Atomistry » Nickel » PDB 5i8s-5mdj » 5jey
Atomistry »
  Nickel »
    PDB 5i8s-5mdj »
      5jey »

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

Go back to Nickel Binding Sites List in 5jey
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

Go back to Nickel Binding Sites List in 5jey
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

Go back to Nickel Binding Sites List in 5jey
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

Go back to Nickel Binding Sites List in 5jey
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

Go back to Nickel Binding Sites List in 5jey
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

Go back to Nickel Binding Sites List in 5jey
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

Go back to Nickel Binding Sites List in 5jey
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

Go back to Nickel Binding Sites List in 5jey
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy