Atomistry » Magnesium » PDB 3d1r-3dev » 3d46
Atomistry »
  Magnesium »
    PDB 3d1r-3dev »
      3d46 »

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

Go back to Magnesium Binding Sites List in 3d46
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

Go back to Magnesium Binding Sites List in 3d46
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

Go back to Magnesium Binding Sites List in 3d46
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

Go back to Magnesium Binding Sites List in 3d46
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

Go back to Magnesium Binding Sites List in 3d46
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

Go back to Magnesium Binding Sites List in 3d46
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

Go back to Magnesium Binding Sites List in 3d46
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

Go back to Magnesium Binding Sites List in 3d46
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy