Vanadium in PDB 9dqr: Crystal Structure of Hrmj From Streptomyces Sp. AG109_G2-6 (Hrmj-Ssa) Complexed with Vanadyl(IV)-Oxo and Succinate

The structure of Crystal Structure of Hrmj From Streptomyces Sp. AG109_G2-6 (Hrmj-Ssa) Complexed with Vanadyl(IV)-Oxo and Succinate, PDB code: 9dqr 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)	40.36 / 2.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	98.622, 44.668, 126.433, 90, 107.11, 90
R / Rfree (%)	17.6 / 21.1

The binding sites of Vanadium atom in the Crystal Structure of Hrmj From Streptomyces Sp. AG109_G2-6 (Hrmj-Ssa) Complexed with Vanadyl(IV)-Oxo and Succinate (pdb code 9dqr). 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. AG109_G2-6 (Hrmj-Ssa) Complexed with Vanadyl(IV)-Oxo and Succinate, PDB code: 9dqr:
Jump to Vanadium binding site number: 1; 2;

Vanadium binding site 1 out of 2 in the Crystal Structure of Hrmj From Streptomyces Sp. AG109_G2-6 (Hrmj-Ssa) Complexed with Vanadyl(IV)-Oxo and Succinate


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. AG109_G2-6 (Hrmj-Ssa) Complexed with Vanadyl(IV)-Oxo and Succinate within 5.0Å range: probe atom residue distance (Å) B Occ A:V302 b:20.0 occ:1.00 V1 A:VVO302 0.0 20.0 1.0 O1 A:VVO302 1.6 31.2 1.0 O2 A:SIN301 2.1 38.1 1.0 OD1 A:ASP159 2.2 17.8 1.0 NE2 A:HIS210 2.3 20.8 1.0 NE2 A:HIS157 2.4 28.8 1.0 O A:HOH414 2.4 22.8 1.0 C1 A:SIN301 3.0 65.8 1.0 O1 A:SIN301 3.1 72.4 1.0 CD2 A:HIS157 3.2 23.2 1.0 CG A:ASP159 3.2 21.9 1.0 CD2 A:HIS210 3.3 19.4 1.0 CE1 A:HIS210 3.3 18.1 1.0 OD2 A:ASP159 3.4 19.0 1.0 CE1 A:HIS157 3.5 28.0 1.0 CG A:HIS157 4.4 25.1 1.0 C2 A:SIN301 4.4 56.9 1.0 ND1 A:HIS210 4.4 16.1 1.0 CG A:HIS210 4.4 18.0 1.0 ND1 A:HIS157 4.5 28.4 1.0 CB A:ASP159 4.6 17.9 1.0 N A:ASP159 4.9 20.2 1.0 C3 A:SIN301 4.9 54.7 1.0 CA A:ASP159 4.9 17.6 1.0 O A:HOH592 5.0 45.0 1.0

Vanadium binding site 2 out of 2 in the Crystal Structure of Hrmj From Streptomyces Sp. AG109_G2-6 (Hrmj-Ssa) Complexed with Vanadyl(IV)-Oxo and Succinate


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. AG109_G2-6 (Hrmj-Ssa) Complexed with Vanadyl(IV)-Oxo and Succinate within 5.0Å range: probe atom residue distance (Å) B Occ B:V302 b:28.8 occ:1.00 V1 B:VVO302 0.0 28.8 1.0 O1 B:VVO302 1.6 41.7 1.0 ND2 B:ASN86 2.1 33.8 1.0 OD1 B:ASP159 2.4 32.3 1.0 NE2 B:HIS210 2.4 32.4 1.0 OD1 B:ASN84 2.4 35.5 1.0 NE2 B:HIS157 2.5 35.4 1.0 CE1 B:HIS210 3.1 35.2 1.0 CG B:ASN86 3.2 41.3 1.0 CG B:ASP159 3.3 38.9 1.0 CE1 B:HIS157 3.3 45.0 1.0 CD2 B:HIS210 3.4 34.1 1.0 OD2 B:ASP159 3.5 39.3 1.0 CD2 B:HIS157 3.5 39.8 1.0 CG B:ASN84 3.5 50.3 1.0 OD1 B:ASN86 3.6 48.4 1.0 ND2 B:ASN84 3.9 46.3 1.0 O B:ASN84 4.1 47.0 1.0 ND1 B:HIS210 4.3 31.1 1.0 ND1 B:HIS157 4.5 40.1 1.0 CG B:HIS210 4.5 30.4 1.0 CB B:ASN86 4.5 44.3 1.0 CG B:HIS157 4.6 42.0 1.0 O2 B:SIN301 4.7 53.6 1.0 CB B:ASP159 4.7 28.2 1.0 N B:ASN84 4.7 35.6 1.0 C B:ASN84 4.8 38.4 1.0 CB B:ASN84 4.8 41.2 1.0 N B:ASN86 4.9 46.3 1.0 CA B:ASN86 4.9 44.2 1.0 N B:ASP159 4.9 33.3 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