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Magnesium in PDB 4f8b: Crystal Structure of the Covalent Thioimide Intermediate of Unimodular Nitrile Reductase Quef

Enzymatic activity of Crystal Structure of the Covalent Thioimide Intermediate of Unimodular Nitrile Reductase Quef

All present enzymatic activity of Crystal Structure of the Covalent Thioimide Intermediate of Unimodular Nitrile Reductase Quef:
1.7.1.13;

Protein crystallography data

The structure of Crystal Structure of the Covalent Thioimide Intermediate of Unimodular Nitrile Reductase Quef, PDB code: 4f8b was solved by B.Stec, M.A.Swairjo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.56 / 2.50
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 93.507, 93.507, 193.696, 90.00, 90.00, 120.00
R / Rfree (%) 18.9 / 27.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Covalent Thioimide Intermediate of Unimodular Nitrile Reductase Quef (pdb code 4f8b). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of the Covalent Thioimide Intermediate of Unimodular Nitrile Reductase Quef, PDB code: 4f8b:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4f8b

Go back to Magnesium Binding Sites List in 4f8b
Magnesium binding site 1 out of 4 in the Crystal Structure of the Covalent Thioimide Intermediate of Unimodular Nitrile Reductase Quef


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Covalent Thioimide Intermediate of Unimodular Nitrile Reductase Quef within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg202

b:53.9
occ:1.00
 O B:HOH301 2.2 46.5 1.0
OXT B:ARG164 2.5 51.0 1.0
O B:HOH302 2.7 50.6 1.0
OD2 B:ASP162 3.0 45.0 1.0
OD1 B:ASP162 3.4 50.1 1.0
CG B:ASP162 3.6 46.1 1.0
C B:ARG164 3.7 50.9 1.0
N B:ARG164 4.4 49.4 1.0
CA B:ARG164 4.4 50.0 1.0
O B:ARG164 4.5 51.8 1.0
CB B:ARG164 4.7 49.0 1.0
N B:ASP162 4.8 44.9 1.0
CB B:ASP162 4.9 45.1 1.0

Magnesium binding site 2 out of 4 in 4f8b

Go back to Magnesium Binding Sites List in 4f8b
Magnesium binding site 2 out of 4 in the Crystal Structure of the Covalent Thioimide Intermediate of Unimodular Nitrile Reductase Quef


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Covalent Thioimide Intermediate of Unimodular Nitrile Reductase Quef within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg202

b:38.4
occ:1.00
 O C:HOH302 1.9 37.1 1.0
O C:HOH301 1.9 35.3 1.0
OD1 C:ASP162 2.2 39.5 1.0
OXT C:ARG164 2.5 42.6 1.0
CG C:ASP162 3.2 41.4 1.0
C C:ARG164 3.6 42.7 1.0
OD2 C:ASP162 3.7 43.8 1.0
N C:ARG164 3.9 43.2 1.0
CA C:ARG164 4.2 42.7 1.0
N C:ASP162 4.2 39.3 1.0
CB C:ARG164 4.4 42.6 1.0
CB C:ASP162 4.5 39.3 1.0
O C:ARG164 4.5 42.8 1.0
N C:ASN163 4.6 41.0 1.0
CA C:ASP162 4.8 39.9 1.0
C C:ASP162 4.9 40.4 1.0
O C:THR160 4.9 35.4 1.0

Magnesium binding site 3 out of 4 in 4f8b

Go back to Magnesium Binding Sites List in 4f8b
Magnesium binding site 3 out of 4 in the Crystal Structure of the Covalent Thioimide Intermediate of Unimodular Nitrile Reductase Quef


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the Covalent Thioimide Intermediate of Unimodular Nitrile Reductase Quef within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg202

b:29.5
occ:1.00
 O D:HOH302 2.0 23.1 1.0
O D:HOH303 2.2 60.8 1.0
O D:HOH301 2.2 32.9 1.0
OD2 D:ASP162 2.2 36.5 1.0
OXT D:ARG164 2.3 45.5 1.0
CG D:ASP162 2.9 37.3 1.0
OD1 D:ASP162 3.0 37.6 1.0
C D:ARG164 3.4 45.2 1.0
N D:ARG164 3.8 43.0 1.0
CA D:ARG164 4.0 44.5 1.0
N D:ASP162 4.1 37.9 1.0
CB D:ASP162 4.2 36.2 1.0
O D:ARG164 4.4 45.6 1.0
CB D:ARG164 4.5 44.4 1.0
CA D:ASP162 4.5 37.6 1.0
N D:ASN163 4.6 39.3 1.0
C D:ASP162 4.7 38.3 1.0
C D:ASN163 5.0 42.1 1.0

Magnesium binding site 4 out of 4 in 4f8b

Go back to Magnesium Binding Sites List in 4f8b
Magnesium binding site 4 out of 4 in the Crystal Structure of the Covalent Thioimide Intermediate of Unimodular Nitrile Reductase Quef


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of the Covalent Thioimide Intermediate of Unimodular Nitrile Reductase Quef within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg202

b:36.5
occ:1.00
 O E:HOH303 2.1 32.3 1.0
O E:HOH301 2.2 49.3 1.0
OD2 E:ASP162 2.2 38.5 1.0
O E:HOH302 2.2 46.3 1.0
OXT E:ARG164 2.5 47.5 1.0
CG E:ASP162 3.1 42.3 1.0
OD1 E:ASP162 3.4 39.9 1.0
C E:ARG164 3.6 46.9 1.0
N E:ARG164 3.9 45.5 1.0
N E:ASP162 4.0 41.8 1.0
CA E:ARG164 4.1 45.6 1.0
CB E:ARG164 4.3 45.3 1.0
CB E:ASP162 4.4 41.0 1.0
O E:ARG164 4.6 46.9 1.0
CA E:ASP162 4.6 42.4 1.0
C E:ASP162 4.7 43.4 1.0
N E:ASN163 4.7 43.6 1.0
O E:THR160 4.9 39.4 1.0

Reference:

V.M.Chikwana, B.Stec, B.W.Lee, V.De Crecy-Lagard, D.Iwata-Reuyl, M.A.Swairjo. Structural Basis of Biological Nitrile Reduction. J.Biol.Chem. V. 287 30560 2012.
ISSN: ISSN 0021-9258
PubMed: 22787148
DOI: 10.1074/JBC.M112.388538
Page generated: Mon Aug 11 12:37:02 2025

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