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Sodium in PDB 1rv8: Class II Fructose-1,6-Bisphosphate Aldolase From Thermus Aquaticus in Complex with Cobalt

Enzymatic activity of Class II Fructose-1,6-Bisphosphate Aldolase From Thermus Aquaticus in Complex with Cobalt

All present enzymatic activity of Class II Fructose-1,6-Bisphosphate Aldolase From Thermus Aquaticus in Complex with Cobalt:
4.1.2.13;

Protein crystallography data

The structure of Class II Fructose-1,6-Bisphosphate Aldolase From Thermus Aquaticus in Complex with Cobalt, PDB code: 1rv8 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) 40.43 / 2.30
Space group P 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 99.354, 57.629, 138.577, 90.00, 90.23, 90.00
R / Rfree (%) 21.1 / 25.2

Other elements in 1rv8:

The structure of Class II Fructose-1,6-Bisphosphate Aldolase From Thermus Aquaticus in Complex with Cobalt also contains other interesting chemical elements:

Cobalt (Co) 5 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Class II Fructose-1,6-Bisphosphate Aldolase From Thermus Aquaticus in Complex with Cobalt (pdb code 1rv8). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Class II Fructose-1,6-Bisphosphate Aldolase From Thermus Aquaticus in Complex with Cobalt, PDB code: 1rv8:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 1rv8

Go back to Sodium Binding Sites List in 1rv8
Sodium binding site 1 out of 4 in the Class II Fructose-1,6-Bisphosphate Aldolase From Thermus Aquaticus in Complex with Cobalt


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Class II Fructose-1,6-Bisphosphate Aldolase From Thermus Aquaticus in Complex with Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1704

b:46.3
occ:1.00
 NE2 A:HIS78 2.8 21.2 1.0
OD2 A:ASP80 2.8 23.4 0.5
OE2 A:GLU130 2.9 28.3 1.0
OD2 A:ASP80 3.0 23.0 0.5
O A:HOH1712 3.1 18.6 1.0
OE1 A:GLU130 3.2 28.0 1.0
NZ A:LYS249 3.3 24.5 1.0
NE2 A:HIS208 3.3 31.8 0.5
CD A:GLU130 3.4 28.3 1.0
CE1 A:HIS208 3.4 31.5 0.5
CG A:ASP80 3.4 23.2 0.5
CE1 A:HIS208 3.5 31.8 0.5
ND2 A:ASN251 3.6 24.7 1.0
CD2 A:HIS78 3.7 21.3 1.0
SD A:MET100 3.7 25.9 1.0
CE1 A:HIS78 3.8 21.3 1.0
CB A:MET100 3.9 24.9 1.0
NE2 A:HIS208 3.9 31.5 0.5
CG A:MET100 4.0 25.2 1.0
OD1 A:ASP80 4.0 23.3 0.5
CG A:ASP80 4.0 22.8 0.5
CA A:ASP80 4.1 23.1 0.5
CA A:ASP80 4.2 22.9 0.5
CB A:ASP80 4.2 23.2 0.5
ND1 A:HIS208 4.3 31.5 0.5
CD2 A:HIS208 4.3 31.8 0.5
O A:HOH1918 4.3 55.1 1.0
N A:HIS81 4.4 23.5 0.5
N A:HIS81 4.4 23.2 0.5
CE A:LYS249 4.5 24.8 1.0
ND1 A:HIS208 4.5 31.8 0.5
CB A:ASP80 4.5 22.8 0.5
CG A:ASN251 4.5 25.0 1.0
CD2 A:HIS81 4.7 24.1 0.5
C A:ASP80 4.7 23.3 0.5
OD1 A:ASN251 4.7 24.8 1.0
O A:LEU79 4.7 22.5 1.0
CG A:GLU130 4.7 28.3 1.0
NE2 A:HIS81 4.8 24.3 0.5
CG A:HIS78 4.8 21.3 1.0
ND1 A:HIS78 4.9 21.2 1.0
C A:ASP80 4.9 23.1 0.5
CD2 A:HIS208 4.9 31.6 0.5
CG A:HIS208 5.0 31.8 0.5
OD1 A:ASP80 5.0 22.8 0.5
CE A:MET100 5.0 25.6 1.0

Sodium binding site 2 out of 4 in 1rv8

Go back to Sodium Binding Sites List in 1rv8
Sodium binding site 2 out of 4 in the Class II Fructose-1,6-Bisphosphate Aldolase From Thermus Aquaticus in Complex with Cobalt


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Class II Fructose-1,6-Bisphosphate Aldolase From Thermus Aquaticus in Complex with Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1702

