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Sodium in PDB 3fw5: Crystal Structure of Siderocalin (Ngal, Lipocalin 2) Complexed with Ferric 4-Methyl-Catechol

Protein crystallography data

The structure of Crystal Structure of Siderocalin (Ngal, Lipocalin 2) Complexed with Ferric 4-Methyl-Catechol, PDB code: 3fw5 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) 40.62 / 2.30
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 114.904, 114.904, 119.164, 90.00, 90.00, 90.00
R / Rfree (%) 24.4 / 29

Other elements in 3fw5:

The structure of Crystal Structure of Siderocalin (Ngal, Lipocalin 2) Complexed with Ferric 4-Methyl-Catechol 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 Ferric 4-Methyl-Catechol (pdb code 3fw5). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the Crystal Structure of Siderocalin (Ngal, Lipocalin 2) Complexed with Ferric 4-Methyl-Catechol, PDB code: 3fw5:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in 3fw5

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Sodium binding site 1 out of 7 in the Crystal Structure of Siderocalin (Ngal, Lipocalin 2) Complexed with Ferric 4-Methyl-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 4-Methyl-Catechol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na181

b:56.0
occ:1.00
 NZ A:LYS30 2.8 33.9 1.0
OH A:TYR32 2.9 32.7 1.0
O C:HOH340 3.1 61.2 1.0
O A:ASP177 3.7 41.2 1.0
N C:ASN21 3.9 26.5 1.0
CA C:ASN21 4.0 26.6 1.0
CE A:LYS30 4.0 33.2 1.0
CB C:ASN21 4.2 26.8 1.0
C A:ASP177 4.2 41.0 1.0
CZ A:TYR32 4.2 31.8 1.0
CA A:ASP177 4.3 40.4 1.0
O A:GLY178 4.5 42.0 0.8
CG C:ASN21 4.7 26.9 1.0
CG C:GLN20 4.7 28.7 1.0
OD1 C:ASN21 4.7 28.4 1.0
O A:ILE176 4.7 38.3 1.0
CD A:LYS30 4.8 32.3 1.0
OD2 A:ASP177 4.8 40.7 1.0
CB A:ASP177 4.9 40.6 1.0
CE2 A:TYR32 4.9 32.1 1.0

Sodium binding site 2 out of 7 in 3fw5

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Sodium binding site 2 out of 7 in the Crystal Structure of Siderocalin (Ngal, Lipocalin 2) Complexed with Ferric 4-Methyl-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 4-Methyl-Catechol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na182

b:60.0
occ:1.00
 N A:SER146 3.9 44.7 1.0
OG A:SER146 4.1 45.4 1.0
O A:HOH258 4.2 51.0 1.0
CA A:THR145 4.3 43.8 1.0
CB A:THR145 4.5 43.8 1.0
CB A:SER146 4.5 45.1 1.0
C A:THR145 4.6 44.3 1.0
CG2 A:THR145 4.7 43.4 1.0
CA A:SER146 4.9 45.0 1.0

Sodium binding site 3 out of 7 in 3fw5

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Sodium binding site 3 out of 7 in the Crystal Structure of Siderocalin (Ngal, Lipocalin 2) Complexed with Ferric 4-Methyl-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 4-Methyl-Catechol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na183

b:42.4
occ:0.50
 N A:LYS73 3.8 39.1 1.0
CG A:ARG72 4.2 39.0 1.0
CA A:ARG72 4.5 38.2 1.0
CG A:LYS73 4.5 40.6 1.0
CA A:LYS73 4.6 39.4 1.0
O A:HOH362 4.6 48.1 1.0
C A:ARG72 4.7 38.7 1.0
CB A:ARG72 4.8 38.5 1.0

Sodium binding site 4 out of 7 in 3fw5

Go back to Sodium Binding Sites List in 3fw5
Sodium binding site 4 out of 7 in the Crystal Structure of Siderocalin (Ngal, Lipocalin 2) Complexed with Ferric 4-Methyl-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 4-Methyl-Catechol within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na181

b:34.1
occ:1.00
 ND1 C:HIS118 3.0 28.2 1.0
OG C:SER112 3.0 24.5 1.0
O C:HOH211 3.4 45.1 1.0
O C:SER112 3.6 23.0 1.0
CE1 C:HIS118 3.7 28.3 1.0
N C:MET120 3.8 24.1 1.0
C C:SER112 3.8 22.7 1.0
CB C:SER112 3.8 22.9 1.0
CA C:ALA119 3.9 24.8 1.0
C C:ALA119 3.9 24.6 1.0
CG C:HIS118 4.1 27.5 1.0
N C:ALA119 4.1 25.2 1.0
N C:THR113 4.2 22.9 1.0
CG C:MET120 4.2 26.4 1.0
C C:HIS118 4.2 25.5 1.0
CE C:MET120 4.3 29.9 1.0
CA C:THR113 4.3 23.3 1.0
CB C:MET120 4.3 24.1 1.0
O C:HIS118 4.3 25.0 1.0
O C:HOH235 4.3 44.3 1.0
CB C:HIS118 4.4 26.4 1.0
CA C:SER112 4.5 22.7 1.0
O C:ALA119 4.6 24.4 1.0
CA C:MET120 4.7 23.8 1.0
NE2 C:HIS118 4.9 29.4 1.0
CD2 C:LEU148 5.0 32.5 1.0

Sodium binding site 5 out of 7 in 3fw5

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Sodium binding site 5 out of 7 in the Crystal Structure of Siderocalin (Ngal, Lipocalin 2) Complexed with Ferric 4-Methyl-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 4-Methyl-Catechol within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na182

b:51.8
occ:1.00
 O C:HOH351 2.2 58.8 1.0
NZ C:LYS157 3.7 34.9 1.0
N C:GLU163 4.0 34.2 1.0
O C:HOH237 4.1 51.9 1.0
CA C:PRO162 4.2 33.3 1.0
CE C:LYS157 4.2 34.2 1.0
CG C:GLU163 4.2 37.2 1.0
CB C:PRO162 4.4 33.4 1.0
O C:HOH384 4.5 46.9 1.0
C C:PRO162 4.6 33.8 1.0
CB C:GLU163 4.8 35.3 1.0
O C:HOH352 4.8 63.2 1.0
CA C:GLU163 5.0 34.7 1.0

Sodium binding site 6 out of 7 in 3fw5

Go back to Sodium Binding Sites List in 3fw5
Sodium binding site 6 out of 7 in the Crystal Structure of Siderocalin (Ngal, Lipocalin 2) Complexed with Ferric 4-Methyl-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 4-Methyl-Catechol within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na183

b:49.6
occ:0.50
 N C:LYS73 4.1 45.2 1.0
CG C:LYS73 4.5 45.6 1.0
CG C:ARG72 4.6 44.9 1.0
CA C:LYS73 4.7 45.4 1.0
CA C:ARG72 4.9 44.1 1.0
C C:ARG72 5.0 44.6 1.0

Sodium binding site 7 out of 7 in 3fw5

Go back to Sodium Binding Sites List in 3fw5
Sodium binding site 7 out of 7 in the Crystal Structure of Siderocalin (Ngal, Lipocalin 2) Complexed with Ferric 4-Methyl-Catechol


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 Ferric 4-Methyl-Catechol within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na184

b:40.1
occ:1.00
 NE2 C:HIS165 3.8 35.2 1.0
CD2 C:HIS165 4.1 35.1 1.0
ND2 C:ASN164 4.3 34.1 1.0
CG C:PRO162 4.4 33.4 1.0
OD1 C:ASN164 4.4 35.4 1.0
CG C:ASN164 4.8 34.6 1.0
CD1 C:ILE8 4.9 32.1 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: Mon Oct 7 09:51:17 2024

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