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Bromine in PDB 3t07: Crystal Structure of S. Aureus Pyruvate Kinase in Complex with A Naturally Occurring Bis-Indole Alkaloid

Enzymatic activity of Crystal Structure of S. Aureus Pyruvate Kinase in Complex with A Naturally Occurring Bis-Indole Alkaloid

All present enzymatic activity of Crystal Structure of S. Aureus Pyruvate Kinase in Complex with A Naturally Occurring Bis-Indole Alkaloid:
2.7.1.40;

Protein crystallography data

The structure of Crystal Structure of S. Aureus Pyruvate Kinase in Complex with A Naturally Occurring Bis-Indole Alkaloid, PDB code: 3t07 was solved by L.J.Worrall, M.Vuckovic, N.C.J.Strynadka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 60.00 / 3.30
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 83.960, 111.910, 112.030, 86.05, 72.14, 80.88
R / Rfree (%) 19.8 / 22.6

Bromine Binding Sites:

The binding sites of Bromine atom in the Crystal Structure of S. Aureus Pyruvate Kinase in Complex with A Naturally Occurring Bis-Indole Alkaloid (pdb code 3t07). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 4 binding sites of Bromine where determined in the Crystal Structure of S. Aureus Pyruvate Kinase in Complex with A Naturally Occurring Bis-Indole Alkaloid, PDB code: 3t07:
Jump to Bromine binding site number: 1; 2; 3; 4;

Bromine binding site 1 out of 4 in 3t07

Go back to Bromine Binding Sites List in 3t07
Bromine binding site 1 out of 4 in the Crystal Structure of S. Aureus Pyruvate Kinase in Complex with A Naturally Occurring Bis-Indole Alkaloid


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Crystal Structure of S. Aureus Pyruvate Kinase in Complex with A Naturally Occurring Bis-Indole Alkaloid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br586

b:0.4
occ:1.00
 BR1 B:09C586 0.0 0.4 1.0
C13 B:09C586 1.9 0.9 1.0
C9 B:09C586 2.7 0.3 1.0
C3 B:09C586 2.9 0.3 1.0
CD2 B:LEU370 3.7 79.2 1.0
CB A:ALA358 3.8 0.9 1.0
CB B:ASN369 3.8 0.8 1.0
CA A:ALA358 3.9 0.2 1.0
C17 B:09C586 4.0 0.9 1.0
CD1 A:ILE361 4.0 88.4 1.0
CG B:LEU370 4.0 86.9 1.0
C5 B:09C586 4.2 0.3 1.0
CA B:THR366 4.2 91.9 1.0
CG2 A:THR353 4.4 0.4 1.0
OG1 B:THR366 4.5 91.2 1.0
CG B:ASN369 4.5 0.6 1.0
C19 B:09C586 4.6 0.2 1.0
ND2 B:ASN369 4.6 0.1 1.0
CD1 B:LEU370 4.6 79.8 1.0
N A:ALA358 4.7 0.8 1.0
O B:THR366 4.7 94.7 1.0
O A:ALA358 4.8 0.2 1.0
C A:ALA358 4.9 0.8 1.0
CB B:THR366 4.9 90.0 1.0
N B:THR366 4.9 99.6 1.0

Bromine binding site 2 out of 4 in 3t07

Go back to Bromine Binding Sites List in 3t07
Bromine binding site 2 out of 4 in the Crystal Structure of S. Aureus Pyruvate Kinase in Complex with A Naturally Occurring Bis-Indole Alkaloid


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Crystal Structure of S. Aureus Pyruvate Kinase in Complex with A Naturally Occurring Bis-Indole Alkaloid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br586

b:0.7
occ:1.00
 BR2 B:09C586 0.0 0.7 1.0
C14 B:09C586 1.9 0.3 1.0
C10 B:09C586 2.8 0.3 1.0
C4 B:09C586 3.0 0.8 1.0
CB A:ASN369 3.8 0.5 1.0
CD2 A:LEU370 3.8 97.2 1.0
CB B:ALA358 3.9 0.8 1.0
CA B:ALA358 3.9 0.6 1.0
CD1 B:ILE361 3.9 98.5 1.0
CG A:LEU370 4.1 0.9 1.0
C18 B:09C586 4.1 0.6 1.0
CA A:THR366 4.1 0.3 1.0
OG1 A:THR366 4.2 0.9 1.0
C6 B:09C586 4.3 0.2 1.0
CG A:ASN369 4.5 0.9 1.0
CG2 B:THR353 4.5 0.0 1.0
ND2 A:ASN369 4.5 0.2 1.0
CB A:THR366 4.7 0.7 1.0
CD1 A:LEU370 4.7 0.5 1.0
O A:THR366 4.7 0.0 1.0
C20 B:09C586 4.7 0.4 1.0
N A:THR366 4.7 0.5 1.0
O B:ALA358 4.8 0.1 1.0
N B:ALA358 4.8 0.8 1.0
C B:ALA358 4.9 1.0 1.0
C A:THR366 4.9 0.5 1.0
O A:HIS365 4.9 91.8 1.0

Bromine binding site 3 out of 4 in 3t07

Go back to Bromine Binding Sites List in 3t07
Bromine binding site 3 out of 4 in the Crystal Structure of S. Aureus Pyruvate Kinase in Complex with A Naturally Occurring Bis-Indole Alkaloid


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Crystal Structure of S. Aureus Pyruvate Kinase in Complex with A Naturally Occurring Bis-Indole Alkaloid within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Br586

b:0.7
occ:1.00
 BR1 D:09C586 0.0 0.7 1.0
C13 D:09C586 1.9 0.5 1.0
C9 D:09C586 2.7 0.9 1.0
C3 D:09C586 3.0 0.4 1.0
CB C:ALA358 3.8 0.6 1.0
CA C:ALA358 3.8 0.8 1.0
CD1 C:ILE361 3.9 0.6 1.0
CB D:ASN369 3.9 0.2 1.0
CD2 D:LEU370 4.0 0.6 1.0
C17 D:09C586 4.1 0.5 1.0
CA D:THR366 4.2 0.3 1.0
CG D:LEU370 4.2 0.6 1.0
OG1 D:THR366 4.3 0.3 1.0
C5 D:09C586 4.3 0.6 1.0
CG D:ASN369 4.5 0.2 1.0
ND2 D:ASN369 4.6 0.7 1.0
CG2 C:THR353 4.6 0.4 1.0
O C:ALA358 4.6 0.8 1.0
N C:ALA358 4.7 0.3 1.0
C C:ALA358 4.7 1.0 1.0
C19 D:09C586 4.7 0.4 1.0
CB D:THR366 4.8 0.8 1.0
N D:THR366 4.8 0.0 1.0
CD1 D:LEU370 4.8 0.8 1.0
O D:THR366 4.9 0.3 1.0

Bromine binding site 4 out of 4 in 3t07

Go back to Bromine Binding Sites List in 3t07
Bromine binding site 4 out of 4 in the Crystal Structure of S. Aureus Pyruvate Kinase in Complex with A Naturally Occurring Bis-Indole Alkaloid


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Crystal Structure of S. Aureus Pyruvate Kinase in Complex with A Naturally Occurring Bis-Indole Alkaloid within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Br586

b:0.1
occ:1.00
 BR2 D:09C586 0.0 0.1 1.0
C14 D:09C586 1.9 0.3 1.0
C10 D:09C586 2.7 0.5 1.0
C4 D:09C586 2.9 0.2 1.0
CD2 C:LEU370 3.8 87.7 1.0
CB C:ASN369 3.8 0.2 1.0
CB D:ALA358 3.9 0.4 1.0
CA D:ALA358 4.0 0.7 1.0
CG C:LEU370 4.0 90.3 1.0
CD1 D:ILE361 4.0 99.1 1.0
C18 D:09C586 4.0 0.6 1.0
CA C:THR366 4.2 0.2 1.0
C6 D:09C586 4.2 0.3 1.0
OG1 C:THR366 4.3 0.5 1.0
CG C:ASN369 4.4 0.9 1.0
CG2 D:THR353 4.4 0.9 1.0
ND2 C:ASN369 4.5 0.8 1.0
CD1 C:LEU370 4.6 87.5 1.0
O C:THR366 4.7 0.7 1.0
C20 D:09C586 4.7 0.4 1.0
CB C:THR366 4.8 0.3 1.0
N C:THR366 4.8 0.8 1.0
N D:ALA358 4.8 0.6 1.0
O C:HIS365 4.9 0.1 1.0
C C:THR366 4.9 0.7 1.0
O D:ALA358 5.0 93.5 1.0
C D:ALA358 5.0 0.2 1.0
N C:LEU370 5.0 98.3 1.0
CA C:ASN369 5.0 0.5 1.0

Reference:

R.Zoraghi, L.Worrall, R.H.See, W.Strangman, W.L.Popplewell, H.Gong, T.Samaai, R.D.Swayze, S.Kaur, M.Vuckovic, B.B.Finlay, R.C.Brunham, W.R.Mcmaster, M.T.Davies-Coleman, N.C.Strynadka, R.J.Andersen, N.E.Reiner. Methicillin-Resistant Staphylococcus Aureus (Mrsa) Pyruvate Kinase As A Target For Bis-Indole Alkaloids with Antibacterial Activities. J.Biol.Chem. V. 286 44716 2011.
ISSN: ISSN 0021-9258
PubMed: 22030393
DOI: 10.1074/JBC.M111.289033
Page generated: Wed Jul 10 20:22:59 2024

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