94 2.6 19.1 1.0
OE1 A:GLU94 2.6 19.5 1.0
CD A:GLU94 2.9 19.0 1.0
CG A:ASP90 3.3 23.3 1.0
CG A:ASN88 3.3 21.4 1.0
CG A:ASP86 3.4 17.8 1.0
C A:GLN92 3.5 18.6 1.0
OD2 A:ASP90 3.8 28.5 1.0
ND2 A:ASN88 3.9 25.2 1.0
N A:GLN92 3.9 19.5 1.0
CA A:ASP86 3.9 16.1 1.0
N A:ASN88 4.0 20.6 1.0
N A:ASP90 4.0 21.9 1.0
N A:LEU87 4.0 18.4 1.0
CB A:ASP86 4.1 17.0 1.0
CA A:GLN92 4.1 18.5 1.0
O A:HOH163 4.2 27.7 0.7
OD2 A:ASP86 4.2 21.1 1.0
N A:GLU94 4.3 15.3 1.0
N A:GLY89 4.4 22.9 1.0
CB A:ASP90 4.4 23.7 1.0
CB A:GLN92 4.4 21.3 1.0
C A:ASP86 4.4 17.1 1.0
CG A:GLU94 4.4 17.4 1.0
N A:LYS91 4.4 20.7 1.0
CA A:ASP90 4.5 21.5 1.0
CB A:ASN88 4.5 22.9 1.0
C A:PRO93 4.5 15.8 1.0
O A:HOH159 4.5 19.9 1.0
N A:PRO93 4.5 17.7 1.0
CA A:ASN88 4.6 22.3 1.0
C A:ASP90 4.6 21.9 1.0
CA A:PRO93 4.7 15.6 1.0
C A:ASN88 4.7 22.6 1.0
C A:LYS91 4.8 20.7 1.0
O A:PRO93 5.0 16.8 1.0

Sodium binding site 2 out of 10 in 3od9

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Sodium binding site 2 out of 10 in the Crystal Structure of Plii-Ah, Periplasmic Lysozyme Inhibitor of I-Type Lysozyme From Aeromonas Hydrophyla


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 Plii-Ah, Periplasmic Lysozyme Inhibitor of I-Type Lysozyme From Aeromonas Hydrophyla within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na8

b:57.4
occ:1.00
 O A:HOH225 3.4 30.9 1.0
O B:HOH473 4.2 34.7 0.6
OG1 A:THR47 4.2 28.8 1.0
OD1 A:ASP76 4.5 28.0 1.0
O B:HOH238 4.5 30.4 0.8
O B:HOH373 4.6 44.8 0.9
O A:HOH271 4.8 46.4 1.0
CG A:ASP76 4.8 27.5 1.0
O A:HOH171 4.9 21.1 0.8

Sodium binding site 3 out of 10 in 3od9

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Sodium binding site 3 out of 10 in the Crystal Structure of Plii-Ah, Periplasmic Lysozyme Inhibitor of I-Type Lysozyme From Aeromonas Hydrophyla


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 Plii-Ah, Periplasmic Lysozyme Inhibitor of I-Type Lysozyme From Aeromonas Hydrophyla within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na9

b:66.4
occ:1.00
 O A:HOH229 3.6 39.7 1.0
O A:HOH682 3.7 52.7 1.0
CA A:PHE23 4.2 23.8 1.0
O A:HOH657 4.3 36.6 1.0
O A:HOH655 4.3 32.0 1.0
N A:PHE23 4.3 27.2 1.0
C A:GLY22 4.5 34.3 1.0
CB A:PHE23 4.6 24.5 1.0
CD1 A:PHE23 4.6 27.5 1.0
O A:GLY22 4.7 35.0 1.0

Sodium binding site 4 out of 10 in 3od9

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Sodium binding site 4 out of 10 in the Crystal Structure of Plii-Ah, Periplasmic Lysozyme Inhibitor of I-Type Lysozyme From Aeromonas Hydrophyla


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 Plii-Ah, Periplasmic Lysozyme Inhibitor of I-Type Lysozyme From Aeromonas Hydrophyla within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na10

b:32.6
occ:0.89
 O A:HOH205 3.1 29.3 0.7
O A:HOH198 3.1 47.6 1.0
O A:HOH165 3.4 20.0 0.8
K A:K2 3.8 16.7 0.8
O A:HOH474 4.3 44.4 0.8

Sodium binding site 5 out of 10 in 3od9

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Sodium binding site 5 out of 10 in the Crystal Structure of Plii-Ah, Periplasmic Lysozyme Inhibitor of I-Type Lysozyme From Aeromonas Hydrophyla


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 Plii-Ah, Periplasmic Lysozyme Inhibitor of I-Type Lysozyme From Aeromonas Hydrophyla within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na11

b:44.6
occ:0.98
 OE2 A:GLU119 2.9 29.3 0.5
ND2 A:ASN88 3.3 25.2 1.0
OE1 A:GLU119 3.4 33.7 0.5
O A:HOH447 3.5 33.4 0.5
CD A:GLU119 3.6 27.7 0.5
O A:HOH166 3.6 38.1 1.0
CG2 A:THR114 3.8 18.0 1.0
O A:HOH579 3.8 60.9 1.0
OE1 A:GLU119 4.0 22.8 0.6
OD2 A:ASP90 4.1 28.5 1.0
O A:HOH219 4.1 37.7 0.9
CB A:THR114 4.2 16.0 1.0
ND2 A:ASN116 4.2 19.5 1.0
OE2 A:GLU119 4.2 30.9 0.6
O A:HOH163 4.2 27.7 0.7
CD A:GLU119 4.3 25.8 0.6
OG1 A:THR114 4.5 17.5 1.0
O A:HOH216 4.5 40.3 0.9
CG A:ASN88 4.6 21.4 1.0
O A:HOH414 4.6 36.6 0.6

Sodium binding site 6 out of 10 in 3od9

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Sodium binding site 6 out of 10 in the Crystal Structure of Plii-Ah, Periplasmic Lysozyme Inhibitor of I-Type Lysozyme From Aeromonas Hydrophyla


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 Plii-Ah, Periplasmic Lysozyme Inhibitor of I-Type Lysozyme From Aeromonas Hydrophyla within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na12

b:42.2
occ:1.00
 OD1 A:ASP122 3.4 23.1 1.0
NZ A:LYS71 3.6 34.2 1.0
O A:HOH340 3.6 40.7 0.8
OG A:SER123 3.7 28.4 0.5
O A:HOH474 3.8 44.4 0.8
O A:HOH413 3.9 57.3 1.0
N A:SER123 4.0 21.2 1.0
CB A:ASP122 4.2 19.4 1.0
CG A:ASP122 4.2 20.1 1.0
CA A:ASP122 4.3 17.2 1.0
CE A:LYS71 4.3 30.7 1.0
O A:HOH347 4.5 48.9 0.9
C A:ASP122 4.6 16.3 1.0
CB A:SER123 4.7 26.0 0.5
CB A:SER123 4.8 25.8 0.5
CA A:SER123 4.9 21.4 0.5
O A:HOH205 4.9 29.3 0.7
CA A:SER123 4.9 21.2 0.5
OG A:SER123 5.0 28.9 0.5

Sodium binding site 7 out of 10 in 3od9

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Sodium binding site 7 out of 10 in the Crystal Structure of Plii-Ah, Periplasmic Lysozyme Inhibitor of I-Type Lysozyme From Aeromonas Hydrophyla


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 Plii-Ah, Periplasmic Lysozyme Inhibitor of I-Type Lysozyme From Aeromonas Hydrophyla within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na3

b:23.4
occ:0.77
 O B:GLN92 2.5 33.0 1.0
OD1 B:ASN88 2.6 32.3 1.0
OD1 B:ASP86 2.6 30.8 1.0
OD1 B:ASP90 2.6 38.1 1.0
OE1 B:GLU94 2.6 24.8 1.0
OE2 B:GLU94 2.7 26.2 1.0
CD B:GLU94 3.0 25.6 1.0
CG B:ASP90 3.4 38.5 1.0
CG B:ASP86 3.5 30.4 1.0
C B:GLN92 3.5 32.2 1.0
O B:HOH182 3.6 30.3 0.8
CG B:ASN88 3.6 34.8 1.0
OD2 B:ASP90 3.7 39.4 1.0
N B:GLN92 3.8 35.6 1.0
CA B:ASP86 4.0 27.8 1.0
N B:ASN88 4.0 29.8 1.0
N B:LEU87 4.0 26.8 1.0
N B:ASP90 4.1 37.2 1.0
CA B:GLN92 4.1 35.0 1.0
ND2 B:ASN88 4.2 37.9 1.0
CB B:ASP86 4.2 28.3 1.0
CB B:GLN92 4.2 38.2 1.0
OD2 B:ASP86 4.2 31.2 1.0
C B:ASP86 4.4 27.7 1.0
N B:GLY89 4.4 34.6 1.0
CB B:ASP90 4.4 36.5 1.0
N B:LYS91 4.5 38.7 1.0
CG B:GLU94 4.5 24.4 1.0
N B:GLU94 4.6 22.1 1.0
CA B:ASP90 4.6 37.9 1.0
N B:PRO93 4.6 27.9 1.0
CA B:ASN88 4.7 32.5 1.0
C B:PRO93 4.7 24.6 1.0
C B:ASP90 4.7 38.8 1.0
CB B:ASN88 4.7 34.3 1.0
O B:HOH160 4.7 22.8 0.9
CA B:PRO93 4.7 26.7 1.0
C B:ASN88 4.8 35.4 1.0
C B:LYS91 4.9 39.4 1.0

Sodium binding site 8 out of 10 in 3od9

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Sodium binding site 8 out of 10 in the Crystal Structure of Plii-Ah, Periplasmic Lysozyme Inhibitor of I-Type Lysozyme From Aeromonas Hydrophyla


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 Plii-Ah, Periplasmic Lysozyme Inhibitor of I-Type Lysozyme From Aeromonas Hydrophyla within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na5

b:25.2
occ:1.00
 O C:GLU119 2.8 31.5 1.0
O C:LEU121 2.9 29.9 1.0
O C:HOH189 2.9 24.2 0.8
OD2 C:ASP122 3.0 33.8 1.0
OD1 C:ASP122 3.1 36.2 1.0
CG C:ASP122 3.3 34.9 1.0
C C:LEU121 3.7 27.1 1.0
N C:LEU121 3.7 25.8 1.0
C C:GLU119 4.0 30.4 1.0
C C:GLY120 4.2 27.8 1.0
CA C:LEU121 4.3 24.9 1.0
O C:HOH281 4.4 28.8 0.5
CA C:GLY120 4.5 26.5 1.0
O C:HOH204 4.5 34.1 0.8
OD2 C:ASP69 4.5 26.5 1.0
N C:ASP122 4.6 27.6 1.0
CB C:ASP122 4.6 32.0 1.0
N C:GLY120 4.7 28.6 1.0
CA C:ASP122 4.8 28.7 1.0
O C:HOH205 4.9 27.8 0.9

Sodium binding site 9 out of 10 in 3od9

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Sodium binding site 9 out of 10 in the Crystal Structure of Plii-Ah, Periplasmic Lysozyme Inhibitor of I-Type Lysozyme From Aeromonas Hydrophyla


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 Plii-Ah, Periplasmic Lysozyme Inhibitor of I-Type Lysozyme From Aeromonas Hydrophyla within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na6

b:23.4
occ:0.59
 O C:GLN92 2.5 38.0 1.0
OD1 C:ASP86 2.6 41.4 1.0
OE1 C:GLU94 2.6 40.3 1.0
OD1 C:ASP90 2.7 45.4 1.0
OD1 C:ASN88 2.7 48.4 1.0
OE2 C:GLU94 2.8 40.0 1.0
CD C:GLU94 3.0 39.8 1.0
CG C:ASP90 3.4 45.7 1.0
CG C:ASP86 3.5 43.0 1.0
CG C:ASN88 3.6 49.3 1.0
C C:GLN92 3.6 36.1 1.0
OD2 C:ASP90 3.7 44.9 1.0
CA C:ASP86 3.9 41.0 1.0
N C:GLN92 3.9 38.2 1.0
N C:LEU87 4.0 41.4 1.0
N C:ASN88 4.1 47.0 1.0
ND2 C:ASN88 4.1 51.4 1.0
N C:ASP90 4.1 45.6 1.0
CB C:ASP86 4.1 40.9 1.0
CA C:GLN92 4.2 37.1 1.0
C C:ASP86 4.3 42.4 1.0
OD2 C:ASP86 4.4 43.7 1.0
N C:GLU94 4.4 32.5 1.0
N C:GLY89 4.4 47.7 1.0
CB C:GLN92 4.4 37.2 1.0
CB C:ASP90 4.5 43.6 1.0
CG C:GLU94 4.5 37.4 1.0
N C:LYS91 4.6 42.2 1.0
C C:PRO93 4.6 33.2 1.0
O C:HOH186 4.6 25.0 0.9
CA C:ASP90 4.6 43.2 1.0
N C:PRO93 4.7 34.4 1.0
CA C:ASN88 4.7 48.2 1.0
CB C:ASN88 4.7 49.3 1.0
C C:ASP90 4.7 43.3 1.0
CA C:PRO93 4.7 34.4 1.0
C C:ASN88 4.8 47.8 1.0
O C:HOH171 4.9 25.4 0.7

Sodium binding site 10 out of 10 in 3od9

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Sodium binding site 10 out of 10 in the Crystal Structure of Plii-Ah, Periplasmic Lysozyme Inhibitor of I-Type Lysozyme From Aeromonas Hydrophyla


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 Plii-Ah, Periplasmic Lysozyme Inhibitor of I-Type Lysozyme From Aeromonas Hydrophyla within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na7

b:60.9
occ:1.00
 NZ C:LYS71 3.6 39.8 1.0
O C:HOH417 3.7 58.5 1.0
OD1 C:ASP122 3.9 36.2 1.0
OG C:SER123 3.9 42.5 1.0
N C:SER123 3.9 31.2 1.0
CE C:LYS71 4.0 37.3 1.0
O C:HOH597 4.4 65.8 1.0
CA C:ASP122 4.4 28.7 1.0
CB C:SER123 4.6 37.0 1.0
CB C:ASP122 4.6 32.0 1.0
CG C:ASP122 4.7 34.9 1.0
C C:ASP122 4.7 30.8 1.0
CA C:SER123 4.8 34.0 1.0
O C:HOH281 4.8 28.8 0.5

Reference:

S.Leysen, J.M.Van Herreweghe, L.Callewaert, M.Heirbaut, P.Buntinx, C.W.Michiels, S.V.Strelkov. Molecular Basis of Bacterial Defense Against Host Lysozymes: X-Ray Structures of Periplasmic Lysozyme Inhibitors Plii and Plic. J.Mol.Biol. V. 405 1233 2011.
ISSN: ISSN 0022-2836
PubMed: 21146533
DOI: 10.1016/J.JMB.2010.12.007
Page generated: Mon Oct 7 11:58:23 2024

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