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Platinum in PDB 5fm0: Crystal Structure of the 6-Carboxyhexanoate-Coa Ligase (Biow)From Bacillus Subtilis (PTCL4 Derivative)

Enzymatic activity of Crystal Structure of the 6-Carboxyhexanoate-Coa Ligase (Biow)From Bacillus Subtilis (PTCL4 Derivative)

All present enzymatic activity of Crystal Structure of the 6-Carboxyhexanoate-Coa Ligase (Biow)From Bacillus Subtilis (PTCL4 Derivative):
6.2.1.14;

Protein crystallography data

The structure of Crystal Structure of the 6-Carboxyhexanoate-Coa Ligase (Biow)From Bacillus Subtilis (PTCL4 Derivative), PDB code: 5fm0 was solved by L.Moynie, M.Wang, D.J.Campopiano, J.H.Naismith, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 83.35 / 2.44
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 50.610, 78.360, 166.700, 90.00, 90.00, 90.00
R / Rfree (%) 19.8 / 24.2

Other elements in 5fm0:

The structure of Crystal Structure of the 6-Carboxyhexanoate-Coa Ligase (Biow)From Bacillus Subtilis (PTCL4 Derivative) also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Platinum Binding Sites:

The binding sites of Platinum atom in the Crystal Structure of the 6-Carboxyhexanoate-Coa Ligase (Biow)From Bacillus Subtilis (PTCL4 Derivative) (pdb code 5fm0). This binding sites where shown within 5.0 Angstroms radius around Platinum atom.
In total 6 binding sites of Platinum where determined in the Crystal Structure of the 6-Carboxyhexanoate-Coa Ligase (Biow)From Bacillus Subtilis (PTCL4 Derivative), PDB code: 5fm0:
Jump to Platinum binding site number: 1; 2; 3; 4; 5; 6;

Platinum binding site 1 out of 6 in 5fm0

Go back to Platinum Binding Sites List in 5fm0
Platinum binding site 1 out of 6 in the Crystal Structure of the 6-Carboxyhexanoate-Coa Ligase (Biow)From Bacillus Subtilis (PTCL4 Derivative)


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 1 of Crystal Structure of the 6-Carboxyhexanoate-Coa Ligase (Biow)From Bacillus Subtilis (PTCL4 Derivative) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt1260

b:83.4
occ:0.50
SD A:MET16 2.3 0.3 1.0
CG A:MET16 3.2 89.3 1.0
CE A:MET16 3.2 84.1 1.0
PT A:PT1262 3.9 0.4 0.5
O A:LYS57 4.1 57.0 1.0
CB A:MET16 4.6 70.6 1.0
N A:LYS57 4.8 82.6 1.0

Platinum binding site 2 out of 6 in 5fm0

Go back to Platinum Binding Sites List in 5fm0
Platinum binding site 2 out of 6 in the Crystal Structure of the 6-Carboxyhexanoate-Coa Ligase (Biow)From Bacillus Subtilis (PTCL4 Derivative)


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 2 of Crystal Structure of the 6-Carboxyhexanoate-Coa Ligase (Biow)From Bacillus Subtilis (PTCL4 Derivative) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt1261

b:0.2
occ:1.00
CG A:MET209 2.6 73.7 0.5
SD A:MET209 2.7 80.5 0.5
CD A:LYS101 3.8 0.5 1.0
CB A:LYS101 4.0 79.2 1.0
CB A:MET209 4.0 67.8 0.5
CE A:MET209 4.3 71.8 0.5
CG A:LYS101 4.5 98.6 1.0
CB A:MET209 4.6 62.4 0.5
CD2 A:LEU98 4.9 62.1 1.0
CE A:LYS101 4.9 1.0 1.0

Platinum binding site 3 out of 6 in 5fm0

Go back to Platinum Binding Sites List in 5fm0
Platinum binding site 3 out of 6 in the Crystal Structure of the 6-Carboxyhexanoate-Coa Ligase (Biow)From Bacillus Subtilis (PTCL4 Derivative)


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 3 of Crystal Structure of the 6-Carboxyhexanoate-Coa Ligase (Biow)From Bacillus Subtilis (PTCL4 Derivative) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt1262

b:0.4
occ:0.50
SD A:MET16 2.3 0.3 1.0
OD1 A:ASN17 3.2 92.0 1.0
CG A:MET16 3.3 89.3 1.0
CE A:MET16 3.5 84.1 1.0
CB A:MET16 3.7 70.6 1.0
PT A:PT1260 3.9 83.4 0.5
CD A:LYS25 4.0 71.5 1.0
CG A:ASN17 4.3 93.1 1.0
NZ A:LYS25 4.6 76.3 1.0
CB A:LYS25 4.7 63.2 1.0
C A:MET16 4.8 73.0 1.0
CE A:LYS25 4.9 78.1 1.0
CA A:MET16 4.9 67.3 1.0
CG A:LYS25 4.9 69.3 1.0
O A:MET16 4.9 64.6 1.0

Platinum binding site 4 out of 6 in 5fm0

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Platinum binding site 4 out of 6 in the Crystal Structure of the 6-Carboxyhexanoate-Coa Ligase (Biow)From Bacillus Subtilis (PTCL4 Derivative)


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 4 of Crystal Structure of the 6-Carboxyhexanoate-Coa Ligase (Biow)From Bacillus Subtilis (PTCL4 Derivative) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Pt1259

b:0.6
occ:0.50
SD B:MET16 2.2 98.3 1.0
OD1 B:ASN17 3.4 88.2 1.0
CG B:MET16 3.4 85.0 1.0
CE B:MET16 3.4 87.2 1.0
CD B:LYS25 3.6 79.7 1.0
CB B:MET16 3.8 66.7 1.0
PT B:PT1261 4.3 90.1 0.5
CB B:LYS25 4.3 72.8 1.0
NZ B:LYS25 4.4 75.8 1.0
CG B:LYS25 4.5 80.8 1.0
CG B:ASN17 4.5 88.4 1.0
CE B:LYS25 4.5 73.3 1.0
C B:MET16 4.9 71.3 1.0
O B:MET16 4.9 59.8 1.0
CA B:MET16 5.0 62.9 1.0

Platinum binding site 5 out of 6 in 5fm0

Go back to Platinum Binding Sites List in 5fm0
Platinum binding site 5 out of 6 in the Crystal Structure of the 6-Carboxyhexanoate-Coa Ligase (Biow)From Bacillus Subtilis (PTCL4 Derivative)


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 5 of Crystal Structure of the 6-Carboxyhexanoate-Coa Ligase (Biow)From Bacillus Subtilis (PTCL4 Derivative) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Pt1260

b:0.9
occ:1.00
SD B:MET209 2.7 73.5 0.5
CG B:MET209 2.9 59.1 0.5
CE B:MET209 3.3 58.8 0.5
CD B:LYS101 3.9 0.3 1.0
CB B:LYS101 4.0 64.0 1.0
CB B:MET209 4.4 57.8 0.5
CG B:LYS101 4.6 82.2 1.0
CE B:MET209 4.6 48.6 0.5
O B:LYS101 4.9 68.8 1.0
CB B:MET209 4.9 36.2 0.5

Platinum binding site 6 out of 6 in 5fm0

Go back to Platinum Binding Sites List in 5fm0
Platinum binding site 6 out of 6 in the Crystal Structure of the 6-Carboxyhexanoate-Coa Ligase (Biow)From Bacillus Subtilis (PTCL4 Derivative)


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 6 of Crystal Structure of the 6-Carboxyhexanoate-Coa Ligase (Biow)From Bacillus Subtilis (PTCL4 Derivative) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Pt1261

b:90.1
occ:0.50
SD B:MET16 2.5 98.3 1.0
CG B:MET16 3.0 85.0 1.0
CE B:MET16 3.2 87.2 1.0
O B:LYS57 3.8 78.8 1.0
PT B:PT1259 4.3 0.6 0.5
CB B:MET16 4.4 66.7 1.0
N B:LYS57 4.6 79.3 1.0
C B:LYS57 4.9 74.6 1.0

Reference:

M.Wang, L.Moynie, P.J.Harrison, V.Kelly, A.Piper, J.H.Naismith, D.J.Campopiano. Using the Pimeloyl-Coa Synthetase Adenylation Fold to Synthesize Fatty Acid Thioesters. Nat. Chem. Biol. V. 13 660 2017.
ISSN: ESSN 1552-4469
PubMed: 28414710
DOI: 10.1038/NCHEMBIO.2361
Page generated: Wed Dec 16 02:05:14 2020

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