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Magnesium in PDB 3d46: Crystal Structure of L-Rhamnonate Dehydratase From Salmonella Typhimurium Complexed with Mg and L-Tartrate

Protein crystallography data

The structure of Crystal Structure of L-Rhamnonate Dehydratase From Salmonella Typhimurium Complexed with Mg and L-Tartrate, PDB code: 3d46 was solved by A.A.Fedorov, E.V.Fedorov, J.M.Sauder, S.K.Burley, J.A.Gerlt, S.C.Almo, Newyork Sgx Research Center For Structural Genomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.97 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 119.524, 147.717, 195.825, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / 20.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of L-Rhamnonate Dehydratase From Salmonella Typhimurium Complexed with Mg and L-Tartrate (pdb code 3d46). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of L-Rhamnonate Dehydratase From Salmonella Typhimurium Complexed with Mg and L-Tartrate, PDB code: 3d46:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 3d46

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Magnesium binding site 1 out of 8 in the Crystal Structure of L-Rhamnonate Dehydratase From Salmonella Typhimurium Complexed with Mg and L-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 L-Rhamnonate Dehydratase From Salmonella Typhimurium Complexed with Mg and L-Tartrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:10.1
occ:1.00
 OE1 A:GLU280 2.0 11.2 1.0
OD2 A:ASP226 2.0 8.5 1.0
OE1 A:GLU252 2.0 10.3 1.0
O A:HOH691 2.1 7.5 1.0
O1 A:TLA502 2.1 14.8 1.0
O2 A:TLA502 2.3 18.2 1.0
CD A:GLU280 3.0 11.8 1.0
C1 A:TLA502 3.0 19.7 1.0
CD A:GLU252 3.0 10.7 1.0
CG A:ASP226 3.0 11.0 1.0
C2 A:TLA502 3.1 21.6 1.0
OE2 A:GLU280 3.3 12.0 1.0
OD1 A:ASP226 3.4 12.1 1.0
CG A:GLU252 3.6 10.1 1.0
O A:HOH555 3.8 12.9 1.0
NZ A:LYS189 3.9 10.3 1.0
OE2 A:GLU252 4.0 7.5 1.0
O A:HOH529 4.0 8.8 1.0
O3 A:TLA502 4.1 24.3 1.0
O11 A:TLA502 4.2 20.2 1.0
C3 A:TLA502 4.2 24.2 1.0
OE1 A:GLU253 4.2 12.2 1.0
CG A:GLU280 4.3 11.3 1.0
CB A:ASP226 4.4 9.5 1.0
CD2 A:HIS329 4.4 16.9 1.0
CE A:LYS189 4.5 7.8 1.0
CB A:GLU252 4.9 9.6 1.0
CB A:GLU280 4.9 11.1 1.0
CB A:GLU253 5.0 12.1 1.0

Magnesium binding site 2 out of 8 in 3d46

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Magnesium binding site 2 out of 8 in the Crystal Structure of L-Rhamnonate Dehydratase From Salmonella Typhimurium Complexed with Mg and L-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 L-Rhamnonate Dehydratase From Salmonella Typhimurium Complexed with Mg and L-Tartrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg501

b:11.5
occ:1.00
 OE1 B:GLU280 2.0 13.2 1.0
OD2 B:ASP226 2.0 11.8 1.0
OE1 B:GLU252 2.0 9.2 1.0
O B:HOH680 2.1 8.5 1.0
O1 B:TLA502 2.2 11.0 1.0
O2 B:TLA502 2.3 17.4 1.0
CD B:GLU280 3.0 14.1 1.0
CD B:GLU252 3.0 7.0 1.0
C1 B:TLA502 3.0 17.1 1.0
CG B:ASP226 3.0 12.3 1.0
C2 B:TLA502 3.1 18.3 1.0
OE2 B:GLU280 3.3 12.7 1.0
OD1 B:ASP226 3.4 12.8 1.0
CG B:GLU252 3.6 8.2 1.0
NZ B:LYS189 3.9 11.5 1.0
O B:HOH681 3.9 6.4 1.0
OE2 B:GLU252 4.0 10.3 1.0
O B:HOH513 4.0 10.1 1.0
O3 B:TLA502 4.1 19.1 1.0
C3 B:TLA502 4.2 20.8 1.0
O11 B:TLA502 4.3 12.9 1.0
OE1 B:GLU253 4.3 13.2 1.0
CG B:GLU280 4.3 12.5 1.0
CB B:ASP226 4.4 11.1 1.0
CD2 B:HIS329 4.4 16.9 1.0
CE B:LYS189 4.5 8.9 1.0
CB B:GLU252 4.9 7.4 1.0
CB B:GLU280 4.9 12.0 1.0
CB B:GLU253 5.0 11.1 1.0

Magnesium binding site 3 out of 8 in 3d46

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Magnesium binding site 3 out of 8 in the Crystal Structure of L-Rhamnonate Dehydratase From Salmonella Typhimurium Complexed with Mg and L-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 L-Rhamnonate Dehydratase From Salmonella Typhimurium Complexed with Mg and L-Tartrate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg501

b:10.6
occ:1.00
 OE1 C:GLU280 2.0 9.4 1.0
OE1 C:GLU252 2.0 9.1 1.0
OD2 C:ASP226 2.0 8.6 1.0
O C:HOH717 2.1 7.2 1.0
O1 C:TLA502 2.1 7.7 1.0
O2 C:TLA502 2.2 9.4 1.0
CD C:GLU280 3.0 10.5 1.0
C1 C:TLA502 3.0 12.9 1.0
CD C:GLU252 3.0 7.9 1.0
CG C:ASP226 3.0 10.3 1.0
C2 C:TLA502 3.1 14.1 1.0
OE2 C:GLU280 3.3 10.2 1.0
OD1 C:ASP226 3.4 9.5 1.0
CG C:GLU252 3.6 6.5 1.0
O C:HOH718 3.9 3.9 1.0
NZ C:LYS189 3.9 10.0 1.0
OE2 C:GLU252 4.0 9.1 1.0
O3 C:TLA502 4.0 15.2 1.0
O C:HOH504 4.1 6.3 1.0
O11 C:TLA502 4.2 12.9 1.0
C3 C:TLA502 4.2 17.1 1.0
OE1 C:GLU253 4.3 11.2 1.0
CG C:GLU280 4.3 10.0 1.0
CB C:ASP226 4.4 8.0 1.0
CD2 C:HIS329 4.4 17.4 1.0
CE C:LYS189 4.5 6.1 1.0
CB C:GLU252 4.9 7.0 1.0
CB C:GLU253 4.9 8.8 1.0
CB C:GLU280 4.9 6.9 1.0

Magnesium binding site 4 out of 8 in 3d46

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Magnesium binding site 4 out of 8 in the Crystal Structure of L-Rhamnonate Dehydratase From Salmonella Typhimurium Complexed with Mg and L-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 L-Rhamnonate Dehydratase From Salmonella Typhimurium Complexed with Mg and L-Tartrate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg501

b:8.6
occ:1.00
 OE1 D:GLU280 2.0 7.7 1.0
OE1 D:GLU252 2.0 10.1 1.0
OD2 D:ASP226 2.0 7.4 1.0
O D:HOH727 2.1 5.0 1.0
O1 D:TLA502 2.2 11.9 1.0
O2 D:TLA502 2.3 11.0 1.0
CD D:GLU280 3.0 9.8 1.0
CD D:GLU252 3.0 8.0 1.0
C1 D:TLA502 3.0 15.1 1.0
CG D:ASP226 3.0 8.9 1.0
C2 D:TLA502 3.2 16.3 1.0
OE2 D:GLU280 3.3 8.8 1.0
OD1 D:ASP226 3.4 8.4 1.0
CG D:GLU252 3.6 6.9 1.0
NZ D:LYS189 3.9 7.3 1.0
O D:HOH535 3.9 9.3 1.0
OE2 D:GLU252 4.0 8.6 1.0
O3 D:TLA502 4.0 15.6 1.0
O D:HOH531 4.1 6.6 1.0
O11 D:TLA502 4.2 13.6 1.0
C3 D:TLA502 4.2 18.1 1.0
OE1 D:GLU253 4.2 8.3 1.0
CG D:GLU280 4.3 8.8 1.0
CB D:ASP226 4.4 8.4 1.0
CD2 D:HIS329 4.4 16.7 1.0
CE D:LYS189 4.5 7.0 1.0
CB D:GLU252 4.9 7.3 1.0
CB D:GLU280 4.9 9.6 1.0
CB D:GLU253 4.9 10.1 1.0

