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Magnesium in PDB 3d47: Crystal Structure of L-Rhamnonate Dehydratase From Salmonella Typhimurium Complexed with Mg and D-Malate

Protein crystallography data

The structure of Crystal Structure of L-Rhamnonate Dehydratase From Salmonella Typhimurium Complexed with Mg and D-Malate, PDB code: 3d47 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) 24.88 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 98.222, 122.003, 141.350, 90.00, 108.24, 90.00
R / Rfree (%) 20.2 / 23.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of L-Rhamnonate Dehydratase From Salmonella Typhimurium Complexed with Mg and D-Malate (pdb code 3d47). 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 D-Malate, PDB code: 3d47:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 3d47

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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 D-Malate


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 D-Malate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:12.8
occ:1.00
 OE1 A:GLU280 2.0 12.1 1.0
OD2 A:ASP226 2.0 10.8 1.0
O A:HOH551 2.1 12.2 1.0
O3 A:MLT502 2.1 12.8 1.0
OE1 A:GLU252 2.2 9.2 1.0
O1 A:MLT502 2.2 14.1 1.0
CD A:GLU280 2.9 12.7 1.0
C1 A:MLT502 2.9 16.7 1.0
C2 A:MLT502 3.0 16.4 1.0
CG A:ASP226 3.1 10.9 1.0
CD A:GLU252 3.1 10.3 1.0
OE2 A:GLU280 3.2 13.4 1.0
OD1 A:ASP226 3.4 11.3 1.0
CG A:GLU252 3.8 8.1 1.0
O A:HOH520 3.9 13.4 1.0
NZ A:LYS189 4.0 13.5 1.0
C3 A:MLT502 4.0 19.0 1.0
OE2 A:GLU252 4.1 11.7 1.0
O2 A:MLT502 4.1 15.3 1.0
O A:HOH522 4.2 13.3 1.0
OE1 A:GLU253 4.2 13.4 1.0
CG A:GLU280 4.3 13.3 1.0
CD2 A:HIS329 4.3 21.2 1.0
CB A:ASP226 4.4 9.4 1.0
CE A:LYS189 4.6 12.9 1.0
CB A:GLU253 4.9 9.8 1.0
CD1 A:TRP228 5.0 12.0 1.0
CB A:GLU280 5.0 13.0 1.0
NE2 A:HIS329 5.0 21.4 1.0

Magnesium binding site 2 out of 8 in 3d47

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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 D-Malate


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 D-Malate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg501

b:17.5
occ:1.00
 O B:HOH506 2.0 17.4 1.0
OD2 B:ASP226 2.0 16.8 1.0
OE1 B:GLU252 2.0 13.9 1.0
OE1 B:GLU280 2.0 17.4 1.0
O3 B:MLT502 2.1 21.8 1.0
O1 B:MLT502 2.1 22.2 1.0
C1 B:MLT502 2.9 25.0 1.0
C2 B:MLT502 3.0 24.7 1.0
CG B:ASP226 3.0 16.1 1.0
CD B:GLU280 3.0 17.3 1.0
CD B:GLU252 3.0 16.6 1.0
OE2 B:GLU280 3.3 17.4 1.0
OD1 B:ASP226 3.3 16.1 1.0
CG B:GLU252 3.7 16.0 1.0
OE2 B:GLU252 3.9 14.6 1.0
NZ B:LYS189 4.0 19.4 1.0
C3 B:MLT502 4.1 27.6 1.0
O2 B:MLT502 4.1 24.3 1.0
O B:HOH590 4.1 19.4 1.0
O B:HOH515 4.2 19.9 1.0
OE1 B:GLU253 4.3 19.0 1.0
CG B:GLU280 4.3 17.6 1.0
CB B:ASP226 4.3 16.7 1.0
CD2 B:HIS329 4.4 26.4 1.0
CE B:LYS189 4.6 18.8 1.0
CB B:GLU252 4.9 18.8 1.0
CD1 B:TRP228 5.0 14.8 1.0
CB B:GLU280 5.0 16.0 1.0

Magnesium binding site 3 out of 8 in 3d47

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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 D-Malate


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 D-Malate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg501

b:15.0
occ:1.00
 OE1 C:GLU252 1.9 8.7 1.0
OD2 C:ASP226 2.0 10.3 1.0
O C:HOH517 2.1 12.6 1.0
OE1 C:GLU280 2.1 13.4 1.0
O1 C:MLT502 2.3 16.8 1.0
O3 C:MLT502 2.3 17.5 1.0
CD C:GLU252 2.9 12.9 1.0
CG C:ASP226 3.0 10.8 1.0
CD C:GLU280 3.1 16.9 1.0
C1 C:MLT502 3.1 19.2 1.0
C2 C:MLT502 3.2 19.1 1.0
OD1 C:ASP226 3.3 12.8 1.0
OE2 C:GLU280 3.5 17.6 1.0
CG C:GLU252 3.5 11.6 1.0
OE2 C:GLU252 3.8 11.0 1.0
NZ C:LYS189 3.9 14.3 1.0
O C:HOH530 4.0 15.7 1.0
O C:HOH539 4.1 19.1 1.0
C3 C:MLT502 4.2 22.1 1.0
OE1 C:GLU253 4.2 13.1 1.0
O2 C:MLT502 4.3 19.4 1.0
CB C:ASP226 4.3 10.7 1.0
CG C:GLU280 4.3 16.1 1.0
CE C:LYS189 4.5 14.8 1.0
CB C:GLU252 4.7 11.9 1.0
CB C:GLU253 4.9 14.7 1.0
CD2 C:HIS329 4.9 24.8 1.0

Magnesium binding site 4 out of 8 in 3d47

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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 D-Malate


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 D-Malate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg501

b:18.4
occ:1.00
 OE1 D:GLU252 2.0 18.7 1.0
OD2 D:ASP226 2.0 20.2 1.0
OE1 D:GLU280 2.1 19.1 1.0
O1 D:MLT502 2.2 26.9 1.0
O D:HOH504 2.2 14.8 1.0
O3 D:MLT502 2.4 27.1 1.0
CD D:GLU252 2.9 21.0 1.0
C1 D:MLT502 3.0 29.4 1.0
CG D:ASP226 3.1 19.9 1.0
CD D:GLU280 3.1 20.9 1.0
C2 D:MLT502 3.2 28.9 1.0
OD1 D:ASP226 3.5 19.9 1.0
OE2 D:GLU280 3.5 21.1 1.0
CG D:GLU252 3.5 19.2 1.0
NZ D:LYS189 3.7 17.0 1.0
OE2 D:GLU252 3.8 20.3 1.0
O D:HOH518 3.9 21.6 1.0
O D:HOH509 4.0 16.6 1.0
O2 D:MLT502 4.2 27.6 1.0
C3 D:MLT502 4.2 31.0 1.0
CB D:ASP226 4.3 19.8 1.0
CD2 D:HIS329 4.4 27.5 1.0
CE D:LYS189 4.4 18.6 1.0
OE1 D:GLU253 4.4 18.4 1.0
CG D:GLU280 4.4 18.4 1.0
CB D:GLU252 4.8 17.8 1.0

Magnesium binding site 5 out of 8 in 3d47

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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 D-Malate


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 D-Malate within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg501

b:20.8
occ:1.00
 OE1 E:GLU280 1.9 20.3 1.0
OD2 E:ASP226 2.0 21.4 1.0
OE1 E:GLU252 2.1 14.3 1.0
O E:HOH541 2.1 16.4 1.0
O3 E:MLT502 2.2 26.9 1.0
O1 E:MLT502 2.3 26.8 1.0
CD E:GLU280 2.9 20.5 1.0
CD E:GLU252 3.0 15.3 1.0
CG E:ASP226 3.0 21.2 1.0
C1 E:MLT502 3.1 28.0 1.0
C2 E:MLT502 3.1 28.2 1.0
OE2 E:GLU280 3.4 18.7 1.0
OD1 E:ASP226 3.4 20.1 1.0
CG E:GLU252 3.6 15.1 1.0
O E:HOH515 3.9 13.8 1.0
OE2 E:GLU252 4.0 17.6 1.0
NZ E:LYS189 4.1 18.9 1.0
C3 E:MLT502 4.1 28.7 1.0
O E:HOH565 4.1 18.3 1.0
OE1 E:GLU253 4.2 16.5 1.0
CG E:GLU280 4.2 20.0 1.0
O2 E:MLT502 4.2 26.3 1.0
CB E:ASP226 4.4 20.0 1.0
CD2 E:HIS329 4.4 25.1 1.0
CE E:LYS189 4.7 15.3 1.0
CB E:GLU252 4.8 15.3 1.0
CB E:GLU253 4.9 16.1 1.0
CB E:GLU280 5.0 18.9 1.0

Magnesium binding site 6 out of 8 in 3d47

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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 D-Malate


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 D-Malate within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg501

b:14.2
occ:1.00
 OE1 F:GLU280 2.0 15.1 1.0
OD2 F:ASP226 2.0 11.6 1.0
O F:HOH542 2.0 13.4 1.0
OE1 F:GLU252 2.1 13.5 1.0
O3 F:MLT502 2.2 18.8 1.0
O1 F:MLT502 2.3 19.9 1.0
CD F:GLU280 2.9 16.6 1.0
CG F:ASP226 3.0 13.6 1.0
C1 F:MLT502 3.1 23.5 1.0
CD F:GLU252 3.1 15.2 1.0
C2 F:MLT502 3.1 21.5 1.0
OE2 F:GLU280 3.3 15.6 1.0
OD1 F:ASP226 3.3 14.0 1.0
CG F:GLU252 3.7 11.8 1.0
OE2 F:GLU252 4.0 12.6 1.0
C3 F:MLT502 4.1 24.1 1.0
NZ F:LYS189 4.1 12.7 1.0
O F:HOH520 4.1 14.2 1.0
OE1 F:GLU253 4.2 13.6 1.0
O F:HOH536 4.2 17.3 1.0
CG F:GLU280 4.3 16.3 1.0
O2 F:MLT502 4.3 20.7 1.0
CB F:ASP226 4.3 12.2 1.0
CD2 F:HIS329 4.5 23.2 1.0
CE F:LYS189 4.6 14.9 1.0
CB F:GLU253 4.9 14.0 1.0
CD1 F:TRP228 4.9 14.6 1.0
CB F:GLU252 5.0 11.5 1.0

Magnesium binding site 7 out of 8 in 3d47

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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 D-Malate


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 D-Malate within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg501

b:15.9
occ:1.00
 OE1 G:GLU280 2.0 14.5 1.0
O G:HOH728 2.0 13.3 1.0
OE1 G:GLU252 2.0 12.0 1.0
OD2 G:ASP226 2.1 14.5 1.0
O1 G:MLT502 2.1 16.1 1.0
O3 G:MLT502 2.3 20.1 1.0
CD G:GLU280 2.9 18.4 1.0
C1 G:MLT502 3.0 21.2 1.0
CD G:GLU252 3.0 15.2 1.0
CG G:ASP226 3.1 13.7 1.0
C2 G:MLT502 3.2 21.4 1.0
OE2 G:GLU280 3.3 18.0 1.0
OD1 G:ASP226 3.5 13.9 1.0
CG G:GLU252 3.6 12.3 1.0
NZ G:LYS189 3.9 12.6 1.0
O G:HOH798 3.9 15.3 1.0
O G:HOH799 4.0 17.0 1.0
OE2 G:GLU252 4.0 12.0 1.0
O2 G:MLT502 4.1 18.2 1.0
C3 G:MLT502 4.2 25.3 1.0
OE1 G:GLU253 4.2 16.9 1.0
CG G:GLU280 4.2 16.0 1.0
CD2 G:HIS329 4.4 28.2 1.0
CB G:ASP226 4.5 13.4 1.0
CE G:LYS189 4.5 13.8 1.0
CB G:GLU253 4.9 14.1 1.0
CB G:GLU252 4.9 10.8 1.0
CB G:GLU280 4.9 15.4 1.0

Magnesium binding site 8 out of 8 in 3d47

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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 D-Malate


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 D-Malate within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg501

b:22.9
occ:1.00
 OE1 H:GLU252 1.9 16.3 1.0
O H:HOH505 2.0 19.6 1.0
OD2 H:ASP226 2.1 20.1 1.0
O1 H:MLT502 2.1 28.4 1.0
OE1 H:GLU280 2.1 18.7 1.0
O3 H:MLT502 2.3 26.6 1.0
CD H:GLU252 2.9 18.3 1.0
C1 H:MLT502 2.9 29.2 1.0
CD H:GLU280 3.1 20.0 1.0
CG H:ASP226 3.1 22.2 1.0
C2 H:MLT502 3.1 28.9 1.0
OE2 H:GLU280 3.4 19.9 1.0
OD1 H:ASP226 3.5 20.2 1.0
CG H:GLU252 3.6 17.9 1.0
NZ H:LYS189 3.7 17.3 1.0
OE2 H:GLU252 3.9 18.6 1.0
O H:HOH522 4.0 20.3 1.0
O H:HOH516 4.1 20.5 1.0
O2 H:MLT502 4.1 29.6 1.0
C3 H:MLT502 4.2 27.1 1.0
CD2 H:HIS329 4.3 26.6 1.0
CG H:GLU280 4.4 19.7 1.0
OE1 H:GLU253 4.4 21.4 1.0
CB H:ASP226 4.4 22.1 1.0
CE H:LYS189 4.5 18.6 1.0
CB H:GLU252 4.8 17.8 1.0
NE2 H:HIS329 4.9 28.1 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 D-Malate. To Be Published.
Page generated: Wed Aug 14 12:23:17 2024

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