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Nickel in PDB 5jey: Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae, Crystallized in Cacodylate Buffer

Enzymatic activity of Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae, Crystallized in Cacodylate Buffer

All present enzymatic activity of Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae, Crystallized in Cacodylate Buffer:
3.5.1.88;

Protein crystallography data

The structure of Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae, Crystallized in Cacodylate Buffer, PDB code: 5jey was solved by S.Fieulaine, C.Giglione, T.Meinnel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.53 / 2.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 41.360, 65.980, 89.450, 90.00, 90.00, 90.00
R / Rfree (%) 18.2 / 24.8

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae, Crystallized in Cacodylate Buffer (pdb code 5jey). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 8 binding sites of Nickel where determined in the Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae, Crystallized in Cacodylate Buffer, PDB code: 5jey:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Nickel binding site 1 out of 8 in 5jey

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Nickel binding site 1 out of 8 in the Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae, Crystallized in Cacodylate Buffer


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae, Crystallized in Cacodylate Buffer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni301

b:21.7
occ:1.00
 OD3 A:OCS131 1.8 26.6 1.0
NE2 A:HIS178 2.0 8.7 1.0
NE2 A:HIS174 2.0 24.9 1.0
O A:HOH421 2.2 9.1 1.0
CE1 A:HIS174 3.0 20.8 1.0
CD2 A:HIS178 3.0 8.3 1.0
CE1 A:HIS178 3.0 11.1 1.0
CD2 A:HIS174 3.0 15.5 1.0
SG A:OCS131 3.1 29.4 1.0
OD2 A:OCS131 3.5 30.2 1.0
O A:HOH446 3.7 10.1 1.0
NE2 A:GLN77 3.8 23.7 1.0
OD1 A:OCS131 3.9 37.8 1.0
OE1 A:GLN77 3.9 17.8 1.0
O A:HOH456 4.0 16.1 1.0
ND1 A:HIS174 4.1 16.9 1.0
ND1 A:HIS178 4.1 11.5 1.0
O A:HOH435 4.1 15.5 1.0
CG A:HIS178 4.1 11.3 1.0
CG A:HIS174 4.1 11.2 1.0
CD A:GLN77 4.1 16.7 1.0
OE1 A:GLU175 4.1 33.6 1.0
CB A:OCS131 4.2 29.5 1.0
OE2 A:GLU175 4.4 31.4 1.0
CA A:OCS131 4.6 30.1 1.0
O A:GLY130 4.6 36.0 1.0
CD A:GLU175 4.7 30.7 1.0
O A:HOH443 5.0 19.4 1.0

Nickel binding site 2 out of 8 in 5jey

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Nickel binding site 2 out of 8 in the Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae, Crystallized in Cacodylate Buffer


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae, Crystallized in Cacodylate Buffer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni302

b:21.9
occ:1.00
 NE2 A:HIS55 1.8 37.3 1.0
CE1 A:HIS55 2.7 37.2 1.0
CD2 A:HIS55 2.9 35.9 1.0
O A:HOH492 2.9 27.5 1.0
ND1 A:HIS55 3.8 34.7 1.0
CG A:HIS55 3.9 34.4 1.0
OE1 A:GLN51 3.9 39.5 1.0
O A:HOH487 4.4 15.1 1.0
CG A:GLN51 4.8 33.3 1.0
CD A:GLN51 4.8 37.0 1.0

Nickel binding site 3 out of 8 in 5jey

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Nickel binding site 3 out of 8 in the Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae, Crystallized in Cacodylate Buffer


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae, Crystallized in Cacodylate Buffer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni303

b:28.9
occ:1.00
 NE2 A:HIS118 2.0 29.1 1.0
O A:HOH441 2.2 32.4 1.0
CE1 A:HIS118 2.8 27.1 1.0
CD2 A:HIS118 3.1 26.6 1.0
ND1 A:HIS118 4.0 23.7 1.0
CG A:HIS118 4.1 23.7 1.0
O A:HOH450 4.4 13.2 1.0
O A:HOH482 4.6 28.5 1.0

Nickel binding site 4 out of 8 in 5jey

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Nickel binding site 4 out of 8 in the Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae, Crystallized in Cacodylate Buffer


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae, Crystallized in Cacodylate Buffer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni304

b:27.0
occ:1.00
 OD1 A:ASP94 2.5 63.2 1.0
CG A:ASP94 3.3 54.1 1.0
CB A:ASP94 3.5 49.8 1.0
O A:HOH468 3.9 29.6 1.0
ND2 A:ASN98 3.9 53.6 1.0
O A:HOH437 4.0 18.2 1.0
CB A:ASN98 4.1 48.5 1.0
OD2 A:ASP94 4.4 65.5 1.0
CG A:ASN98 4.5 51.7 1.0
O A:ASN98 4.5 41.6 1.0
NE2 A:GLN96 4.7 73.4 1.0
CA A:ASP94 5.0 49.5 1.0

