Atomistry » Sodium » PDB 1qtk-1s3x » 1rv8
Atomistry »
  Sodium »
    PDB 1qtk-1s3x »
      1rv8 »

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: Sun Oct 6 22:02:24 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