b:48.0
occ:1.00
 NE2 B:HIS78 2.9 21.2 1.0
OE2 B:GLU130 2.9 29.5 1.0
OD2 B:ASP80 2.9 23.2 1.0
O B:HOH1704 3.3 18.7 1.0
OE1 B:GLU130 3.3 29.5 1.0
CD B:GLU130 3.3 29.6 1.0
NZ B:LYS249 3.4 25.2 1.0
ND2 B:ASN251 3.5 28.0 1.0
CE1 B:HIS78 3.6 21.3 1.0
CG B:MET100 3.7 30.7 1.0
NE2 B:HIS208 3.8 38.1 1.0
CB B:MET100 3.9 30.1 1.0
N B:HIS81 3.9 24.0 1.0
CA B:ASP80 3.9 23.2 1.0
CD2 B:HIS78 4.0 21.1 1.0
CG B:ASP80 4.0 23.2 1.0
ND1 B:HIS81 4.0 25.4 1.0
SD B:MET100 4.0 31.4 1.0
CE B:MET100 4.1 31.2 1.0
CE1 B:HIS208 4.1 38.0 1.0
CE1 B:HIS81 4.2 25.4 1.0
CB B:ASP80 4.4 23.1 1.0
C B:ASP80 4.4 23.6 1.0
CG B:ASN251 4.4 28.1 1.0
OD1 B:ASN251 4.5 28.2 1.0
CE B:LYS249 4.5 25.7 1.0
O B:LEU79 4.5 22.2 1.0
CG B:GLU130 4.6 29.6 1.0
CD2 B:HIS208 4.7 38.0 1.0
ND1 B:HIS78 4.8 21.2 1.0
CG B:HIS81 4.9 25.2 1.0
CA B:HIS81 4.9 24.5 1.0
N B:ASP80 5.0 22.7 1.0
OD1 B:ASP80 5.0 23.0 1.0

Sodium binding site 3 out of 4 in 1rv8

Go back to Sodium Binding Sites List in 1rv8
Sodium binding site 3 out of 4 in the Class II Fructose-1,6-Bisphosphate Aldolase From Thermus Aquaticus in Complex with Cobalt


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Class II Fructose-1,6-Bisphosphate Aldolase From Thermus Aquaticus in Complex with Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na1708

b:48.9
occ:1.00
 OD2 C:ASP80 2.8 23.5 1.0
OE2 C:GLU130 2.9 29.0 1.0
NE2 C:HIS78 3.0 22.1 1.0
O C:HOH1709 3.0 12.9 1.0
OD1 C:ASN251 3.2 32.6 1.0
NZ C:LYS249 3.3 33.4 1.0
NE2 C:HIS208 3.4 43.3 1.0
OE1 C:GLU130 3.4 29.2 1.0
CD C:GLU130 3.5 29.1 1.0
CE1 C:HIS208 3.8 43.4 1.0
CG C:ASP80 3.9 23.6 1.0
CE1 C:HIS78 3.9 22.3 1.0
CD2 C:HIS78 3.9 22.2 1.0
ND1 C:HIS81 4.0 26.0 1.0
SD C:MET100 4.1 29.9 1.0
CG C:MET100 4.1 29.4 1.0
N C:HIS81 4.1 24.6 1.0
CA C:ASP80 4.1 23.8 1.0
CG C:ASN251 4.2 32.8 1.0
CE1 C:HIS81 4.2 26.2 1.0
CD2 C:HIS208 4.3 43.4 1.0
CB C:MET100 4.3 29.0 1.0
O C:HOH1834 4.3 43.6 1.0
ND2 C:ASN251 4.4 32.6 1.0
CB C:ASP80 4.5 23.6 1.0
CE C:LYS249 4.6 33.6 1.0
C C:ASP80 4.6 24.1 1.0
ND1 C:HIS208 4.7 43.4 1.0
CE C:MET100 4.7 29.6 1.0
O C:LEU79 4.8 23.1 1.0
CG C:GLU130 4.8 29.2 1.0
OD1 C:ASP80 4.8 23.5 1.0
CG C:HIS81 5.0 25.8 1.0

Sodium binding site 4 out of 4 in 1rv8

Go back to Sodium Binding Sites List in 1rv8
Sodium binding site 4 out of 4 in the Class II Fructose-1,6-Bisphosphate Aldolase From Thermus Aquaticus in Complex with Cobalt


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Class II Fructose-1,6-Bisphosphate Aldolase From Thermus Aquaticus in Complex with Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na1706

b:30.0
occ:1.00
 OE2 D:GLU130 2.8 24.5 1.0
NE2 D:HIS78 2.8 20.9 1.0
OD2 D:ASP80 2.9 23.4 1.0
O D:HOH1716 3.0 21.6 1.0
NZ D:LYS249 3.2 25.5 1.0
OE1 D:GLU130 3.3 24.7 1.0
CD D:GLU130 3.3 24.7 1.0
ND2 D:ASN251 3.4 28.4 1.0
NE2 D:HIS208 3.7 33.7 1.0
CE1 D:HIS78 3.7 21.1 1.0
CG D:ASP80 3.8 23.1 1.0
CD2 D:HIS78 3.8 20.9 1.0
CA D:ASP80 4.0 22.5 1.0
N D:HIS81 4.1 22.8 1.0
CG D:MET100 4.1 26.5 1.0
CE1 D:HIS208 4.2 33.7 1.0
ND1 D:HIS81 4.2 23.1 1.0
OD1 D:ASN251 4.2 28.6 1.0
SD D:MET100 4.2 27.4 1.0
CG D:ASN251 4.3 28.7 1.0
CB D:ASP80 4.3 22.6 1.0
CB D:MET100 4.3 26.0 1.0
CE D:LYS249 4.4 25.7 1.0
CE1 D:HIS81 4.4 23.0 1.0
CE D:MET100 4.5 27.0 1.0
O D:LEU79 4.5 22.0 1.0
C D:ASP80 4.6 22.6 1.0
CD2 D:HIS208 4.6 33.7 1.0
CG D:GLU130 4.6 24.8 1.0
OD1 D:ASP80 4.8 23.4 1.0
ND1 D:HIS78 4.9 21.0 1.0
CG D:HIS78 5.0 21.1 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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