Iron in PDB 7kov: Crystal Structure of Azotobacter Vinelandii 3-Mercaptopropionic Acid Dioxygenase in Complex with Thiocyanate

The structure of Crystal Structure of Azotobacter Vinelandii 3-Mercaptopropionic Acid Dioxygenase in Complex with Thiocyanate, PDB code: 7kov was solved by P.D.Kiser, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.88 / 2.95
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	102.182, 102.182, 301.935, 90, 90, 120
R / Rfree (%)	21.5 / 24.1

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

Chlorine

(Cl)

2 atoms

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

Iron binding site 1 out of 4 in the Crystal Structure of Azotobacter Vinelandii 3-Mercaptopropionic Acid Dioxygenase in Complex with Thiocyanate


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 Thiocyanate within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:81.0 occ:1.00 NE2 B:HIS92 2.2 73.8 1.0 N B:SCN302 2.2 105.2 1.0 NE2 B:HIS90 2.2 80.5 1.0 NE2 B:HIS142 2.2 80.8 1.0 O B:HOH405 2.2 77.9 1.0 O B:HOH404 2.5 63.9 1.0 CE1 B:HIS142 3.0 83.6 1.0 CD2 B:HIS92 3.2 78.7 1.0 CD2 B:HIS90 3.2 82.0 1.0 CE1 B:HIS92 3.2 78.0 1.0 CE1 B:HIS90 3.2 78.3 1.0 CD2 B:HIS142 3.3 79.8 1.0 C B:SCN302 3.3 115.4 1.0 OH B:TYR159 4.0 76.8 1.0 ND1 B:HIS142 4.2 81.1 1.0 ND1 B:HIS92 4.3 76.8 1.0 ND1 B:HIS90 4.3 78.5 1.0 CG B:HIS92 4.3 80.2 1.0 CG B:HIS90 4.3 84.8 1.0 CG B:HIS142 4.4 81.3 1.0 CG2 B:VAL144 4.6 92.3 1.0 ND1 B:HIS157 4.8 86.5 1.0 CE1 B:TYR159 4.8 82.7 1.0 NH1 B:ARG168 4.8 94.6 1.0 CZ B:TYR159 4.9 80.8 1.0 CE1 B:HIS157 4.9 87.8 1.0 S B:SCN302 4.9 126.7 1.0

Iron binding site 2 out of 4 in the Crystal Structure of Azotobacter Vinelandii 3-Mercaptopropionic Acid Dioxygenase in Complex with Thiocyanate


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 Thiocyanate within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:85.4 occ:1.00 N A:SCN302 2.2 88.8 1.0 NE2 A:HIS90 2.2 71.8 1.0 NE2 A:HIS92 2.2 96.1 1.0 O A:HOH403 2.2 82.1 1.0 NE2 A:HIS142 2.2 91.3 1.0 O A:HOH402 2.5 59.7 1.0 CE1 A:HIS142 3.1 93.6 1.0 CD2 A:HIS92 3.2 95.0 1.0 CD2 A:HIS90 3.2 75.3 1.0 CE1 A:HIS90 3.2 73.5 1.0 CE1 A:HIS92 3.2 98.8 1.0 CD2 A:HIS142 3.3 89.5 1.0 C A:SCN302 3.3 107.5 1.0 OH A:TYR159 3.9 91.7 1.0 ND1 A:HIS142 4.2 89.2 1.0 ND1 A:HIS90 4.3 73.5 1.0 ND1 A:HIS92 4.3 94.9 1.0 CG A:HIS90 4.3 79.6 1.0 CG A:HIS92 4.3 93.6 1.0 CG A:HIS142 4.4 89.2 1.0 ND1 A:HIS157 4.7 92.1 1.0 CG2 A:VAL144 4.7 89.4 1.0 CE1 A:TYR159 4.8 95.8 1.0 NH1 A:ARG168 4.8 104.2 1.0 CZ A:TYR159 4.8 91.3 1.0 CE1 A:HIS157 4.8 93.5 1.0 S A:SCN302 4.9 123.7 1.0

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


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 Thiocyanate within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe301 b:83.0 occ:1.00 NE2 C:HIS92 2.2 95.2 1.0 N C:SCN302 2.2 133.0 1.0 NE2 C:HIS90 2.2 84.0 1.0 NE2 C:HIS142 2.2 90.7 1.0 O C:HOH406 2.2 87.1 1.0 O C:HOH404 2.5 65.9 1.0 CE1 C:HIS142 3.0 91.9 1.0 CD2 C:HIS92 3.2 98.4 1.0 CD2 C:HIS90 3.2 83.2 1.0 CE1 C:HIS90 3.2 84.0 1.0 CE1 C:HIS92 3.2 99.2 1.0 CD2 C:HIS142 3.3 94.2 1.0 C C:SCN302 3.3 138.6 1.0 OH C:TYR159 3.9 90.4 1.0 ND1 C:HIS142 4.2 89.1 1.0 ND1 C:HIS90 4.3 82.5 1.0 ND1 C:HIS92 4.3 97.5 1.0 CG C:HIS92 4.3 99.7 1.0 CG C:HIS90 4.3 86.2 1.0 CG C:HIS142 4.4 92.1 1.0 CG2 C:VAL144 4.7 87.5 1.0 ND1 C:HIS157 4.8 87.6 1.0 CE1 C:TYR159 4.8 87.8 1.0 NH1 C:ARG168 4.8 97.2 1.0 CZ C:TYR159 4.9 88.6 1.0 CE1 C:HIS157 4.9 86.1 1.0 S C:SCN302 4.9 140.1 1.0 O C:HOH405 4.9 79.0 1.0

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


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 Thiocyanate within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe301 b:94.6 occ:1.00 NE2 D:HIS90 2.2 86.8 1.0 N D:SCN302 2.2 126.6 1.0 NE2 D:HIS142 2.2 100.7 1.0 NE2 D:HIS92 2.2 91.4 1.0 O D:HOH407 2.2 88.8 1.0 O D:HOH406 2.5 60.9 1.0 CE1 D:HIS142 3.1 103.0 1.0 CD2 D:HIS90 3.2 86.4 1.0 CD2 D:HIS92 3.2 92.3 1.0 CE1 D:HIS90 3.2 90.0 1.0 CE1 D:HIS92 3.2 93.3 1.0 CD2 D:HIS142 3.3 102.3 1.0 C D:SCN302 3.3 128.3 1.0 OH D:TYR159 4.0 93.4 1.0 ND1 D:HIS142 4.2 99.6 1.0 ND1 D:HIS90 4.3 89.3 1.0 ND1 D:HIS92 4.3 89.0 1.0 CG D:HIS90 4.3 90.1 1.0 CG D:HIS92 4.3 89.4 1.0 CG D:HIS142 4.4 103.2 1.0 CG2 D:VAL144 4.6 105.5 1.0 ND1 D:HIS157 4.8 113.2 1.0 CE1 D:TYR159 4.8 93.9 1.0 NH1 D:ARG168 4.8 104.8 1.0 S D:SCN302 4.8 126.7 1.0 CZ D:TYR159 4.9 90.5 1.0 O D:HOH408 4.9 75.3 1.0 CE1 D:HIS157 4.9 116.1 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