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Cobalt in PDB 1ofa: Crystal Structure of the Tyrosine-Regulated 3-Deoxy-D-Arabino-Heptulosonate-7-Phosphate Synthase From Saccharomyces Cerevisiae in Complex with Phosphoenolpyruvate and Cobalt(II)

Enzymatic activity of Crystal Structure of the Tyrosine-Regulated 3-Deoxy-D-Arabino-Heptulosonate-7-Phosphate Synthase From Saccharomyces Cerevisiae in Complex with Phosphoenolpyruvate and Cobalt(II)

All present enzymatic activity of Crystal Structure of the Tyrosine-Regulated 3-Deoxy-D-Arabino-Heptulosonate-7-Phosphate Synthase From Saccharomyces Cerevisiae in Complex with Phosphoenolpyruvate and Cobalt(II):
4.1.2.15;

Protein crystallography data

The structure of Crystal Structure of the Tyrosine-Regulated 3-Deoxy-D-Arabino-Heptulosonate-7-Phosphate Synthase From Saccharomyces Cerevisiae in Complex with Phosphoenolpyruvate and Cobalt(II), PDB code: 1ofa was solved by V.Koenig, A.Pfeil, G.Heinrich, G.H.Braus, T.R.Schneider, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 17.57 / 2.01
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 196.210, 50.610, 64.980, 90.00, 106.33, 90.00
R / Rfree (%) 15.5 / 20.4

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Crystal Structure of the Tyrosine-Regulated 3-Deoxy-D-Arabino-Heptulosonate-7-Phosphate Synthase From Saccharomyces Cerevisiae in Complex with Phosphoenolpyruvate and Cobalt(II) (pdb code 1ofa). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 2 binding sites of Cobalt where determined in the Crystal Structure of the Tyrosine-Regulated 3-Deoxy-D-Arabino-Heptulosonate-7-Phosphate Synthase From Saccharomyces Cerevisiae in Complex with Phosphoenolpyruvate and Cobalt(II), PDB code: 1ofa:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in 1ofa

Go back to Cobalt Binding Sites List in 1ofa
Cobalt binding site 1 out of 2 in the Crystal Structure of the Tyrosine-Regulated 3-Deoxy-D-Arabino-Heptulosonate-7-Phosphate Synthase From Saccharomyces Cerevisiae in Complex with Phosphoenolpyruvate and Cobalt(II)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Crystal Structure of the Tyrosine-Regulated 3-Deoxy-D-Arabino-Heptulosonate-7-Phosphate Synthase From Saccharomyces Cerevisiae in Complex with Phosphoenolpyruvate and Cobalt(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co400

b:26.5
occ:1.00
 OE2 B:GLU316 1.9 22.1 1.0
OD2 B:ASP342 2.0 22.3 1.0
O A:HOH2143 2.1 29.9 1.0
NE2 B:HIS282 2.2 18.2 1.0
SG B:CYS76 2.6 22.3 1.0
CD B:GLU316 2.7 20.8 1.0
OE1 B:GLU316 2.9 27.7 1.0
CG B:ASP342 3.0 26.2 1.0
CD2 B:HIS282 3.1 18.8 1.0
CE1 B:HIS282 3.2 18.7 1.0
CB B:ASP342 3.3 24.1 1.0
CB B:CYS76 3.6 19.4 1.0
O1 B:PEP508 3.7 27.8 1.0
O2 B:GOL603 3.9 36.9 1.0
CG B:GLU316 4.0 19.7 1.0
O B:HOH2125 4.1 25.5 1.0
OD1 B:ASP342 4.1 25.4 1.0
NH2 B:ARG107 4.1 19.2 1.0
C1 B:PEP508 4.1 30.0 1.0
CA B:CYS76 4.2 22.3 1.0
NZ B:LYS112 4.2 18.4 1.0
ND1 B:HIS282 4.2 18.4 1.0
CG B:HIS282 4.3 18.8 1.0
C2 B:PEP508 4.6 25.7 1.0
CA B:ASP342 4.7 25.2 1.0
O2' B:PEP508 4.7 32.3 1.0
C3 B:PEP508 4.7 21.7 1.0
C3 B:GOL603 4.8 44.5 1.0
O B:CYS76 4.8 24.5 1.0
N B:ASP342 4.8 23.8 1.0
C2 B:GOL603 4.9 44.6 1.0
CZ B:ARG107 4.9 21.2 1.0
C B:CYS76 4.9 24.2 1.0
CE B:LYS112 4.9 18.1 1.0

Cobalt binding site 2 out of 2 in 1ofa

Go back to Cobalt Binding Sites List in 1ofa
Cobalt binding site 2 out of 2 in the Crystal Structure of the Tyrosine-Regulated 3-Deoxy-D-Arabino-Heptulosonate-7-Phosphate Synthase From Saccharomyces Cerevisiae in Complex with Phosphoenolpyruvate and Cobalt(II)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Crystal Structure of the Tyrosine-Regulated 3-Deoxy-D-Arabino-Heptulosonate-7-Phosphate Synthase From Saccharomyces Cerevisiae in Complex with Phosphoenolpyruvate and Cobalt(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co400

b:27.3
occ:1.00
 OE2 A:GLU316 1.8 26.6 1.0
OD1 A:ASP342 2.1 31.2 1.0
O B:HOH2141 2.1 31.6 1.0
NE2 A:HIS282 2.1 19.0 1.0
SG A:CYS76 2.6 21.3 1.0
CD A:GLU316 2.7 22.6 1.0
OE1 A:GLU316 3.0 27.3 1.0
CE1 A:HIS282 3.1 24.0 1.0
CG A:ASP342 3.1 25.1 1.0
CD2 A:HIS282 3.2 18.9 1.0
CB A:ASP342 3.4 26.2 1.0
CB A:CYS76 3.6 20.7 1.0
O1 A:PEP508 3.7 27.8 1.0
CG A:GLU316 4.0 22.4 1.0
C1 A:PEP508 4.1 30.0 1.0
O A:HOH2118 4.1 29.9 1.0
NZ A:LYS112 4.1 20.3 1.0
OD2 A:ASP342 4.1 32.0 1.0
NH2 A:ARG107 4.2 20.1 1.0
ND1 A:HIS282 4.2 22.4 1.0
CA A:CYS76 4.2 22.3 1.0
CG A:HIS282 4.3 22.7 1.0
O A:HOH2132 4.5 37.9 1.0
C2 A:PEP508 4.5 25.7 1.0
C3 A:PEP508 4.6 21.7 1.0
O2' A:PEP508 4.6 32.3 1.0
CA A:ASP342 4.7 25.9 1.0
N A:ASP342 4.8 24.6 1.0
O A:CYS76 4.8 23.9 1.0
CE A:LYS112 4.9 21.7 1.0
CZ A:ARG107 4.9 23.7 1.0
C A:CYS76 4.9 22.8 1.0

Reference:

V.Koenig, A.Pfeil, G.H.Braus, T.R.Schneider. Substrate and Metal Complexes of 3-Deoxy-D- Arabino-Heptulosonate-7-Phosphate Synthase From Saccharomyces Cerevisiae Provide New Insights Into the Catalytic Mechanism J.Mol.Biol. V. 337 675 2004.
ISSN: ISSN 0022-2836
PubMed: 15019786
DOI: 10.1016/J.JMB.2004.01.055
Page generated: Tue Jul 30 14:29:35 2024

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