Iron in PDB 5oyn: Crystal Structure of D-Xylonate Dehydratase in Holo-Form

The structure of Crystal Structure of D-Xylonate Dehydratase in Holo-Form, PDB code: 5oyn 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)	29.94 / 2.70
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	270.420, 236.130, 65.160, 90.00, 97.38, 90.00
R / Rfree (%)	17.7 / 21.8

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

Magnesium

(Mg)

4 atoms

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

Iron binding site 1 out of 8 in the Crystal Structure of D-Xylonate 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 D-Xylonate Dehydratase in Holo-Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe602 b:73.5 occ:1.00 FE1 A:FES602 0.0 73.5 1.0 S2 A:FES602 2.2 56.2 1.0 S1 A:FES602 2.2 67.1 1.0 SG A:CYS60 2.3 63.5 1.0 SG A:CYS128 2.3 70.4 1.0 FE2 A:FES602 3.1 79.4 1.0 CB A:CYS60 3.2 54.3 1.0 CB A:CYS128 3.2 61.9 1.0 CA A:CYS128 3.6 60.9 1.0 NH1 B:ARG30 4.1 62.5 1.0 N A:ASP129 4.4 62.6 1.0 CD1 A:PHE91 4.5 62.4 1.0 C A:CYS128 4.5 63.1 1.0 N A:GLU92 4.6 61.8 1.0 CA A:CYS60 4.6 53.6 1.0 N A:CYS128 4.6 53.8 1.0 CB A:GLU92 4.6 66.3 1.0 CE1 A:PHE91 4.6 60.5 1.0 SG A:CYS201 4.8 61.7 1.0 CB A:HIS200 4.9 49.2 1.0 OD1 A:ASP129 4.9 72.7 1.0

Iron binding site 2 out of 8 in the Crystal Structure of D-Xylonate 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 D-Xylonate Dehydratase in Holo-Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe602 b:79.4 occ:1.00 FE2 A:FES602 0.0 79.4 1.0 S2 A:FES602 2.2 56.2 1.0 S1 A:FES602 2.2 67.1 1.0 SG A:CYS201 2.3 61.7 1.0 FE1 A:FES602 3.1 73.5 1.0 O A:HOH722 3.7 52.7 1.0 CB A:CYS201 3.7 50.4 1.0 NH1 B:ARG30 3.9 62.5 1.0 OD1 A:ASP129 3.9 72.7 1.0 OD2 A:ASP129 4.1 80.5 1.0 OD1 A:ASN93 4.2 74.8 1.0 CG A:ASP129 4.3 74.8 1.0 NH2 B:ARG30 4.3 59.8 1.0 N A:CYS201 4.4 49.3 1.0 CZ B:ARG30 4.5 57.0 1.0 SG A:CYS60 4.6 63.5 1.0 CA A:CYS201 4.6 52.3 1.0 SG A:CYS128 4.7 70.4 1.0 O A:HOH753 4.8 52.7 1.0 CG A:ASN93 4.8 67.7 1.0 CB A:GLU92 4.9 66.3 1.0

Iron binding site 3 out of 8 in the Crystal Structure of D-Xylonate 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 D-Xylonate Dehydratase in Holo-Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe602 b:85.6 occ:1.00 FE1 B:FES602 0.0 85.6 1.0 S2 B:FES602 2.2 85.9 1.0 S1 B:FES602 2.2 90.8 1.0 SG B:CYS60 2.3 71.5 1.0 SG B:CYS128 2.3 84.0 1.0 FE2 B:FES602 3.1 0.7 1.0 CB B:CYS60 3.3 64.4 1.0 CB B:CYS128 3.5 67.9 1.0 CA B:CYS128 3.8 64.2 1.0 NH1 A:ARG30 4.2 78.6 1.0 CB B:GLU92 4.4 81.2 1.0 OD1 B:ASP129 4.5 80.6 1.0 CD1 B:PHE91 4.5 64.4 1.0 N B:GLU92 4.5 76.7 1.0 CE1 B:PHE91 4.6 73.0 1.0 N B:ASP129 4.7 67.0 1.0 CA B:CYS60 4.7 62.0 1.0 N B:CYS128 4.8 72.2 1.0 C B:CYS128 4.8 65.4 1.0 CB B:HIS200 4.8 63.4 1.0 CZ A:ARG30 4.9 79.6 1.0

Iron binding site 4 out of 8 in the Crystal Structure of D-Xylonate 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 D-Xylonate Dehydratase in Holo-Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe602 b:0.7 occ:1.00 FE2 B:FES602 0.0 0.7 1.0 S1 B:FES602 2.2 90.8 1.0 S2 B:FES602 2.2 85.9 1.0 SG B:CYS201 2.3 75.8 1.0 FE1 B:FES602 3.1 85.6 1.0 CB B:CYS201 3.5 66.7 1.0 NH1 A:ARG30 3.7 78.6 1.0 NH2 A:ARG30 3.8 76.3 1.0 OD1 B:ASP129 3.8 80.6 1.0 N B:CYS201 4.1 64.4 1.0 CZ A:ARG30 4.1 79.6 1.0 CA B:CYS201 4.3 65.9 1.0 SG B:CYS60 4.5 71.5 1.0 OD1 B:ASN93 4.5 86.6 1.0 CG B:ASP129 4.7 80.9 1.0 O B:HOH706 4.8 73.5 1.0 OD2 B:ASP129 4.9 88.8 1.0 SG B:CYS128 4.9 84.0 1.0 CG B:GLU92 4.9 86.1 1.0 CG B:ASN93 5.0 83.7 1.0

Iron binding site 5 out of 8 in the Crystal Structure of D-Xylonate 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 D-Xylonate Dehydratase in Holo-Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe602 b:69.5 occ:1.00 FE1 C:FES602 0.0 69.5 1.0 S1 C:FES602 2.2 76.7 1.0 S2 C:FES602 2.2 65.0 1.0 SG C:CYS60 2.3 58.8 1.0 SG C:CYS128 2.3 62.9 1.0 FE2 C:FES602 3.1 77.0 1.0 CB C:CYS60 3.2 52.4 1.0 CB C:CYS128 3.3 60.0 1.0 CA C:CYS128 3.8 56.6 1.0 NH1 D:ARG30 4.0 64.2 1.0 CB C:GLU92 4.5 62.9 1.0 N C:GLU92 4.5 61.8 1.0 N C:ASP129 4.6 61.1 1.0 CA C:CYS60 4.6 52.9 1.0 CD1 C:PHE91 4.6 56.0 1.0 CB C:HIS200 4.7 51.6 1.0 OD1 C:ASP129 4.7 61.9 1.0 C C:CYS128 4.7 55.8 1.0 CE1 C:PHE91 4.8 56.3 1.0 N C:CYS128 4.8 55.0 1.0 SG C:CYS201 4.8 59.8 1.0 CZ D:ARG30 4.9 62.4 1.0 CA C:HIS200 5.0 51.6 1.0 N C:CYS60 5.0 51.4 1.0

Iron binding site 6 out of 8 in the Crystal Structure of D-Xylonate 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 D-Xylonate Dehydratase in Holo-Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe602 b:77.0 occ:1.00 FE2 C:FES602 0.0 77.0 1.0 S2 C:FES602 2.2 65.0 1.0 S1 C:FES602 2.2 76.7 1.0 SG C:CYS201 2.3 59.8 1.0 FE1 C:FES602 3.1 69.5 1.0 O C:HOH749 3.4 50.9 1.0 OD1 C:ASP129 3.6 61.9 1.0 CB C:CYS201 3.8 51.8 1.0 NH1 D:ARG30 3.9 64.2 1.0 NH2 D:ARG30 4.0 59.4 1.0 CZ D:ARG30 4.3 62.4 1.0 CG C:ASP129 4.4 67.1 1.0 N C:CYS201 4.4 53.2 1.0 OD2 C:ASP129 4.4 73.9 1.0 CB C:GLU92 4.5 62.9 1.0 OD1 C:ASN93 4.6 63.0 1.0 SG C:CYS128 4.6 62.9 1.0 CA C:CYS201 4.7 58.3 1.0 SG C:CYS60 4.8 58.8 1.0 CG C:GLU92 4.9 68.0 1.0 O C:HOH753 4.9 48.4 1.0

