Iron in PDB 5j84: Crystal Structure of L-Arabinonate Dehydratase in Holo-Form

All present enzymatic activity of Crystal Structure of L-Arabinonate Dehydratase in Holo-Form:
4.2.1.9;

The structure of Crystal Structure of L-Arabinonate Dehydratase in Holo-Form, PDB code: 5j84 was solved by M.M.Rahman, J.Rouvinen, N.Hakulinen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.89 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	106.070, 208.610, 147.090, 90.00, 90.43, 90.00
R / Rfree (%)	15.6 / 18.5

The structure of Crystal Structure of L-Arabinonate Dehydratase in Holo-Form also contains other interesting chemical elements:

Magnesium

(Mg)

8 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Iron atom in the Crystal Structure of L-Arabinonate Dehydratase in Holo-Form (pdb code 5j84). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 16 binding sites of Iron where determined in the Crystal Structure of L-Arabinonate Dehydratase in Holo-Form, PDB code: 5j84:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 16 in the Crystal Structure of L-Arabinonate Dehydratase in Holo-Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of L-Arabinonate Dehydratase in Holo-Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe602 b:61.2 occ:1.00 FE1 A:FES602 0.0 61.2 1.0 S1 A:FES602 2.2 73.9 1.0 S2 A:FES602 2.2 41.2 1.0 SG A:CYS127 2.3 68.9 1.0 SG A:CYS59 2.3 45.1 1.0 CB A:CYS59 3.0 34.5 1.0 FE2 A:FES602 3.1 66.0 1.0 CB A:CYS127 3.3 29.3 1.0 CA A:CYS127 3.5 29.3 1.0 ND2 A:ASN92 4.0 60.8 1.0 N A:ASP128 4.0 36.4 1.0 C A:CYS127 4.3 35.9 1.0 CA A:CYS59 4.5 21.2 1.0 CG2 A:THR199 4.5 22.9 1.0 OD1 A:ASP128 4.5 53.3 1.0 N A:CYS127 4.6 28.1 1.0 CA A:THR199 4.7 27.2 1.0 CB A:THR199 4.7 28.9 1.0 CB A:GLU91 4.8 44.1 1.0 CG A:ASP128 4.8 51.7 1.0 CD1 B:TRP30 4.9 43.6 1.0 NE1 B:TRP30 4.9 51.0 1.0 N A:CYS200 4.9 29.1 1.0 SG A:CYS200 4.9 42.1 1.0

Iron binding site 2 out of 16 in the Crystal Structure of L-Arabinonate Dehydratase in Holo-Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of L-Arabinonate Dehydratase in Holo-Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe602 b:66.0 occ:1.00 FE2 A:FES602 0.0 66.0 1.0 S1 A:FES602 2.2 73.9 1.0 S2 A:FES602 2.2 41.2 1.0 SG A:CYS200 2.4 42.1 1.0 FE1 A:FES602 3.1 61.2 1.0 CB A:CYS200 3.6 32.5 1.0 OD1 A:ASP128 3.8 53.3 1.0 NE1 B:TRP30 3.8 51.0 1.0 OD2 A:ASP128 4.1 42.6 1.0 N A:CYS200 4.1 29.1 1.0 CG A:ASP128 4.2 51.7 1.0 SG A:CYS59 4.3 45.1 1.0 CA A:CYS200 4.5 40.4 1.0 O A:HOH816 4.5 30.4 1.0 CD1 B:TRP30 4.6 43.6 1.0 OH B:TYR26 4.7 30.5 1.0 CE2 B:TRP30 4.8 62.9 1.0 SG A:CYS127 5.0 68.9 1.0

Iron binding site 3 out of 16 in the Crystal Structure of L-Arabinonate Dehydratase in Holo-Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of L-Arabinonate Dehydratase in Holo-Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe602 b:58.8 occ:1.00 FE1 B:FES602 0.0 58.8 1.0 S1 B:FES602 2.2 57.5 1.0 S2 B:FES602 2.2 67.1 1.0 SG B:CYS59 2.3 54.4 1.0 SG B:CYS127 2.3 63.7 1.0 FE2 B:FES602 3.1 50.9 1.0 ND2 B:ASN92 3.3 57.9 1.0 CB B:CYS59 3.3 35.4 1.0 CB B:CYS127 3.6 40.8 1.0 CA B:CYS127 3.9 41.1 1.0 CD1 A:TRP30 4.3 39.9 1.0 NE1 A:TRP30 4.4 53.2 1.0 O B:HOH838 4.4 49.1 1.0 N B:ASP128 4.4 48.4 1.0 CG B:ASN92 4.5 54.2 1.0 CB B:GLU91 4.6 41.6 1.0 CA B:CYS59 4.7 31.4 1.0 C B:CYS127 4.8 33.5 1.0 OD1 B:ASP128 4.8 51.2 1.0 N B:GLU91 4.8 50.0 1.0 SG B:CYS200 4.9 46.2 1.0 CB B:ASN92 4.9 39.0 1.0 N B:ASN92 5.0 33.5 1.0

Iron binding site 4 out of 16 in the Crystal Structure of L-Arabinonate Dehydratase in Holo-Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of L-Arabinonate Dehydratase in Holo-Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe602 b:50.9 occ:1.00 FE2 B:FES602 0.0 50.9 1.0 O B:HOH838 2.2 49.1 1.0 S1 B:FES602 2.2 57.5 1.0 S2 B:FES602 2.2 67.1 1.0 SG B:CYS200 2.4 46.2 1.0 FE1 B:FES602 3.1 58.8 1.0 O B:HOH702 3.4 30.7 1.0 CB B:CYS200 3.8 27.3 1.0 OD1 B:ASP128 3.8 51.2 1.0 O B:HOH868 3.8 33.4 1.0 NE1 A:TRP30 3.9 53.2 1.0 OD2 B:ASP128 4.1 41.9 1.0 CG B:ASP128 4.2 48.6 1.0 N B:CYS200 4.3 36.4 1.0 CA B:CYS200 4.6 36.8 1.0 SG B:CYS59 4.7 54.4 1.0 CD1 A:TRP30 4.7 39.9 1.0 OH A:TYR26 4.7 49.1 1.0 CE2 A:TRP30 4.8 54.2 1.0 SG B:CYS127 4.9 63.7 1.0 CB B:GLU91 5.0 41.6 1.0

Iron binding site 5 out of 16 in the Crystal Structure of L-Arabinonate Dehydratase in Holo-Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of L-Arabinonate Dehydratase in Holo-Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe602 b:52.4 occ:1.00 FE1 C:FES602 0.0 52.4 1.0 S1 C:FES602 2.2 65.3 1.0 S2 C:FES602 2.2 47.8 1.0 SG C:CYS59 2.3 57.4 1.0 SG C:CYS127 2.3 61.4 1.0 FE2 C:FES602 3.1 66.3 1.0 CB C:CYS59 3.2 33.3 1.0 CB C:CYS127 3.4 36.8 1.0 CA C:CYS127 3.7 29.5 1.0 ND2 C:ASN92 3.8 55.4 1.0 N C:ASP128 4.3 26.8 1.0 CD1 D:TRP30 4.5 54.8 1.0 NE1 D:TRP30 4.6 48.9 1.0 C C:CYS127 4.6 29.7 1.0 CA C:CYS59 4.6 29.8 1.0 CG2 C:THR199 4.7 22.9 1.0 OD1 C:ASP128 4.7 52.1 1.0 CB C:GLU91 4.8 51.0 1.0 N C:CYS127 4.8 24.0 1.0 N C:GLU91 5.0 40.7 1.0 CA C:THR199 5.0 27.0 1.0

Iron binding site 6 out of 16 in the Crystal Structure of L-Arabinonate Dehydratase in Holo-Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of L-Arabinonate Dehydratase in Holo-Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe602 b:66.3 occ:1.00 FE2 C:FES602 0.0 66.3 1.0 S2 C:FES602 2.2 47.8 1.0 S1 C:FES602 2.2 65.3 1.0 SG C:CYS200 2.3 55.5 1.0 FE1 C:FES602 3.1 52.4 1.0 O C:HOH872 3.4 26.0 1.0 CB C:CYS200 3.6 37.1 1.0 NE1 D:TRP30 3.8 48.9 1.0 OD1 C:ASP128 3.9 52.1 1.0 N C:CYS200 4.0 39.0 1.0 O C:HOH888 4.1 34.2 1.0 OD2 C:ASP128 4.4 40.6 1.0 OE2 C:GLU91 4.4 73.2 1.0 CA C:CYS200 4.4 29.6 1.0 CG C:ASP128 4.4 44.1 1.0 SG C:CYS59 4.5 57.4 1.0 CD1 D:TRP30 4.7 54.8 1.0 CE2 D:TRP30 4.7 46.2 1.0 CZ2 D:TRP30 4.9 51.9 1.0

Iron binding site 7 out of 16 in the Crystal Structure of L-Arabinonate Dehydratase in Holo-Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of L-Arabinonate Dehydratase in Holo-Form within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe602 b:43.8 occ:1.00 FE1 D:FES602 0.0 43.8 1.0 S1 D:FES602 2.2 87.6 1.0 S2 D:FES602 2.2 48.0 1.0 SG D:CYS127 2.3 57.6 1.0 SG D:CYS59 2.3 51.4 1.0 FE2 D:FES602 3.1 51.9 1.0 CB D:CYS59 3.3 33.2 1.0 CB D:CYS127 3.5 30.6 1.0 ND2 D:ASN92 3.7 44.4 1.0 CA D:CYS127 3.8 39.2 1.0 CB D:GLU91 4.3 33.7 1.0 CD1 C:TRP30 4.4 47.0 1.0 NE1 C:TRP30 4.4 52.3 1.0 N D:ASP128 4.5 36.1 1.0 C D:CYS127 4.7 33.8 1.0 CA D:CYS59 4.8 31.3 1.0 CG2 D:THR199 4.8 20.9 1.0 N D:GLU91 4.8 37.9 1.0 N D:CYS127 4.9 34.5 1.0 OD1 D:ASP128 4.9 58.5 1.0 SG D:CYS200 4.9 50.2 1.0 CG D:ASN92 4.9 38.5 1.0

Iron binding site 8 out of 16 in the Crystal Structure of L-Arabinonate Dehydratase in Holo-Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of L-Arabinonate Dehydratase in Holo-Form within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe602 b:51.9 occ:1.00 FE2 D:FES602 0.0 51.9 1.0 S1 D:FES602 2.2 87.6 1.0 S2 D:FES602 2.2 48.0 1.0 SG D:CYS200 2.4 50.2 1.0 FE1 D:FES602 3.1 43.8 1.0 O D:HOH827 3.3 16.1 1.0 CB D:CYS200 3.7 31.5 1.0 OD1 D:ASP128 3.8 58.5 1.0 NE1 C:TRP30 4.1 52.3 1.0 OD2 D:ASP128 4.2 49.1 1.0 N D:CYS200 4.2 26.5 1.0 CG D:ASP128 4.3 37.8 1.0 CA D:CYS200 4.6 34.8 1.0 SG D:CYS59 4.6 51.4 1.0 CG D:GLU91 4.7 35.5 1.0 CB D:GLU91 4.7 33.7 1.0 SG D:CYS127 4.8 57.6 1.0 CE2 C:TRP30 4.9 56.7 1.0 CD1 C:TRP30 4.9 47.0 1.0 OH C:TYR26 4.9 44.3 1.0

Iron binding site 9 out of 16 in the Crystal Structure of L-Arabinonate Dehydratase in Holo-Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Crystal Structure of L-Arabinonate Dehydratase in Holo-Form within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe602 b:45.8 occ:1.00 FE1 E:FES602 0.0 45.8 1.0 S1 E:FES602 2.2 43.2 1.0 S2 E:FES602 2.2 42.5 1.0 SG E:CYS59 2.3 59.5 1.0 SG E:CYS127 2.3 47.3 1.0 FE2 E:FES602 3.1 60.4 1.0 ND2 E:ASN92 3.3 42.4 1.0 CB E:CYS59 3.5 31.9 1.0 O E:HOH859 3.5 33.2 1.0 CB E:CYS127 3.6 29.1 1.0 CA E:CYS127 4.1 31.1 1.0 CD1 F:TRP30 4.4 43.9 1.0 CB E:GLU91 4.4 43.7 1.0 NE1 F:TRP30 4.5 50.0 1.0 CG E:ASN92 4.6 49.4 1.0 N E:ASP128 4.6 38.6 1.0 N E:GLU91 4.7 33.0 1.0 CA E:CYS59 4.8 29.1 1.0 OD1 E:ASP128 4.8 59.1 1.0 C E:CYS127 4.9 24.9 1.0 SG E:CYS200 4.9 46.3 1.0 N E:ASN92 5.0 28.5 1.0 CB E:ASN92 5.0 36.9 1.0

Iron binding site 10 out of 16 in the Crystal Structure of L-Arabinonate Dehydratase in Holo-Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Crystal Structure of L-Arabinonate Dehydratase in Holo-Form within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe602 b:60.4 occ:1.00 FE2 E:FES602 0.0 60.4 1.0 S1 E:FES602 2.2 43.2 1.0 S2 E:FES602 2.2 42.5 1.0 SG E:CYS200 2.4 46.3 1.0 FE1 E:FES602 3.1 45.8 1.0 O E:HOH845 3.1 11.5 1.0 OD1 E:ASP128 3.6 59.1 1.0 CB E:CYS200 3.6 36.4 1.0 O E:HOH905 3.9 25.2 1.0 OD2 E:ASP128 3.9 40.0 1.0 CG E:ASP128 4.1 43.6 1.0 N E:CYS200 4.2 23.7 1.0 NE1 F:TRP30 4.2 50.0 1.0 CA E:CYS200 4.5 33.5 1.0 SG E:CYS59 4.6 59.5 1.0 O E:HOH785 4.7 37.0 1.0 SG E:CYS127 4.8 47.3 1.0 OH F:TYR26 4.9 44.2 1.0 CD1 F:TRP30 4.9 43.9 1.0 CB E:GLU91 4.9 43.7 1.0

M.M.Rahman, M.Andberg, S.K.Thangaraj, T.Parkkinen, M.Penttila, J.Janis, A.Koivula, J.Rouvinen, N.Hakulinen. The Crystal Structure of A Bacterial L-Arabinonate Dehydratase Contains A [2FE-2S] Cluster. Acs Chem. Biol. V. 12 1919 2017.
ISSN: ESSN 1554-8937
PubMed: 28574691
DOI: 10.1021/ACSCHEMBIO.7B00304