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Iron in PDB 9dqq: Crystal Structure of Hrmj From Streptomyces Sp. AG109_G2-6 (Hrmj-Ssa) Complexed with Ferric Iron(III) and 2-Oxoglutarate

Protein crystallography data

The structure of Crystal Structure of Hrmj From Streptomyces Sp. AG109_G2-6 (Hrmj-Ssa) Complexed with Ferric Iron(III) and 2-Oxoglutarate, PDB code: 9dqq 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) 17.68 / 2.45
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 96.871, 43.616, 126.201, 90, 106.95, 90
R / Rfree (%) 20.7 / 28

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Hrmj From Streptomyces Sp. AG109_G2-6 (Hrmj-Ssa) Complexed with Ferric Iron(III) and 2-Oxoglutarate (pdb code 9dqq). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 3 binding sites of Iron where determined in the Crystal Structure of Hrmj From Streptomyces Sp. AG109_G2-6 (Hrmj-Ssa) Complexed with Ferric Iron(III) and 2-Oxoglutarate, PDB code: 9dqq:
Jump to Iron binding site number: 1; 2; 3;

Iron binding site 1 out of 3 in 9dqq

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Iron binding site 1 out of 3 in the Crystal Structure of Hrmj From Streptomyces Sp. AG109_G2-6 (Hrmj-Ssa) Complexed with Ferric Iron(III) and 2-Oxoglutarate


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 Hrmj From Streptomyces Sp. AG109_G2-6 (Hrmj-Ssa) Complexed with Ferric Iron(III) and 2-Oxoglutarate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe302

b:37.5
occ:1.00
NE2 A:HIS210 2.1 34.2 1.0
O A:HOH423 2.1 39.0 1.0
OD1 A:ASP159 2.2 43.9 1.0
NE2 A:HIS157 2.2 45.7 1.0
O5 A:AKG301 2.4 47.5 1.0
O2 A:AKG301 2.7 61.4 1.0
CG A:ASP159 2.9 32.0 1.0
OD2 A:ASP159 3.0 31.2 1.0
CE1 A:HIS210 3.0 40.1 1.0
CE1 A:HIS157 3.1 43.9 1.0
CD2 A:HIS210 3.1 36.8 1.0
CD2 A:HIS157 3.1 41.9 1.0
C2 A:AKG301 3.2 58.0 1.0
C1 A:AKG301 3.4 65.1 1.0
ND1 A:HIS210 4.2 35.1 1.0
ND1 A:HIS157 4.2 41.5 1.0
CG A:HIS157 4.2 46.4 1.0
CG A:HIS210 4.2 39.8 1.0
CB A:ASP159 4.4 28.8 1.0
C3 A:AKG301 4.7 50.7 1.0
O1 A:AKG301 4.7 61.0 1.0
CA A:ASP159 4.9 37.5 1.0
N A:ASP159 4.9 40.2 1.0
CZ2 A:TRP203 5.0 29.7 1.0
O A:HOH477 5.0 38.1 1.0
O A:HOH405 5.0 56.6 1.0

Iron binding site 2 out of 3 in 9dqq

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Iron binding site 2 out of 3 in the Crystal Structure of Hrmj From Streptomyces Sp. AG109_G2-6 (Hrmj-Ssa) Complexed with Ferric Iron(III) and 2-Oxoglutarate


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 Hrmj From Streptomyces Sp. AG109_G2-6 (Hrmj-Ssa) Complexed with Ferric Iron(III) and 2-Oxoglutarate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe303

b:118.8
occ:1.00
NH1 B:ARG67 2.0 40.3 0.5
OG1 A:THR195 2.5 40.0 1.0
OD2 A:ASP199 2.5 38.8 1.0
O B:ARG67 2.9 45.4 0.5
O B:ARG67 2.9 44.3 0.5
CZ B:ARG67 3.2 44.6 0.5
CG A:ASP199 3.5 27.4 1.0
O A:CYS193 3.5 29.3 1.0
CB A:THR195 3.8 38.7 1.0
N A:THR195 3.8 27.0 1.0
NH2 B:ARG67 3.8 37.6 0.5
OD1 A:ASP199 3.9 32.1 1.0
C B:ARG67 4.1 38.7 0.5
C B:ARG67 4.1 37.6 0.5
CG2 A:THR195 4.2 41.8 1.0
N A:GLU196 4.2 34.2 1.0
CA A:THR195 4.3 30.2 1.0
NE B:ARG67 4.3 47.4 0.5
CA B:THR68 4.4 33.9 1.0
CD B:ARG67 4.6 44.8 0.5
CB A:ASP199 4.7 35.6 1.0
C A:CYS193 4.7 29.6 1.0
N B:THR68 4.7 33.1 1.0
C A:THR195 4.7 27.1 1.0
CG A:GLU196 4.7 46.7 1.0
C A:LEU194 4.8 27.6 1.0
C B:THR68 4.9 40.2 1.0
CA A:LEU194 4.9 29.5 1.0
O B:THR68 4.9 28.4 1.0
CB A:GLU196 5.0 31.6 1.0
CB A:PRO18 5.0 36.4 1.0

Iron binding site 3 out of 3 in 9dqq

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Iron binding site 3 out of 3 in the Crystal Structure of Hrmj From Streptomyces Sp. AG109_G2-6 (Hrmj-Ssa) Complexed with Ferric Iron(III) and 2-Oxoglutarate


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 Hrmj From Streptomyces Sp. AG109_G2-6 (Hrmj-Ssa) Complexed with Ferric Iron(III) and 2-Oxoglutarate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:69.8
occ:1.00
O5 B:AKG301 2.1 68.0 1.0
OD1 B:ASP159 2.2 69.3 1.0
NE2 B:HIS210 2.2 55.7 1.0
O2 B:AKG301 2.5 62.4 1.0
OD2 B:ASP159 2.6 67.2 1.0
CG B:ASP159 2.8 66.6 1.0
C2 B:AKG301 2.9 78.5 1.0
NE2 B:HIS157 2.9 68.7 1.0
CE1 B:HIS210 3.0 56.1 1.0
CE1 B:HIS157 3.1 73.2 1.0
C1 B:AKG301 3.1 74.4 1.0
CD2 B:HIS210 3.3 55.7 1.0
CD2 B:HIS157 4.1 68.8 1.0
ND1 B:HIS210 4.2 54.8 1.0
ND1 B:HIS157 4.2 75.5 1.0
CB B:ASP159 4.3 66.7 1.0
CG B:HIS210 4.3 61.1 1.0
O1 B:AKG301 4.4 69.5 1.0
C3 B:AKG301 4.4 73.1 1.0
OE1 B:GLU154 4.7 91.0 1.0
CG B:HIS157 4.7 69.5 1.0
CA B:ASP159 4.9 67.7 1.0
N B:ASP159 5.0 72.6 1.0
C4 B:AKG301 5.0 66.0 1.0

Reference:

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
Page generated: Tue Feb 25 09:58:27 2025

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