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Sodium in PDB 5ucp: Class II Fructose-1,6-Bisphosphate Aldolase E142A Variant of Helicobacter Pylori with Fbp and Cleavage Products

Enzymatic activity of Class II Fructose-1,6-Bisphosphate Aldolase E142A Variant of Helicobacter Pylori with Fbp and Cleavage Products

All present enzymatic activity of Class II Fructose-1,6-Bisphosphate Aldolase E142A Variant of Helicobacter Pylori with Fbp and Cleavage Products:
4.1.2.13;

Protein crystallography data

The structure of Class II Fructose-1,6-Bisphosphate Aldolase E142A Variant of Helicobacter Pylori with Fbp and Cleavage Products, PDB code: 5ucp was solved by B.Jacques, J.Sygusch, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.21 / 1.44
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 39.476, 64.633, 62.845, 82.15, 74.39, 75.78
R / Rfree (%) 16.2 / 19.6

Other elements in 5ucp:

The structure of Class II Fructose-1,6-Bisphosphate Aldolase E142A Variant of Helicobacter Pylori with Fbp and Cleavage Products also contains other interesting chemical elements:

Zinc (Zn) 6 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Class II Fructose-1,6-Bisphosphate Aldolase E142A Variant of Helicobacter Pylori with Fbp and Cleavage Products (pdb code 5ucp). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Class II Fructose-1,6-Bisphosphate Aldolase E142A Variant of Helicobacter Pylori with Fbp and Cleavage Products, PDB code: 5ucp:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5ucp

Go back to Sodium Binding Sites List in 5ucp
Sodium binding site 1 out of 2 in the Class II Fructose-1,6-Bisphosphate Aldolase E142A Variant of Helicobacter Pylori with Fbp and Cleavage Products


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 E142A Variant of Helicobacter Pylori with Fbp and Cleavage Products within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:27.2
occ:1.00
 HE2 A:HIS80 2.1 14.2 1.0
HD21 A:ASN253 2.4 19.4 1.0
HE1 A:HIS210 2.7 22.2 0.2
HZ1 A:LYS251 2.7 21.0 1.0
OD1 A:ASP82 2.8 16.7 1.0
NE2 A:HIS80 2.9 11.8 1.0
HZ2 A:LYS251 3.0 21.0 1.0
HA A:ASP82 3.1 14.7 1.0
OE2 A:GLU132 3.1 19.6 1.0
HE1 A:HIS210 3.1 14.6 0.3
HE2 A:HIS210 3.2 14.5 0.3
ND2 A:ASN253 3.2 16.2 1.0
NZ A:LYS251 3.2 17.5 1.0
CE1 A:HIS210 3.2 18.5 0.2
HE2 A:HIS210 3.3 18.2 0.4
HE2 A:HIS210 3.3 21.1 0.2
HB2 A:MET102 3.4 18.6 1.0
OE1 A:GLU132 3.4 14.1 1.0
CE1 A:HIS210 3.4 12.3 0.3
NE2 A:HIS210 3.5 12.2 0.3
H A:HIS83 3.5 8.7 0.4
H A:HIS83 3.5 13.4 0.2
CD A:GLU132 3.5 16.1 1.0
H A:HIS83 3.5 26.4 0.3
OE1 A:GLN47 3.5 19.6 1.0
HD22 A:ASN253 3.5 19.4 1.0
NE2 A:HIS210 3.5 17.5 0.2
HZ3 A:LYS251 3.6 21.0 1.0
HD2 A:HIS80 3.7 13.4 1.0
CD2 A:HIS80 3.7 11.1 1.0
SD A:MET102 3.7 21.5 1.0
HG3 A:MET102 3.7 22.7 1.0
NE2 A:HIS210 3.8 15.2 0.4
CG A:ASP82 3.8 19.8 1.0
HB3 A:MET102 3.8 18.6 1.0
CB A:MET102 3.9 15.5 1.0
CG A:MET102 4.0 18.9 1.0
CE1 A:HIS80 4.0 11.6 1.0
CA A:ASP82 4.0 12.2 1.0
HD1 A:HIS83 4.0 19.6 0.4
HE1 A:HIS80 4.2 13.9 1.0
HE22 A:GLN47 4.2 17.0 1.0
N A:HIS83 4.2 7.3 0.4
CG A:ASN253 4.2 10.7 1.0
N A:HIS83 4.2 11.2 0.2
N A:HIS83 4.2 22.0 0.3
CB A:ASP82 4.3 15.8 1.0
HB2 A:ASP82 4.3 19.0 1.0
HG11 A:VAL208 4.3 21.6 1.0
ND1 A:HIS210 4.3 12.6 0.2
OD1 A:ASN253 4.4 14.7 1.0
CD A:GLN47 4.4 15.8 1.0
ND1 A:HIS83 4.4 16.3 0.4
CD2 A:HIS210 4.4 17.5 0.4
HD2 A:HIS210 4.4 21.1 0.4
HE3 A:LYS251 4.5 14.4 1.0
CE A:LYS251 4.5 12.0 1.0
ND1 A:HIS210 4.5 33.8 0.3
HE1 A:HIS83 4.5 33.5 0.4
O3 A:P6F405 4.5 25.5 0.7
CD2 A:HIS210 4.6 14.1 0.3
CE1 A:HIS210 4.6 12.5 0.4
HD2 A:HIS83 4.6 21.6 0.2
NE2 A:GLN47 4.6 14.1 1.0
HE3 A:MET102 4.6 18.1 1.0
C A:ASP82 4.6 10.2 1.0
HO3 A:P6F405 4.6 30.6 0.7
CE1 A:HIS83 4.7 27.9 0.4
O A:LEU81 4.7 12.7 1.0
CD2 A:HIS210 4.7 12.5 0.2
HD2 A:HIS83 4.8 11.4 0.3
HE1 A:HIS210 4.8 14.9 0.4
CD2 A:HIS83 4.8 17.9 0.2
HB3 A:GLU132 4.8 13.0 1.0
CE A:MET102 4.8 15.1 1.0
OD2 A:ASP82 4.8 25.1 1.0
CG A:GLU132 4.8 13.1 1.0
CG A:HIS80 4.9 9.9 1.0
HG2 A:MET102 4.9 22.7 1.0
CD2 A:HIS83 4.9 9.5 0.3
HE2 A:LYS251 4.9 14.4 1.0

Sodium binding site 2 out of 2 in 5ucp

Go back to Sodium Binding Sites List in 5ucp
Sodium binding site 2 out of 2 in the Class II Fructose-1,6-Bisphosphate Aldolase E142A Variant of Helicobacter Pylori with Fbp and Cleavage Products


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 E142A Variant of Helicobacter Pylori with Fbp and Cleavage Products within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na401

b:24.5
occ:1.00
 HE2 B:HIS80 2.1 16.6 1.0
HD21 B:ASN253 2.4 18.9 1.0
HE1 B:HIS210 2.6 36.3 0.2
HZ1 B:LYS251 2.6 17.2 1.0
HZ2 B:LYS251 2.9 17.2 1.0
NE2 B:HIS80 2.9 13.8 1.0
OE2 B:GLU132 2.9 18.0 1.0
OD1 B:ASP82 3.0 17.3 1.0
HE2 B:HIS210 3.1 9.7 0.3
NZ B:LYS251 3.1 14.3 1.0
HA B:ASP82 3.1 15.6 1.0
HE2 B:HIS210 3.2 15.5 0.4
ND2 B:ASN253 3.2 15.7 1.0
CE1 B:HIS210 3.2 30.2 0.2
OE1 B:GLU132 3.3 17.4 1.0
HE2 B:HIS210 3.4 31.5 0.2
HB2 B:MET102 3.4 18.0 1.0
CD B:GLU132 3.4 20.3 1.0
HE1 B:HIS210 3.5 14.1 0.3
NE2 B:HIS210 3.5 8.2 0.3
HZ3 B:LYS251 3.5 17.2 1.0
OE1 B:GLN47 3.5 20.7 1.0
HD22 B:ASN253 3.5 18.9 1.0
H B:HIS83 3.6 14.6 0.4
NE2 B:HIS210 3.6 26.2 0.2
H B:HIS83 3.6 14.8 0.2
H B:HIS83 3.6 15.2 0.3
HG3 B:MET102 3.6 19.0 1.0
CE1 B:HIS210 3.7 11.7 0.3
CD2 B:HIS80 3.7 11.4 1.0
HD2 B:HIS80 3.7 13.7 1.0
NE2 B:HIS210 3.8 12.9 0.4
SD B:MET102 3.8 22.5 1.0
HB3 B:MET102 3.8 18.0 1.0
CB B:MET102 3.9 15.0 1.0
CE1 B:HIS80 3.9 11.7 1.0
CG B:ASP82 3.9 22.5 1.0
CG B:MET102 3.9 15.8 1.0
CA B:ASP82 4.0 12.9 1.0
HE1 B:HIS80 4.1 14.0 1.0
HD1 B:HIS83 4.1 19.7 0.4
CG B:ASN253 4.2 11.8 1.0
HO3 B:13P405 4.2 33.6 0.8
HG11 B:VAL208 4.2 13.9 1.0
HE22 B:GLN47 4.2 16.3 1.0
ND1 B:HIS210 4.3 12.4 0.2
N B:HIS83 4.3 12.2 0.4
N B:HIS83 4.3 12.3 0.2
N B:HIS83 4.3 12.6 0.3
HD2 B:HIS210 4.3 12.0 0.4
HB2 B:ASP82 4.3 20.3 1.0
OD1 B:ASN253 4.3 15.4 1.0
CB B:ASP82 4.3 16.9 1.0
CD2 B:HIS210 4.4 10.0 0.4
HE3 B:LYS251 4.4 17.7 1.0
CE B:LYS251 4.4 14.7 1.0
CD B:GLN47 4.4 13.4 1.0
HD2 B:HIS83 4.4 24.4 0.2
ND1 B:HIS83 4.5 16.4 0.4
HE3 B:MET102 4.5 16.5 1.0
CD2 B:HIS210 4.5 20.3 0.3
HE1 B:HIS83 4.5 35.1 0.4
HD1 B:HIS210 4.6 15.0 0.2
HD2 B:HIS83 4.6 28.8 0.3
NE2 B:GLN47 4.7 13.6 1.0
CE1 B:HIS83 4.7 29.2 0.4
CE1 B:HIS210 4.7 10.8 0.4
C B:ASP82 4.7 13.8 1.0
ND1 B:HIS210 4.7 21.7 0.3
CD2 B:HIS83 4.7 20.4 0.2
O3 B:13P405 4.7 28.0 0.8
O B:LEU81 4.8 12.7 1.0
HB3 B:GLU132 4.8 14.3 1.0
CG B:GLU132 4.8 14.2 1.0
CD2 B:HIS210 4.8 8.5 0.2
CE B:MET102 4.8 13.7 1.0
CD2 B:HIS83 4.9 23.9 0.3
HE2 B:LYS251 4.9 17.7 1.0
HE1 B:HIS210 4.9 13.0 0.4
HG2 B:MET102 4.9 19.0 1.0
HD2 B:HIS210 4.9 24.4 0.3
CG B:HIS80 4.9 12.1 1.0
HG2 B:GLU132 5.0 17.1 1.0
OD2 B:ASP82 5.0 25.8 1.0
ND1 B:HIS80 5.0 14.4 1.0

Reference:

B.Jacques, M.Coincon, J.Sygusch. Active Site Remodeling During the Catalytic Cycle in Metal-Dependent Fructose-1,6-Bisphosphate Aldolases. J. Biol. Chem. V. 293 7737 2018.
ISSN: ESSN 1083-351X
PubMed: 29593097
DOI: 10.1074/JBC.RA117.001098
Page generated: Tue Oct 8 00:28:10 2024

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