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Magnesium in PDB 2d0q: Complex of Fe-Type Nhase with Cyclohexyl Isocyanide, Photo- Activated For 1HR at 277K

Enzymatic activity of Complex of Fe-Type Nhase with Cyclohexyl Isocyanide, Photo- Activated For 1HR at 277K

All present enzymatic activity of Complex of Fe-Type Nhase with Cyclohexyl Isocyanide, Photo- Activated For 1HR at 277K:
4.2.1.84;

Protein crystallography data

The structure of Complex of Fe-Type Nhase with Cyclohexyl Isocyanide, Photo- Activated For 1HR at 277K, PDB code: 2d0q was solved by M.Nojiri, Y.Kawano, K.Hashimoto, N.Kamiya, Riken Structuralgenomics/Proteomics Initiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.22 / 1.65
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 114.352, 60.201, 81.585, 90.00, 125.10, 90.00
R / Rfree (%) 15.4 / 16.5

Other elements in 2d0q:

The structure of Complex of Fe-Type Nhase with Cyclohexyl Isocyanide, Photo- Activated For 1HR at 277K also contains other interesting chemical elements:

Iron (Fe) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Complex of Fe-Type Nhase with Cyclohexyl Isocyanide, Photo- Activated For 1HR at 277K (pdb code 2d0q). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Complex of Fe-Type Nhase with Cyclohexyl Isocyanide, Photo- Activated For 1HR at 277K, PDB code: 2d0q:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 2d0q

Go back to Magnesium Binding Sites List in 2d0q
Magnesium binding site 1 out of 6 in the Complex of Fe-Type Nhase with Cyclohexyl Isocyanide, Photo- Activated For 1HR at 277K


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Complex of Fe-Type Nhase with Cyclohexyl Isocyanide, Photo- Activated For 1HR at 277K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1410

b:21.5
occ:0.50
 O A:HOH1771 2.0 40.7 1.0
O A:HOH1613 2.1 29.1 1.0
O A:HOH1799 2.2 50.9 1.0
O B:HOH1811 2.2 54.3 1.0
O B:HOH1780 2.4 35.5 1.0
O A:HOH1666 4.1 28.3 1.0
O A:HOH1711 4.1 35.0 1.0
OE2 A:GLU92 4.2 21.7 1.0
O B:HOH1774 4.2 36.7 1.0
OE1 A:GLU92 4.4 24.4 1.0
CD A:GLU92 4.7 20.5 1.0

Magnesium binding site 2 out of 6 in 2d0q

Go back to Magnesium Binding Sites List in 2d0q
Magnesium binding site 2 out of 6 in the Complex of Fe-Type Nhase with Cyclohexyl Isocyanide, Photo- Activated For 1HR at 277K


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Complex of Fe-Type Nhase with Cyclohexyl Isocyanide, Photo- Activated For 1HR at 277K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1439

b:13.2
occ:0.50
 O A:HOH1616 2.2 25.1 1.0
O A:GLY180 3.9 14.3 1.0
OE1 A:GLN185 4.2 19.6 1.0
O A:HOH1752 4.2 35.8 1.0
O A:HOH1634 4.2 19.5 1.0
NE2 A:GLN185 4.7 23.0 1.0
C A:GLY180 4.8 13.5 1.0
CD A:GLN185 4.9 19.7 1.0
N A:SER182 5.0 14.2 1.0

Magnesium binding site 3 out of 6 in 2d0q

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Magnesium binding site 3 out of 6 in the Complex of Fe-Type Nhase with Cyclohexyl Isocyanide, Photo- Activated For 1HR at 277K


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Complex of Fe-Type Nhase with Cyclohexyl Isocyanide, Photo- Activated For 1HR at 277K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1517

b:24.2
occ:0.50
 O B:HOH1866 1.8 25.7 1.0
O B:HOH1750 1.9 21.1 1.0
O A:HOH1754 2.0 35.4 1.0
OE2 A:GLU139 2.6 24.6 1.0
O B:HOH1769 3.1 27.4 1.0
O B:HOH1749 3.2 21.9 1.0
CD A:GLU139 3.6 19.6 1.0
O A:HOH1637 3.9 24.1 1.0
O B:HOH1727 4.1 26.1 1.0
OD1 B:ASP193 4.2 17.4 1.0
OE1 A:GLU139 4.3 19.8 1.0
CB A:GLU139 4.4 12.0 1.0
O A:HOH1723 4.4 34.2 1.0
NE2 B:GLN11 4.4 11.3 1.0
CG A:GLU139 4.5 15.5 1.0
CG B:ASP193 5.0 16.7 1.0

Magnesium binding site 4 out of 6 in 2d0q

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Magnesium binding site 4 out of 6 in the Complex of Fe-Type Nhase with Cyclohexyl Isocyanide, Photo- Activated For 1HR at 277K


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Complex of Fe-Type Nhase with Cyclohexyl Isocyanide, Photo- Activated For 1HR at 277K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1560

b:24.0
occ:0.50
 O A:HOH1747 1.9 31.6 1.0
O A:HOH1665 1.9 25.8 1.0
O A:HOH1725 2.0 37.2 1.0
O A:HOH1735 2.1 39.4 1.0
OD1 A:ASP37 3.2 27.6 1.0
OD1 A:ASP30 3.9 18.2 1.0
OD2 A:ASP30 4.0 15.3 1.0
CG A:ASP37 4.1 23.4 1.0
O A:HOH1593 4.3 17.4 1.0
O A:HOH1813 4.3 52.9 1.0
CG A:ASP30 4.4 14.9 1.0
O A:HOH1688 4.5 40.1 1.0
OD2 A:ASP37 4.5 27.3 1.0
O A:HOH1716 4.6 29.2 1.0

Magnesium binding site 5 out of 6 in 2d0q

Go back to Magnesium Binding Sites List in 2d0q
Magnesium binding site 5 out of 6 in the Complex of Fe-Type Nhase with Cyclohexyl Isocyanide, Photo- Activated For 1HR at 277K


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Complex of Fe-Type Nhase with Cyclohexyl Isocyanide, Photo- Activated For 1HR at 277K within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1438

b:11.5
occ:0.50
 O B:HOH1741 2.0 26.5 1.0
O B:HOH1673 2.1 23.6 1.0
O B:HOH1739 4.1 32.8 1.0
O B:HOH1730 4.1 23.4 1.0
OE1 B:GLU96 4.3 13.9 1.0
O B:HOH1697 4.3 14.6 1.0

Magnesium binding site 6 out of 6 in 2d0q

Go back to Magnesium Binding Sites List in 2d0q
Magnesium binding site 6 out of 6 in the Complex of Fe-Type Nhase with Cyclohexyl Isocyanide, Photo- Activated For 1HR at 277K


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Complex of Fe-Type Nhase with Cyclohexyl Isocyanide, Photo- Activated For 1HR at 277K within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1612

b:18.0
occ:0.50
 O B:HOH1755 1.9 27.1 1.0
O B:HOH1827 1.9 32.0 1.0
O B:HOH1716 2.1 24.2 1.0
O B:HOH1802 2.2 35.0 1.0
O B:HOH1635 4.2 11.8 1.0
O A:HOH1706 4.2 35.5 1.0
O A:HOH1602 4.3 21.8 1.0
OE1 B:GLU74 4.3 11.9 1.0
O B:MET69 4.4 10.5 1.0
O B:HOH1809 4.5 42.5 1.0
CD B:PRO71 4.6 10.2 1.0
SD B:MET69 4.7 18.7 0.3
OE2 B:GLU74 5.0 11.1 1.0

Reference:

M.Nojiri, Y.Kawano, K.Hashimoto, N.Kamiya. X-Ray Snap Shots of Inhibitor Binding Process in Photo-Reactive Nitrile Hydratase To Be Published.
Page generated: Sun Aug 10 10:22:51 2025

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