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Magnesium in PDB 2dw7: Crystal Structure of D-Tartrate Dehydratase From Bradyrhizobium Japonicum Complexed with Mg++ and Meso- Tartrate

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

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

Protein crystallography data

The structure of Crystal Structure of D-Tartrate Dehydratase From Bradyrhizobium Japonicum Complexed with Mg++ and Meso- Tartrate, PDB code: 2dw7 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 / 2.50
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 74.837, 162.542, 168.181, 117.76, 90.03, 90.67
R / Rfree (%) 24.1 / 26.5

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of D-Tartrate Dehydratase From Bradyrhizobium Japonicum Complexed with Mg++ and Meso- Tartrate (pdb code 2dw7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 16 binding sites of Magnesium where determined in the Crystal Structure of D-Tartrate Dehydratase From Bradyrhizobium Japonicum Complexed with Mg++ and Meso- Tartrate, PDB code: 2dw7:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 16 in 2dw7

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Magnesium binding site 1 out of 16 in the Crystal Structure of D-Tartrate Dehydratase From Bradyrhizobium Japonicum Complexed with Mg++ and Meso- 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 D-Tartrate Dehydratase From Bradyrhizobium Japonicum Complexed with Mg++ and Meso- Tartrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2001

b:20.3
occ:1.00
 OE1 A:GLU265 1.8 13.7 1.0
O2 A:SRT1001 2.0 30.8 1.0
OE2 A:GLU239 2.1 6.6 1.0
OD2 A:ASP213 2.4 24.0 1.0
CD A:GLU265 2.7 16.1 1.0
O1 A:SRT1001 2.8 30.2 1.0
OE2 A:GLU265 3.1 19.1 1.0
CG A:ASP213 3.1 22.8 1.0
OD1 A:ASP213 3.1 25.5 1.0
C2 A:SRT1001 3.2 31.8 1.0
CD A:GLU239 3.2 8.5 1.0
C1 A:SRT1001 3.4 32.4 1.0
O A:HOH2015 3.4 24.1 1.0
OE1 A:GLU240 3.5 33.8 1.0
CG A:GLU239 3.8 9.6 1.0
OD1 A:ASN215 3.8 27.9 1.0
CG A:GLU265 3.9 18.3 1.0
OE1 A:GLU239 4.2 8.2 1.0
C3 A:SRT1001 4.3 31.8 1.0
CB A:GLU240 4.4 23.7 1.0
CD A:GLU240 4.4 30.1 1.0
CG A:ASN215 4.5 22.8 1.0
NZ A:LYS184 4.5 32.2 1.0
CB A:ASP213 4.5 21.5 1.0
O11 A:SRT1001 4.6 30.0 1.0
CA A:ASN215 4.7 20.4 1.0
NZ A:LYS182 4.7 9.2 1.0
CB A:GLU265 4.8 17.0 1.0
N A:ASN215 4.9 20.9 1.0

Magnesium binding site 2 out of 16 in 2dw7

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Magnesium binding site 2 out of 16 in the Crystal Structure of D-Tartrate Dehydratase From Bradyrhizobium Japonicum Complexed with Mg++ and Meso- 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 D-Tartrate Dehydratase From Bradyrhizobium Japonicum Complexed with Mg++ and Meso- Tartrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2002

b:62.4
occ:1.00
 O2 B:SRT1002 2.1 44.1 1.0
OE2 B:GLU239 2.1 45.2 1.0
OD2 B:ASP213 2.1 48.3 1.0
OE1 B:GLU265 2.2 46.1 1.0
CG B:ASP213 2.8 47.1 1.0
OD1 B:ASP213 2.8 45.3 1.0
O1 B:SRT1002 2.9 54.8 1.0
CD B:GLU265 3.0 44.4 1.0
CD B:GLU239 3.1 46.0 1.0
C2 B:SRT1002 3.2 49.3 1.0
OE2 B:GLU265 3.4 46.1 1.0
OE1 B:GLU240 3.5 41.2 1.0
C1 B:SRT1002 3.5 51.4 1.0
CG B:GLU239 3.6 44.6 1.0
OD1 B:ASN215 3.7 48.5 1.0
OE1 B:GLU239 4.2 47.9 1.0
CG B:GLU265 4.2 40.7 1.0
NZ B:LYS182 4.2 43.4 1.0
CB B:ASP213 4.2 44.6 1.0
CG B:ASN215 4.3 48.5 1.0
CB B:GLU240 4.3 37.1 1.0
C3 B:SRT1002 4.4 49.9 1.0
CD B:GLU240 4.4 41.3 1.0
CA B:ASN215 4.4 44.9 1.0
NZ B:LYS184 4.5 52.4 1.0
N B:ASN215 4.7 44.0 1.0
O11 B:SRT1002 4.7 53.7 1.0
CB B:GLU239 4.8 41.4 1.0
ND2 B:ASN215 4.8 49.2 1.0
CB B:ASN215 5.0 45.8 1.0
CG B:GLU240 5.0 39.0 1.0

Magnesium binding site 3 out of 16 in 2dw7

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Magnesium binding site 3 out of 16 in the Crystal Structure of D-Tartrate Dehydratase From Bradyrhizobium Japonicum Complexed with Mg++ and Meso- 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 D-Tartrate Dehydratase From Bradyrhizobium Japonicum Complexed with Mg++ and Meso- Tartrate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg2003

b:26.6
occ:1.00
 OE1 C:GLU265 2.0 29.6 1.0
O2 C:SRT1003 2.2 26.9 1.0
OE2 C:GLU239 2.2 16.4 1.0
OD2 C:ASP213 2.3 16.6 1.0
O1 C:SRT1003 2.8 21.0 1.0
CD C:GLU265 2.8 28.8 1.0
OD1 C:ASP213 2.9 17.8 1.0
CG C:ASP213 3.0 18.4 1.0
OE2 C:GLU265 3.2 31.3 1.0
CD C:GLU239 3.3 19.5 1.0
C2 C:SRT1003 3.3 28.0 1.0
OE1 C:GLU240 3.4 30.3 1.0
C1 C:SRT1003 3.5 24.9 1.0
OD1 C:ASN215 3.7 30.4 1.0
CG C:GLU239 3.8 16.5 1.0
CG C:GLU265 4.0 26.9 1.0
O C:HOH2044 4.2 16.6 1.0
CG C:ASN215 4.3 29.5 1.0
CB C:GLU240 4.3 22.7 1.0
CD C:GLU240 4.3 27.4 1.0
OE1 C:GLU239 4.4 20.9 1.0
CA C:ASN215 4.4 23.7 1.0
CB C:ASP213 4.4 18.9 1.0
C3 C:SRT1003 4.5 34.2 1.0
NZ C:LYS184 4.6 28.3 1.0
NZ C:LYS182 4.7 20.5 1.0
O11 C:SRT1003 4.7 18.2 1.0
N C:ASN215 4.7 20.5 1.0
ND2 C:ASN215 4.8 32.0 1.0
CB C:ASN215 5.0 25.9 1.0
CG C:GLU240 5.0 25.3 1.0
CB C:GLU265 5.0 21.2 1.0

Magnesium binding site 4 out of 16 in 2dw7

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Magnesium binding site 4 out of 16 in the Crystal Structure of D-Tartrate Dehydratase From Bradyrhizobium Japonicum Complexed with Mg++ and Meso- 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 D-Tartrate Dehydratase From Bradyrhizobium Japonicum Complexed with Mg++ and Meso- Tartrate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2004

b:27.3
occ:1.00
 OE2 D:GLU239 1.9 13.5 1.0
OD2 D:ASP213 2.0 31.4 1.0
O2 D:SRT1004 2.1 34.5 1.0
OE1 D:GLU265 2.2 22.0 1.0
O1 D:SRT1004 2.2 21.7 1.0
CG D:ASP213 2.8 26.2 1.0
OD1 D:ASP213 2.9 27.4 1.0
C2 D:SRT1004 3.0 31.2 1.0
C1 D:SRT1004 3.0 28.4 1.0
CD D:GLU265 3.0 22.9 1.0
CD D:GLU239 3.0 18.8 1.0
OE2 D:GLU265 3.4 21.4 1.0
CG D:GLU239 3.7 16.9 1.0
OE1 D:GLU240 3.8 27.5 1.0
OD1 D:ASN215 3.9 27.7 1.0
OE1 D:GLU239 4.0 22.1 1.0
O11 D:SRT1004 4.2 23.6 1.0
NZ D:LYS182 4.2 19.6 1.0
CB D:ASP213 4.2 25.2 1.0
CG D:GLU265 4.2 19.7 1.0
C3 D:SRT1004 4.2 35.1 1.0
O D:HOH2012 4.3 26.8 1.0
NZ D:LYS184 4.4 34.0 1.0
CG D:ASN215 4.4 26.9 1.0
O D:HOH2022 4.4 15.8 1.0
CB D:GLU240 4.6 17.5 1.0
CA D:ASN215 4.7 18.6 1.0
CD D:GLU240 4.8 26.7 1.0
ND2 D:ASN215 4.8 29.2 1.0
CB D:GLU239 4.9 18.8 1.0
N D:ASN215 4.9 19.2 1.0

