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Sodium in PDB 3fw4: Crystal Structure of Siderocalin (Ngal, Lipocalin 2) Complexed with Ferric Catechol

Protein crystallography data

The structure of Crystal Structure of Siderocalin (Ngal, Lipocalin 2) Complexed with Ferric Catechol, PDB code: 3fw4 was solved by M.C.Clifton, R.K.Strong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.79 / 2.30
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 115.421, 115.421, 118.801, 90.00, 90.00, 90.00
R / Rfree (%) 25.6 / 28.4

Other elements in 3fw4:

The structure of Crystal Structure of Siderocalin (Ngal, Lipocalin 2) Complexed with Ferric Catechol also contains other interesting chemical elements:

Iron (Fe) 3 atoms
Chlorine (Cl) 8 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Siderocalin (Ngal, Lipocalin 2) Complexed with Ferric Catechol (pdb code 3fw4). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Crystal Structure of Siderocalin (Ngal, Lipocalin 2) Complexed with Ferric Catechol, PDB code: 3fw4:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 3fw4

Go back to Sodium Binding Sites List in 3fw4
Sodium binding site 1 out of 6 in the Crystal Structure of Siderocalin (Ngal, Lipocalin 2) Complexed with Ferric Catechol


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 Ferric Catechol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na181

b:73.9
occ:1.00
O A:HOH191 3.9 61.1 1.0
CD2 A:LEU13 3.9 48.5 1.0
CD1 A:LEU13 4.0 48.7 1.0
CB A:LEU13 4.2 48.5 1.0
CG A:LEU13 4.2 48.7 1.0
N A:LEU13 4.5 48.1 1.0
O A:HOH265 4.6 48.2 1.0

Sodium binding site 2 out of 6 in 3fw4

Go back to Sodium Binding Sites List in 3fw4
Sodium binding site 2 out of 6 in the Crystal Structure of Siderocalin (Ngal, Lipocalin 2) Complexed with Ferric Catechol


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 Ferric Catechol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na182

b:75.7
occ:1.00
N A:LYS73 4.2 39.2 1.0
CG A:ARG72 4.3 39.7 1.0
CA A:ARG72 4.5 38.8 1.0
CB A:ARG72 4.7 39.1 1.0
C A:ARG72 4.9 39.0 1.0

Sodium binding site 3 out of 6 in 3fw4

Go back to Sodium Binding Sites List in 3fw4
Sodium binding site 3 out of 6 in the Crystal Structure of Siderocalin (Ngal, Lipocalin 2) Complexed with Ferric Catechol


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 Ferric Catechol within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na181

b:72.6
occ:1.00
O C:HOH272 2.7 61.4 1.0
O C:HOH273 3.4 51.4 1.0
NE2 A:GLN117 3.6 41.9 1.0
ND2 C:ASN114 3.7 26.8 1.0
CB C:ASN114 3.9 26.4 1.0
OE1 A:GLN117 4.0 43.7 1.0
CD A:GLN117 4.2 41.7 1.0
CG C:ASN114 4.4 26.4 1.0
O C:HOH275 4.6 60.4 1.0
NE2 C:HIS118 4.9 29.9 1.0

Sodium binding site 4 out of 6 in 3fw4

Go back to Sodium Binding Sites List in 3fw4
Sodium binding site 4 out of 6 in the Crystal Structure of Siderocalin (Ngal, Lipocalin 2) Complexed with Ferric Catechol


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 Ferric Catechol within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na182

b:50.0
occ:1.00
NE2 C:HIS165 3.8 34.3 1.0
CD2 C:HIS165 4.1 34.9 1.0
CG C:PRO162 4.4 32.8 1.0
ND2 C:ASN164 4.4 35.2 1.0
OD1 C:ASN164 4.5 34.6 1.0
CD1 C:ILE8 4.8 31.0 1.0
CG C:ASN164 4.9 34.4 1.0

Sodium binding site 5 out of 6 in 3fw4

Go back to Sodium Binding Sites List in 3fw4
Sodium binding site 5 out of 6 in the Crystal Structure of Siderocalin (Ngal, Lipocalin 2) Complexed with Ferric Catechol


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 Ferric Catechol within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na183

b:59.0
occ:1.00
OG C:SER146 3.6 33.6 0.5
OG C:SER146 3.6 33.2 0.5
N C:SER146 3.9 34.1 1.0
CB C:SER146 4.2 33.6 0.5
CB C:SER146 4.2 33.7 0.5
O C:HOH305 4.2 52.4 1.0
CA C:THR145 4.5 35.8 1.0
CA C:SER146 4.7 33.8 0.5
CA C:SER146 4.7 33.7 0.5
C C:THR145 4.8 35.0 1.0
CB C:THR145 4.8 35.9 1.0

Sodium binding site 6 out of 6 in 3fw4

Go back to Sodium Binding Sites List in 3fw4
Sodium binding site 6 out of 6 in the Crystal Structure of Siderocalin (Ngal, Lipocalin 2) Complexed with Ferric Catechol


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 Ferric Catechol within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na184

b:66.5
occ:1.00
O C:HOH266 3.1 52.5 1.0
N C:LYS73 4.1 43.6 1.0
OD2 C:ASP47 4.4 52.5 1.0
CA C:ARG72 4.6 42.9 1.0
CG C:ARG72 4.9 43.4 1.0
NZ C:LYS50 4.9 46.0 1.0
C C:ARG72 4.9 43.3 1.0
O C:PHE71 4.9 41.9 1.0
CE C:LYS50 5.0 45.0 1.0
CA C:LYS73 5.0 43.7 1.0

Reference:

G.Bao, M.Clifton, T.M.Hoette, K.Mori, S.X.Deng, A.Qiu, M.Viltard, D.Williams, N.Paragas, T.Leete, R.Kulkarni, X.Li, B.Lee, A.Kalandadze, A.J.Ratner, J.C.Pizarro, K.M.Schmidt-Ott, D.W.Landry, K.N.Raymond, R.K.Strong, J.Barasch. Iron Traffics in Circulation Bound to A Siderocalin (Ngal)-Catechol Complex. Nat.Chem.Biol. V. 6 602 2010.
ISSN: ISSN 1552-4450
PubMed: 20581821
DOI: 10.1038/NCHEMBIO.402
Page generated: Tue Dec 15 06:11:12 2020

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