Nickel binding site 5 out of 8 in 5jey

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Nickel binding site 5 out of 8 in the Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae, Crystallized in Cacodylate Buffer


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae, Crystallized in Cacodylate Buffer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni305

b:15.3
occ:1.00
 OE1 A:GLU158 1.7 36.9 1.0
CD A:GLU158 2.5 34.4 1.0
OE2 A:GLU158 2.7 41.3 1.0
O A:HOH460 3.3 36.9 1.0
CG A:GLU158 4.0 30.8 1.0
O A:HOH423 4.0 15.8 1.0
CE1 A:HIS160 4.4 28.7 1.0
NE2 A:HIS160 4.9 24.6 1.0
O A:HOH403 5.0 22.0 1.0

Nickel binding site 6 out of 8 in 5jey

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Nickel binding site 6 out of 8 in the Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae, Crystallized in Cacodylate Buffer


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 6 of Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae, Crystallized in Cacodylate Buffer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni306

b:38.1
occ:1.00
 OD1 A:ASP18 2.2 44.7 1.0
NE2 A:HIS12 2.4 62.2 1.0
OD2 A:ASP18 2.5 41.2 1.0
O A:HOH412 2.6 29.6 1.0
CG A:ASP18 2.6 42.5 1.0
O A:HOH464 2.7 44.0 1.0
CE1 A:HIS12 2.7 58.7 1.0
O A:HOH442 2.8 25.9 1.0
O A:HOH480 3.0 24.3 1.0
OD1 A:ASP15 3.2 47.6 1.0
CD2 A:HIS12 3.7 63.8 1.0
ND1 A:HIS12 4.0 59.1 1.0
CG A:ASP15 4.1 44.6 1.0
CB A:ASP18 4.2 38.9 1.0
O A:LEU13 4.2 41.7 1.0
OD2 A:ASP15 4.4 52.7 1.0
CG A:HIS12 4.5 55.9 1.0
O A:HOH500 4.6 35.5 1.0
N A:ASP18 4.6 38.5 1.0
N A:ASP15 4.7 38.2 1.0
CA A:ASP18 4.8 38.4 1.0
CA A:ILE14 4.9 36.6 1.0

Nickel binding site 7 out of 8 in 5jey

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Nickel binding site 7 out of 8 in the Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae, Crystallized in Cacodylate Buffer


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 7 of Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae, Crystallized in Cacodylate Buffer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni307

b:51.1
occ:1.00
 O A:HOH448 2.4 38.9 1.0
OE1 A:GLU47 2.4 63.4 1.0
OE1 A:GLU43 2.6 50.7 1.0
CD A:GLU43 3.1 46.5 1.0
CD A:GLU47 3.2 57.8 1.0
OE2 A:GLU47 3.2 61.0 1.0
NZ A:LYS155 3.6 41.8 1.0
OE2 A:GLU43 3.6 60.9 1.0
CG A:GLU43 3.8 43.2 1.0
O A:HOH406 4.0 11.0 1.0
O A:HOH451 4.0 27.0 1.0
CE A:LYS155 4.3 42.0 1.0
O A:HOH520 4.6 29.1 1.0
CG A:GLU47 4.7 42.7 1.0

Nickel binding site 8 out of 8 in 5jey

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Nickel binding site 8 out of 8 in the Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae, Crystallized in Cacodylate Buffer


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 8 of Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae, Crystallized in Cacodylate Buffer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni308

b:47.6
occ:1.00
 OE1 A:GLU151 2.1 45.5 1.0
O A:HOH436 2.6 16.3 1.0
CD A:GLU151 2.9 37.9 1.0
OE2 A:GLU151 3.2 43.5 1.0
O A:HOH419 3.4 48.4 1.0
NH1 A:ARG161 3.7 32.8 1.0
NE A:ARG161 3.8 38.5 1.0
NZ A:LYS159 3.9 37.8 1.0
CZ A:ARG161 4.1 35.6 1.0
O A:HOH494 4.2 3.2 1.0
CG A:GLU151 4.2 24.4 1.0
CG1 A:VAL116 4.7 17.7 1.0
CE A:LYS159 4.7 31.5 1.0
CD A:ARG161 4.8 35.0 1.0

Reference:

S.Fieulaine, R.Alves De Sousa, L.Maigre, K.Hamiche, M.Alimi, J.M.Bolla, A.Taleb, A.Denis, J.M.Pages, I.Artaud, T.Meinnel, C.Giglione. A Unique Peptide Deformylase Platform to Rationally Design and Challenge Novel Active Compounds. Sci Rep V. 6 35429 2016.
ISSN: ESSN 2045-2322
PubMed: 27762275
DOI: 10.1038/SREP35429
Page generated: Thu Oct 10 06:31:52 2024

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