Atomistry » Magnesium » PDB 2vu9-2wb1 » 2vwt
Atomistry »
  Magnesium »
    PDB 2vu9-2wb1 »
      2vwt »

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: Sun Aug 10 15:33:48 2025

Last articles

Mg in 5Y9Z
Mg in 5Y8V
Mg in 5Y88
Mg in 5Y8H
Mg in 5Y8B
Mg in 5Y5P
Mg in 5Y5Q
Mg in 5Y6Z
Mg in 5XYM
Mg in 5XYU
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy