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Sodium in PDB 1rvg: Crystal Strcuture of Class II Fructose-Bisphosphate Aldolase From Thermus Aquaticus in Complex with Y

Enzymatic activity of Crystal Strcuture of Class II Fructose-Bisphosphate Aldolase From Thermus Aquaticus in Complex with Y

All present enzymatic activity of Crystal Strcuture of Class II Fructose-Bisphosphate Aldolase From Thermus Aquaticus in Complex with Y:
4.1.2.13;

Protein crystallography data

The structure of Crystal Strcuture of Class II Fructose-Bisphosphate Aldolase From Thermus Aquaticus in Complex with Y, PDB code: 1rvg was solved by T.Izard, J.Sygusch, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 2.00
Space group P 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 99.860, 57.550, 138.617, 90.00, 90.26, 90.00
R / Rfree (%) 22.5 / 25.9

Other elements in 1rvg:

The structure of Crystal Strcuture of Class II Fructose-Bisphosphate Aldolase From Thermus Aquaticus in Complex with Y also contains other interesting chemical elements:

Cobalt (Co) 5 atoms
Yttrium (Y) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Strcuture of Class II Fructose-Bisphosphate Aldolase From Thermus Aquaticus in Complex with Y (pdb code 1rvg). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Strcuture of Class II Fructose-Bisphosphate Aldolase From Thermus Aquaticus in Complex with Y, PDB code: 1rvg:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 1rvg

Go back to Sodium Binding Sites List in 1rvg
Sodium binding site 1 out of 4 in the Crystal Strcuture of Class II Fructose-Bisphosphate Aldolase From Thermus Aquaticus in Complex with Y


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Strcuture of Class II Fructose-Bisphosphate Aldolase From Thermus Aquaticus in Complex with Y within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1704

b:39.7
occ:1.00
 NE2 A:HIS78 2.8 19.1 1.0
OD2 A:ASP80 2.8 21.9 0.5
OE2 A:GLU130 2.9 21.4 1.0
OD2 A:ASP80 3.0 21.4 0.5
O A:HOH1803 3.0 16.2 1.0
OE1 A:GLU130 3.1 21.1 1.0
CE1 A:HIS208 3.3 25.3 0.5
CD A:GLU130 3.3 21.8 1.0
NZ A:LYS249 3.4 19.8 1.0
CE1 A:HIS208 3.4 25.2 0.5
SD A:MET100 3.4 22.6 1.0
NE2 A:HIS208 3.6 25.4 0.5
CD2 A:HIS78 3.7 19.4 1.0
CG A:ASP80 3.7 21.9 0.5
CB A:MET100 3.7 21.9 1.0
CE1 A:HIS78 3.8 19.7 1.0
ND2 A:ASN251 3.8 23.5 1.0
NE2 A:HIS208 3.8 25.3 0.5
CG A:MET100 3.9 22.0 1.0
CG A:ASP80 4.0 21.5 0.5
CA A:ASP80 4.1 21.8 0.5
N A:HIS81 4.2 22.3 0.5
CA A:ASP80 4.2 21.6 0.5
ND1 A:HIS208 4.3 25.4 0.5
CB A:ASP80 4.4 21.9 0.5
ND1 A:HIS208 4.4 25.5 0.5
N A:HIS81 4.4 22.1 0.5
OD1 A:ASP80 4.4 22.0 0.5
CE A:LYS249 4.5 20.5 1.0
CE A:MET100 4.5 22.5 1.0
CB A:ASP80 4.6 21.6 0.5
CG A:GLU130 4.6 21.7 1.0
CG A:ASN251 4.7 23.8 1.0
O A:LEU79 4.7 21.0 1.0
C A:ASP80 4.7 22.0 0.5
OD1 A:ASN251 4.7 23.7 1.0
O A:HOH1944 4.7 39.0 1.0
CG A:HIS78 4.9 19.6 1.0
ND1 A:HIS78 4.9 19.7 1.0
CD2 A:HIS208 4.9 25.3 0.5
C A:ASP80 4.9 21.9 0.5
CD2 A:HIS208 4.9 25.3 0.5

Sodium binding site 2 out of 4 in 1rvg

Go back to Sodium Binding Sites List in 1rvg
Sodium binding site 2 out of 4 in the Crystal Strcuture of Class II Fructose-Bisphosphate Aldolase From Thermus Aquaticus in Complex with Y


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Strcuture of Class II Fructose-Bisphosphate Aldolase From Thermus Aquaticus in Complex with Y within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1702

b:40.8
occ:1.00
 OD2 B:ASP80 2.9 22.3 1.0
NE2 B:HIS78 2.9 18.1 1.0
OE2 B:GLU130 2.9 27.2 1.0
O B:HOH1704 3.0 18.4 1.0
NZ B:LYS249 3.2 21.4 1.0
ND2 B:ASN251 3.4 24.4 1.0
OE1 B:GLU130 3.4 26.6 1.0
NE2 B:HIS208 3.4 33.4 1.0
CD B:GLU130 3.5 27.1 1.0
CE B:MET100 3.5 30.9 1.0
CG B:MET100 3.7 29.8 1.0
CE1 B:HIS78 3.8 18.1 1.0
CE1 B:HIS208 3.8 33.4 1.0
CD2 B:HIS78 3.9 18.2 1.0
CG B:ASP80 4.0 21.9 1.0
CB B:MET100 4.0 28.5 1.0
N B:HIS81 4.1 22.8 1.0
CA B:ASP80 4.1 21.6 1.0
ND1 B:HIS81 4.1 25.1 1.0
CE1 B:HIS81 4.2 24.8 1.0
CG B:ASN251 4.3 24.4 1.0
SD B:MET100 4.4 31.7 1.0
OD1 B:ASN251 4.4 24.4 1.0
CD2 B:HIS208 4.4 33.3 1.0
CE B:LYS249 4.4 21.7 1.0
CB B:ASP80 4.5 21.7 1.0
C B:ASP80 4.6 22.1 1.0
O B:LEU79 4.8 20.3 1.0
CG B:GLU130 4.8 27.2 1.0
ND1 B:HIS208 4.9 33.5 1.0
ND1 B:HIS78 4.9 18.1 1.0
OD1 B:ASP80 5.0 22.2 1.0

Sodium binding site 3 out of 4 in 1rvg

Go back to Sodium Binding Sites List in 1rvg
Sodium binding site 3 out of 4 in the Crystal Strcuture of Class II Fructose-Bisphosphate Aldolase From Thermus Aquaticus in Complex with Y


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Strcuture of Class II Fructose-Bisphosphate Aldolase From Thermus Aquaticus in Complex with Y within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na1706

b:30.5
occ:1.00
 NE2 C:HIS78 2.9 19.3 1.0
OE2 C:GLU130 2.9 25.1 1.0
OD2 C:ASP80 2.9 23.6 1.0
O C:HOH1709 3.2 18.6 1.0
NZ C:LYS249 3.2 20.7 1.0
OE1 C:GLU130 3.3 24.6 1.0
CD C:GLU130 3.4 24.4 1.0
ND2 C:ASN251 3.5 24.9 1.0
NE2 C:HIS208 3.6 28.2 1.0
CE1 C:HIS78 3.8 19.3 1.0
CD2 C:HIS78 3.9 19.4 1.0
CG C:ASP80 3.9 23.2 1.0
ND1 C:HIS81 4.0 24.4 1.0
CE1 C:HIS208 4.1 28.1 1.0
CA C:ASP80 4.1 22.4 1.0
N C:HIS81 4.1 23.2 1.0
CE1 C:HIS81 4.2 24.3 1.0
SD C:MET100 4.2 27.1 1.0
CG C:MET100 4.3 25.9 1.0
OD1 C:ASN251 4.3 25.1 1.0
CG C:ASN251 4.3 24.8 1.0
CE C:MET100 4.4 26.9 1.0
CB C:ASP80 4.4 22.7 1.0
CB C:MET100 4.5 25.1 1.0
CE C:LYS249 4.5 21.0 1.0
CD2 C:HIS208 4.5 28.2 1.0
C C:ASP80 4.6 22.8 1.0
O C:LEU79 4.6 21.5 1.0
CG C:GLU130 4.7 24.2 1.0
OD1 C:ASP80 4.9 23.8 1.0
CG C:HIS81 5.0 24.1 1.0
ND1 C:HIS78 5.0 19.1 1.0

Sodium binding site 4 out of 4 in 1rvg

Go back to Sodium Binding Sites List in 1rvg
Sodium binding site 4 out of 4 in the Crystal Strcuture of Class II Fructose-Bisphosphate Aldolase From Thermus Aquaticus in Complex with Y


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Strcuture of Class II Fructose-Bisphosphate Aldolase From Thermus Aquaticus in Complex with Y within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na1708

b:35.2
occ:1.00
 OE2 D:GLU130 2.9 25.9 1.0
NE2 D:HIS78 2.9 22.0 1.0
OD2 D:ASP80 2.9 24.3 1.0
O D:HOH1715 3.1 20.5 1.0
OE1 D:GLU130 3.4 26.2 1.0
CD D:GLU130 3.4 26.0 1.0
NZ D:LYS249 3.4 28.4 1.0
OD1 D:ASN251 3.5 29.7 1.0
NE2 D:HIS208 3.6 38.0 1.0
CD2 D:HIS78 3.7 21.9 1.0
CE1 D:HIS208 3.9 38.4 1.0
CE1 D:HIS78 3.9 22.3 1.0
CG D:ASP80 4.0 24.4 1.0
SD D:MET100 4.0 29.4 1.0
CA D:ASP80 4.0 23.9 1.0
N D:HIS81 4.0 24.7 1.0
CG D:MET100 4.1 28.5 1.0
ND1 D:HIS81 4.2 27.5 1.0
CB D:MET100 4.2 27.9 1.0
CE1 D:HIS81 4.3 27.8 1.0
CG D:ASN251 4.4 29.3 1.0
CB D:ASP80 4.5 24.1 1.0
CD2 D:HIS208 4.5 38.3 1.0
ND2 D:ASN251 4.5 29.1 1.0
C D:ASP80 4.6 24.3 1.0
O D:LEU79 4.6 22.8 1.0
O D:HOH1867 4.6 45.7 1.0
CE D:LYS249 4.7 28.7 1.0
CG D:GLU130 4.8 26.3 1.0
ND1 D:HIS208 4.8 38.4 1.0
CE D:MET100 4.9 28.8 1.0
CG D:HIS78 5.0 22.3 1.0
OD1 D:ASP80 5.0 25.1 1.0

Reference:

T.Izard, J.Sygusch. Induced Fit Movements and Metal Cofactor Selectivity of Class II Aldolases: Structure of Thermus Aquaticus Fructose-1,6-Bisphosphate Aldolase. J.Biol.Chem. V. 279 11825 2004.
ISSN: ISSN 0021-9258
PubMed: 14699122
DOI: 10.1074/JBC.M311375200
Page generated: Tue Dec 15 05:35:17 2020

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