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Sodium in PDB 4lrt: Crystal and Solution Structures of the Bifunctional Enzyme (Aldolase/Aldehyde Dehydrogenase) From Thermomonospora Curvata, Reveal A Cofactor-Binding Domain Motion During Nad+ and Coa Accommodation Whithin the Shared Cofactor-Binding Site

Enzymatic activity of Crystal and Solution Structures of the Bifunctional Enzyme (Aldolase/Aldehyde Dehydrogenase) From Thermomonospora Curvata, Reveal A Cofactor-Binding Domain Motion During Nad+ and Coa Accommodation Whithin the Shared Cofactor-Binding Site

All present enzymatic activity of Crystal and Solution Structures of the Bifunctional Enzyme (Aldolase/Aldehyde Dehydrogenase) From Thermomonospora Curvata, Reveal A Cofactor-Binding Domain Motion During Nad+ and Coa Accommodation Whithin the Shared Cofactor-Binding Site:
1.2.1.10; 4.1.3.39;

Protein crystallography data

The structure of Crystal and Solution Structures of the Bifunctional Enzyme (Aldolase/Aldehyde Dehydrogenase) From Thermomonospora Curvata, Reveal A Cofactor-Binding Domain Motion During Nad+ and Coa Accommodation Whithin the Shared Cofactor-Binding Site, PDB code: 4lrt was solved by B.Fischer, G.Branlant, F.Talfournier, A.Gruez, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.45 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 94.500, 116.700, 131.500, 90.00, 90.00, 90.00
R / Rfree (%) 15.1 / 17

Other elements in 4lrt:

The structure of Crystal and Solution Structures of the Bifunctional Enzyme (Aldolase/Aldehyde Dehydrogenase) From Thermomonospora Curvata, Reveal A Cofactor-Binding Domain Motion During Nad+ and Coa Accommodation Whithin the Shared Cofactor-Binding Site also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal and Solution Structures of the Bifunctional Enzyme (Aldolase/Aldehyde Dehydrogenase) From Thermomonospora Curvata, Reveal A Cofactor-Binding Domain Motion During Nad+ and Coa Accommodation Whithin the Shared Cofactor-Binding Site (pdb code 4lrt). 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 and Solution Structures of the Bifunctional Enzyme (Aldolase/Aldehyde Dehydrogenase) From Thermomonospora Curvata, Reveal A Cofactor-Binding Domain Motion During Nad+ and Coa Accommodation Whithin the Shared Cofactor-Binding Site, PDB code: 4lrt:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 4lrt

Go back to Sodium Binding Sites List in 4lrt
Sodium binding site 1 out of 4 in the Crystal and Solution Structures of the Bifunctional Enzyme (Aldolase/Aldehyde Dehydrogenase) From Thermomonospora Curvata, Reveal A Cofactor-Binding Domain Motion During Nad+ and Coa Accommodation Whithin the Shared Cofactor-Binding Site


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal and Solution Structures of the Bifunctional Enzyme (Aldolase/Aldehyde Dehydrogenase) From Thermomonospora Curvata, Reveal A Cofactor-Binding Domain Motion During Nad+ and Coa Accommodation Whithin the Shared Cofactor-Binding Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:24.7
occ:1.00
 O C:HOH622 2.9 25.8 1.0
OG A:SER182 3.0 22.3 1.0
NE2 C:GLN221 3.3 20.6 1.0
O A:HOH655 3.3 33.9 1.0
N A:SER182 3.4 15.4 1.0
O A:VAL180 3.5 20.6 1.0
CB A:SER182 3.6 18.0 1.0
CB A:LEU181 3.8 16.2 1.0
CA A:SER182 4.1 16.3 1.0
CD2 C:LEU253 4.1 22.0 1.0
CD C:GLN221 4.2 19.3 1.0
OE1 C:GLN221 4.2 20.8 1.0
CG1 A:VAL180 4.2 20.3 1.0
C A:VAL180 4.3 17.9 1.0
C A:LEU181 4.4 16.2 1.0
CA A:LEU181 4.5 15.7 1.0
CG1 C:VAL217 4.6 15.1 1.0
CG A:LEU181 4.6 17.6 1.0
CD1 A:LEU181 4.6 21.3 1.0
N A:LEU181 4.8 16.9 1.0
CB A:VAL180 4.9 18.0 1.0
O A:HOH675 4.9 29.3 1.0

Sodium binding site 2 out of 4 in 4lrt

Go back to Sodium Binding Sites List in 4lrt
Sodium binding site 2 out of 4 in the Crystal and Solution Structures of the Bifunctional Enzyme (Aldolase/Aldehyde Dehydrogenase) From Thermomonospora Curvata, Reveal A Cofactor-Binding Domain Motion During Nad+ and Coa Accommodation Whithin the Shared Cofactor-Binding Site


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal and Solution Structures of the Bifunctional Enzyme (Aldolase/Aldehyde Dehydrogenase) From Thermomonospora Curvata, Reveal A Cofactor-Binding Domain Motion During Nad+ and Coa Accommodation Whithin the Shared Cofactor-Binding Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na402

b:31.1
occ:1.00
 O B:LYS98 2.7 14.2 0.2
O B:LYS98 2.7 14.2 0.2
O B:LYS98 2.7 13.8 0.4
C B:LYS98 3.7 14.0 0.4
C B:LYS98 3.7 14.1 0.2
C B:LYS98 3.7 14.1 0.2
CG B:LYS98 3.7 15.7 0.2
N B:ALA102 3.8 15.6 1.0
CB B:LEU101 3.9 15.1 1.0
CA B:LYS98 3.9 14.4 0.4
CB B:ALA102 3.9 16.5 1.0
CG B:LYS98 4.0 15.3 0.2
CA B:LYS98 4.0 14.2 0.2
CA B:LYS98 4.0 14.3 0.2
CB B:LYS98 4.0 14.6 0.4
CA B:ALA102 4.2 16.1 1.0
CB B:LYS98 4.3 14.2 0.2
C B:LEU101 4.3 15.6 1.0
CB B:LYS98 4.4 14.3 0.2
O B:HOH729 4.6 42.1 1.0
CA B:LEU101 4.7 14.6 1.0
N B:ALA99 4.9 14.0 1.0
CD1 B:LEU101 4.9 16.5 1.0
CD B:LYS98 4.9 16.2 0.2

Sodium binding site 3 out of 4 in 4lrt

Go back to Sodium Binding Sites List in 4lrt
Sodium binding site 3 out of 4 in the Crystal and Solution Structures of the Bifunctional Enzyme (Aldolase/Aldehyde Dehydrogenase) From Thermomonospora Curvata, Reveal A Cofactor-Binding Domain Motion During Nad+ and Coa Accommodation Whithin the Shared Cofactor-Binding Site


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal and Solution Structures of the Bifunctional Enzyme (Aldolase/Aldehyde Dehydrogenase) From Thermomonospora Curvata, Reveal A Cofactor-Binding Domain Motion During Nad+ and Coa Accommodation Whithin the Shared Cofactor-Binding Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na403

b:16.7
occ:1.00
 SG B:CYS146 2.4 22.9 0.3
O B:HOH790 3.1 19.6 1.0
O B:HOH545 3.1 19.4 1.0
O B:HOH656 3.2 27.9 1.0
ND2 B:ASN296 3.3 15.6 1.0
CB B:ASN296 3.7 15.3 1.0
C2P B:COA405 3.7 14.3 0.8
CD1 B:ILE173 3.9 16.2 1.0
CG B:ASN296 4.0 15.1 1.0
CD1 B:ILE210 4.0 16.8 1.0
CB B:CYS146 4.1 17.9 0.3
CB B:CYS146 4.2 16.6 0.7
S1P B:COA405 4.3 13.2 0.6
CG2 B:ILE173 4.4 15.6 1.0
OG1 B:THR182 4.6 23.3 1.0
CG2 B:THR182 4.7 21.9 1.0
CG1 B:ILE173 4.9 16.0 1.0
N B:GLY147 4.9 16.6 1.0
CE1 B:PHE189 4.9 18.6 1.0
SG B:CYS146 5.0 15.5 0.7

Sodium binding site 4 out of 4 in 4lrt

Go back to Sodium Binding Sites List in 4lrt
Sodium binding site 4 out of 4 in the Crystal and Solution Structures of the Bifunctional Enzyme (Aldolase/Aldehyde Dehydrogenase) From Thermomonospora Curvata, Reveal A Cofactor-Binding Domain Motion During Nad+ and Coa Accommodation Whithin the Shared Cofactor-Binding Site


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal and Solution Structures of the Bifunctional Enzyme (Aldolase/Aldehyde Dehydrogenase) From Thermomonospora Curvata, Reveal A Cofactor-Binding Domain Motion During Nad+ and Coa Accommodation Whithin the Shared Cofactor-Binding Site within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na402

b:15.0
occ:1.00
 SG D:CYS146 2.5 20.4 0.2
O D:HOH819 3.1 18.8 1.0
O D:HOH570 3.1 16.5 1.0
O D:HOH824 3.2 22.9 1.0
ND2 D:ASN296 3.3 14.6 1.0
CB D:ASN296 3.7 13.3 1.0
C2P D:COA403 3.8 16.7 1.0
CD1 D:ILE173 4.0 13.8 1.0
CG D:ASN296 4.0 15.0 1.0
CD1 D:ILE210 4.0 16.8 1.0
CB D:CYS146 4.2 16.3 0.2
CB D:CYS146 4.2 15.9 0.8
S1P D:COA403 4.3 11.5 0.6
CG2 D:ILE173 4.4 12.4 1.0
OG1 D:THR182 4.6 22.0 1.0
CG2 D:THR182 4.6 19.5 1.0
N D:GLY147 4.9 14.9 1.0
CG1 D:ILE173 5.0 13.2 1.0
SG D:CYS146 5.0 14.9 0.8

Reference:

B.Fischer, G.Branlant, F.Talfournier, A.Gruez. Crystal and Solution Structures of the Bifunctional Enzyme (Aldolase/Aldehyde Dehydrogenase) From Thermomonospora Curvata, Reveal A Cofactor-Binding Domain Motion During Nad+ and Coa Accommodation Whithin the Shared Cofactor-Binding Site To Be Published.
Page generated: Mon Oct 7 16:50:27 2024

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