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Iron in PDB 7v4f: Unique Non-Heme Hydroxylase in Biosynthesis of Nucleoside Antibiotic Pathway Uncover Mechanism of Reaction

Protein crystallography data

The structure of Unique Non-Heme Hydroxylase in Biosynthesis of Nucleoside Antibiotic Pathway Uncover Mechanism of Reaction, PDB code: 7v4f was solved by T.L.Li, M.Z.Saeid, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.46 / 1.98
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 82.049, 82.049, 103.893, 90, 90, 90
R / Rfree (%) 19.1 / 25.1

Iron Binding Sites:

The binding sites of Iron atom in the Unique Non-Heme Hydroxylase in Biosynthesis of Nucleoside Antibiotic Pathway Uncover Mechanism of Reaction (pdb code 7v4f). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Unique Non-Heme Hydroxylase in Biosynthesis of Nucleoside Antibiotic Pathway Uncover Mechanism of Reaction, PDB code: 7v4f:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 7v4f

Go back to Iron Binding Sites List in 7v4f
Iron binding site 1 out of 4 in the Unique Non-Heme Hydroxylase in Biosynthesis of Nucleoside Antibiotic Pathway Uncover Mechanism of Reaction


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Unique Non-Heme Hydroxylase in Biosynthesis of Nucleoside Antibiotic Pathway Uncover Mechanism of Reaction within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe204

b:64.4
occ:1.00
O2 B:CO2203 1.9 34.5 1.0
OG1 B:5KC201 2.3 44.0 1.0
NE2 B:HIS115 2.3 25.6 1.0
OD1 B:ASP117 2.4 34.4 1.0
HG1 B:5KC201 2.6 52.8 1.0
OD2 B:ASP117 2.6 25.4 1.0
CG B:ASP117 2.8 29.8 1.0
CE1 B:HIS115 2.9 22.9 1.0
C B:CO2203 3.0 40.9 1.0
O B:5KC201 3.1 49.4 1.0
CB B:5KC201 3.3 49.3 1.0
CG2 B:5KC201 3.4 41.9 1.0
NE2 B:HIS160 3.5 23.4 1.0
CD2 B:HIS115 3.5 22.6 1.0
CE1 B:HIS160 3.6 21.1 1.0
C B:5KC201 3.7 49.8 1.0
CA B:5KC201 4.0 51.9 1.0
H1 B:5KC201 4.1 61.1 1.0
ND1 B:HIS115 4.1 22.6 1.0
O1 B:CO2203 4.2 40.5 1.0
CB B:ASP117 4.3 25.3 1.0
CG B:HIS115 4.5 20.0 1.0
N B:5KC201 4.6 50.9 1.0
O1 B:SIN202 4.6 36.3 1.0
OXT B:5KC201 4.7 46.7 1.0
CD2 B:HIS160 4.8 22.0 1.0
NAL B:5KC201 4.8 46.7 1.0
CD2 B:TYR112 4.8 28.4 1.0
N B:ASP117 4.9 18.1 1.0
ND1 B:HIS160 4.9 18.5 1.0
C1 B:SIN202 4.9 35.5 1.0
CB B:THR156 4.9 20.6 1.0
CA B:ASP117 5.0 22.0 1.0
CE2 B:TYR112 5.0 29.7 1.0

Iron binding site 2 out of 4 in 7v4f

Go back to Iron Binding Sites List in 7v4f
Iron binding site 2 out of 4 in the Unique Non-Heme Hydroxylase in Biosynthesis of Nucleoside Antibiotic Pathway Uncover Mechanism of Reaction


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Unique Non-Heme Hydroxylase in Biosynthesis of Nucleoside Antibiotic Pathway Uncover Mechanism of Reaction within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe205

b:42.5
occ:0.50
OD2 B:ASP92 2.4 22.2 1.0
OE1 B:GLU89 2.4 19.1 1.0
CG B:ASP92 3.4 23.2 1.0
CD B:GLU89 3.6 27.3 1.0
CB B:ASP92 3.9 25.8 1.0
OE2 B:GLU89 4.3 31.6 1.0
CA B:GLU89 4.3 27.0 1.0
OD1 B:ASP92 4.4 25.9 1.0
CB B:GLU89 4.5 26.4 1.0
CG B:GLU89 4.6 30.8 1.0
O B:HOH378 4.8 35.3 1.0
N B:GLU89 5.0 22.1 1.0

Iron binding site 3 out of 4 in 7v4f

Go back to Iron Binding Sites List in 7v4f
Iron binding site 3 out of 4 in the Unique Non-Heme Hydroxylase in Biosynthesis of Nucleoside Antibiotic Pathway Uncover Mechanism of Reaction


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Unique Non-Heme Hydroxylase in Biosynthesis of Nucleoside Antibiotic Pathway Uncover Mechanism of Reaction within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe202

b:65.9
occ:1.00
NE2 A:HIS160 2.6 25.5 1.0
OD2 A:ASP117 2.7 40.7 1.0
O1 A:SIN201 2.9 47.0 1.0
OD1 A:ASP117 3.0 39.1 1.0
NE2 A:HIS115 3.0 30.5 1.0
CE1 A:HIS160 3.2 24.3 1.0
CG A:ASP117 3.2 41.6 1.0
CE1 A:HIS115 3.3 23.7 1.0
OH A:TYR112 3.5 32.5 1.0
C1 A:SIN201 3.6 48.0 1.0
CD2 A:HIS160 3.8 22.8 1.0
CZ A:TYR112 3.9 25.8 1.0
O2 A:SIN201 4.0 36.9 1.0
CE1 A:TYR112 4.1 24.2 1.0
CD2 A:HIS115 4.2 27.7 1.0
CB A:THR156 4.4 29.1 1.0
ND1 A:HIS160 4.4 25.6 1.0
CG2 A:THR156 4.4 32.5 1.0
ND1 A:HIS115 4.5 27.8 1.0
C2 A:SIN201 4.5 32.2 1.0
CB A:ASP117 4.7 29.9 1.0
CE2 A:TYR112 4.8 23.0 1.0
CG A:HIS160 4.8 20.6 1.0
OG1 A:THR156 4.9 34.0 1.0
CG A:HIS115 5.0 26.5 1.0

Iron binding site 4 out of 4 in 7v4f

Go back to Iron Binding Sites List in 7v4f
Iron binding site 4 out of 4 in the Unique Non-Heme Hydroxylase in Biosynthesis of Nucleoside Antibiotic Pathway Uncover Mechanism of Reaction


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Unique Non-Heme Hydroxylase in Biosynthesis of Nucleoside Antibiotic Pathway Uncover Mechanism of Reaction within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe203

b:33.0
occ:1.00
O A:ASP140 2.4 20.7 1.0
O A:HOH340 2.5 28.7 1.0
O A:HOH336 2.6 32.1 1.0
C A:ASP140 3.5 20.4 1.0
CD A:LYS141 4.0 34.3 1.0
OD2 A:ASP140 4.0 31.4 1.0
CB A:ASP140 4.3 19.8 1.0
CG A:ASP140 4.3 23.1 1.0
NZ A:LYS141 4.3 42.3 1.0
N A:LYS141 4.4 17.7 1.0
CA A:LYS141 4.5 20.2 1.0
O A:HOH351 4.5 37.4 1.0
CA A:ASP140 4.5 23.3 1.0
O A:HIS139 4.6 22.4 1.0
CE A:LYS141 4.7 37.5 1.0

Reference:

S.M.Zadeh, M.H.Chen, Z.C.Wang, E.K.Astani, I.W.Lo, K.H.Lin, N.S.Hsu, K.Adhikari, S.Y.Lyu, H.Y.Tsai, Y.Terasawa, M.Yabe, K.Yamamoto, S.Ichikawa, T.L.Li. Beta-Hydroxylation of Alpha-Amino-Beta-Hydroxylbutanoyl-Glycyluridine Catalyzed By A Nonheme Hydroxylase Ensures the Maturation of Caprazamycin Commun Chem V. 5 87 2022.
ISSN: ESSN 2399-3669
DOI: 10.1038/S42004-022-00703-6
Page generated: Fri Aug 9 05:23:04 2024

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