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Sodium in PDB 3hwf: Crystal Structure of Siderocalin (Ngal, Lipocalin 2) Complexed with Fe-TRENCAM2-Hopo

Protein crystallography data

The structure of Crystal Structure of Siderocalin (Ngal, Lipocalin 2) Complexed with Fe-TRENCAM2-Hopo, PDB code: 3hwf 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) 48.00 / 3.20
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 114.802, 114.802, 118.352, 90.00, 90.00, 90.00
R / Rfree (%) 21.6 / 27.2

Other elements in 3hwf:

The structure of Crystal Structure of Siderocalin (Ngal, Lipocalin 2) Complexed with Fe-TRENCAM2-Hopo also contains other interesting chemical elements:

Iron (Fe) 3 atoms
Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Siderocalin (Ngal, Lipocalin 2) Complexed with Fe-TRENCAM2-Hopo (pdb code 3hwf). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Siderocalin (Ngal, Lipocalin 2) Complexed with Fe-TRENCAM2-Hopo, PDB code: 3hwf:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 3hwf

Go back to Sodium Binding Sites List in 3hwf
Sodium binding site 1 out of 4 in the Crystal Structure of Siderocalin (Ngal, Lipocalin 2) Complexed with Fe-TRENCAM2-Hopo


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-TRENCAM2-Hopo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na182

b:22.3
occ:1.00
O A:CYS175 3.8 26.4 1.0
O A:ASP177 4.4 29.8 1.0
CD1 A:ILE55 4.5 23.1 1.0
CG1 A:VAL69 4.5 23.5 1.0

Sodium binding site 2 out of 4 in 3hwf

Go back to Sodium Binding Sites List in 3hwf
Sodium binding site 2 out of 4 in the Crystal Structure of Siderocalin (Ngal, Lipocalin 2) Complexed with Fe-TRENCAM2-Hopo


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-TRENCAM2-Hopo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na185

b:36.0
occ:1.00
O A:ASN129 2.9 31.4 1.0
ND2 A:ASN129 3.6 33.8 1.0
C A:ASN129 4.0 31.6 1.0
CA A:ASN129 4.4 32.2 1.0
CG A:ASN129 4.6 33.5 1.0
CB A:ASN129 4.7 32.3 1.0
CG1 A:VAL126 4.9 28.4 1.0

Sodium binding site 3 out of 4 in 3hwf

Go back to Sodium Binding Sites List in 3hwf
Sodium binding site 3 out of 4 in the Crystal Structure of Siderocalin (Ngal, Lipocalin 2) Complexed with Fe-TRENCAM2-Hopo


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-TRENCAM2-Hopo within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na180

b:41.7
occ:1.00
NE2 B:HIS165 3.7 48.0 1.0
CD2 B:HIS165 4.5 47.5 1.0
ND2 B:ASN164 4.6 48.0 1.0
CE1 B:HIS165 4.7 47.9 1.0

Sodium binding site 4 out of 4 in 3hwf

Go back to Sodium Binding Sites List in 3hwf
Sodium binding site 4 out of 4 in the Crystal Structure of Siderocalin (Ngal, Lipocalin 2) Complexed with Fe-TRENCAM2-Hopo


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-TRENCAM2-Hopo within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na185

b:23.2
occ:1.00
N C:SER146 3.7 25.7 1.0
OG C:SER146 4.1 26.5 1.0
CA C:THR145 4.2 24.7 1.0
CB C:SER146 4.2 25.9 1.0
CB C:THR145 4.3 24.6 1.0
C C:THR145 4.5 25.2 1.0
CG2 C:THR145 4.6 24.3 1.0
CA C:SER146 4.6 26.0 1.0

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: Tue Dec 15 06:13:38 2020

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