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Magnesium in PDB 5tds: Toluene Bound in the Resting Active Site of Toluene 4-Monooxygenase (T4MOH)

Protein crystallography data

The structure of Toluene Bound in the Resting Active Site of Toluene 4-Monooxygenase (T4MOH), PDB code: 5tds was solved by J.F.Acheson, B.G.Fox, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.78 / 1.72
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 169.386, 176.906, 55.944, 90.00, 90.00, 90.00
R / Rfree (%) 13 / 17.3

Other elements in 5tds:

The structure of Toluene Bound in the Resting Active Site of Toluene 4-Monooxygenase (T4MOH) also contains other interesting chemical elements:

Iron (Fe) 4 atoms
Chlorine (Cl) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Toluene Bound in the Resting Active Site of Toluene 4-Monooxygenase (T4MOH) (pdb code 5tds). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the Toluene Bound in the Resting Active Site of Toluene 4-Monooxygenase (T4MOH), PDB code: 5tds:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 5tds

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Magnesium binding site 1 out of 9 in the Toluene Bound in the Resting Active Site of Toluene 4-Monooxygenase (T4MOH)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Toluene Bound in the Resting Active Site of Toluene 4-Monooxygenase (T4MOH) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:25.6
occ:1.00
 O A:HOH1079 2.0 34.6 1.0
O A:HOH772 2.1 28.0 1.0
O A:HOH680 2.1 26.6 1.0
O A:HOH1051 2.2 30.3 1.0
OD1 A:ASP383 4.2 28.1 1.0
OD2 A:ASP383 4.3 25.8 1.0
CG A:MET385 4.6 22.6 1.0
CG A:ASP383 4.7 26.1 1.0

Magnesium binding site 2 out of 9 in 5tds

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Magnesium binding site 2 out of 9 in the Toluene Bound in the Resting Active Site of Toluene 4-Monooxygenase (T4MOH)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Toluene Bound in the Resting Active Site of Toluene 4-Monooxygenase (T4MOH) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg401

b:10.7
occ:1.00
 O B:HOH679 2.0 9.8 1.0
O B:HOH612 2.0 13.4 1.0
OE1 B:GLU298 3.8 21.9 1.0
OE2 B:GLU298 4.1 24.1 1.0
OD2 B:ASP294 4.3 14.5 1.0
CD B:GLU298 4.4 21.9 1.0
CB B:ASP294 4.4 9.9 1.0
CG B:ASP294 4.8 14.4 1.0

Magnesium binding site 3 out of 9 in 5tds

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Magnesium binding site 3 out of 9 in the Toluene Bound in the Resting Active Site of Toluene 4-Monooxygenase (T4MOH)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Toluene Bound in the Resting Active Site of Toluene 4-Monooxygenase (T4MOH) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:29.4
occ:1.00
 O B:HOH616 2.1 19.4 1.0
O B:HOH877 2.1 27.4 1.0
O B:HOH796 2.1 27.4 1.0
O B:HOH871 2.2 29.6 1.0
O B:HOH536 2.2 19.1 1.0
O B:HOH816 2.3 22.6 1.0
O B:HOH822 3.8 29.5 1.0
O B:HOH865 4.0 32.4 1.0
O B:HOH633 4.1 21.4 1.0
O B:HOH727 4.2 15.7 1.0
O B:HOH628 4.2 31.2 1.0
O B:HOH724 4.2 34.8 1.0
OE2 B:GLU274 4.3 19.4 1.0
ND1 B:HIS271 4.4 11.3 1.0
O B:ALA71 4.4 10.7 1.0
CE1 B:HIS271 4.7 8.8 1.0
O B:HOH706 5.0 32.9 1.0

Magnesium binding site 4 out of 9 in 5tds

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Magnesium binding site 4 out of 9 in the Toluene Bound in the Resting Active Site of Toluene 4-Monooxygenase (T4MOH)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Toluene Bound in the Resting Active Site of Toluene 4-Monooxygenase (T4MOH) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg403

b:41.3
occ:1.00
 O B:HOH644 2.0 30.4 1.0
O B:HOH795 2.1 36.1 1.0
O B:HOH746 2.2 40.7 1.0
O E:HOH581 2.3 40.9 1.0
O A:HOH839 3.7 37.1 1.0
OE2 B:GLU184 4.0 36.5 1.0
O B:HOH545 4.0 32.5 1.0
ND1 B:HIS171 4.0 12.6 1.0
OG B:SER174 4.1 13.1 1.0
O A:HOH1077 4.2 39.6 1.0
O A:HOH804 4.3 29.0 1.0
OE2 E:GLU184 4.4 36.5 1.0
CE1 B:HIS171 4.5 14.0 1.0
O B:HOH508 4.7 36.1 1.0
O B:LEU182 4.7 15.7 1.0
O E:HOH686 4.8 34.7 1.0
CB B:SER174 5.0 13.7 1.0

Magnesium binding site 5 out of 9 in 5tds

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Magnesium binding site 5 out of 9 in the Toluene Bound in the Resting Active Site of Toluene 4-Monooxygenase (T4MOH)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Toluene Bound in the Resting Active Site of Toluene 4-Monooxygenase (T4MOH) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg404

b:42.5
occ:1.00
 O B:HOH517 2.2 30.5 1.0
O B:HOH693 2.2 21.1 1.0
OD1 B:ASP40 3.7 14.2 1.0
O B:HOH527 3.7 14.7 1.0
NZ B:LYS56 4.0 9.0 1.0
OD2 B:ASP48 4.4 22.9 1.0
O B:HOH869 4.5 28.6 1.0
CG B:ASP40 4.7 15.5 1.0
OD2 B:ASP40 4.8 15.3 1.0

Magnesium binding site 6 out of 9 in 5tds

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Magnesium binding site 6 out of 9 in the Toluene Bound in the Resting Active Site of Toluene 4-Monooxygenase (T4MOH)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Toluene Bound in the Resting Active Site of Toluene 4-Monooxygenase (T4MOH) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg101

b:34.8
occ:1.00
 O C:HOH267 1.9 33.2 1.0
O C:HOH228 1.9 29.3 1.0
O C:HOH273 2.0 30.8 1.0
O C:HOH287 2.2 28.4 1.0
O C:HOH266 2.3 38.1 1.0
O C:HOH229 4.0 27.1 1.0
O C:HOH279 4.1 31.6 1.0
NE2 C:GLN29 4.1 26.0 1.0
O C:HOH224 4.2 25.0 1.0
OE1 C:GLN29 4.3 20.5 1.0
O C:ASN24 4.3 20.7 1.0
CD C:GLN29 4.7 21.9 1.0
O C:HOH205 4.7 37.5 1.0
O C:HOH288 4.9 34.4 1.0

Magnesium binding site 7 out of 9 in 5tds

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Magnesium binding site 7 out of 9 in the Toluene Bound in the Resting Active Site of Toluene 4-Monooxygenase (T4MOH)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Toluene Bound in the Resting Active Site of Toluene 4-Monooxygenase (T4MOH) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg503

b:17.8
occ:1.00
 O D:HOH683 2.4 15.4 1.0
O D:SER389 2.4 13.7 1.0
O D:HOH777 2.4 16.6 1.0
O D:ASP386 2.5 15.1 1.0
OG D:SER389 2.5 18.6 1.0
C D:SER389 3.3 14.9 1.0
C D:ASP386 3.4 15.1 1.0
CB D:SER389 3.6 15.9 1.0
CA D:ASP386 3.7 17.6 1.0
CA D:SER389 3.9 14.2 1.0
NH1 F:ARG41 4.1 13.2 1.0
N D:SER389 4.2 13.9 1.0
CB D:ASP386 4.3 18.1 1.0
O D:PRO390 4.3 13.9 1.0
NH2 F:ARG41 4.3 17.6 1.0
N D:PRO390 4.3 12.9 1.0
CG D:GLU391 4.4 18.5 1.0
O D:HOH1032 4.5 40.5 1.0
C D:PRO390 4.5 13.3 1.0
O D:MET385 4.6 23.9 1.0
N D:LEU387 4.7 14.7 1.0
CZ F:ARG41 4.7 15.3 1.0
OE2 D:GLU391 4.7 19.8 1.0
CA D:PRO390 4.8 12.0 1.0
N D:ASP386 5.0 17.9 1.0

Magnesium binding site 8 out of 9 in 5tds

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Magnesium binding site 8 out of 9 in the Toluene Bound in the Resting Active Site of Toluene 4-Monooxygenase (T4MOH)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Toluene Bound in the Resting Active Site of Toluene 4-Monooxygenase (T4MOH) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg401

b:28.2
occ:1.00
 O E:HOH801 2.0 24.3 1.0
O E:HOH773 2.1 28.0 1.0
O E:HOH600 2.1 22.5 1.0
O E:HOH556 2.2 17.5 1.0
O E:HOH806 2.2 30.3 1.0
O E:HOH752 3.9 40.6 1.0
O E:THR36 3.9 9.9 1.0
O E:HOH518 4.1 28.0 1.0
O E:HOH656 4.1 15.9 1.0
OD1 E:ASN37 4.2 11.6 1.0
O E:HOH718 4.4 42.3 1.0
CA E:ASN37 4.5 8.9 1.0
C E:THR36 4.6 9.2 1.0
OG1 E:THR36 4.6 10.3 1.0
N E:ASN37 4.9 7.9 1.0
O E:ASN37 5.0 11.9 1.0
NZ E:LYS31 5.0 26.0 1.0

Magnesium binding site 9 out of 9 in 5tds

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Magnesium binding site 9 out of 9 in the Toluene Bound in the Resting Active Site of Toluene 4-Monooxygenase (T4MOH)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Toluene Bound in the Resting Active Site of Toluene 4-Monooxygenase (T4MOH) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg402

b:34.7
occ:1.00
 O E:HOH798 2.0 31.6 1.0
O E:HOH842 2.0 32.0 1.0
O E:HOH880 2.1 36.2 1.0
O E:HOH863 2.1 30.6 1.0
O E:HOH612 2.1 25.7 1.0
O E:HOH539 2.2 18.2 1.0
O E:HOH810 4.0 26.5 1.0
O E:HOH862 4.1 42.6 1.0
OE2 E:GLU274 4.2 21.3 1.0
O E:HOH864 4.2 36.1 1.0
O E:HOH717 4.2 17.7 1.0
ND1 E:HIS271 4.3 11.9 1.0
O E:HOH639 4.4 28.9 1.0
O E:ALA71 4.4 11.0 1.0
CE1 E:HIS271 4.7 10.5 1.0
O E:HOH591 4.8 44.6 1.0
O E:HOH681 4.9 22.7 1.0

Reference:

J.F.Acheson, L.J.Bailey, T.C.Brunold, B.G.Fox. In-Crystal Reaction Cycle of A Toluene-Bound Diiron Hydroxylase. Nature V. 544 191 2017.
ISSN: ESSN 1476-4687
PubMed: 28346937
DOI: 10.1038/NATURE21681
Page generated: Mon Sep 30 04:48:56 2024

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