Iron in PDB 6xb9: Crystal Structure of Azotobacter Vinelandii 3-Mercaptopropionic Acid Dioxygenase in Complex with 3-Hydroxypropionic Acid

The structure of Crystal Structure of Azotobacter Vinelandii 3-Mercaptopropionic Acid Dioxygenase in Complex with 3-Hydroxypropionic Acid, PDB code: 6xb9 was solved by P.D.Kiser, N.Khadka, W.Shi, B.S.Pierce, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.26 / 2.25
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	178.219, 178.219, 75.915, 90, 90, 120
R / Rfree (%)	19.6 / 22.6

The structure of Crystal Structure of Azotobacter Vinelandii 3-Mercaptopropionic Acid Dioxygenase in Complex with 3-Hydroxypropionic Acid also contains other interesting chemical elements:

Magnesium	(Mg)	4 atoms
Chlorine	(Cl)	13 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Iron atom in the Crystal Structure of Azotobacter Vinelandii 3-Mercaptopropionic Acid Dioxygenase in Complex with 3-Hydroxypropionic Acid (pdb code 6xb9). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 12 binding sites of Iron where determined in the Crystal Structure of Azotobacter Vinelandii 3-Mercaptopropionic Acid Dioxygenase in Complex with 3-Hydroxypropionic Acid, PDB code: 6xb9:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 12 in the Crystal Structure of Azotobacter Vinelandii 3-Mercaptopropionic Acid Dioxygenase in Complex with 3-Hydroxypropionic Acid


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 Azotobacter Vinelandii 3-Mercaptopropionic Acid Dioxygenase in Complex with 3-Hydroxypropionic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:49.0 occ:1.00 NE2 A:HIS90 2.2 41.4 1.0 O3 A:3OH302 2.2 47.1 1.0 O2 A:3OH302 2.2 57.2 1.0 NE2 A:HIS142 2.2 42.3 1.0 NE2 A:HIS92 2.2 42.9 1.0 CL A:CL303 2.4 54.0 1.0 C3 A:3OH302 2.6 53.7 1.0 C1 A:3OH302 2.8 53.7 1.0 CE1 A:HIS92 3.1 44.1 1.0 CE1 A:HIS142 3.1 40.4 1.0 CD2 A:HIS90 3.1 41.1 1.0 C2 A:3OH302 3.1 53.3 1.0 CE1 A:HIS90 3.1 36.9 1.0 CD2 A:HIS142 3.2 43.5 1.0 CD2 A:HIS92 3.2 48.6 1.0 O1 A:3OH302 3.9 53.3 1.0 OH A:TYR159 4.1 52.7 1.0 ND1 A:HIS92 4.2 42.4 1.0 ND1 A:HIS142 4.2 40.4 1.0 ND1 A:HIS90 4.3 37.6 1.0 CG A:HIS90 4.3 37.8 1.0 CG A:HIS142 4.3 42.6 1.0 CG A:HIS92 4.3 45.7 1.0 CG2 A:VAL144 4.7 40.5 1.0 NH1 A:ARG168 4.8 44.6 1.0

Iron binding site 2 out of 12 in the Crystal Structure of Azotobacter Vinelandii 3-Mercaptopropionic Acid Dioxygenase in Complex with 3-Hydroxypropionic Acid


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 Azotobacter Vinelandii 3-Mercaptopropionic Acid Dioxygenase in Complex with 3-Hydroxypropionic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:44.3 occ:1.00 O3 B:3OH302 2.1 47.9 1.0 O1 B:3OH302 2.1 48.0 1.0 NE2 B:HIS92 2.1 47.5 1.0 NE2 B:HIS90 2.2 39.6 1.0 NE2 B:HIS142 2.2 44.8 1.0 CL B:CL303 2.4 54.1 1.0 CE1 B:HIS92 3.1 51.8 1.0 C1 B:3OH302 3.1 48.2 1.0 C3 B:3OH302 3.1 48.1 1.0 CD2 B:HIS90 3.1 45.0 1.0 CE1 B:HIS142 3.2 49.1 1.0 CE1 B:HIS90 3.2 45.2 1.0 CD2 B:HIS92 3.2 52.6 1.0 CD2 B:HIS142 3.2 42.0 1.0 C2 B:3OH302 3.5 47.6 1.0 OH B:TYR159 4.0 53.0 1.0 ND1 B:HIS92 4.2 44.3 1.0 ND1 B:HIS90 4.3 48.5 1.0 O2 B:3OH302 4.3 43.0 1.0 CG B:HIS90 4.3 42.8 1.0 CG B:HIS92 4.3 49.4 1.0 ND1 B:HIS142 4.3 45.4 1.0 CG B:HIS142 4.4 45.6 1.0 NH1 B:ARG168 4.7 37.9 1.0 CG2 B:VAL144 4.8 41.9 1.0 ND1 B:HIS157 4.9 54.5 1.0 CE1 B:TYR159 4.9 46.1 1.0 CZ B:TYR159 5.0 50.3 1.0

Iron binding site 3 out of 12 in the Crystal Structure of Azotobacter Vinelandii 3-Mercaptopropionic Acid Dioxygenase in Complex with 3-Hydroxypropionic Acid


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 Azotobacter Vinelandii 3-Mercaptopropionic Acid Dioxygenase in Complex with 3-Hydroxypropionic Acid within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe301 b:48.7 occ:1.00 O3 C:3OH302 2.1 48.9 1.0 O2 C:3OH302 2.2 51.0 1.0 NE2 C:HIS142 2.2 40.9 1.0 NE2 C:HIS92 2.2 56.3 1.0 NE2 C:HIS90 2.2 44.9 1.0 CL C:CL303 2.4 60.5 1.0 C1 C:3OH302 3.1 52.2 1.0 CE1 C:HIS142 3.1 45.6 1.0 CE1 C:HIS92 3.1 51.0 1.0 CD2 C:HIS142 3.2 40.9 1.0 CD2 C:HIS90 3.2 46.9 1.0 CE1 C:HIS90 3.2 51.6 1.0 CD2 C:HIS92 3.2 53.2 1.0 C3 C:3OH302 3.3 50.7 1.0 C2 C:3OH302 3.5 53.2 1.0 OH C:TYR159 4.0 48.4 1.0 ND1 C:HIS142 4.2 44.4 1.0 O1 C:3OH302 4.3 45.1 1.0 ND1 C:HIS92 4.3 55.0 1.0 CG C:HIS142 4.3 39.8 1.0 ND1 C:HIS90 4.3 45.9 1.0 CG C:HIS92 4.4 50.1 1.0 CG C:HIS90 4.4 42.8 1.0 CG2 C:VAL144 4.7 37.6 1.0 NH1 C:ARG168 4.8 47.4 1.0 ND1 C:HIS157 4.8 39.4 1.0 CE1 C:TYR159 4.9 50.6 1.0 CZ C:TYR159 5.0 48.3 1.0 CE1 C:HIS157 5.0 44.6 1.0

Iron binding site 4 out of 12 in the Crystal Structure of Azotobacter Vinelandii 3-Mercaptopropionic Acid Dioxygenase in Complex with 3-Hydroxypropionic Acid


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 Azotobacter Vinelandii 3-Mercaptopropionic Acid Dioxygenase in Complex with 3-Hydroxypropionic Acid within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe301 b:47.6 occ:1.00 NE2 D:HIS92 2.1 45.6 1.0 O3 D:3OH302 2.1 54.1 1.0 NE2 D:HIS90 2.1 41.8 1.0 O1 D:3OH302 2.1 51.3 1.0 NE2 D:HIS142 2.2 38.4 1.0 CL D:CL303 2.4 68.0 1.0 CE1 D:HIS92 3.0 50.7 1.0 C1 D:3OH302 3.1 47.2 1.0 CD2 D:HIS90 3.1 40.0 1.0 CE1 D:HIS142 3.1 44.0 1.0 CE1 D:HIS90 3.1 42.5 1.0 CD2 D:HIS92 3.2 50.6 1.0 CD2 D:HIS142 3.2 37.2 1.0 C3 D:3OH302 3.2 53.3 1.0 C2 D:3OH302 3.6 51.8 1.0 OH D:TYR159 4.2 44.2 1.0 O2 D:3OH302 4.2 38.6 1.0 ND1 D:HIS92 4.2 51.7 1.0 ND1 D:HIS90 4.2 35.1 1.0 CG D:HIS90 4.3 36.5 1.0 ND1 D:HIS142 4.3 39.0 1.0 CG D:HIS92 4.3 49.2 1.0 CG D:HIS142 4.3 37.6 1.0 CG2 D:VAL144 4.7 39.6 1.0 NH1 D:ARG168 4.7 49.4 1.0 CE1 D:TYR159 5.0 39.8 1.0

