Iodine in PDB 9dq1: Crystal Structure of Hrmj From Streptomyces Sp. Cfmr 7 (Hrmj-Ssc) Complexed with Manganese (II), 2-Oxoglutarate and 6-Nitronorleucine

The structure of Crystal Structure of Hrmj From Streptomyces Sp. Cfmr 7 (Hrmj-Ssc) Complexed with Manganese (II), 2-Oxoglutarate and 6-Nitronorleucine, PDB code: 9dq1 was solved by Y.-C.Zheng, P.Swartz, W.-C.Chang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	17.49 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	44.342, 74.971, 87.295, 90, 90.03, 90
R / Rfree (%)	17.5 / 20.4

The structure of Crystal Structure of Hrmj From Streptomyces Sp. Cfmr 7 (Hrmj-Ssc) Complexed with Manganese (II), 2-Oxoglutarate and 6-Nitronorleucine also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

The binding sites of Iodine atom in the Crystal Structure of Hrmj From Streptomyces Sp. Cfmr 7 (Hrmj-Ssc) Complexed with Manganese (II), 2-Oxoglutarate and 6-Nitronorleucine (pdb code 9dq1). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 7 binding sites of Iodine where determined in the Crystal Structure of Hrmj From Streptomyces Sp. Cfmr 7 (Hrmj-Ssc) Complexed with Manganese (II), 2-Oxoglutarate and 6-Nitronorleucine, PDB code: 9dq1:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7;

Iodine binding site 1 out of 7 in the Crystal Structure of Hrmj From Streptomyces Sp. Cfmr 7 (Hrmj-Ssc) Complexed with Manganese (II), 2-Oxoglutarate and 6-Nitronorleucine


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Crystal Structure of Hrmj From Streptomyces Sp. Cfmr 7 (Hrmj-Ssc) Complexed with Manganese (II), 2-Oxoglutarate and 6-Nitronorleucine within 5.0Å range: probe atom residue distance (Å) B Occ A:I304 b:54.8 occ:1.00 O A:HOH602 3.1 43.0 1.0 O A:HOH627 3.1 35.5 1.0 CE A:LYS46 3.4 25.8 1.0 NZ A:LYS46 3.5 19.3 1.0 CD A:LYS58 3.6 27.8 1.0 CE A:LYS58 4.4 40.2 1.0 O A:HOH583 4.7 17.8 1.0 NZ A:LYS58 4.8 42.2 1.0 CD A:6HN307 4.8 42.9 1.0 CB A:LYS58 4.8 14.8 1.0 CG A:LYS58 4.8 24.1 1.0 O2 A:6HN307 4.8 19.8 1.0 CD A:LYS46 4.9 28.4 1.0 O A:HOH414 5.0 28.0 1.0

Iodine binding site 2 out of 7 in the Crystal Structure of Hrmj From Streptomyces Sp. Cfmr 7 (Hrmj-Ssc) Complexed with Manganese (II), 2-Oxoglutarate and 6-Nitronorleucine


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Crystal Structure of Hrmj From Streptomyces Sp. Cfmr 7 (Hrmj-Ssc) Complexed with Manganese (II), 2-Oxoglutarate and 6-Nitronorleucine within 5.0Å range: probe atom residue distance (Å) B Occ A:I305 b:67.7 occ:1.00 O A:HOH494 3.3 8.7 1.0 N A:GLY122 3.7 15.7 1.0 CA A:GLY122 3.8 17.8 1.0 O B:HOH557 4.0 28.1 1.0 C A:GLY122 4.1 18.2 1.0 CG A:PRO124 4.1 15.1 1.0 CD A:PRO124 4.3 10.0 1.0 N A:ARG123 4.3 10.4 1.0 CD2 A:LEU192 4.5 11.5 1.0 O A:GLY122 4.6 17.9 1.0 N A:PRO124 4.7 8.1 1.0 O A:ASP120 4.7 10.3 1.0 O B:HOH489 4.7 40.6 1.0 O A:HOH469 4.8 13.1 1.0 C A:GLY121 4.9 15.9 1.0

Iodine binding site 3 out of 7 in the Crystal Structure of Hrmj From Streptomyces Sp. Cfmr 7 (Hrmj-Ssc) Complexed with Manganese (II), 2-Oxoglutarate and 6-Nitronorleucine


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Crystal Structure of Hrmj From Streptomyces Sp. Cfmr 7 (Hrmj-Ssc) Complexed with Manganese (II), 2-Oxoglutarate and 6-Nitronorleucine within 5.0Å range: probe atom residue distance (Å) B Occ A:I306 b:27.4 occ:1.00 O A:HOH511 3.1 43.7 1.0 N A:GLY34 3.5 8.8 1.0 ND2 B:ASN35 3.7 7.4 1.0 CG A:PRO129 3.8 14.2 1.0 CB A:PRO129 3.8 8.8 1.0 CA A:MET33 4.0 8.6 1.0 ND2 A:ASN35 4.1 6.2 1.0 O A:HOH573 4.2 12.2 1.0 CG2 A:VAL74 4.3 14.8 1.0 C A:MET33 4.3 6.3 1.0 I B:IOD304 4.3 24.6 1.0 O B:HOH420 4.3 25.1 1.0 CB A:MET33 4.4 8.8 1.0 CB A:VAL74 4.4 11.9 1.0 CA A:GLY34 4.4 7.2 1.0 CG A:MET33 4.5 16.2 1.0 CE A:MET33 4.6 13.3 1.0 CG B:ASN35 4.6 6.8 1.0 OD1 B:ASN35 4.6 8.4 1.0 O A:TYR32 4.8 8.6 1.0 O A:HOH428 5.0 18.4 1.0 CG1 A:VAL74 5.0 13.4 1.0 N A:ASN35 5.0 4.6 1.0

Iodine binding site 4 out of 7 in the Crystal Structure of Hrmj From Streptomyces Sp. Cfmr 7 (Hrmj-Ssc) Complexed with Manganese (II), 2-Oxoglutarate and 6-Nitronorleucine


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Crystal Structure of Hrmj From Streptomyces Sp. Cfmr 7 (Hrmj-Ssc) Complexed with Manganese (II), 2-Oxoglutarate and 6-Nitronorleucine within 5.0Å range: probe atom residue distance (Å) B Occ B:I304 b:24.6 occ:1.00 CG B:MET33 3.6 17.1 0.6 N B:GLY34 3.6 9.7 1.0 ND2 A:ASN35 3.7 6.2 1.0 CG B:PRO129 3.7 17.2 1.0 CB B:PRO129 3.8 14.2 1.0 SD B:MET33 4.1 32.5 0.6 ND2 B:ASN35 4.1 7.4 1.0 O B:HOH515 4.1 13.4 1.0 CA B:MET33 4.1 10.1 0.6 CA B:MET33 4.1 10.1 0.4 O A:HOH428 4.3 18.4 1.0 CG2 B:VAL74 4.3 12.3 1.0 I A:IOD306 4.3 27.4 1.0 CB B:VAL74 4.3 15.3 1.0 C B:MET33 4.4 8.3 0.4 C B:MET33 4.4 8.3 0.6 CB B:MET33 4.5 10.0 0.6 CA B:GLY34 4.5 6.9 1.0 SD B:MET33 4.5 29.6 0.4 OD1 A:ASN35 4.5 9.6 1.0 CB B:MET33 4.6 10.0 0.4 CG A:ASN35 4.6 8.1 1.0 CE B:MET33 4.6 7.4 0.4 O A:HOH511 4.8 43.7 1.0 O B:TYR32 4.8 10.1 1.0 CG1 B:VAL74 4.9 15.8 1.0

Iodine binding site 5 out of 7 in the Crystal Structure of Hrmj From Streptomyces Sp. Cfmr 7 (Hrmj-Ssc) Complexed with Manganese (II), 2-Oxoglutarate and 6-Nitronorleucine


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Crystal Structure of Hrmj From Streptomyces Sp. Cfmr 7 (Hrmj-Ssc) Complexed with Manganese (II), 2-Oxoglutarate and 6-Nitronorleucine within 5.0Å range: probe atom residue distance (Å) B Occ B:I305 b:72.0 occ:1.00 O B:HOH510 3.0 36.2 1.0 CG B:GLU6 3.8 36.4 1.0 CE1 B:PHE8 3.9 16.8 1.0 CZ B:PHE8 4.1 25.0 1.0 CD1 B:TRP167 4.3 19.2 1.0 CE2 B:PHE166 4.3 18.7 1.0 CD2 B:PHE166 4.3 11.2 1.0 CB B:GLU6 4.3 29.2 1.0 CB B:TRP167 4.7 17.4 1.0 CG B:TRP167 4.9 18.7 1.0 CD B:GLU6 4.9 51.9 1.0 O B:PHE166 4.9 15.1 1.0

Iodine binding site 6 out of 7 in the Crystal Structure of Hrmj From Streptomyces Sp. Cfmr 7 (Hrmj-Ssc) Complexed with Manganese (II), 2-Oxoglutarate and 6-Nitronorleucine


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Crystal Structure of Hrmj From Streptomyces Sp. Cfmr 7 (Hrmj-Ssc) Complexed with Manganese (II), 2-Oxoglutarate and 6-Nitronorleucine within 5.0Å range: probe atom residue distance (Å) B Occ B:I306 b:84.0 occ:1.00 O B:HOH455 3.4 12.6 1.0 N B:GLY122 3.7 17.2 1.0 CA B:GLY122 3.8 22.3 1.0 O A:HOH585 3.9 32.3 1.0 C B:GLY122 4.1 17.2 1.0 CD B:PRO124 4.1 15.0 1.0 N B:ARG123 4.3 11.0 1.0 CD2 B:LEU192 4.4 18.4 1.0 CG B:PRO124 4.5 18.2 1.0 O B:GLY122 4.6 17.7 1.0 N B:PRO124 4.6 11.1 1.0 O B:HOH425 4.6 15.1 1.0 O B:ASP120 4.7 17.2 1.0 C B:GLY121 4.9 14.7 1.0

Iodine binding site 7 out of 7 in the Crystal Structure of Hrmj From Streptomyces Sp. Cfmr 7 (Hrmj-Ssc) Complexed with Manganese (II), 2-Oxoglutarate and 6-Nitronorleucine


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Crystal Structure of Hrmj From Streptomyces Sp. Cfmr 7 (Hrmj-Ssc) Complexed with Manganese (II), 2-Oxoglutarate and 6-Nitronorleucine within 5.0Å range: probe atom residue distance (Å) B Occ B:I307 b:105.5 occ:1.00 OG B:SER94 3.5 27.6 1.0 CB B:SER94 3.8 23.1 1.0 N B:TRP55 3.9 34.0 1.0 CB B:TRP55 4.1 32.9 1.0 CD1 B:TRP55 4.2 26.1 1.0 O B:TRP55 4.4 26.8 1.0 CA B:SER94 4.4 23.6 1.0 CA B:TRP55 4.5 31.8 1.0 CG B:TRP55 4.6 25.3 1.0 CA B:THR54 4.7 48.9 1.0 O B:HOH427 4.7 35.7 1.0 C B:THR54 4.7 37.7 1.0 O B:SER94 4.7 20.5 1.0 C B:TRP55 5.0 24.8 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