Vanadium in PDB 9dq2: Crystal Structure of Hrmj From Streptomyces Sp. Cfmr 7 (Hrmj-Ssc) Complexed with Vanadyl(IV)-Oxo, Succinate and 6-Nitronorleucine

The structure of Crystal Structure of Hrmj From Streptomyces Sp. Cfmr 7 (Hrmj-Ssc) Complexed with Vanadyl(IV)-Oxo, Succinate and 6-Nitronorleucine, PDB code: 9dq2 was solved by Y.-C.Zheng, W.-C.Chang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.36 / 1.55
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	75.113, 78.836, 97.166, 90, 90, 90
R / Rfree (%)	19.6 / 21.1

The structure of Crystal Structure of Hrmj From Streptomyces Sp. Cfmr 7 (Hrmj-Ssc) Complexed with Vanadyl(IV)-Oxo, Succinate and 6-Nitronorleucine also contains other interesting chemical elements:

Bromine

(Br)

4 atoms

The binding sites of Vanadium atom in the Crystal Structure of Hrmj From Streptomyces Sp. Cfmr 7 (Hrmj-Ssc) Complexed with Vanadyl(IV)-Oxo, Succinate and 6-Nitronorleucine (pdb code 9dq2). This binding sites where shown within 5.0 Angstroms radius around Vanadium atom.
In total 2 binding sites of Vanadium where determined in the Crystal Structure of Hrmj From Streptomyces Sp. Cfmr 7 (Hrmj-Ssc) Complexed with Vanadyl(IV)-Oxo, Succinate and 6-Nitronorleucine, PDB code: 9dq2:
Jump to Vanadium binding site number: 1; 2;

Vanadium binding site 1 out of 2 in the Crystal Structure of Hrmj From Streptomyces Sp. Cfmr 7 (Hrmj-Ssc) Complexed with Vanadyl(IV)-Oxo, Succinate and 6-Nitronorleucine


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 1 of Crystal Structure of Hrmj From Streptomyces Sp. Cfmr 7 (Hrmj-Ssc) Complexed with Vanadyl(IV)-Oxo, Succinate and 6-Nitronorleucine within 5.0Å range: probe atom residue distance (Å) B Occ A:V302 b:10.9 occ:1.00 V1 A:VVO302 0.0 10.9 1.0 O1 A:VVO302 1.6 13.4 1.0 O1 A:SIN303 2.1 11.6 1.0 OD1 A:ASP135 2.2 10.5 1.0 O A:HOH419 2.2 17.2 1.0 NE2 A:HIS133 2.2 11.5 1.0 NE2 A:HIS186 2.3 10.9 1.0 C1 A:SIN303 3.0 20.6 1.0 CG A:ASP135 3.1 16.8 1.0 O2 A:SIN303 3.1 23.9 1.0 CE1 A:HIS133 3.2 9.9 1.0 CE1 A:HIS186 3.2 11.3 1.0 CD2 A:HIS133 3.2 11.1 1.0 OD2 A:ASP135 3.3 16.8 1.0 CD2 A:HIS186 3.3 10.1 1.0 O A:HOH413 3.9 30.7 1.0 ND1 A:HIS133 4.3 8.9 1.0 ND1 A:HIS186 4.3 10.8 1.0 CG A:HIS133 4.3 9.9 1.0 C2 A:SIN303 4.4 16.4 1.0 CG A:HIS186 4.4 8.2 1.0 CB A:ASP135 4.5 11.8 1.0 CG A:6HN301 4.6 19.1 1.0 N A:6HN301 4.6 20.2 1.0 CA A:ASP135 4.9 8.6 1.0 N A:ASP135 5.0 8.9 1.0

Vanadium binding site 2 out of 2 in the Crystal Structure of Hrmj From Streptomyces Sp. Cfmr 7 (Hrmj-Ssc) Complexed with Vanadyl(IV)-Oxo, Succinate and 6-Nitronorleucine


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 2 of Crystal Structure of Hrmj From Streptomyces Sp. Cfmr 7 (Hrmj-Ssc) Complexed with Vanadyl(IV)-Oxo, Succinate and 6-Nitronorleucine within 5.0Å range: probe atom residue distance (Å) B Occ B:V302 b:10.9 occ:1.00 V1 B:VVO302 0.0 10.9 1.0 O1 B:VVO302 1.6 13.0 1.0 O B:HOH428 2.1 14.1 1.0 OD1 B:ASP135 2.1 10.1 1.0 O3 B:SIN303 2.1 14.5 1.0 NE2 B:HIS133 2.2 10.4 1.0 NE2 B:HIS186 2.3 11.1 1.0 C4 B:SIN303 3.0 20.7 1.0 O4 B:SIN303 3.1 23.3 1.0 CG B:ASP135 3.1 14.8 1.0 CE1 B:HIS186 3.2 12.3 1.0 CD2 B:HIS133 3.2 11.0 1.0 CE1 B:HIS133 3.2 9.2 1.0 CD2 B:HIS186 3.3 8.8 1.0 OD2 B:ASP135 3.3 16.8 1.0 O B:HOH407 4.0 30.2 1.0 ND1 B:HIS186 4.3 10.7 1.0 ND1 B:HIS133 4.3 9.7 1.0 CG B:HIS133 4.4 8.2 1.0 C3 B:SIN303 4.4 16.7 1.0 CG B:HIS186 4.4 7.5 1.0 CB B:ASP135 4.5 11.2 1.0 CG B:6HN301 4.6 17.3 1.0 N B:6HN301 4.6 23.2 1.0 CA B:ASP135 4.9 10.3 1.0 N B:ASP135 5.0 8.8 1.0

Y.C.Zheng, X.Li, L.Cha, J.C.Paris, C.Michael, R.Ushimaru, Y.Ogasawara, I.Abe, Y.Guo, W.C.Chang. Comparison of A Nonheme Iron Cyclopropanase with A Homologous Hydroxylase Reveals Mechanistic Features Associated with Distinct Reaction Outcomes. J.Am.Chem.Soc. 2025.
ISSN: ESSN 1520-5126
PubMed: 39901767
DOI: 10.1021/JACS.4C17741