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Iron in PDB 6b9t: Crystal Structure of Mpns with Substrate 2-Hydroxyethylphosphonate (2- Hep) and Fe(II) Bound

Enzymatic activity of Crystal Structure of Mpns with Substrate 2-Hydroxyethylphosphonate (2- Hep) and Fe(II) Bound

All present enzymatic activity of Crystal Structure of Mpns with Substrate 2-Hydroxyethylphosphonate (2- Hep) and Fe(II) Bound:
1.13.11.73;

Protein crystallography data

The structure of Crystal Structure of Mpns with Substrate 2-Hydroxyethylphosphonate (2- Hep) and Fe(II) Bound, PDB code: 6b9t was solved by D.A.Born, C.L.Drennan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.10 / 2.35
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 70.850, 351.250, 76.870, 90.00, 103.36, 90.00
R / Rfree (%) 19 / 23.8

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Mpns with Substrate 2-Hydroxyethylphosphonate (2- Hep) and Fe(II) Bound (pdb code 6b9t). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 9 binding sites of Iron where determined in the Crystal Structure of Mpns with Substrate 2-Hydroxyethylphosphonate (2- Hep) and Fe(II) Bound, PDB code: 6b9t:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Iron binding site 1 out of 9 in 6b9t

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Iron binding site 1 out of 9 in the Crystal Structure of Mpns with Substrate 2-Hydroxyethylphosphonate (2- Hep) and Fe(II) Bound


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 Mpns with Substrate 2-Hydroxyethylphosphonate (2- Hep) and Fe(II) Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:43.2
occ:1.00
 O2 A:2HE502 1.8 42.0 1.0
O4 A:2HE502 1.9 41.7 1.0
NE2 A:HIS148 2.1 38.9 1.0
NE2 A:HIS190 2.1 38.8 1.0
OE1 A:GLN152 2.3 38.2 1.0
O A:HOH601 2.6 37.2 1.0
CE1 A:HIS190 2.9 38.9 1.0
CE1 A:HIS148 3.0 40.5 1.0
CD2 A:HIS148 3.1 38.6 1.0
CB A:2HE502 3.1 45.4 1.0
P A:2HE502 3.2 39.4 1.0
CD A:GLN152 3.3 35.7 1.0
CD2 A:HIS190 3.3 38.8 1.0
CA A:2HE502 3.5 38.8 1.0
NE2 A:GLN152 3.7 35.7 1.0
NZ B:LYS28 3.8 42.2 1.0
ND2 A:ASN145 4.1 39.7 1.0
ND1 A:HIS190 4.1 36.4 1.0
O3 A:2HE502 4.1 38.3 1.0
ND1 A:HIS148 4.2 36.4 1.0
O1 A:2HE502 4.2 40.9 1.0
CG A:HIS148 4.2 39.0 1.0
CG A:HIS190 4.3 37.5 1.0
CG A:GLN152 4.6 34.9 1.0
CE B:LYS28 4.8 40.8 1.0
CB A:GLN152 5.0 36.3 1.0

Iron binding site 2 out of 9 in 6b9t

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Iron binding site 2 out of 9 in the Crystal Structure of Mpns with Substrate 2-Hydroxyethylphosphonate (2- Hep) and Fe(II) Bound


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 Mpns with Substrate 2-Hydroxyethylphosphonate (2- Hep) and Fe(II) Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:40.1
occ:1.00
 O4 B:2HE503 2.0 41.8 1.0
O3 B:2HE503 2.1 38.5 1.0
OE1 B:GLN152 2.1 36.6 1.0
NE2 B:HIS148 2.2 40.2 1.0
NE2 B:HIS190 2.2 38.6 1.0
O B:HOH621 2.4 30.4 1.0
CD2 B:HIS148 2.9 38.5 1.0
CD B:GLN152 3.1 39.1 1.0
CE1 B:HIS190 3.1 39.3 1.0
CB B:2HE503 3.2 42.5 1.0
CD2 B:HIS190 3.3 37.7 1.0
P B:2HE503 3.3 43.4 1.0
CE1 B:HIS148 3.3 37.5 1.0
NE2 B:GLN152 3.4 37.4 1.0
CA B:2HE503 3.5 38.1 1.0
NZ A:LYS28 3.6 38.2 1.0
O1 B:2HE503 4.0 40.0 1.0
ND2 B:ASN145 4.1 40.3 1.0
CG B:HIS148 4.2 38.1 1.0
ND1 B:HIS190 4.3 38.7 1.0
ND1 B:HIS148 4.3 38.1 1.0
CG B:HIS190 4.4 38.9 1.0
CG B:GLN152 4.5 38.4 1.0
O2 B:2HE503 4.5 44.9 1.0
CE A:LYS28 4.7 43.3 1.0
CB B:GLN152 4.9 38.9 1.0

Iron binding site 3 out of 9 in 6b9t

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Iron binding site 3 out of 9 in the Crystal Structure of Mpns with Substrate 2-Hydroxyethylphosphonate (2- Hep) and Fe(II) Bound


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 Mpns with Substrate 2-Hydroxyethylphosphonate (2- Hep) and Fe(II) Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe502

b:60.7
occ:1.00
 O B:HOH609 2.0 52.7 1.0
OE1 B:GLU159 3.2 52.7 1.0
O B:HOH707 3.4 39.1 1.0
CD B:GLU159 4.0 51.5 1.0
NE B:ARG195 4.1 40.9 1.0
NH1 B:ARG195 4.5 39.9 1.0
OE2 B:GLU159 4.6 51.8 1.0
CZ B:ARG195 4.8 40.3 1.0
CG B:GLU159 4.9 47.0 1.0

Iron binding site 4 out of 9 in 6b9t

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Iron binding site 4 out of 9 in the Crystal Structure of Mpns with Substrate 2-Hydroxyethylphosphonate (2- Hep) and Fe(II) Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of Mpns with Substrate 2-Hydroxyethylphosphonate (2- Hep) and Fe(II) Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe501

b:38.2
occ:1.00
 O4 C:2HE502 2.0 39.3 1.0
NE2 C:HIS148 2.1 35.4 1.0
OE1 C:GLN152 2.1 33.9 1.0
NE2 C:HIS190 2.2 38.6 1.0
O2 C:2HE502 2.2 42.1 1.0
O C:HOH601 2.5 37.5 1.0
CE1 C:HIS190 2.9 35.8 1.0
CD2 C:HIS148 3.0 35.6 1.0
CE1 C:HIS148 3.1 32.7 1.0
CD C:GLN152 3.2 33.8 1.0
CB C:2HE502 3.3 42.9 1.0
CD2 C:HIS190 3.3 36.5 1.0
P C:2HE502 3.4 43.5 1.0
NE2 C:GLN152 3.7 38.2 1.0
CA C:2HE502 3.7 37.1 1.0
NZ D:LYS28 3.8 39.5 1.0
ND2 C:ASN145 4.1 35.4 1.0
ND1 C:HIS190 4.1 34.0 1.0
CG C:HIS148 4.2 34.1 1.0
ND1 C:HIS148 4.2 32.3 1.0
CG C:HIS190 4.4 35.8 1.0
O1 C:2HE502 4.5 38.5 1.0
O3 C:2HE502 4.5 36.7 1.0
CG C:GLN152 4.5 33.2 1.0
CB C:GLN152 4.8 31.1 1.0
CE D:LYS28 4.8 37.9 1.0

Iron binding site 5 out of 9 in 6b9t

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Iron binding site 5 out of 9 in the Crystal Structure of Mpns with Substrate 2-Hydroxyethylphosphonate (2- Hep) and Fe(II) Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of Mpns with Substrate 2-Hydroxyethylphosphonate (2- Hep) and Fe(II) Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe501

b:31.0
occ:1.00
 O1 D:2HE502 2.0 32.6 1.0
O4 D:2HE502 2.1 35.3 1.0
NE2 D:HIS148 2.2 30.1 1.0
O D:HOH601 2.2 27.1 1.0
NE2 D:HIS190 2.2 32.4 1.0
OE1 D:GLN152 2.2 28.8 1.0
CE1 D:HIS190 3.1 31.6 1.0
CD2 D:HIS148 3.1 32.9 1.0
CE1 D:HIS148 3.2 30.1 1.0
CD D:GLN152 3.2 30.9 1.0
P D:2HE502 3.2 36.8 1.0
CB D:2HE502 3.2 37.4 1.0
CD2 D:HIS190 3.2 31.9 1.0
CA D:2HE502 3.5 31.2 1.0
NE2 D:GLN152 3.5 27.7 1.0
NZ C:LYS28 3.7 30.8 1.0
O3 D:2HE502 4.0 34.2 1.0
ND2 D:ASN145 4.0 31.3 1.0
ND1 D:HIS190 4.2 32.3 1.0
CG D:HIS148 4.3 32.4 1.0
ND1 D:HIS148 4.3 31.5 1.0
CG D:HIS190 4.3 33.5 1.0
O2 D:2HE502 4.4 33.4 1.0
CG D:GLN152 4.6 29.1 1.0
CE C:LYS28 4.8 30.5 1.0
CE1 D:PHE192 4.9 33.3 1.0
CB D:GLN152 5.0 26.9 1.0

Iron binding site 6 out of 9 in 6b9t

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Iron binding site 6 out of 9 in the Crystal Structure of Mpns with Substrate 2-Hydroxyethylphosphonate (2- Hep) and Fe(II) Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of Mpns with Substrate 2-Hydroxyethylphosphonate (2- Hep) and Fe(II) Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe501

b:34.0
occ:1.00
 O4 E:2HE502 1.9 39.2 1.0
O2 E:2HE502 2.0 33.3 1.0
NE2 E:HIS148 2.1 32.2 1.0
OE1 E:GLN152 2.2 36.0 1.0
NE2 E:HIS190 2.2 35.3 1.0
O E:HOH608 2.4 32.5 1.0
CD2 E:HIS148 2.9 32.5 1.0
CE1 E:HIS190 3.0 34.8 1.0
CE1 E:HIS148 3.2 32.5 1.0
CB E:2HE502 3.2 38.1 1.0
CD E:GLN152 3.2 36.2 1.0
CD2 E:HIS190 3.4 34.0 1.0
P E:2HE502 3.4 38.5 1.0
NE2 E:GLN152 3.6 35.2 1.0
NZ F:LYS28 3.6 37.2 1.0
CA E:2HE502 3.8 34.9 1.0
CG E:HIS148 4.1 32.7 1.0
ND2 E:ASN145 4.2 31.2 1.0
ND1 E:HIS148 4.2 31.8 1.0
O3 E:2HE502 4.2 39.2 1.0
ND1 E:HIS190 4.2 36.7 1.0
CG E:HIS190 4.4 37.3 1.0
O1 E:2HE502 4.5 33.7 1.0
CG E:GLN152 4.6 32.5 1.0
CE F:LYS28 4.8 40.0 1.0
CB E:GLN152 4.9 29.9 1.0

Iron binding site 7 out of 9 in 6b9t

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Iron binding site 7 out of 9 in the Crystal Structure of Mpns with Substrate 2-Hydroxyethylphosphonate (2- Hep) and Fe(II) Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of Mpns with Substrate 2-Hydroxyethylphosphonate (2- Hep) and Fe(II) Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe501

b:42.4
occ:1.00
 O F:HOH601 1.9 34.9 1.0
NE2 F:HIS190 2.0 38.3 1.0
O4 F:2HE502 2.1 42.0 1.0
O1 F:2HE502 2.2 43.1 1.0
OE1 F:GLN152 2.2 39.3 1.0
NE2 F:HIS148 2.2 41.6 1.0
CE1 F:HIS190 2.8 40.7 1.0
CD2 F:HIS148 3.0 40.5 1.0
CD F:GLN152 3.2 38.1 1.0
CD2 F:HIS190 3.2 41.7 1.0
CB F:2HE502 3.2 44.5 1.0
P F:2HE502 3.2 45.3 1.0
CE1 F:HIS148 3.3 42.0 1.0
CA F:2HE502 3.3 42.4 1.0
NE2 F:GLN152 3.5 41.9 1.0
NZ E:LYS28 3.7 40.1 1.0
ND1 F:HIS190 4.0 43.1 1.0
ND2 F:ASN145 4.1 41.9 1.0
O2 F:2HE502 4.2 39.1 1.0
CG F:HIS190 4.2 43.3 1.0
CG F:HIS148 4.2 42.9 1.0
ND1 F:HIS148 4.3 39.1 1.0
O3 F:2HE502 4.4 43.0 1.0
CG F:GLN152 4.5 38.9 1.0
CE E:LYS28 4.8 38.0 1.0
CB F:GLN152 4.9 35.5 1.0

Iron binding site 8 out of 9 in 6b9t

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Iron binding site 8 out of 9 in the Crystal Structure of Mpns with Substrate 2-Hydroxyethylphosphonate (2- Hep) and Fe(II) Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of Mpns with Substrate 2-Hydroxyethylphosphonate (2- Hep) and Fe(II) Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe501

b:56.3
occ:1.00
 NE2 G:HIS148 2.0 57.7 1.0
O4 G:2HE502 2.1 59.8 1.0
O2 G:2HE502 2.2 68.4 1.0
NE2 G:HIS190 2.4 58.6 1.0
OE1 G:GLN152 2.4 52.1 1.0
CD2 G:HIS148 2.8 58.2 1.0
CB G:2HE502 3.0 62.8 1.0
CE1 G:HIS190 3.0 58.0 1.0
CE1 G:HIS148 3.1 56.1 1.0
P G:2HE502 3.4 69.8 1.0
NZ H:LYS28 3.4 64.2 1.0
CD G:GLN152 3.5 52.8 1.0
CD2 G:HIS190 3.5 59.0 1.0
CA G:2HE502 3.6 56.2 1.0
NE2 G:GLN152 4.0 55.0 1.0
CG G:HIS148 4.0 55.8 1.0
ND1 G:HIS148 4.1 56.0 1.0
ND2 G:ASN145 4.1 61.9 1.0
ND1 G:HIS190 4.3 56.0 1.0
O1 G:2HE502 4.3 67.4 1.0
O3 G:2HE502 4.5 65.4 1.0
CG G:HIS190 4.5 56.3 1.0
CE H:LYS28 4.7 65.2 1.0
CG G:GLN152 4.8 47.9 1.0
CG2 G:THR208 5.0 53.4 1.0

Iron binding site 9 out of 9 in 6b9t

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Iron binding site 9 out of 9 in the Crystal Structure of Mpns with Substrate 2-Hydroxyethylphosphonate (2- Hep) and Fe(II) Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Crystal Structure of Mpns with Substrate 2-Hydroxyethylphosphonate (2- Hep) and Fe(II) Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Fe501

b:48.2
occ:1.00
 O4 H:2HE502 1.9 46.6 1.0
O2 H:2HE502 2.1 51.2 1.0
NE2 H:HIS190 2.1 46.6 1.0
NE2 H:HIS148 2.1 48.2 1.0
OE1 H:GLN152 2.2 46.1 1.0
O H:HOH601 2.9 48.6 1.0
CD2 H:HIS148 3.0 50.0 1.0
CD2 H:HIS190 3.1 47.4 1.0
CB H:2HE502 3.1 50.9 1.0
CE1 H:HIS190 3.1 46.9 1.0
P H:2HE502 3.2 53.6 1.0
CE1 H:HIS148 3.2 47.2 1.0
CD H:GLN152 3.2 42.7 1.0
CA H:2HE502 3.3 50.5 1.0
NE2 H:GLN152 3.6 42.8 1.0
NZ G:LYS28 3.7 58.9 1.0
ND2 H:ASN145 4.1 51.7 1.0
O1 H:2HE502 4.1 53.4 1.0
CG H:HIS148 4.2 49.7 1.0
ND1 H:HIS190 4.2 46.1 1.0
CG H:HIS190 4.2 47.6 1.0
ND1 H:HIS148 4.3 48.4 1.0
O3 H:2HE502 4.3 54.2 1.0
CG H:GLN152 4.6 42.3 1.0
CE G:LYS28 4.9 57.6 1.0
CB H:GLN152 4.9 42.8 1.0

Reference:

D.A.Born, E.C.Ulrich, K.S.Ju, S.C.Peck, W.A.Van Der Donk, C.L.Drennan. Structural Basis For Methylphosphonate Biosynthesis. Science V. 358 1336 2017.
ISSN: ESSN 1095-9203
PubMed: 29217579
DOI: 10.1126/SCIENCE.AAO3435
Page generated: Tue Aug 6 14:08:52 2024

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