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Sodium in PDB 3hwg: Crystal Structure of Siderocalin (Ngal, Lipocalin 2) Complexed with Fe-Trencam-HOPO2

Protein crystallography data

The structure of Crystal Structure of Siderocalin (Ngal, Lipocalin 2) Complexed with Fe-Trencam-HOPO2, PDB code: 3hwg was solved by M.C.Clifton, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.93 / 2.19
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 114.084, 114.084, 118.422, 90.00, 90.00, 90.00
R / Rfree (%) 24.2 / 26.8

Other elements in 3hwg:

The structure of Crystal Structure of Siderocalin (Ngal, Lipocalin 2) Complexed with Fe-Trencam-HOPO2 also contains other interesting chemical elements:

Iron (Fe) 3 atoms
Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Siderocalin (Ngal, Lipocalin 2) Complexed with Fe-Trencam-HOPO2 (pdb code 3hwg). 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 Siderocalin (Ngal, Lipocalin 2) Complexed with Fe-Trencam-HOPO2, PDB code: 3hwg:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 3hwg

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Sodium binding site 1 out of 8 in the Crystal Structure of Siderocalin (Ngal, Lipocalin 2) Complexed with Fe-Trencam-HOPO2


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 Siderocalin (Ngal, Lipocalin 2) Complexed with Fe-Trencam-HOPO2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na186

b:62.3
occ:1.00
 OG A:SER5 3.9 47.0 1.0
O A:HOH230 4.6 63.7 1.0
O A:THR4 4.9 47.7 1.0

Sodium binding site 2 out of 8 in 3hwg

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Sodium binding site 2 out of 8 in the Crystal Structure of Siderocalin (Ngal, Lipocalin 2) Complexed with Fe-Trencam-HOPO2


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 Siderocalin (Ngal, Lipocalin 2) Complexed with Fe-Trencam-HOPO2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na187

b:77.9
occ:1.00
 N A:GLU163 4.1 36.1 1.0
CB A:PRO162 4.1 35.1 1.0
CG A:GLU163 4.2 38.8 1.0
CA A:PRO162 4.4 35.1 1.0
CB A:GLU163 4.6 37.2 1.0
C A:PRO162 4.8 35.7 1.0
CA A:GLU163 5.0 36.6 1.0

Sodium binding site 3 out of 8 in 3hwg

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Sodium binding site 3 out of 8 in the Crystal Structure of Siderocalin (Ngal, Lipocalin 2) Complexed with Fe-Trencam-HOPO2


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 Siderocalin (Ngal, Lipocalin 2) Complexed with Fe-Trencam-HOPO2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na188

b:50.6
occ:1.00
 O A:GLY95 2.6 43.1 1.0
OH A:TYR100 3.3 48.3 1.0
N A:THR82 3.5 34.1 1.0
C A:GLY95 3.6 42.8 1.0
CE1 A:TYR100 3.8 47.5 1.0
OG1 A:THR82 3.9 34.3 1.0
CA A:ARG81 3.9 34.8 1.0
CB A:THR82 4.0 34.0 1.0
CZ A:TYR100 4.0 47.7 1.0
C A:ARG81 4.2 34.4 1.0
CB A:ASN96 4.2 45.3 1.0
CA A:THR82 4.4 33.9 1.0
CA A:GLY95 4.4 41.7 1.0
O A:ASN96 4.4 46.1 1.0
CB A:ARG81 4.4 34.8 1.0
N A:GLY95 4.5 40.5 1.0
N A:ASN96 4.5 44.1 1.0
CG A:LEU94 4.7 37.6 1.0
O A:THR82 4.7 33.5 1.0
CA A:ASN96 4.7 45.1 1.0
C A:ASN96 4.8 45.8 1.0
CD1 A:LEU94 4.8 37.0 1.0
OG A:SER99 4.9 48.2 1.0
O A:ILE80 4.9 35.5 1.0

Sodium binding site 4 out of 8 in 3hwg

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Sodium binding site 4 out of 8 in the Crystal Structure of Siderocalin (Ngal, Lipocalin 2) Complexed with Fe-Trencam-HOPO2