Iron binding site 7 out of 8 in the Crystal Structure of D-Xylonate 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 D-Xylonate Dehydratase in Holo-Form within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe602 b:65.4 occ:1.00 FE1 D:FES602 0.0 65.4 1.0 S1 D:FES602 2.2 64.2 1.0 S2 D:FES602 2.2 60.4 1.0 SG D:CYS60 2.3 60.4 1.0 SG D:CYS128 2.3 64.5 1.0 FE2 D:FES602 3.0 77.9 1.0 CB D:CYS60 3.0 44.2 1.0 CB D:CYS128 3.4 47.4 1.0 CA D:CYS128 3.8 52.8 1.0 NH1 C:ARG30 3.8 60.7 1.0 CA D:CYS60 4.5 44.3 1.0 N D:ASP129 4.5 55.5 1.0 N D:GLU92 4.6 58.9 1.0 CD1 D:PHE91 4.6 55.2 1.0 CB D:GLU92 4.6 66.1 1.0 SG D:CYS201 4.7 65.1 1.0 O D:HOH764 4.7 71.9 1.0 C D:CYS128 4.7 55.1 1.0 CB D:HIS200 4.7 42.5 1.0 N D:CYS128 4.8 48.8 1.0 CE1 D:PHE91 4.8 58.0 1.0 OD2 D:ASP129 4.8 63.8 1.0 CZ C:ARG30 4.9 64.0 1.0 N D:CYS60 5.0 49.3 1.0 CA D:HIS200 5.0 46.8 1.0

Iron binding site 8 out of 8 in the Crystal Structure of D-Xylonate 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 D-Xylonate Dehydratase in Holo-Form within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe602 b:77.9 occ:1.00 FE2 D:FES602 0.0 77.9 1.0 O D:HOH764 2.1 71.9 1.0 S2 D:FES602 2.2 60.4 1.0 S1 D:FES602 2.2 64.2 1.0 SG D:CYS201 2.3 65.1 1.0 FE1 D:FES602 3.0 65.4 1.0 O D:HOH786 3.5 52.9 1.0 NH1 C:ARG30 3.6 60.7 1.0 CB D:CYS201 3.7 49.4 1.0 OD2 D:ASP129 3.7 63.8 1.0 NH2 C:ARG30 4.1 60.5 1.0 CZ C:ARG30 4.3 64.0 1.0 OD1 D:ASN93 4.4 61.9 1.0 N D:CYS201 4.4 48.7 1.0 CG D:ASP129 4.5 72.2 1.0 CG D:GLU92 4.6 69.3 1.0 SG D:CYS128 4.6 64.5 1.0 CA D:CYS201 4.6 47.7 1.0 OD1 D:ASP129 4.7 80.2 1.0 SG D:CYS60 4.7 60.4 1.0 CB D:GLU92 4.8 66.1 1.0 O D:HOH778 4.9 45.6 1.0 CG D:ASN93 4.9 65.1 1.0

M.M.Rahman, M.Andberg, A.Koivula, J.Rouvinen, N.Hakulinen. The Crystal Structure of D-Xylonate Dehydratase Reveals Functional Features of Enzymes From the Ilv/Ed Dehydratase Family. Sci Rep V. 8 865 2018.
ISSN: ESSN 2045-2322
PubMed: 29339766
DOI: 10.1038/S41598-018-19192-6