Atomistry » Magnesium » PDB 3d1r-3dev » 3d47
Atomistry »
  Magnesium »
    PDB 3d1r-3dev »
      3d47 »

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

Go back to Magnesium Binding Sites List in 3d47
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

Go back to Magnesium Binding Sites List in 3d47
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

Go back to Magnesium Binding Sites List in 3d47
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

Go back to Magnesium Binding Sites List in 3d47
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

Go back to Magnesium Binding Sites List in 3d47
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

Go back to Magnesium Binding Sites List in 3d47
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

Go back to Magnesium Binding Sites List in 3d47
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

Go back to Magnesium Binding Sites List in 3d47
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

Last articles

Cl in 2VJ0
Cl in 2VIO
Cl in 2VIW
Cl in 2VIV
Cl in 2VH6
Cl in 2VH0
Cl in 2VG3
Cl in 2VGC
Cl in 2VG5
Cl in 2VG2
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy