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Magnesium in PDB 2dw6: Crystal Structure of the Mutant K184A of D-Tartrate Dehydratase From Bradyrhizobium Japonicum Complexed with Mg++ and D-Tartrate

Enzymatic activity of Crystal Structure of the Mutant K184A of D-Tartrate Dehydratase From Bradyrhizobium Japonicum Complexed with Mg++ and D-Tartrate

All present enzymatic activity of Crystal Structure of the Mutant K184A of D-Tartrate Dehydratase From Bradyrhizobium Japonicum Complexed with Mg++ and D-Tartrate:
4.2.1.81;

Protein crystallography data

The structure of Crystal Structure of the Mutant K184A of D-Tartrate Dehydratase From Bradyrhizobium Japonicum Complexed with Mg++ and D-Tartrate, PDB code: 2dw6 was solved by A.A.Fedorov, E.V.Fedorov, W.S.Yew, B.M.Wood, J.A.Gerlt, S.C.Almo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 2.30
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 150.997, 150.997, 444.101, 90.00, 90.00, 120.00
R / Rfree (%) 20.9 / 23.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Mutant K184A of D-Tartrate Dehydratase From Bradyrhizobium Japonicum Complexed with Mg++ and D-Tartrate (pdb code 2dw6). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of the Mutant K184A of D-Tartrate Dehydratase From Bradyrhizobium Japonicum Complexed with Mg++ and D-Tartrate, PDB code: 2dw6:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 2dw6

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Magnesium binding site 1 out of 4 in the Crystal Structure of the Mutant K184A of D-Tartrate Dehydratase From Bradyrhizobium Japonicum Complexed with Mg++ and D-Tartrate


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 the Mutant K184A of D-Tartrate Dehydratase From Bradyrhizobium Japonicum Complexed with Mg++ and D-Tartrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2001

b:39.1
occ:1.00
 O A:HOH2002 1.9 27.6 1.0
OD2 A:ASP213 2.0 36.5 1.0
OE2 A:GLU239 2.1 40.4 1.0
O2 A:TAR1001 2.1 37.8 1.0
O11 A:TAR1001 2.1 40.9 1.0
OE1 A:GLU265 2.1 41.2 1.0
C1 A:TAR1001 2.7 39.3 1.0
C2 A:TAR1001 2.8 37.6 1.0
CD A:GLU265 3.0 40.2 1.0
CG A:ASP213 3.0 39.0 1.0
CD A:GLU239 3.2 40.4 1.0
OE2 A:GLU265 3.3 40.4 1.0
OD1 A:ASP213 3.4 38.3 1.0
NZ A:LYS182 3.8 37.9 1.0
O1 A:TAR1001 3.9 39.8 1.0
OD1 A:ASN215 4.0 39.2 1.0
OE1 A:GLU239 4.0 41.1 1.0
CG A:GLU239 4.0 39.8 1.0
C3 A:TAR1001 4.1 38.6 1.0
O A:HOH2025 4.2 30.6 1.0
CB A:ASP213 4.4 38.9 1.0
CG A:GLU265 4.4 38.5 1.0
O3 A:TAR1001 4.4 41.5 1.0
CE A:LYS182 4.6 37.8 1.0
CD2 A:HIS322 4.6 35.5 1.0
CG A:ASN215 4.7 38.7 1.0
OE1 A:GLU240 4.7 55.7 1.0
C4 A:TAR1001 4.9 37.9 1.0

Magnesium binding site 2 out of 4 in 2dw6

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Magnesium binding site 2 out of 4 in the Crystal Structure of the Mutant K184A of D-Tartrate Dehydratase From Bradyrhizobium Japonicum Complexed with Mg++ and D-Tartrate


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 the Mutant K184A of D-Tartrate Dehydratase From Bradyrhizobium Japonicum Complexed with Mg++ and D-Tartrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2002

b:39.9
occ:1.00
 OE2 B:GLU239 1.9 32.6 1.0
O B:HOH2003 2.0 29.8 1.0
OD2 B:ASP213 2.0 39.6 1.0
OE1 B:GLU265 2.1 31.4 1.0
O11 B:TAR1002 2.1 40.0 1.0
O2 B:TAR1002 2.2 35.2 1.0
C1 B:TAR1002 2.8 38.0 1.0
C2 B:TAR1002 2.9 38.9 1.0
CD B:GLU265 3.0 33.9 1.0
CD B:GLU239 3.1 33.7 1.0
CG B:ASP213 3.1 38.1 1.0
OE2 B:GLU265 3.3 34.7 1.0
OD1 B:ASP213 3.4 37.4 1.0
NZ B:LYS182 3.8 36.7 1.0
OE1 B:GLU239 3.9 35.9 1.0
CG B:GLU239 4.0 33.2 1.0
O B:HOH2073 4.0 35.2 1.0
O1 B:TAR1002 4.0 39.6 1.0
OD1 B:ASN215 4.1 36.8 1.0
O B:HOH2100 4.1 31.7 1.0
C3 B:TAR1002 4.2 39.0 1.0
CB B:ASP213 4.4 38.9 1.0
CG B:GLU265 4.4 31.3 1.0
O3 B:TAR1002 4.6 41.9 1.0
CE B:LYS182 4.6 33.8 1.0
CD2 B:HIS322 4.6 30.1 1.0
OE1 B:GLU240 4.7 51.8 1.0
CG B:ASN215 4.8 38.8 1.0
C4 B:TAR1002 5.0 40.8 1.0

