Atomistry » Sodium » PDB 3fvs-3gdg » 3fw5
Atomistry »
  Sodium »
    PDB 3fvs-3gdg »
      3fw5 »

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

Go back to Sodium Binding Sites List in 3fw5
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

Go back to Sodium Binding Sites List in 3fw5
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

Go back to Sodium Binding Sites List in 3fw5
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

Go back to Sodium Binding Sites List in 3fw5
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy