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Nickel in PDB 5jf0: Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Tripeptide Met-Ala-Arg

Enzymatic activity of Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Tripeptide Met-Ala-Arg

All present enzymatic activity of Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Tripeptide Met-Ala-Arg:
3.5.1.88;

Protein crystallography data

The structure of Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Tripeptide Met-Ala-Arg, PDB code: 5jf0 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) 44.28 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 41.210, 65.430, 88.540, 90.00, 90.00, 90.00
R / Rfree (%) 17.3 / 20

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Tripeptide Met-Ala-Arg (pdb code 5jf0). 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 in Complex with Tripeptide Met-Ala-Arg, PDB code: 5jf0:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Nickel binding site 1 out of 8 in 5jf0

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Nickel binding site 1 out of 8 in the Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Tripeptide Met-Ala-Arg


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 in Complex with Tripeptide Met-Ala-Arg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni302

b:11.2
occ:1.00
 OD3 A:OCS131 2.0 13.4 1.0
NE2 A:HIS174 2.1 9.3 1.0
NE2 A:HIS178 2.1 10.1 1.0
O A:HOH418 2.2 12.0 1.0
O A:HOH637 2.3 3.9 1.0
CD2 A:HIS178 3.0 10.3 1.0
CD2 A:HIS174 3.0 10.6 1.0
CE1 A:HIS174 3.1 10.5 1.0
CE1 A:HIS178 3.1 9.9 1.0
SG A:OCS131 3.3 13.8 1.0
OD2 A:OCS131 3.5 14.3 1.0
NE2 A:GLN77 3.6 12.0 1.0
N D:MET1 3.9 18.1 1.0
OE1 A:GLN77 3.9 11.1 1.0
CD A:GLN77 4.0 10.1 1.0
CA D:MET1 4.1 17.2 1.0
O A:HOH500 4.1 14.4 1.0
CG A:HIS178 4.2 8.4 1.0
CG A:HIS174 4.2 8.1 1.0
OD1 A:OCS131 4.2 16.7 1.0
ND1 A:HIS174 4.2 9.4 1.0
ND1 A:HIS178 4.2 8.7 1.0
OE1 A:GLU175 4.3 15.1 1.0
CB A:OCS131 4.4 14.2 1.0
CA A:OCS131 4.5 14.0 1.0
O A:HOH536 4.6 11.7 1.0
OE2 A:GLU175 4.7 17.5 1.0
N A:LEU132 4.9 14.2 1.0
CD A:GLU175 4.9 13.3 1.0
O A:GLY130 4.9 15.2 1.0

Nickel binding site 2 out of 8 in 5jf0

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Nickel binding site 2 out of 8 in the Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Tripeptide Met-Ala-Arg


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 in Complex with Tripeptide Met-Ala-Arg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni303

b:21.0
occ:1.00
 O A:HOH582 1.8 32.6 1.0
NE2 A:HIS55 2.0 17.7 1.0
O A:HOH640 2.1 29.6 1.0
CE1 A:HIS55 3.0 17.7 1.0
CD2 A:HIS55 3.0 17.4 1.0
NE2 A:GLN51 4.1 20.6 1.0
ND1 A:HIS55 4.1 15.2 1.0
CG A:HIS55 4.2 16.2 1.0
CE A:MET61 4.4 32.4 1.0
O A:HOH688 4.5 32.8 1.0
CG A:GLN51 4.6 17.2 1.0
CD A:GLN51 4.8 18.5 1.0

Nickel binding site 3 out of 8 in 5jf0

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Nickel binding site 3 out of 8 in the Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Tripeptide Met-Ala-Arg


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 in Complex with Tripeptide Met-Ala-Arg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni304

b:20.6
occ:1.00
 NE2 A:HIS118 2.0 14.1 1.0
O A:HOH623 2.1 26.9 1.0
O A:HOH645 2.2 28.4 1.0
O A:HOH629 2.3 29.2 1.0
CD2 A:HIS118 3.0 13.7 1.0
CE1 A:HIS118 3.0 15.7 1.0
ND1 A:HIS118 4.1 13.5 1.0
CG A:HIS118 4.1 12.4 1.0
O A:HOH656 4.2 41.2 1.0
O A:HOH683 4.3 48.3 1.0
O A:HOH634 4.3 20.6 1.0
O A:HOH612 4.4 20.0 1.0
O A:HOH698 4.4 29.5 1.0
CE1 A:HIS145 4.9 13.8 1.0

Nickel binding site 4 out of 8 in 5jf0

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Nickel binding site 4 out of 8 in the Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Tripeptide Met-Ala-Arg


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 in Complex with Tripeptide Met-Ala-Arg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni305

b:15.0
occ:1.00
 OE2 A:GLU190 1.9 23.9 1.0
O A:HOH447 2.0 16.3 1.0
O A:HOH526 2.1 14.6 1.0
CD A:GLU190 2.6 22.4 1.0
OE1 A:GLU190 2.7 22.0 1.0
O A:HOH424 3.8 31.6 1.0
CG A:GLU190 4.1 22.9 1.0
O A:TYR185 4.1 11.4 1.0
O A:ILE188 4.5 14.6 1.0
CA A:GLU190 4.6 22.1 1.0
CB A:GLU190 4.6 22.4 1.0

Nickel binding site 5 out of 8 in 5jf0

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Nickel binding site 5 out of 8 in the Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Tripeptide Met-Ala-Arg


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 in Complex with Tripeptide Met-Ala-Arg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni306

b:13.8
occ:1.00
 NE2 A:HIS145 2.0 11.6 1.0
O A:ACT301 2.0 14.4 1.0
O A:HOH634 2.3 20.6 1.0
C A:ACT301 2.8 14.8 1.0
CH3 A:ACT301 2.9 11.8 1.0
CD2 A:HIS145 3.0 11.7 1.0
CE1 A:HIS145 3.0 13.8 1.0
O A:HOH648 3.8 26.1 1.0
O A:HOH623 4.1 26.9 1.0
OXT A:ACT301 4.1 16.8 1.0
CG A:HIS145 4.1 11.2 1.0
ND1 A:HIS145 4.1 11.6 1.0
O A:HOH452 4.2 25.9 1.0
CD2 A:HIS118 4.6 13.7 1.0
O A:HOH677 4.6 26.7 1.0
NE2 A:HIS118 4.9 14.1 1.0
CG1 A:VAL115 5.0 11.7 1.0

Nickel binding site 6 out of 8 in 5jf0

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Nickel binding site 6 out of 8 in the Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Tripeptide Met-Ala-Arg


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 in Complex with Tripeptide Met-Ala-Arg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni307

b:34.6
occ:1.00
 O A:HOH429 1.9 25.4 1.0
O A:HOH481 2.1 15.6 1.0
OD2 A:ASP18 2.2 19.2 1.0
NE2 A:HIS12 2.2 26.4 1.0
OD1 A:ASP18 2.3 20.6 1.0
O A:HOH426 2.3 34.9 1.0
O A:HOH647 2.5 32.6 1.0
CG A:ASP18 2.5 19.2 1.0
CE1 A:HIS12 3.0 26.4 1.0
O A:HOH697 3.2 20.0 1.0
CD2 A:HIS12 3.3 26.4 1.0
O A:LEU13 3.9 18.4 1.0
OD2 A:ASP15 3.9 20.7 1.0
CB A:ASP18 4.1 17.5 1.0
ND1 A:HIS12 4.2 26.2 1.0
CG A:ASP15 4.2 20.2 1.0
OD1 A:ASP15 4.3 21.4 1.0
CG A:HIS12 4.4 24.6 1.0
N A:ASP15 4.5 17.5 1.0
O A:HOH712 4.5 50.3 1.0
N A:ASP18 4.7 18.6 1.0
O A:HOH414 4.7 33.0 1.0
CA A:ASP18 4.8 17.9 1.0
CA A:ILE14 4.8 17.0 1.0
C A:LEU13 4.8 17.9 1.0
O A:HOH662 4.9 21.4 1.0

Nickel binding site 7 out of 8 in 5jf0

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Nickel binding site 7 out of 8 in the Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Tripeptide Met-Ala-Arg


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 in Complex with Tripeptide Met-Ala-Arg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni308

b:39.6
occ:1.00
 OE2 A:GLU47 2.2 26.6 1.0
O A:HOH565 2.2 39.4 1.0
OE1 A:GLU43 2.3 30.3 1.0
CD A:GLU47 3.0 21.8 1.0
OE1 A:GLU47 3.0 25.9 1.0
CD A:GLU43 3.1 27.8 1.0
CG A:GLU43 3.7 23.2 1.0
OE2 A:GLU43 3.9 30.1 1.0
NZ A:LYS155 4.0 30.0 1.0
O A:HOH450 4.3 49.1 1.0
CG A:GLU47 4.4 19.6 1.0
CE A:LYS155 4.4 28.4 1.0
O A:HOH718 4.5 50.8 1.0

Nickel binding site 8 out of 8 in 5jf0

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Nickel binding site 8 out of 8 in the Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Tripeptide Met-Ala-Arg


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 in Complex with Tripeptide Met-Ala-Arg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni309

b:29.2
occ:1.00
 OE2 A:GLU151 2.0 20.3 1.0
O A:HOH619 2.6 30.3 1.0
CD A:GLU151 2.8 18.9 1.0
OE1 A:GLU151 2.9 19.9 1.0
O A:HOH630 3.8 38.2 1.0
NH2 A:ARG161 3.9 21.3 1.0
NZ A:LYS159 3.9 25.7 1.0
NE A:ARG161 4.0 17.3 1.0
CG A:GLU151 4.2 15.3 1.0
CZ A:ARG161 4.3 18.9 1.0
CG1 A:VAL116 4.6 15.4 1.0
CE A:LYS159 4.7 22.9 1.0
O A:HOH603 4.9 37.6 1.0
CD A:ARG161 5.0 16.3 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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