Iron in PDB 2pyb: Napa Protein From Borrelia Burgdorferi

The structure of Napa Protein From Borrelia Burgdorferi, PDB code: 2pyb was solved by G.Zanotti, E.Papinutto, M.De Bernard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.99 / 2.60
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	93.078, 93.078, 227.500, 90.00, 90.00, 120.00
R / Rfree (%)	24.2 / 27.5

The binding sites of Iron atom in the Napa Protein From Borrelia Burgdorferi (pdb code 2pyb). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Napa Protein From Borrelia Burgdorferi, PDB code: 2pyb:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in the Napa Protein From Borrelia Burgdorferi


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Napa Protein From Borrelia Burgdorferi within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:72.0 occ:1.00 O B:HOH503 1.9 23.4 1.0 FE B:FE501 2.9 35.3 1.0 NE2 A:HIS50 2.9 34.9 1.0 OE2 B:GLU69 3.0 29.4 1.0 CE1 A:HIS50 3.6 34.9 1.0 OE1 B:GLU69 3.6 31.0 1.0 CD B:GLU69 3.7 36.2 1.0 CD2 A:HIS50 3.9 35.6 1.0 NE2 A:HIS38 4.0 40.7 1.0 O B:HOH510 4.2 40.6 1.0 CE1 A:HIS38 4.2 40.6 1.0 OD2 B:ASP65 4.4 37.8 1.0 NZ C:LYS148 4.4 54.7 1.0 NE2 A:GLN54 4.5 43.6 1.0 CH2 C:TRP151 4.6 57.5 1.0 ND1 A:HIS50 4.7 36.6 1.0 CG A:HIS50 4.9 37.2 1.0 CZ3 C:TRP151 5.0 56.8 1.0

Iron binding site 2 out of 8 in the Napa Protein From Borrelia Burgdorferi


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Napa Protein From Borrelia Burgdorferi within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe503 b:35.3 occ:1.00 OE2 A:GLU69 2.4 29.3 1.0 OD2 A:ASP65 2.4 44.1 1.0 OD1 A:ASP65 2.4 43.3 1.0 NE2 B:HIS38 2.5 39.1 1.0 CG A:ASP65 2.7 45.0 1.0 FE A:FE504 2.7 79.0 1.0 O B:HOH502 3.3 11.7 1.0 CD2 B:HIS38 3.4 39.2 1.0 CE1 B:HIS38 3.5 39.3 1.0 CD A:GLU69 3.6 37.2 1.0 CB A:ASP65 4.1 44.1 1.0 OE1 A:GLU69 4.3 33.7 1.0 OH B:TYR57 4.3 60.8 1.0 CE1 B:HIS50 4.4 37.0 1.0 NE1 B:TRP39 4.5 48.8 1.0 NE2 B:HIS50 4.6 37.8 1.0 CG B:HIS38 4.6 40.6 1.0 O B:HOH505 4.6 23.4 1.0 CG A:GLU69 4.7 38.4 1.0 ND1 B:HIS38 4.7 40.1 1.0 CD1 B:TRP39 4.7 48.7 1.0 NE2 B:GLN54 4.8 44.2 1.0 CD B:GLN54 4.8 42.0 1.0 OE1 B:GLN54 4.9 41.8 1.0

Iron binding site 3 out of 8 in the Napa Protein From Borrelia Burgdorferi


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Napa Protein From Borrelia Burgdorferi within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe504 b:79.0 occ:1.00 O B:HOH502 1.8 11.7 1.0 FE A:FE503 2.7 35.3 1.0 OE2 A:GLU69 3.2 29.3 1.0 NE2 B:HIS50 3.4 37.8 1.0 OE1 A:GLU69 3.8 33.7 1.0 CD A:GLU69 3.9 37.2 1.0 O B:HOH505 4.0 23.4 1.0 CE1 B:HIS50 4.1 37.0 1.0 NE2 B:HIS38 4.1 39.1 1.0 OD2 A:ASP65 4.2 44.1 1.0 CD2 B:HIS50 4.3 38.5 1.0 CE1 B:HIS38 4.4 39.3 1.0 NE2 B:GLN54 4.4 44.2 1.0

Iron binding site 4 out of 8 in the Napa Protein From Borrelia Burgdorferi


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Napa Protein From Borrelia Burgdorferi within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:35.3 occ:1.00 OD2 B:ASP65 2.2 37.8 1.0 O B:HOH503 2.3 23.4 1.0 OE2 B:GLU69 2.3 29.4 1.0 OD1 B:ASP65 2.4 42.8 1.0 CG B:ASP65 2.6 43.2 1.0 NE2 A:HIS38 2.6 40.7 1.0 FE A:FE502 2.9 72.0 1.0 CD2 A:HIS38 3.4 40.2 1.0 CD B:GLU69 3.5 36.2 1.0 CE1 A:HIS38 3.7 40.6 1.0 CB B:ASP65 4.0 42.9 1.0 O B:HOH510 4.0 40.6 1.0 OE1 B:GLU69 4.3 31.0 1.0 OH A:TYR57 4.3 59.2 1.0 NE1 A:TRP39 4.4 48.3 1.0 CE1 A:HIS50 4.6 34.9 1.0 CG B:GLU69 4.6 38.6 1.0 CD1 A:TRP39 4.7 48.1 1.0 CG A:HIS38 4.7 39.3 1.0 NE2 A:HIS50 4.7 34.9 1.0 ND1 A:HIS38 4.8 40.1 1.0 NE2 A:GLN54 4.8 43.6 1.0 CD A:GLN54 4.9 41.3 1.0 OE1 A:GLN54 5.0 39.5 1.0

Iron binding site 5 out of 8 in the Napa Protein From Borrelia Burgdorferi


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Napa Protein From Borrelia Burgdorferi within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe506 b:72.5 occ:1.00 O C:HOH511 2.1 17.7 1.0 O C:HOH510 2.4 26.2 1.0 NE2 C:HIS50 2.7 30.9 1.0 FE D:FE505 3.3 36.6 1.0 OE2 D:GLU69 3.3 34.1 1.0 CE1 C:HIS50 3.6 33.3 1.0 CD2 C:HIS50 3.6 34.9 1.0 OE1 D:GLU69 3.8 34.4 1.0 CD D:GLU69 4.0 38.8 1.0 NE2 C:HIS38 4.2 35.9 1.0 CE1 C:HIS38 4.4 36.7 1.0 NE2 C:GLN54 4.5 46.0 1.0 ND1 C:HIS50 4.6 32.2 1.0 CG C:HIS50 4.7 35.1 1.0 OD2 D:ASP65 4.8 43.9 1.0

Iron binding site 6 out of 8 in the Napa Protein From Borrelia Burgdorferi


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Napa Protein From Borrelia Burgdorferi within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe507 b:41.3 occ:1.00 O D:HOH511 2.3 33.7 1.0 OE2 C:GLU69 2.3 36.8 1.0 OD1 C:ASP65 2.3 46.1 1.0 OD2 C:ASP65 2.4 43.1 1.0 NE2 D:HIS38 2.4 39.3 1.0 CG C:ASP65 2.7 45.1 1.0 FE C:FE508 3.0 75.5 1.0 O C:HOH512 3.1 14.7 1.0 CD2 D:HIS38 3.2 40.3 1.0 CE1 D:HIS38 3.5 37.9 1.0 CD C:GLU69 3.5 40.8 1.0 CB C:ASP65 4.2 45.2 1.0 OE1 C:GLU69 4.2 33.9 1.0 OH D:TYR57 4.2 58.7 1.0 CE1 D:HIS50 4.3 35.7 1.0 NE1 D:TRP39 4.3 49.0 1.0 CG D:HIS38 4.4 39.3 1.0 NE2 D:HIS50 4.5 36.2 1.0 CD1 D:TRP39 4.5 49.9 1.0 ND1 D:HIS38 4.5 40.0 1.0 CG C:GLU69 4.6 40.9 1.0 NE2 D:GLN54 4.8 43.6 1.0 CD D:GLN54 4.9 42.8 1.0 OE1 D:GLN54 5.0 41.6 1.0

Iron binding site 7 out of 8 in the Napa Protein From Borrelia Burgdorferi


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Napa Protein From Borrelia Burgdorferi within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe508 b:75.5 occ:1.00 O C:HOH512 2.0 14.7 1.0 O D:HOH511 2.3 33.7 1.0 FE C:FE507 3.0 41.3 1.0 NE2 D:HIS50 3.2 36.2 1.0 OE2 C:GLU69 3.3 36.8 1.0 OE1 C:GLU69 3.7 33.9 1.0 CD C:GLU69 3.9 40.8 1.0 CE1 D:HIS50 4.0 35.7 1.0 CD2 D:HIS50 4.2 37.5 1.0 NE2 D:HIS38 4.3 39.3 1.0 OD2 C:ASP65 4.3 43.1 1.0 NE2 D:GLN54 4.5 43.6 1.0 CE1 D:HIS38 4.5 37.9 1.0

Iron binding site 8 out of 8 in the Napa Protein From Borrelia Burgdorferi


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Napa Protein From Borrelia Burgdorferi within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe505 b:36.6 occ:1.00 OD2 D:ASP65 2.3 43.9 1.0 OD1 D:ASP65 2.3 44.5 1.0 O C:HOH510 2.4 26.2 1.0 OE2 D:GLU69 2.4 34.1 1.0 NE2 C:HIS38 2.6 35.9 1.0 CG D:ASP65 2.6 46.2 1.0 FE C:FE506 3.3 72.5 1.0 CD2 C:HIS38 3.4 38.1 1.0 CE1 C:HIS38 3.6 36.7 1.0 CD D:GLU69 3.6 38.8 1.0 O C:HOH511 3.7 17.7 1.0 CB D:ASP65 4.1 44.4 1.0 OH C:TYR57 4.2 57.2 1.0 OE1 D:GLU69 4.3 34.4 1.0 NE1 C:TRP39 4.4 47.3 1.0 CE1 C:HIS50 4.5 33.3 1.0 CG C:HIS38 4.6 38.0 1.0 NE2 C:HIS50 4.6 30.9 1.0 CG D:GLU69 4.7 39.4 1.0 NE2 C:GLN54 4.7 46.0 1.0 ND1 C:HIS38 4.7 39.9 1.0 CD1 C:TRP39 4.7 46.2 1.0 CD C:GLN54 4.8 43.4 1.0 OE1 C:GLN54 4.8 42.9 1.0

G.Codolo, E.Papinutto, A.Polenghi, M.M.D'elios, G.Zanotti, M.De Bernard. Structure and Immunomodulatory Property Relationship in Napa of Borrelia Burgdorferi. Biochim.Biophys.Acta V.1804 2191 2010.
ISSN: ISSN 0006-3002
PubMed: 20851780
DOI: 10.1016/J.BBAPAP.2010.09.004