Iron binding site 5 out of 12 in the Crystal Structure of Azotobacter Vinelandii 3-Mercaptopropionic Acid Dioxygenase in Complex with 3-Hydroxypropionic Acid


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 Azotobacter Vinelandii 3-Mercaptopropionic Acid Dioxygenase in Complex with 3-Hydroxypropionic Acid within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe301 b:49.5 occ:1.00 O3 E:3OH302 2.1 48.9 1.0 NE2 E:HIS142 2.2 50.1 1.0 O2 E:3OH302 2.2 55.0 1.0 NE2 E:HIS92 2.2 44.1 1.0 NE2 E:HIS90 2.2 46.8 1.0 CL E:CL303 2.4 62.6 1.0 C3 E:3OH302 2.9 57.5 1.0 C1 E:3OH302 3.0 57.4 1.0 CE1 E:HIS142 3.1 51.5 1.0 CE1 E:HIS92 3.1 49.3 1.0 CD2 E:HIS90 3.2 47.7 1.0 CD2 E:HIS142 3.2 49.8 1.0 CE1 E:HIS90 3.2 53.4 1.0 CD2 E:HIS92 3.2 42.4 1.0 C2 E:3OH302 3.3 58.0 1.0 OH E:TYR159 4.0 49.1 1.0 O1 E:3OH302 4.2 53.2 1.0 ND1 E:HIS142 4.2 48.9 1.0 ND1 E:HIS92 4.2 44.9 1.0 CG E:HIS142 4.3 49.6 1.0 ND1 E:HIS90 4.3 41.0 1.0 CG E:HIS90 4.3 44.4 1.0 CG E:HIS92 4.3 44.9 1.0 CG2 E:VAL144 4.7 51.9 1.0 NH1 E:ARG168 4.8 45.1 1.0 ND1 E:HIS157 4.8 44.0 1.0 CE1 E:TYR159 5.0 42.6 1.0 CZ E:TYR159 5.0 40.7 1.0 CE1 E:HIS157 5.0 37.6 1.0

Iron binding site 6 out of 12 in the Crystal Structure of Azotobacter Vinelandii 3-Mercaptopropionic Acid Dioxygenase in Complex with 3-Hydroxypropionic Acid


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 Azotobacter Vinelandii 3-Mercaptopropionic Acid Dioxygenase in Complex with 3-Hydroxypropionic Acid within 5.0Å range: probe atom residue distance (Å) B Occ F:Fe301 b:60.2 occ:1.00 NE2 F:HIS90 2.1 42.1 1.0 NE2 F:HIS92 2.1 85.9 1.0 O3 F:3OH302 2.1 65.8 1.0 O1 F:3OH302 2.2 68.4 1.0 NE2 F:HIS142 2.2 59.1 1.0 CL F:CL303 2.3 59.4 1.0 C1 F:3OH302 2.9 69.0 1.0 CD2 F:HIS90 3.0 49.0 1.0 CE1 F:HIS92 3.0 86.4 1.0 C3 F:3OH302 3.0 71.6 1.0 CE1 F:HIS90 3.1 44.2 1.0 CD2 F:HIS142 3.1 58.2 1.0 C2 F:3OH302 3.2 67.3 1.0 CE1 F:HIS142 3.2 57.1 1.0 CD2 F:HIS92 3.2 87.9 1.0 O2 F:3OH302 4.1 63.2 1.0 ND1 F:HIS90 4.2 48.9 1.0 CG F:HIS90 4.2 47.8 1.0 OH F:TYR159 4.2 79.1 1.0 ND1 F:HIS92 4.2 85.4 1.0 ND1 F:HIS142 4.3 54.2 1.0 CG F:HIS92 4.3 85.2 1.0 CG F:HIS142 4.3 57.9 1.0 NH1 F:ARG168 4.7 70.7 1.0 CG2 F:VAL144 4.8 46.9 1.0

Iron binding site 7 out of 12 in the Crystal Structure of Azotobacter Vinelandii 3-Mercaptopropionic Acid Dioxygenase in Complex with 3-Hydroxypropionic Acid


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 Azotobacter Vinelandii 3-Mercaptopropionic Acid Dioxygenase in Complex with 3-Hydroxypropionic Acid within 5.0Å range: probe atom residue distance (Å) B Occ G:Fe301 b:58.6 occ:1.00 O3 G:3OH302 2.1 51.2 1.0 O2 G:3OH302 2.2 65.6 1.0 NE2 G:HIS90 2.2 58.4 1.0 NE2 G:HIS92 2.2 54.5 1.0 NE2 G:HIS142 2.2 75.5 1.0 CL G:CL303 2.4 70.0 1.0 C1 G:3OH302 2.9 62.0 1.0 C3 G:3OH302 2.9 59.8 1.0 C2 G:3OH302 3.0 56.9 1.0 CE1 G:HIS92 3.1 58.5 1.0 CD2 G:HIS90 3.1 58.9 1.0 CE1 G:HIS90 3.2 57.0 1.0 CE1 G:HIS142 3.2 74.5 1.0 CD2 G:HIS92 3.2 61.2 1.0 CD2 G:HIS142 3.3 76.1 1.0 OH G:TYR159 4.1 52.2 1.0 O1 G:3OH302 4.1 57.4 1.0 ND1 G:HIS92 4.2 54.6 1.0 ND1 G:HIS90 4.3 54.7 1.0 CG G:HIS90 4.3 63.7 1.0 ND1 G:HIS142 4.3 71.8 1.0 CG G:HIS92 4.3 57.6 1.0 CG G:HIS142 4.4 73.0 1.0 NH1 G:ARG168 4.7 73.6 1.0 CG2 G:VAL144 4.8 49.6 1.0 CE1 G:TYR159 4.9 50.1 1.0 CZ G:TYR159 5.0 51.2 1.0

Iron binding site 8 out of 12 in the Crystal Structure of Azotobacter Vinelandii 3-Mercaptopropionic Acid Dioxygenase in Complex with 3-Hydroxypropionic Acid


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 Azotobacter Vinelandii 3-Mercaptopropionic Acid Dioxygenase in Complex with 3-Hydroxypropionic Acid within 5.0Å range: probe atom residue distance (Å) B Occ H:Fe301 b:52.2 occ:1.00 O1 H:3OH302 2.1 55.8 1.0 O3 H:3OH302 2.1 45.9 1.0 NE2 H:HIS90 2.2 41.9 1.0 NE2 H:HIS142 2.2 53.1 1.0 NE2 H:HIS92 2.2 36.5 1.0 CL H:CL303 2.4 72.2 1.0 C1 H:3OH302 2.7 47.1 1.0 C3 H:3OH302 2.8 46.9 1.0 CE1 H:HIS92 3.1 37.5 1.0 CE1 H:HIS142 3.1 54.3 1.0 CD2 H:HIS90 3.1 41.8 1.0 CE1 H:HIS90 3.1 42.6 1.0 CD2 H:HIS142 3.2 50.4 1.0 C2 H:3OH302 3.2 44.5 1.0 CD2 H:HIS92 3.2 41.4 1.0 O2 H:3OH302 3.7 44.9 1.0 OH H:TYR159 4.2 56.0 1.0 ND1 H:HIS92 4.2 36.5 1.0 ND1 H:HIS142 4.2 54.0 1.0 ND1 H:HIS90 4.2 36.1 1.0 CG H:HIS90 4.3 41.5 1.0 CG H:HIS142 4.3 50.3 1.0 CG H:HIS92 4.3 42.2 1.0 CG2 H:VAL144 4.7 51.4 1.0 NH1 H:ARG168 4.7 55.7 1.0 CE1 H:TYR159 5.0 43.9 1.0

Iron binding site 9 out of 12 in the Crystal Structure of Azotobacter Vinelandii 3-Mercaptopropionic Acid Dioxygenase in Complex with 3-Hydroxypropionic Acid


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 Azotobacter Vinelandii 3-Mercaptopropionic Acid Dioxygenase in Complex with 3-Hydroxypropionic Acid within 5.0Å range: probe atom residue distance (Å) B Occ I:Fe301 b:51.5 occ:1.00 NE2 I:HIS142 2.1 46.0 1.0 NE2 I:HIS90 2.1 38.8 1.0 O3 I:3OH302 2.1 49.8 1.0 O2 I:3OH302 2.1 55.7 1.0 NE2 I:HIS92 2.2 47.9 1.0 CL I:CL303 2.3 60.0 1.0 C1 I:3OH302 3.0 44.8 1.0 C3 I:3OH302 3.0 52.5 1.0 CE1 I:HIS142 3.1 51.7 1.0 CE1 I:HIS92 3.1 46.0 1.0 CD2 I:HIS90 3.1 41.1 1.0 CE1 I:HIS90 3.1 36.2 1.0 CD2 I:HIS142 3.1 50.3 1.0 CD2 I:HIS92 3.3 48.0 1.0 C2 I:3OH302 3.4 48.4 1.0 O1 I:3OH302 4.1 45.2 1.0 OH I:TYR159 4.2 57.5 1.0 ND1 I:HIS142 4.2 46.2 1.0 ND1 I:HIS90 4.2 35.5 1.0 ND1 I:HIS92 4.2 45.2 1.0 CG I:HIS90 4.2 39.8 1.0 CG I:HIS142 4.2 42.4 1.0 CG I:HIS92 4.4 44.6 1.0 CG2 I:VAL144 4.6 43.9 1.0 NH1 I:ARG168 4.8 59.0 1.0 ND1 I:HIS157 5.0 53.2 1.0

Iron binding site 10 out of 12 in the Crystal Structure of Azotobacter Vinelandii 3-Mercaptopropionic Acid Dioxygenase in Complex with 3-Hydroxypropionic Acid


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 Azotobacter Vinelandii 3-Mercaptopropionic Acid Dioxygenase in Complex with 3-Hydroxypropionic Acid within 5.0Å range: probe atom residue distance (Å) B Occ J:Fe301 b:53.4 occ:1.00 O3 J:3OH302 2.1 53.8 1.0 NE2 J:HIS92 2.2 50.1 1.0 NE2 J:HIS142 2.2 49.8 1.0 O1 J:3OH302 2.2 57.2 1.0 NE2 J:HIS90 2.2 48.6 1.0 CL J:CL303 2.4 58.7 1.0 C1 J:3OH302 3.0 50.1 1.0 CE1 J:HIS92 3.1 52.2 1.0 CE1 J:HIS142 3.1 53.5 1.0 CD2 J:HIS90 3.2 52.0 1.0 CE1 J:HIS90 3.2 54.1 1.0 CD2 J:HIS92 3.2 52.6 1.0 CD2 J:HIS142 3.2 48.2 1.0 C3 J:3OH302 3.3 60.0 1.0 C2 J:3OH302 3.5 52.0 1.0 OH J:TYR159 4.1 63.6 1.0 O2 J:3OH302 4.1 40.5 1.0 ND1 J:HIS92 4.2 46.4 1.0 ND1 J:HIS142 4.3 46.6 1.0 ND1 J:HIS90 4.3 53.1 1.0 CG J:HIS92 4.3 45.3 1.0 CG J:HIS90 4.3 49.5 1.0 CG J:HIS142 4.3 47.0 1.0 CG2 J:VAL144 4.7 39.1 1.0 NH1 J:ARG168 4.8 57.1 1.0 CE1 J:TYR159 4.9 43.7 1.0 CZ J:TYR159 5.0 49.4 1.0 ND1 J:HIS157 5.0 37.8 1.0

N.J.York, M.M.Lockart, S.Sardar, N.Khadka, W.Shi, R.E.Stenkamp, J.Zhang, P.D.Kiser, B.S.Pierce. Structure of 3-Mercaptopropionic Acid Dioxygenase with A Substrate Analog Reveals Bidentate Substrate Binding at the Iron Center J.Biol.Chem. 2021.
ISSN: ESSN 1083-351X