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 Siderocalin (Ngal, Lipocalin 2) Complexed with Fe-Trencam-HOPO2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na189

b:41.6
occ:1.00
 O A:HOH240 2.3 52.5 1.0
OG1 A:THR93 2.8 36.6 1.0
O A:TYR106 3.7 29.6 1.0
N A:TYR106 3.7 30.3 1.0
CB A:THR93 4.1 36.1 1.0
CA A:SER105 4.2 32.3 1.0
OG A:SER105 4.2 32.8 1.0
C A:TYR106 4.3 29.2 1.0
C A:SER105 4.4 31.3 1.0
CA A:TYR106 4.5 29.7 1.0
CD1 A:ILE97 4.6 47.2 1.0
CB A:SER105 4.8 32.1 1.0
O A:THR104 4.8 34.6 1.0
N A:LEU94 5.0 37.4 1.0
CA A:THR93 5.0 36.0 1.0
CG2 A:THR93 5.0 35.9 1.0

Sodium binding site 5 out of 8 in 3hwg

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Sodium binding site 5 out of 8 in the Crystal Structure of Siderocalin (Ngal, Lipocalin 2) Complexed with Fe-Trencam-HOPO2


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 Siderocalin (Ngal, Lipocalin 2) Complexed with Fe-Trencam-HOPO2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na188

b:55.4
occ:1.00
 O C:LEU18 3.2 20.9 1.0
O C:HOH213 3.9 32.4 1.0
CA C:GLN20 3.9 21.6 1.0
C C:LEU18 4.1 21.0 1.0
O C:HOH215 4.1 51.4 1.0
CB C:LEU18 4.1 21.1 1.0
N C:GLN20 4.2 21.2 1.0
O2 A:GOL185 4.2 47.6 1.0
C1 A:GOL185 4.3 48.2 1.0
CB C:GLN20 4.3 22.1 1.0
O C:GLN19 4.3 20.7 1.0
C C:GLN19 4.4 20.9 1.0
CG C:LEU18 4.4 21.6 1.0
CD2 C:LEU18 4.5 21.5 1.0
O1 A:GOL185 4.6 49.0 1.0
C2 A:GOL185 4.6 48.0 1.0
CG C:GLN20 4.6 23.8 1.0
CA C:LEU18 4.6 21.0 1.0
N C:LEU18 4.9 21.0 1.0

Sodium binding site 6 out of 8 in 3hwg

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Sodium binding site 6 out of 8 in the Crystal Structure of Siderocalin (Ngal, Lipocalin 2) Complexed with Fe-Trencam-HOPO2


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 Siderocalin (Ngal, Lipocalin 2) Complexed with Fe-Trencam-HOPO2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na189

b:72.2
occ:1.00
 N C:LYS73 4.2 33.5 1.0
CA C:LYS73 4.8 34.0 1.0

Sodium binding site 7 out of 8 in 3hwg

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Sodium binding site 7 out of 8 in the Crystal Structure of Siderocalin (Ngal, Lipocalin 2) Complexed with Fe-Trencam-HOPO2


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 Siderocalin (Ngal, Lipocalin 2) Complexed with Fe-Trencam-HOPO2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na190

b:42.6
occ:1.00
 O C:HOH291 3.7 33.8 1.0
N C:SER146 3.8 25.5 1.0
OG C:SER146 4.0 26.3 1.0
CA C:THR145 4.2 26.5 1.0
CB C:SER146 4.3 25.2 1.0
CB C:THR145 4.3 26.6 1.0
C C:THR145 4.6 26.1 1.0
CG2 C:THR145 4.7 26.8 1.0
CA C:SER146 4.7 25.2 1.0

Sodium binding site 8 out of 8 in 3hwg

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Sodium binding site 8 out of 8 in the Crystal Structure of Siderocalin (Ngal, Lipocalin 2) Complexed with Fe-Trencam-HOPO2


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 Siderocalin (Ngal, Lipocalin 2) Complexed with Fe-Trencam-HOPO2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na191

b:54.5
occ:0.50
 OE2 C:GLU91 3.6 24.5 1.0
OE1 C:GLN88 3.8 24.7 0.5
OE1 C:GLU91 4.0 24.4 1.0
CB C:SER87 4.2 22.6 1.0
CD C:GLU91 4.2 22.8 1.0
NH2 C:ARG109 4.2 25.8 1.0
CG C:GLN88 4.3 23.5 0.5
CD C:GLN88 4.6 23.7 0.5
OG C:SER87 4.7 22.4 1.0
CG C:GLN88 4.7 23.0 0.5
NE2 C:GLN88 4.9 25.6 0.5

Reference:

M.C.Clifton, P.B.Rupert, T.M.Hoette, K.N.Raymond, R.J.Abergel, R.K.Strong. Parsing the Functional Specificity of Siderocalin / Lipocalin 2 / Ngal For Siderophores and Related Small-Molecule Ligands To Be Published.
Page generated: Mon Oct 7 10:29:06 2024

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