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Calcium in PDB 4fgc: Crystal Structure of Active Site Mutant C55A of Nitrile Reductase Quef, Bound to Substrate PREQ0

Enzymatic activity of Crystal Structure of Active Site Mutant C55A of Nitrile Reductase Quef, Bound to Substrate PREQ0

All present enzymatic activity of Crystal Structure of Active Site Mutant C55A of Nitrile Reductase Quef, Bound to Substrate PREQ0:
1.7.1.13;

Protein crystallography data

The structure of Crystal Structure of Active Site Mutant C55A of Nitrile Reductase Quef, Bound to Substrate PREQ0, PDB code: 4fgc 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) 22.15 / 2.50
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 93.048, 93.048, 193.651, 90.00, 90.00, 120.00
R / Rfree (%) 22.8 / 30.5

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Active Site Mutant C55A of Nitrile Reductase Quef, Bound to Substrate PREQ0 (pdb code 4fgc). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of Active Site Mutant C55A of Nitrile Reductase Quef, Bound to Substrate PREQ0, PDB code: 4fgc:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 4fgc

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Calcium binding site 1 out of 8 in the Crystal Structure of Active Site Mutant C55A of Nitrile Reductase Quef, Bound to Substrate PREQ0


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Active Site Mutant C55A of Nitrile Reductase Quef, Bound to Substrate PREQ0 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca202

b:31.0
occ:1.00
 OD2 B:ASP162 2.4 21.9 1.0
O B:HOH301 2.5 17.4 1.0
O B:HOH341 2.5 29.0 1.0
O B:HOH302 2.5 13.7 1.0
O B:HOH347 2.8 30.0 1.0
OXT B:ARG164 2.9 30.2 1.0
CG B:ASP162 3.3 26.3 1.0
OD1 B:ASP162 3.6 29.0 1.0
C B:ARG164 4.0 29.4 1.0
N B:ASP162 4.0 26.6 1.0
N B:ARG164 4.1 29.3 1.0
CA B:ARG164 4.4 29.1 1.0
CB B:ASP162 4.4 27.1 1.0
CB B:ARG164 4.5 29.4 1.0
N B:ASN163 4.5 28.8 1.0
O B:THR160 4.5 27.9 1.0
CA B:ASP162 4.7 27.3 1.0
CA B:ILE161 4.8 25.6 1.0
C B:ILE161 4.8 25.9 1.0
O B:ARG164 4.9 29.3 1.0
C B:ASP162 5.0 28.2 1.0

Calcium binding site 2 out of 8 in 4fgc

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Calcium binding site 2 out of 8 in the Crystal Structure of Active Site Mutant C55A of Nitrile Reductase Quef, Bound to Substrate PREQ0


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Active Site Mutant C55A of Nitrile Reductase Quef, Bound to Substrate PREQ0 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca204

b:50.0
occ:1.00
 O B:ASP94 2.4 41.4 1.0
OD1 B:ASP62 2.4 42.0 1.0
O B:HOH342 2.4 30.7 1.0
OG B:SER53 2.6 32.3 1.0
O B:LEU54 2.6 35.3 1.0
OD2 B:ASP94 2.7 46.6 1.0
CG B:ASP62 3.2 38.6 1.0
OD2 B:ASP62 3.3 36.8 1.0
C B:LEU54 3.4 35.5 1.0
C B:ASP94 3.5 41.2 1.0
N B:LEU54 3.7 32.3 1.0
CB B:SER53 3.7 30.4 1.0
CG B:ASP94 3.9 45.2 1.0
N B:ASP94 3.9 41.2 1.0
ND1 B:HIS96 3.9 38.4 1.0
CA B:LEU54 4.1 34.4 1.0
C B:SER53 4.1 30.9 1.0
CE1 B:HIS96 4.2 37.6 1.0
CA B:ASP94 4.2 41.8 1.0
N B:ALA55 4.2 38.1 1.0
CA B:SER53 4.5 30.7 1.0
CA B:ALA55 4.5 40.4 1.0
O B:PHE95 4.5 40.3 1.0
C B:PHE95 4.6 39.4 1.0
CB B:ASP62 4.6 35.7 1.0
N B:PHE95 4.6 40.8 1.0
O B:SER53 4.7 30.2 1.0
CB B:ASP94 4.7 42.4 1.0
O B:HIS92 4.7 40.6 1.0
OD1 B:ASP94 4.8 47.0 1.0
C B:GLY93 4.8 41.2 1.0
CA B:PHE95 4.9 40.1 1.0
N B:HIS96 4.9 38.4 1.0
N11 B:PQ0201 4.9 43.2 1.0

Calcium binding site 3 out of 8 in 4fgc

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Calcium binding site 3 out of 8 in the Crystal Structure of Active Site Mutant C55A of Nitrile Reductase Quef, Bound to Substrate PREQ0


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Active Site Mutant C55A of Nitrile Reductase Quef, Bound to Substrate PREQ0 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca202

b:40.4
occ:1.00
 OD1 C:ASP162 2.3 29.0 1.0
O C:HOH301 2.3 12.0 1.0
O C:HOH302 2.4 13.8 1.0
OXT C:ARG164 2.6 26.5 1.0
CG C:ASP162 3.3 30.2 1.0
OD2 C:ASP162 3.7 27.7 1.0
C C:ARG164 3.7 26.3 1.0
N C:ASP162 4.1 28.7 1.0
N C:ARG164 4.3 27.5 1.0
O C:THR160 4.4 28.6 1.0
CB C:ASP162 4.5 28.6 1.0
O C:ARG164 4.5 27.1 1.0
CA C:ARG164 4.6 26.6 1.0
CB C:ARG164 4.7 26.3 1.0
N C:ASN163 4.8 29.1 1.0
CA C:ASP162 4.8 29.1 1.0
CA C:ILE161 4.9 28.3 1.0

Calcium binding site 4 out of 8 in 4fgc

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Calcium binding site 4 out of 8 in the Crystal Structure of Active Site Mutant C55A of Nitrile Reductase Quef, Bound to Substrate PREQ0


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Active Site Mutant C55A of Nitrile Reductase Quef, Bound to Substrate PREQ0 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca203

b:56.2
occ:1.00
 OD1 C:ASP94 2.3 48.2 0.5
O C:ASP94 2.4 41.8 0.5
O C:HOH336 2.4 45.5 1.0
O C:ASP94 2.4 41.8 0.5
O C:LEU54 2.7 40.8 1.0
OG C:SER53 2.7 33.5 1.0
OD1 C:ASP62 3.0 41.2 1.0
C C:ASP94 3.3 41.4 0.5
C C:ASP94 3.3 41.4 0.5
OD2 C:ASP62 3.4 38.1 1.0
CG C:ASP94 3.5 46.5 0.5
C C:LEU54 3.6 40.3 1.0
CG C:ASP62 3.6 40.5 1.0
N C:ASP94 3.7 43.0 0.5
N C:ASP94 3.8 43.0 0.5
CB C:SER53 3.9 33.8 1.0
CA C:ASP94 4.0 42.4 0.5
ND1 C:HIS96 4.0 28.7 1.0
CA C:ASP94 4.0 42.4 0.5
N C:LEU54 4.1 36.9 1.0
CE1 C:HIS96 4.2 30.4 1.0
N C:PHE95 4.3 40.1 1.0
C C:PHE95 4.4 38.0 1.0
CB C:ASP94 4.4 42.9 0.5
C C:SER53 4.4 35.6 1.0
CB C:ASP94 4.4 42.9 0.5
OD2 C:ASP94 4.4 48.1 0.5
N C:ALA55 4.4 42.3 1.0
CA C:LEU54 4.4 38.7 1.0
O C:PHE95 4.5 37.6 1.0
CA C:PHE95 4.5 38.8 1.0
CA C:ALA55 4.6 44.0 1.0
O C:HIS92 4.7 44.9 1.0
N C:HIS96 4.8 36.7 1.0
CA C:SER53 4.8 34.4 1.0
O C:SER53 4.8 35.7 1.0
C C:GLY93 4.9 43.9 1.0

Calcium binding site 5 out of 8 in 4fgc

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Calcium binding site 5 out of 8 in the Crystal Structure of Active Site Mutant C55A of Nitrile Reductase Quef, Bound to Substrate PREQ0


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Active Site Mutant C55A of Nitrile Reductase Quef, Bound to Substrate PREQ0 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca202

b:31.3
occ:1.00
 O D:HOH301 2.2 16.4 1.0
O D:HOH302 2.3 37.2 1.0
O D:HOH330 2.4 27.1 1.0
OD2 D:ASP162 2.4 28.0 1.0
OXT D:ARG164 2.6 35.2 1.0
CG D:ASP162 3.4 30.9 1.0
C D:ARG164 3.4 35.6 1.0
OD1 D:ASP162 3.7 28.9 1.0
N D:ARG164 3.9 35.1 1.0
O D:ARG164 4.1 35.9 1.0
CA D:ARG164 4.1 35.0 1.0
N D:ASP162 4.2 33.1 1.0
O D:HOH332 4.4 36.1 1.0
CB D:ARG164 4.6 35.1 1.0
CB D:ASP162 4.6 32.3 1.0
N D:ASN163 4.8 34.0 1.0
CA D:ASP162 4.8 33.1 1.0
C D:ASP162 5.0 33.4 1.0

Calcium binding site 6 out of 8 in 4fgc

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Calcium binding site 6 out of 8 in the Crystal Structure of Active Site Mutant C55A of Nitrile Reductase Quef, Bound to Substrate PREQ0


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Active Site Mutant C55A of Nitrile Reductase Quef, Bound to Substrate PREQ0 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca203

b:55.8
occ:1.00
 O D:HOH324 2.3 27.4 1.0
O D:ASP94 2.4 45.5 1.0
OG D:SER53 2.4 34.0 1.0
OD1 D:ASP62 2.6 39.8 1.0
OD2 D:ASP94 2.8 54.2 1.0
O D:LEU54 2.9 41.3 1.0
CB D:SER53 3.4 35.1 1.0
C D:ASP94 3.4 45.3 1.0
CG D:ASP62 3.5 38.8 1.0
N D:ASP94 3.7 46.4 1.0
OD2 D:ASP62 3.7 35.6 1.0
CG D:ASP94 3.7 50.4 1.0
C D:LEU54 3.8 40.8 1.0
N D:LEU54 3.9 37.8 1.0
CA D:ASP94 4.0 46.2 1.0
C D:SER53 4.2 36.3 1.0
O D:HIS92 4.4 44.5 1.0
CA D:SER53 4.4 35.2 1.0
N D:PHE95 4.5 44.2 1.0
CA D:LEU54 4.5 39.9 1.0
CB D:ASP94 4.5 47.0 1.0
OD1 D:ASP94 4.5 51.0 1.0
C D:PHE95 4.6 41.5 1.0
ND1 D:HIS96 4.6 36.8 1.0
N D:ALA55 4.6 42.6 1.0
SG D:CYS99 4.7 40.8 1.0
O D:PHE95 4.7 41.0 1.0
CA D:PHE95 4.7 43.0 1.0
C D:GLY93 4.8 46.2 1.0
O D:SER53 4.9 36.3 1.0
CA D:ALA55 4.9 44.2 1.0
N D:HIS96 4.9 40.0 1.0
CB D:ASP62 4.9 36.7 1.0
CE1 D:HIS96 4.9 37.0 1.0
CA D:GLY93 5.0 45.6 1.0

Calcium binding site 7 out of 8 in 4fgc

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Calcium binding site 7 out of 8 in the Crystal Structure of Active Site Mutant C55A of Nitrile Reductase Quef, Bound to Substrate PREQ0


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Active Site Mutant C55A of Nitrile Reductase Quef, Bound to Substrate PREQ0 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca202

b:26.8
occ:1.00
 O E:HOH342 2.0 30.0 1.0
O E:HOH302 2.1 26.9 1.0
O E:HOH301 2.4 26.9 1.0
OD2 E:ASP162 2.5 33.1 1.0
OXT E:ARG164 2.7 31.7 1.0
CG E:ASP162 3.3 34.9 1.0
C E:ARG164 3.7 31.9 1.0
OD1 E:ASP162 3.7 35.2 1.0
N E:ASP162 3.9 33.7 1.0
N E:ARG164 4.0 32.4 1.0
CA E:ARG164 4.3 31.9 1.0
CB E:ASP162 4.4 33.8 1.0
O E:HOH325 4.4 14.1 1.0
CB E:ARG164 4.6 31.9 1.0
O E:ARG164 4.6 32.3 1.0
CA E:ASP162 4.6 33.6 1.0
N E:ASN163 4.6 33.1 1.0
O E:THR160 4.6 33.5 1.0
C E:ASP162 4.8 33.1 1.0
CA E:ILE161 4.8 33.9 1.0
C E:ILE161 4.8 33.9 1.0

Calcium binding site 8 out of 8 in 4fgc

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Calcium binding site 8 out of 8 in the Crystal Structure of Active Site Mutant C55A of Nitrile Reductase Quef, Bound to Substrate PREQ0


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Active Site Mutant C55A of Nitrile Reductase Quef, Bound to Substrate PREQ0 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca203

b:41.8
occ:1.00
 OG E:SER53 2.1 42.8 1.0
O E:LEU54 2.4 48.6 1.0
OD2 E:ASP94 2.4 49.0 1.0
O E:HOH339 2.6 29.7 1.0
OD1 E:ASP62 2.8 41.6 1.0
O E:ASP94 2.9 43.9 1.0
CB E:SER53 3.1 42.8 1.0
N E:LEU54 3.1 45.8 1.0
C E:LEU54 3.2 48.5 1.0
OD2 E:ASP62 3.4 36.5 1.0
CG E:ASP62 3.4 38.5 1.0
CG E:ASP94 3.6 48.6 1.0
CA E:LEU54 3.7 47.4 1.0
O E:HIS92 3.8 46.1 1.0
C E:ASP94 3.9 44.2 1.0
N E:ASP94 3.9 45.3 1.0
C E:SER53 4.0 44.1 1.0
CA E:SER53 4.1 42.7 1.0
N E:ALA55 4.2 50.1 1.0
CA E:ASP94 4.3 45.0 1.0
OD1 E:ASP94 4.3 51.2 1.0
CB E:ASP94 4.6 45.4 1.0
CA E:ALA55 4.6 51.5 1.0
C E:GLY93 4.8 45.6 1.0
N E:SER53 4.8 41.0 1.0
ND1 E:HIS96 4.9 47.1 1.0
CB E:ASP62 4.9 37.8 1.0
C E:HIS92 4.9 46.6 1.0
O E:PHE95 4.9 43.8 1.0
CB E:LEU54 4.9 47.4 1.0
CA E:GLY93 5.0 45.7 1.0
N E:PHE95 5.0 44.1 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: Sun Jul 14 00:17:56 2024

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