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Chlorine in PDB 2ypp: 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase in Complex with 3 Tyrosine Molecules

Enzymatic activity of 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase in Complex with 3 Tyrosine Molecules

All present enzymatic activity of 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase in Complex with 3 Tyrosine Molecules:
2.5.1.54;

Protein crystallography data

The structure of 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase in Complex with 3 Tyrosine Molecules, PDB code: 2ypp was solved by N.J.Blackmore, S.Reichau, W.Jiao, R.D.Hutton, E.N.Baker, G.B.Jameson, E.J.Parker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.02 / 2.30
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 203.449, 203.449, 66.490, 90.00, 90.00, 120.00
R / Rfree (%) 13.923 / 16.375

Other elements in 2ypp:

The structure of 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase in Complex with 3 Tyrosine Molecules also contains other interesting chemical elements:

Manganese (Mn) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase in Complex with 3 Tyrosine Molecules (pdb code 2ypp). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase in Complex with 3 Tyrosine Molecules, PDB code: 2ypp:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 2ypp

Go back to Chlorine Binding Sites List in 2ypp
Chlorine binding site 1 out of 3 in the 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase in Complex with 3 Tyrosine Molecules


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase in Complex with 3 Tyrosine Molecules within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl903

b:39.4
occ:1.00
OG A:SER62 3.2 16.4 1.0
N A:SER62 3.4 15.1 1.0
CB A:SER62 3.5 15.3 1.0
CD A:PRO61 3.8 14.3 1.0
N A:PRO61 3.9 14.3 1.0
CB A:VAL60 4.0 13.7 1.0
CG2 A:VAL60 4.0 13.5 1.0
CA A:SER62 4.1 15.2 1.0
CB A:PRO61 4.3 14.8 1.0
C A:PRO61 4.3 15.1 1.0
CA A:PRO61 4.4 14.7 1.0
C A:VAL60 4.4 13.9 1.0
CG A:PRO61 4.6 14.7 1.0
CB B:SER189 4.7 27.5 1.0
CA A:VAL60 4.8 13.8 1.0
O A:VAL60 5.0 14.0 1.0

Chlorine binding site 2 out of 3 in 2ypp

Go back to Chlorine Binding Sites List in 2ypp
Chlorine binding site 2 out of 3 in the 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase in Complex with 3 Tyrosine Molecules


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase in Complex with 3 Tyrosine Molecules within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl901

b:35.8
occ:1.00
O B:HOH2001 3.0 22.0 1.0
N B:LEU18 3.2 25.3 1.0
NH2 B:ARG23 3.2 18.2 1.0
NE B:ARG23 3.4 18.9 1.0
CZ B:ARG23 3.8 18.4 1.0
CA B:PRO17 3.8 30.6 1.0
CB B:LEU18 3.9 21.7 1.0
CG B:LEU18 3.9 20.9 1.0
C B:PRO17 4.0 27.8 1.0
CA B:LEU18 4.1 22.8 1.0
CB B:PRO17 4.3 33.0 1.0
CD1 B:TYR801 4.4 17.7 1.0
CD1 B:LEU18 4.4 20.0 1.0
CE1 B:TYR801 4.5 16.6 1.0
O B:LEU18 4.6 23.2 1.0
CD B:ARG23 4.6 19.6 1.0
CB B:ARG23 4.8 20.3 1.0
CG B:ARG23 4.8 20.1 1.0
C B:LEU18 4.9 23.2 1.0

Chlorine binding site 3 out of 3 in 2ypp

Go back to Chlorine Binding Sites List in 2ypp
Chlorine binding site 3 out of 3 in the 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase in Complex with 3 Tyrosine Molecules


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase in Complex with 3 Tyrosine Molecules within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl905

b:39.0
occ:1.00
OG B:SER62 3.0 13.8 1.0
O A:HOH2061 3.4 28.1 1.0
N B:SER62 3.4 12.6 1.0
CB B:SER62 3.6 13.3 1.0
CD B:PRO61 3.8 12.1 1.0
N B:PRO61 3.9 12.0 1.0
CG2 B:VAL60 3.9 12.1 1.0
CB B:VAL60 4.0 12.0 1.0
CA B:SER62 4.1 12.9 1.0
CB B:PRO61 4.2 12.4 1.0
C B:PRO61 4.4 12.4 1.0
CA B:PRO61 4.4 12.2 1.0
CG B:PRO61 4.5 12.3 1.0
C B:VAL60 4.5 11.9 1.0
NH1 A:ARG100 4.7 18.8 0.5
CA B:VAL60 4.9 11.8 1.0
CB A:SER189 4.9 31.9 1.0

Reference:

N.J.Blackmore, S.Reichau, W.Jiao, R.D.Hutton, E.N.Baker, G.B.Jameson, E.J.Parker. Three Sites and You Are Out: Ternary Synergistic Allostery Controls Aromatic Aminoacid Biosynthesis in Mycobacterium Tuberculosis. J.Mol.Biol. V. 425 1582 2013.
ISSN: ISSN 0022-2836
PubMed: 23274137
DOI: 10.1016/J.JMB.2012.12.019
Page generated: Sat Jul 20 15:16:29 2024

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