Bromine 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:

Vanadium

(V)

2 atoms

The binding sites of Bromine 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 Bromine atom.
In total 4 binding sites of Bromine 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 Bromine binding site number: 1; 2; 3; 4;

Bromine binding site 1 out of 4 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 Bromine with other atoms in the Br 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:Br306 b:22.7 occ:1.00 O A:HOH643 1.9 20.8 1.0 CG1 A:VAL74 3.3 11.9 0.5 O B:HOH651 3.3 20.1 1.0 N A:GLY34 3.4 6.4 1.0 ND2 B:ASN35 3.4 7.8 1.0 CG A:MET33 3.7 15.4 0.4 CG A:PRO129 3.8 16.4 1.0 CB A:PRO129 3.9 18.0 1.0 ND2 A:ASN35 3.9 8.6 1.0 O A:HOH566 3.9 15.9 1.0 CA A:MET33 3.9 8.8 0.6 SD A:MET33 4.0 11.4 0.4 CA A:MET33 4.0 8.9 0.4 C A:MET33 4.2 7.7 1.0 CA A:GLY34 4.2 9.6 1.0 BR B:BR307 4.3 23.7 1.0 CG2 A:VAL74 4.3 12.8 0.5 CG B:ASN35 4.3 8.5 1.0 CB A:MET33 4.3 10.3 0.6 OD1 B:ASN35 4.3 8.6 1.0 CB A:MET33 4.4 10.3 0.4 CB A:VAL74 4.5 13.1 0.5 CB A:VAL74 4.5 13.5 0.5 CE A:MET33 4.6 15.5 0.6 O B:HOH557 4.6 23.9 1.0 CG A:MET33 4.6 8.2 0.6 O A:TYR32 4.7 12.2 1.0 CG1 B:VAL74 4.8 15.1 0.6 N A:ASN35 4.8 7.6 1.0 CG2 B:VAL74 4.9 18.6 0.4 CG2 A:VAL74 4.9 17.9 0.5 C A:GLY34 4.9 10.4 1.0

Bromine binding site 2 out of 4 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 Bromine with other atoms in the Br 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 A:Br307 b:35.8 occ:1.00 O A:HOH696 2.7 34.8 1.0 O A:HOH594 3.0 29.8 1.0 N A:THR170 3.3 12.2 1.0 CB A:THR170 3.9 12.3 1.0 O A:HOH626 4.0 40.7 1.0 O A:THR170 4.0 13.7 1.0 CA A:GLY169 4.1 10.5 1.0 CA A:THR170 4.1 11.7 1.0 OG1 A:THR170 4.1 13.3 1.0 C A:GLY169 4.2 12.2 1.0 C A:THR170 4.5 13.9 1.0 O A:HOH468 4.6 27.2 1.0 O A:HOH443 4.8 21.6 1.0 O A:HOH640 4.8 28.0 1.0

Bromine binding site 3 out of 4 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 Bromine with other atoms in the Br binding site number 3 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:Br308 b:43.8 occ:1.00 O A:HOH461 2.5 34.1 1.0 NZ A:LYS46 3.2 11.6 1.0 O A:HOH674 3.7 35.0 1.0 NZ A:LYS58 3.8 57.3 1.0 CD A:LYS46 3.8 10.9 1.0 CE A:LYS46 4.0 15.8 1.0 CE A:LYS58 4.2 44.5 1.0 CD A:LYS58 4.2 32.0 1.0 O A:HOH406 4.6 30.9 1.0

Bromine binding site 4 out of 4 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 Bromine with other atoms in the Br binding site number 4 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:Br307 b:23.7 occ:1.00 O B:HOH651 2.0 20.1 1.0 CG1 B:VAL74 3.3 15.1 0.6 N B:GLY34 3.3 7.6 1.0 CG2 B:VAL74 3.4 18.6 0.4 O A:HOH643 3.4 20.8 1.0 ND2 A:ASN35 3.4 8.6 1.0 CG B:PRO129 3.8 14.4 1.0 CA B:MET33 3.9 8.8 0.5 O B:HOH574 3.9 14.6 1.0 CB B:PRO129 3.9 14.4 1.0 ND2 B:ASN35 3.9 7.8 1.0 CA B:MET33 3.9 8.9 0.5 SD B:MET33 4.0 15.2 0.5 C B:MET33 4.1 8.6 1.0 CB B:MET33 4.2 10.9 0.5 CA B:GLY34 4.2 9.3 1.0 BR A:BR306 4.3 22.7 1.0 CG A:ASN35 4.3 8.8 1.0 OD1 A:ASN35 4.3 8.8 1.0 CE B:MET33 4.4 15.7 0.5 O A:HOH541 4.5 22.8 1.0 CB B:VAL74 4.5 11.7 0.4 CG B:MET33 4.5 10.8 0.5 CG1 B:VAL74 4.5 11.7 0.4 CB B:MET33 4.5 10.1 0.5 CB B:VAL74 4.6 13.1 0.6 O B:TYR32 4.7 12.4 1.0 N B:ASN35 4.8 6.8 1.0 CE B:MET33 4.8 15.4 0.5 C B:GLY34 4.9 8.2 1.0 CG1 A:VAL74 4.9 11.9 0.5 CG B:MET33 5.0 11.7 0.5

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