Magnesium binding site 5 out of 8 in 3d46

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Magnesium binding site 5 out of 8 in the Crystal Structure of L-Rhamnonate Dehydratase From Salmonella Typhimurium Complexed with Mg and L-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 L-Rhamnonate Dehydratase From Salmonella Typhimurium Complexed with Mg and L-Tartrate within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg501

b:7.3
occ:1.00
 OE1 E:GLU280 2.0 8.2 1.0
OE1 E:GLU252 2.0 8.8 1.0
OD2 E:ASP226 2.0 8.6 1.0
O E:HOH711 2.1 5.9 1.0
O1 E:TLA502 2.2 11.3 1.0
O2 E:TLA502 2.3 13.0 1.0
CD E:GLU280 3.0 9.1 1.0
CD E:GLU252 3.0 10.2 1.0
C1 E:TLA502 3.0 14.7 1.0
CG E:ASP226 3.0 7.8 1.0
C2 E:TLA502 3.2 15.9 1.0
OE2 E:GLU280 3.3 9.3 1.0
OD1 E:ASP226 3.4 9.3 1.0
CG E:GLU252 3.6 9.0 1.0
NZ E:LYS189 3.9 10.1 1.0
O E:HOH543 3.9 9.7 1.0
O E:HOH508 4.0 8.1 1.0
OE2 E:GLU252 4.0 8.9 1.0
O3 E:TLA502 4.0 19.7 1.0
C3 E:TLA502 4.2 19.8 1.0
O11 E:TLA502 4.2 11.0 1.0
OE1 E:GLU253 4.3 7.5 1.0
CG E:GLU280 4.3 10.4 1.0
CB E:ASP226 4.4 8.5 1.0
CD2 E:HIS329 4.4 16.9 1.0
CE E:LYS189 4.5 8.5 1.0
CB E:GLU252 4.9 9.8 1.0
CB E:GLU253 4.9 8.1 1.0
CB E:GLU280 4.9 9.5 1.0

Magnesium binding site 6 out of 8 in 3d46

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Magnesium binding site 6 out of 8 in the Crystal Structure of L-Rhamnonate Dehydratase From Salmonella Typhimurium Complexed with Mg and L-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 L-Rhamnonate Dehydratase From Salmonella Typhimurium Complexed with Mg and L-Tartrate within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg501

b:9.9
occ:1.00
 OE1 F:GLU280 2.0 9.0 1.0
OE1 F:GLU252 2.0 7.2 1.0
OD2 F:ASP226 2.0 7.6 1.0
O1 F:TLA502 2.1 5.9 1.0
O F:HOH733 2.1 8.1 1.0
O2 F:TLA502 2.2 5.7 1.0
C1 F:TLA502 2.9 8.4 1.0
CD F:GLU280 3.0 9.6 1.0
CD F:GLU252 3.0 8.0 1.0
CG F:ASP226 3.0 7.8 1.0
C2 F:TLA502 3.1 9.7 1.0
OE2 F:GLU280 3.3 9.0 1.0
OD1 F:ASP226 3.4 9.0 1.0
CG F:GLU252 3.6 6.8 1.0
O F:HOH604 3.8 12.2 1.0
NZ F:LYS189 3.9 8.0 1.0
OE2 F:GLU252 4.0 8.1 1.0
O F:HOH503 4.0 7.3 1.0
O3 F:TLA502 4.0 11.0 1.0
O11 F:TLA502 4.1 6.2 1.0
C3 F:TLA502 4.2 13.9 1.0
OE1 F:GLU253 4.3 9.1 1.0
CG F:GLU280 4.3 7.9 1.0
CB F:ASP226 4.4 8.5 1.0
CD2 F:HIS329 4.4 13.5 1.0
CE F:LYS189 4.5 6.0 1.0
CB F:GLU252 4.9 8.3 1.0
CB F:GLU280 4.9 8.9 1.0
CB F:GLU253 4.9 7.2 1.0

Magnesium binding site 7 out of 8 in 3d46

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Magnesium binding site 7 out of 8 in the Crystal Structure of L-Rhamnonate Dehydratase From Salmonella Typhimurium Complexed with Mg and L-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 L-Rhamnonate Dehydratase From Salmonella Typhimurium Complexed with Mg and L-Tartrate within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg501

b:10.7
occ:1.00
 OE1 G:GLU280 2.0 11.4 1.0
OD2 G:ASP226 2.0 10.1 1.0
OE1 G:GLU252 2.0 9.8 1.0
O G:HOH692 2.1 8.3 1.0
O1 G:TLA502 2.2 16.5 1.0
O2 G:TLA502 2.3 11.0 1.0
CD G:GLU280 3.0 11.8 1.0
C1 G:TLA502 3.0 17.1 1.0
CD G:GLU252 3.0 9.9 1.0
CG G:ASP226 3.0 10.0 1.0
C2 G:TLA502 3.1 17.0 1.0
OE2 G:GLU280 3.3 12.1 1.0
OD1 G:ASP226 3.4 11.0 1.0
CG G:GLU252 3.6 9.6 1.0
NZ G:LYS189 3.9 9.4 1.0
O G:HOH555 3.9 11.2 1.0
OE2 G:GLU252 4.0 10.4 1.0
O3 G:TLA502 4.1 19.3 1.0
O G:HOH522 4.1 8.9 1.0
O11 G:TLA502 4.2 16.0 1.0
C3 G:TLA502 4.2 19.9 1.0
OE1 G:GLU253 4.3 10.6 1.0
CG G:GLU280 4.3 11.3 1.0
CB G:ASP226 4.4 9.4 1.0
CD2 G:HIS329 4.4 15.4 1.0
CE G:LYS189 4.5 9.3 1.0
CB G:GLU252 4.9 9.2 1.0
CB G:GLU253 4.9 10.6 1.0
CB G:GLU280 4.9 10.1 1.0

Magnesium binding site 8 out of 8 in 3d46

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Magnesium binding site 8 out of 8 in the Crystal Structure of L-Rhamnonate Dehydratase From Salmonella Typhimurium Complexed with Mg and L-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 L-Rhamnonate Dehydratase From Salmonella Typhimurium Complexed with Mg and L-Tartrate within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg501

b:12.6
occ:1.00
 OE1 H:GLU280 2.0 9.3 1.0
OD2 H:ASP226 2.0 10.2 1.0
OE1 H:GLU252 2.0 10.3 1.0
O H:HOH705 2.1 7.9 1.0
O1 H:TLA502 2.2 9.9 1.0
O2 H:TLA502 2.2 13.8 1.0
CD H:GLU280 3.0 10.4 1.0
CD H:GLU252 3.0 9.7 1.0
C1 H:TLA502 3.0 13.8 1.0
CG H:ASP226 3.0 10.6 1.0
C2 H:TLA502 3.1 15.7 1.0
OE2 H:GLU280 3.4 9.1 1.0
OD1 H:ASP226 3.4 9.5 1.0
CG H:GLU252 3.6 6.9 1.0
NZ H:LYS189 3.9 9.4 1.0
O H:HOH614 3.9 15.4 1.0
OE2 H:GLU252 4.0 9.0 1.0
O H:HOH508 4.1 7.9 1.0
O3 H:TLA502 4.1 17.6 1.0
O11 H:TLA502 4.2 9.3 1.0
C3 H:TLA502 4.3 19.2 1.0
OE1 H:GLU253 4.3 11.3 1.0
CG H:GLU280 4.3 9.3 1.0
CB H:ASP226 4.4 10.4 1.0
CD2 H:HIS329 4.4 13.8 1.0
CE H:LYS189 4.5 7.2 1.0
CB H:GLU252 4.9 8.9 1.0
CB H:GLU280 4.9 9.7 1.0
CB H:GLU253 4.9 9.0 1.0

Reference:

A.A.Fedorov, E.V.Fedorov, J.M.Sauder, S.K.Burley, J.A.Gerlt, S.C.Almo. Crystal Structure of L-Rhamnonate Dehydratase From Salmonella Typhimurium Complexed with Mg and L-Tartrate. To Be Published.
Page generated: Wed Aug 14 12:23:18 2024

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