Magnesium binding site 3 out of 4 in 2dw6

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Magnesium binding site 3 out of 4 in the Crystal Structure of the Mutant K184A of D-Tartrate Dehydratase From Bradyrhizobium Japonicum Complexed with Mg++ and D-Tartrate


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 the Mutant K184A of D-Tartrate Dehydratase From Bradyrhizobium Japonicum Complexed with Mg++ and D-Tartrate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg2003

b:36.3
occ:1.00
 OE2 C:GLU239 2.0 36.5 1.0
OE1 C:GLU265 2.0 36.0 1.0
O2 C:TAR1003 2.1 34.6 1.0
OD2 C:ASP213 2.1 40.1 1.0
O C:HOH2004 2.2 29.0 1.0
O11 C:TAR1003 2.2 38.4 1.0
C2 C:TAR1003 2.9 38.8 1.0
C1 C:TAR1003 2.9 38.7 1.0
CD C:GLU265 2.9 36.2 1.0
CD C:GLU239 3.1 37.8 1.0
CG C:ASP213 3.2 42.7 1.0
OE2 C:GLU265 3.2 34.3 1.0
OD1 C:ASP213 3.5 41.7 1.0
O C:HOH2040 3.8 35.6 1.0
NZ C:LYS182 3.8 29.1 1.0
OE1 C:GLU239 3.9 36.3 1.0
CG C:GLU239 4.0 35.5 1.0
O1 C:TAR1003 4.1 40.1 1.0
OD1 C:ASN215 4.1 38.0 1.0
C3 C:TAR1003 4.2 39.9 1.0
O C:HOH2105 4.2 38.7 1.0
CG C:GLU265 4.3 34.1 1.0
O3 C:TAR1003 4.4 41.6 1.0
CB C:ASP213 4.5 39.5 1.0
CD2 C:HIS322 4.5 33.9 1.0
CE C:LYS182 4.6 32.4 1.0
OE1 C:GLU240 4.7 49.2 1.0
O C:HOH2107 4.7 51.1 1.0
CG C:ASN215 4.8 38.5 1.0
CB C:GLU265 5.0 33.7 1.0
C4 C:TAR1003 5.0 40.2 1.0

Magnesium binding site 4 out of 4 in 2dw6

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Magnesium binding site 4 out of 4 in the Crystal Structure of the Mutant K184A of D-Tartrate Dehydratase From Bradyrhizobium Japonicum Complexed with Mg++ and D-Tartrate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of the Mutant K184A of D-Tartrate Dehydratase From Bradyrhizobium Japonicum Complexed with Mg++ and D-Tartrate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2004

b:34.9
occ:1.00
 OE2 D:GLU239 2.0 37.0 1.0
O1 D:TLA1004 2.0 34.0 1.0
OD2 D:ASP213 2.0 33.8 1.0
OE1 D:GLU265 2.1 32.2 1.0
O D:HOH2005 2.1 24.9 1.0
O2 D:TLA1004 2.3 35.7 1.0
C1 D:TLA1004 2.8 35.8 1.0
C2 D:TLA1004 3.0 37.3 1.0
CD D:GLU239 3.0 34.8 1.0
CG D:ASP213 3.1 33.5 1.0
CD D:GLU265 3.2 36.1 1.0
OD1 D:ASP213 3.5 33.7 1.0
NZ D:LYS182 3.6 30.8 1.0
OE2 D:GLU265 3.6 38.2 1.0
OE1 D:GLU239 3.6 35.1 1.0
O11 D:TLA1004 4.0 33.3 1.0
CG D:GLU239 4.0 34.0 1.0
O D:HOH2054 4.1 34.7 1.0
C3 D:TLA1004 4.2 40.8 1.0
O3 D:TLA1004 4.3 40.4 1.0
OD1 D:ASN215 4.4 34.5 1.0
CB D:ASP213 4.4 31.4 1.0
CG D:GLU265 4.4 32.6 1.0
CE D:LYS182 4.5 28.6 1.0
OE1 D:GLU240 4.7 43.7 1.0
CB D:GLU265 4.9 31.1 1.0
CD2 D:HIS322 5.0 33.3 1.0

Reference:

W.S.Yew, A.A.Fedorov, E.V.Fedorov, B.M.Wood, S.C.Almo, J.A.Gerlt. Evolution of Enzymatic Activities in the Enolase Superfamily: D-Tartrate Dehydratase From Bradyrhizobium Japonicum Biochemistry V. 45 14598 2006.
ISSN: ISSN 0006-2960
PubMed: 17144653
DOI: 10.1021/BI061688G
Page generated: Tue Aug 13 22:36:15 2024

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