Magnesium binding site 5 out of 16 in 2dw7

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Magnesium binding site 5 out of 16 in the Crystal Structure of D-Tartrate Dehydratase From Bradyrhizobium Japonicum Complexed with Mg++ and Meso- Tartrate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of D-Tartrate Dehydratase From Bradyrhizobium Japonicum Complexed with Mg++ and Meso- Tartrate within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg2005

b:39.5
occ:1.00
 OE2 E:GLU239 2.0 31.5 1.0
O2 E:SRT1005 2.0 47.5 1.0
OD2 E:ASP213 2.1 39.8 1.0
OE1 E:GLU265 2.1 36.5 1.0
O1 E:SRT1005 2.7 51.0 1.0
CG E:ASP213 2.8 38.2 1.0
OD1 E:ASP213 2.9 37.9 1.0
CD E:GLU265 3.0 36.7 1.0
CD E:GLU239 3.1 33.5 1.0
C2 E:SRT1005 3.1 48.4 1.0
OE2 E:GLU265 3.4 37.6 1.0
C1 E:SRT1005 3.4 49.1 1.0
OE1 E:GLU240 3.7 41.5 1.0
CG E:GLU239 3.7 31.8 1.0
OD1 E:ASN215 3.8 37.4 1.0
O E:HOH2032 4.1 20.7 1.0
OE1 E:GLU239 4.1 33.9 1.0
CG E:GLU265 4.2 35.4 1.0
CB E:ASP213 4.2 37.2 1.0
NZ E:LYS184 4.3 39.3 1.0
C3 E:SRT1005 4.3 46.8 1.0
CG E:ASN215 4.3 38.8 1.0
CB E:GLU240 4.4 30.5 1.0
O11 E:SRT1005 4.6 50.1 1.0
CA E:ASN215 4.6 38.9 1.0
CD E:GLU240 4.6 35.9 1.0
NZ E:LYS182 4.7 27.1 1.0
N E:ASN215 4.8 37.0 1.0
ND2 E:ASN215 4.9 38.0 1.0
CB E:GLU239 4.9 30.9 1.0

Magnesium binding site 6 out of 16 in 2dw7

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Magnesium binding site 6 out of 16 in the Crystal Structure of D-Tartrate Dehydratase From Bradyrhizobium Japonicum Complexed with Mg++ and Meso- Tartrate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of D-Tartrate Dehydratase From Bradyrhizobium Japonicum Complexed with Mg++ and Meso- Tartrate within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg2006

b:19.5
occ:1.00
 O2 F:SRT1006 2.1 35.7 1.0
OE1 F:GLU265 2.2 29.5 1.0
OD2 F:ASP213 2.3 16.4 1.0
OE2 F:GLU239 2.3 15.2 1.0
O1 F:SRT1006 2.7 26.4 1.0
OD1 F:ASP213 2.8 14.7 1.0
CD F:GLU265 2.9 29.5 1.0
CG F:ASP213 2.9 19.2 1.0
OE1 F:GLU240 3.2 34.1 1.0
C2 F:SRT1006 3.2 33.1 1.0
OE2 F:GLU265 3.3 31.9 1.0
CD F:GLU239 3.3 14.4 1.0
C1 F:SRT1006 3.4 32.1 1.0
OD1 F:ASN215 3.6 26.0 1.0
CG F:GLU239 3.7 10.6 1.0
CG F:GLU265 4.1 26.4 1.0
CB F:GLU240 4.2 21.1 1.0
CG F:ASN215 4.2 26.6 1.0
CD F:GLU240 4.2 29.3 1.0
CA F:ASN215 4.3 24.5 1.0
O F:HOH2020 4.3 18.0 1.0
CB F:ASP213 4.4 20.6 1.0
OE1 F:GLU239 4.4 12.9 1.0
C3 F:SRT1006 4.4 35.7 1.0
N F:ASN215 4.6 20.3 1.0
O11 F:SRT1006 4.6 25.6 1.0
ND2 F:ASN215 4.8 25.2 1.0
CG F:GLU240 4.8 25.2 1.0
CB F:ASN215 4.8 24.6 1.0
CB F:GLU239 4.9 14.9 1.0

