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Magnesium in PDB 2vwt: Crystal Structure of Yfau, A Metal Ion Dependent Class II Aldolase From Escherichia Coli K12 - Mg-Pyruvate Product Complex

Enzymatic activity of Crystal Structure of Yfau, A Metal Ion Dependent Class II Aldolase From Escherichia Coli K12 - Mg-Pyruvate Product Complex

All present enzymatic activity of Crystal Structure of Yfau, A Metal Ion Dependent Class II Aldolase From Escherichia Coli K12 - Mg-Pyruvate Product Complex:
4.1.2.20;

Protein crystallography data

The structure of Crystal Structure of Yfau, A Metal Ion Dependent Class II Aldolase From Escherichia Coli K12 - Mg-Pyruvate Product Complex, PDB code: 2vwt was solved by D.Rea, J.F.Rakus, J.A.Gerlt, V.Fulop, T.D.H.Bugg, D.I.Roper, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 52.70 / 1.93
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 105.600, 137.700, 124.100, 90.00, 90.00, 90.00
R / Rfree (%) 16.8 / 20.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Yfau, A Metal Ion Dependent Class II Aldolase From Escherichia Coli K12 - Mg-Pyruvate Product Complex (pdb code 2vwt). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Yfau, A Metal Ion Dependent Class II Aldolase From Escherichia Coli K12 - Mg-Pyruvate Product Complex, PDB code: 2vwt:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 2vwt

Go back to Magnesium Binding Sites List in 2vwt
Magnesium binding site 1 out of 3 in the Crystal Structure of Yfau, A Metal Ion Dependent Class II Aldolase From Escherichia Coli K12 - Mg-Pyruvate Product Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Yfau, A Metal Ion Dependent Class II Aldolase From Escherichia Coli K12 - Mg-Pyruvate Product Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:46.5
occ:1.00
 OE1 A:GLU153 2.1 44.1 1.0
O A:HOH2154 2.1 44.2 1.0
OD2 A:ASP179 2.2 37.2 1.0
O A:HOH2040 2.3 40.6 1.0
O3 A:PYR302 2.4 59.3 1.0
O2 A:PYR302 2.5 58.1 1.0
CD A:GLU153 3.1 42.1 1.0
C2 A:PYR302 3.1 59.5 1.0
C1 A:PYR302 3.2 59.2 1.0
CG A:ASP179 3.3 40.6 1.0
NE2 A:GLN151 3.4 30.5 1.0
OE2 A:GLU153 3.5 38.5 1.0
CB A:ASP179 3.9 40.6 1.0
O A:HOH2039 4.2 43.2 1.0
NH1 A:ARG74 4.2 33.7 1.0
OD1 A:ASP179 4.3 42.6 1.0
CG A:GLU153 4.4 39.8 1.0
O1 A:PYR302 4.4 59.3 1.0
C3 A:PYR302 4.6 58.5 1.0
CD A:GLN151 4.6 32.2 1.0
CB A:GLU153 4.7 39.1 1.0
O A:HOH2067 4.7 38.5 1.0
OE1 A:GLU48 4.8 31.8 1.0
O B:VAL122 4.9 43.6 1.0
OE1 A:GLN151 5.0 36.1 1.0
CG2 B:VAL122 5.0 44.6 1.0

Magnesium binding site 2 out of 3 in 2vwt

Go back to Magnesium Binding Sites List in 2vwt
Magnesium binding site 2 out of 3 in the Crystal Structure of Yfau, A Metal Ion Dependent Class II Aldolase From Escherichia Coli K12 - Mg-Pyruvate Product Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Yfau, A Metal Ion Dependent Class II Aldolase From Escherichia Coli K12 - Mg-Pyruvate Product Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg301

b:37.8
occ:1.00
 OE1 B:GLU153 2.2 34.8 1.0
O C:HOH2094 2.2 35.3 1.0
OD2 B:ASP179 2.2 35.2 1.0
O B:HOH2035 2.2 34.8 1.0
O2 B:PYR302 2.2 40.7 1.0
O3 B:PYR302 2.2 38.6 1.0
C2 B:PYR302 2.9 41.3 1.0
C1 B:PYR302 2.9 40.8 1.0
CD B:GLU153 3.1 38.0 1.0
CG B:ASP179 3.3 36.7 1.0
OE2 B:GLU153 3.5 38.3 1.0
NE2 B:GLN151 3.6 35.4 1.0
CB B:ASP179 3.7 36.5 1.0
O B:HOH2038 3.8 38.9 1.0
NH1 B:ARG74 4.2 30.8 1.0
O1 B:PYR302 4.2 40.3 1.0
O C:VAL122 4.3 36.5 1.0
OD1 B:ASP179 4.3 36.0 1.0
C3 B:PYR302 4.4 36.9 1.0
CG B:GLU153 4.5 36.6 1.0
N B:ASP179 4.5 35.7 1.0
OE1 B:GLU48 4.5 31.7 1.0
O B:HOH2061 4.6 26.2 1.0
CD B:GLN151 4.6 36.3 1.0
CB B:GLU153 4.7 38.4 1.0
CA B:ASP179 4.7 36.4 1.0
NE2 B:HIS49 4.8 33.6 1.0
CA B:GLY176 4.9 36.4 1.0
OE1 B:GLN151 4.9 37.1 1.0

Magnesium binding site 3 out of 3 in 2vwt

Go back to Magnesium Binding Sites List in 2vwt
Magnesium binding site 3 out of 3 in the Crystal Structure of Yfau, A Metal Ion Dependent Class II Aldolase From Escherichia Coli K12 - Mg-Pyruvate Product Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Yfau, A Metal Ion Dependent Class II Aldolase From Escherichia Coli K12 - Mg-Pyruvate Product Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg301

b:47.4
occ:1.00
 OE1 C:GLU153 2.2 42.7 1.0
O A:HOH2112 2.3 46.5 1.0
OD2 C:ASP179 2.3 46.0 1.0
O2 C:PYR302 2.3 51.4 1.0
O3 C:PYR302 2.3 53.6 1.0
O C:HOH2112 2.3 41.5 1.0
CD C:GLU153 3.0 42.3 1.0
C2 C:PYR302 3.0 54.0 1.0
C1 C:PYR302 3.1 53.6 1.0
OE2 C:GLU153 3.3 39.6 1.0
CG C:ASP179 3.3 42.3 1.0
NE2 C:GLN151 3.3 37.9 1.0
CB C:ASP179 3.8 40.5 1.0
CG C:GLU153 4.2 39.1 1.0
NH1 C:ARG74 4.2 34.5 1.0
OD1 C:ASP179 4.3 44.3 1.0
O1 C:PYR302 4.4 50.2 1.0
CD C:GLN151 4.5 38.4 1.0
C3 C:PYR302 4.5 55.3 1.0
O C:HOH2156 4.5 40.8 1.0
O C:HOH2027 4.6 37.8 1.0
CB C:GLU153 4.6 40.3 1.0
O A:VAL122 4.6 35.7 1.0
OE1 C:GLU48 4.7 36.4 1.0
OE1 C:GLN151 4.9 37.3 1.0

Reference:

D.Rea, R.Hovington, J.F.Rakus, J.A.Gerlt, V.Fulop, T.D.H.Bugg, D.I.Roper. Crystal Structure and Functional Assignment of Yfau, A Metal Ion Dependent Class II Aldolase From Escherichia Coli K12. Biochemistry V. 47 9955 2008.
ISSN: ISSN 0006-2960
PubMed: 18754683
DOI: 10.1021/BI800943G
Page generated: Wed Aug 14 05:55:08 2024

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