Magnesium binding site 7 out of 16 in 2dw7

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Magnesium binding site 7 out of 16 in the Crystal Structure of D-Tartrate Dehydratase From Bradyrhizobium Japonicum Complexed with Mg++ and Meso- Tartrate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of D-Tartrate Dehydratase From Bradyrhizobium Japonicum Complexed with Mg++ and Meso- Tartrate within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg2007

b:31.1
occ:1.00
 O2 G:SRT1007 2.3 40.4 1.0
OE1 G:GLU265 2.6 23.8 1.0
OD2 G:ASP213 2.7 23.8 1.0
OE1 G:GLU240 2.7 34.8 1.0
OD1 G:ASP213 2.7 25.0 1.0
OE2 G:GLU239 3.0 10.5 1.0
CG G:ASP213 3.0 21.9 1.0
CD G:GLU265 3.1 28.8 1.0
OD1 G:ASN215 3.3 19.8 1.0
O1 G:SRT1007 3.3 33.4 1.0
OE2 G:GLU265 3.3 28.0 1.0
C2 G:SRT1007 3.6 36.6 1.0
CA G:ASN215 3.6 19.2 1.0
CG G:ASN215 3.7 20.9 1.0
CD G:GLU240 3.7 30.6 1.0
O G:HOH2037 3.8 28.4 1.0
CB G:GLU240 3.8 25.7 1.0
CD G:GLU239 3.9 14.4 1.0
C1 G:SRT1007 3.9 36.1 1.0
N G:ASN215 4.0 17.8 1.0
CG G:GLU239 4.1 14.8 1.0
CG G:GLU265 4.2 28.9 1.0
CB G:ASN215 4.2 18.8 1.0
O G:HOH2018 4.3 21.3 1.0
CG G:GLU240 4.3 26.1 1.0
ND2 G:ASN215 4.4 21.5 1.0
CB G:ASP213 4.6 19.0 1.0
C G:ASN215 4.6 18.8 1.0
OE2 G:GLU240 4.7 29.4 1.0
C3 G:SRT1007 4.7 37.6 1.0
OE1 G:GLU239 5.0 12.2 1.0

Magnesium binding site 8 out of 16 in 2dw7

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Magnesium binding site 8 out of 16 in the Crystal Structure of D-Tartrate Dehydratase From Bradyrhizobium Japonicum Complexed with Mg++ and Meso- Tartrate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of D-Tartrate Dehydratase From Bradyrhizobium Japonicum Complexed with Mg++ and Meso- Tartrate within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg2008

b:42.6
occ:1.00
 OD2 H:ASP213 2.0 33.4 1.0
OE2 H:GLU239 2.2 39.9 1.0
O2 H:SRT1008 2.2 57.1 1.0
OE1 H:GLU265 2.3 40.0 1.0
O1 H:SRT1008 2.5 50.1 1.0
OD1 H:ASP213 2.6 35.9 1.0
CG H:ASP213 2.7 35.6 1.0
CD H:GLU265 3.1 41.9 1.0
CD H:GLU239 3.2 39.0 1.0
C2 H:SRT1008 3.2 54.5 1.0
C1 H:SRT1008 3.3 52.9 1.0
OE2 H:GLU265 3.5 43.7 1.0
OE1 H:GLU240 3.5 32.1 1.0
OD1 H:ASN215 3.6 41.9 1.0
CG H:GLU239 3.7 38.1 1.0
CB H:ASP213 4.1 37.1 1.0
CG H:ASN215 4.2 42.9 1.0
OE1 H:GLU239 4.2 40.4 1.0
O H:HOH2014 4.3 39.5 1.0
CB H:GLU240 4.3 32.1 1.0
CA H:ASN215 4.3 39.8 1.0
CG H:GLU265 4.3 39.3 1.0
CD H:GLU240 4.4 33.4 1.0
O11 H:SRT1008 4.5 51.4 1.0
C3 H:SRT1008 4.5 55.9 1.0
N H:ASN215 4.5 38.1 1.0
NZ H:LYS182 4.6 38.2 1.0
ND2 H:ASN215 4.7 42.1 1.0
CB H:GLU239 4.8 36.0 1.0
CB H:ASN215 4.9 40.8 1.0
CG H:GLU240 5.0 33.4 1.0

Magnesium binding site 9 out of 16 in 2dw7

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Magnesium binding site 9 out of 16 in the Crystal Structure of D-Tartrate Dehydratase From Bradyrhizobium Japonicum Complexed with Mg++ and Meso- Tartrate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of D-Tartrate Dehydratase From Bradyrhizobium Japonicum Complexed with Mg++ and Meso- Tartrate within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg2009

b:25.4
occ:1.00
 O2 I:SRT1009 2.1 36.5 1.0
OE1 I:GLU265 2.3 24.7 1.0
OD2 I:ASP213 2.6 41.4 1.0
OE2 I:GLU239 2.7 19.2 1.0
CD I:GLU265 2.9 25.3 1.0
OD1 I:ASP213 2.9 40.1 1.0
OE1 I:GLU240 3.0 34.1 1.0
CG I:ASP213 3.1 39.9 1.0
OE2 I:GLU265 3.1 23.8 1.0
O1 I:SRT1009 3.1 22.8 1.0
OD1 I:ASN215 3.3 34.2 1.0
C2 I:SRT1009 3.4 30.6 1.0
CD I:GLU239 3.7 24.5 1.0
C1 I:SRT1009 3.7 26.7 1.0
CG I:ASN215 3.9 30.9 1.0
CA I:ASN215 3.9 28.7 1.0
CD I:GLU240 4.0 32.6 1.0
CG I:GLU265 4.0 24.1 1.0
CB I:GLU240 4.1 23.8 1.0
CG I:GLU239 4.1 23.7 1.0
N I:ASN215 4.3 29.4 1.0
CB I:ASN215 4.5 28.1 1.0
C3 I:SRT1009 4.5 34.1 1.0
CB I:ASP213 4.6 38.8 1.0
ND2 I:ASN215 4.6 32.4 1.0
CG I:GLU240 4.6 29.7 1.0
NZ I:LYS184 4.8 35.6 1.0
OE1 I:GLU239 4.8 24.6 1.0
OE2 I:GLU240 4.9 31.1 1.0
C I:ASN215 4.9 27.5 1.0
O11 I:SRT1009 4.9 20.7 1.0

Magnesium binding site 10 out of 16 in 2dw7

Go back to Magnesium Binding Sites List in 2dw7
Magnesium binding site 10 out of 16 in the Crystal Structure of D-Tartrate Dehydratase From Bradyrhizobium Japonicum Complexed with Mg++ and Meso- Tartrate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of D-Tartrate Dehydratase From Bradyrhizobium Japonicum Complexed with Mg++ and Meso- Tartrate within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg2010

b:41.5
occ:1.00
 OE2 J:GLU239 2.0 43.0 1.0
OE1 J:GLU265 2.2 56.1 1.0
OD2 J:ASP213 2.2 55.1 1.0
O2 J:SRT1010 2.2 45.7 1.0
OD1 J:ASP213 2.8 57.2 1.0
CG J:ASP213 2.8 56.0 1.0
CD J:GLU239 3.0 44.3 1.0
CD J:GLU265 3.0 53.3 1.0
O1 J:SRT1010 3.0 46.1 1.0
OE1 J:GLU240 3.4 50.1 1.0
C2 J:SRT1010 3.5 47.2 1.0
OE2 J:GLU265 3.5 52.3 1.0
CG J:GLU239 3.5 44.0 1.0
C1 J:SRT1010 3.7 46.9 1.0
OD1 J:ASN215 3.9 51.4 1.0
OE1 J:GLU239 4.1 45.1 1.0
CB J:GLU240 4.1 44.3 1.0
CG J:GLU265 4.1 50.4 1.0
CB J:ASP213 4.3 54.5 1.0
CD J:GLU240 4.3 48.5 1.0
CG J:ASN215 4.4 52.2 1.0
CA J:ASN215 4.4 47.1 1.0
C3 J:SRT1010 4.6 49.0 1.0
N J:ASN215 4.7 46.9 1.0
CB J:GLU239 4.7 44.6 1.0
NZ J:LYS184 4.8 50.5 1.0
CG J:GLU240 4.9 47.1 1.0
O11 J:SRT1010 4.9 47.3 1.0
ND2 J:ASN215 5.0 54.0 1.0
OE1 J:GLN290 5.0 44.1 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 22:36:26 2024

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