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Sodium in PDB 5vjd: Class II Fructose-1,6-Bisphosphate Aldolase of Escherichia Coli with Dhap

Enzymatic activity of Class II Fructose-1,6-Bisphosphate Aldolase of Escherichia Coli with Dhap

All present enzymatic activity of Class II Fructose-1,6-Bisphosphate Aldolase of Escherichia Coli with Dhap:
4.1.2.13;

Protein crystallography data

The structure of Class II Fructose-1,6-Bisphosphate Aldolase of Escherichia Coli with Dhap, PDB code: 5vjd was solved by J.Sygusch, M.Coincon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.87 / 1.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 57.174, 71.454, 88.185, 90.00, 108.94, 90.00
R / Rfree (%) 14.8 / 17.3

Other elements in 5vjd:

The structure of Class II Fructose-1,6-Bisphosphate Aldolase of Escherichia Coli with Dhap also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Class II Fructose-1,6-Bisphosphate Aldolase of Escherichia Coli with Dhap (pdb code 5vjd). 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 of Escherichia Coli with Dhap, PDB code: 5vjd:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 5vjd

Go back to Sodium Binding Sites List in 5vjd
Sodium binding site 1 out of 4 in the Class II Fructose-1,6-Bisphosphate Aldolase of Escherichia Coli with Dhap


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 of Escherichia Coli with Dhap within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:33.4
occ:1.00
 O A:GLY227 2.3 59.0 1.0
O2P A:13P404 2.4 25.1 1.0
O A:HOH812 2.5 50.5 1.0
O A:SER267 2.6 24.5 1.0
O A:VAL225 2.7 47.2 1.0
O A:GLY265 2.9 25.1 1.0
H A:GLY227 3.1 65.6 1.0
HB2 A:SER267 3.2 27.6 1.0
HA2 A:GLY265 3.2 27.1 1.0
C A:GLY265 3.3 23.7 1.0
C A:GLY227 3.3 56.6 1.0
N A:GLY227 3.4 54.7 1.0
C A:SER267 3.6 26.6 1.0
HA3 A:GLY265 3.6 27.1 1.0
H A:SER267 3.6 29.2 1.0
CA A:GLY265 3.6 22.6 1.0
N A:SER267 3.7 24.4 1.0
HA A:HIS226 3.8 65.0 1.0
O A:HOH557 3.9 30.9 1.0
P A:13P404 3.9 23.4 1.0
C A:VAL225 3.9 46.2 1.0
CA A:GLY227 3.9 57.3 1.0
CA A:SER267 4.0 24.9 1.0
C A:HIS226 4.0 55.5 1.0
CB A:SER267 4.0 23.0 1.0
HA A:VAL228 4.1 65.7 1.0
HG11 A:VAL228 4.1 61.8 1.0
N A:GLY266 4.2 22.4 1.0
CA A:HIS226 4.3 54.1 1.0
C A:GLY266 4.3 23.4 1.0
O A:HOH816 4.3 38.7 1.0
N A:VAL228 4.4 53.1 1.0
HA2 A:GLY227 4.4 68.8 1.0
O1P A:13P404 4.5 23.4 1.0
H A:VAL225 4.5 49.6 1.0
HB3 A:SER267 4.5 27.6 1.0
N A:HIS226 4.6 52.3 1.0
HE1 A:TYR229 4.7 0.1 1.0
O A:HOH618 4.7 44.9 1.0
O1 A:13P404 4.7 21.2 1.0
HA3 A:GLY268 4.7 37.3 1.0
H A:GLY266 4.7 26.9 1.0
HA3 A:GLY227 4.7 68.8 1.0
N A:GLY268 4.7 29.0 1.0
CA A:VAL228 4.8 54.8 1.0
O A:HIS226 4.8 56.5 1.0
CA A:GLY266 4.8 23.0 1.0
HB A:VAL225 4.8 51.5 1.0
O A:GLY266 4.9 22.9 1.0
O3P A:13P404 4.9 20.6 1.0
HD1 A:TYR229 4.9 1.0 1.0
HA A:SER267 4.9 29.9 1.0
HG A:SER269 5.0 35.2 1.0

Sodium binding site 2 out of 4 in 5vjd

Go back to Sodium Binding Sites List in 5vjd
Sodium binding site 2 out of 4 in the Class II Fructose-1,6-Bisphosphate Aldolase of Escherichia Coli with Dhap


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 of Escherichia Coli with Dhap within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:23.3
occ:1.00
 HD21 A:ASN286 2.2 17.7 1.0
HE2 A:HIS107 2.3 14.6 1.0
HZ3 A:LYS284 2.6 13.7 1.0
OD2 A:ASP109 2.7 14.9 1.0
HZ2 A:LYS284 2.7 13.7 1.0
OE2 A:GLU172 2.7 12.9 1.0
HE1 A:HIS264 2.9 18.3 0.5
NZ A:LYS284 3.0 11.4 1.0
NE2 A:HIS107 3.1 12.2 1.0
ND2 A:ASN286 3.1 14.8 1.0
HA A:ASP109 3.1 17.0 1.0
HE2 A:HIS264 3.2 17.6 0.5
OE1 A:GLU172 3.2 12.5 1.0
CD A:GLU172 3.2 12.7 1.0
HE2 A:HIS264 3.2 18.3 0.5
HB2 A:MET142 3.3 22.8 1.0
CE1 A:HIS264 3.4 15.2 0.5
HZ1 A:LYS284 3.4 13.7 1.0
HG3 A:MET142 3.4 25.7 1.0
HD22 A:ASN286 3.5 17.7 1.0
HD2 A:HIS107 3.6 14.3 1.0
NE2 A:HIS264 3.6 15.2 0.5
HE22 A:GLN59 3.6 20.0 1.0
CD2 A:HIS107 3.7 11.9 1.0
NE2 A:HIS264 3.7 14.7 0.5
CG A:ASP109 3.8 14.7 1.0
OE1 A:GLN59 3.8 13.1 1.0
SD A:MET142 3.9 24.1 1.0
CG A:MET142 3.9 21.4 1.0
CB A:MET142 3.9 19.0 1.0
HG11 A:VAL262 4.0 13.2 1.0
CA A:ASP109 4.0 14.2 1.0
HB3 A:MET142 4.1 22.8 1.0
CG A:ASN286 4.1 15.3 1.0
OD1 A:ASN286 4.2 16.4 1.0
NE2 A:GLN59 4.2 16.7 1.0
H A:HIS110 4.2 20.2 0.5
H A:HIS110 4.2 20.2 0.5
CE1 A:HIS107 4.2 12.0 1.0
HE1 A:HIS264 4.2 15.7 0.5
CE1 A:HIS264 4.2 13.0 0.5
HE3 A:LYS284 4.3 13.5 1.0
CE A:LYS284 4.3 11.2 1.0
HO3 A:13P404 4.3 28.0 1.0
CD A:GLN59 4.3 13.9 1.0
CB A:ASP109 4.4 15.0 1.0
HE1 A:HIS107 4.5 14.4 1.0
O A:THR108 4.5 11.0 1.0
ND1 A:HIS264 4.5 15.8 0.5
CD2 A:HIS264 4.6 14.4 0.5
CG A:GLU172 4.6 12.7 1.0
HE2 A:MET142 4.6 29.7 1.0
HB2 A:ASP109 4.6 18.0 1.0
N A:HIS110 4.7 16.8 1.0
OD1 A:ASP109 4.7 15.8 1.0
HB3 A:GLU172 4.7 15.4 1.0
C A:ASP109 4.8 16.8 1.0
HG2 A:GLU172 4.8 15.2 1.0
HD2 A:HIS264 4.8 17.3 0.5
CD2 A:HIS264 4.8 15.4 0.5
O3 A:13P404 4.8 23.3 1.0
HE2 A:LYS284 4.8 13.5 1.0
HG2 A:MET142 4.8 25.7 1.0
CG1 A:VAL262 4.9 11.0 1.0
HE21 A:GLN59 4.9 20.0 1.0
CE A:MET142 4.9 24.7 1.0
N A:ASP109 4.9 12.3 1.0
HG12 A:VAL262 5.0 13.2 1.0
CG A:HIS107 5.0 11.8 1.0

Sodium binding site 3 out of 4 in 5vjd

Go back to Sodium Binding Sites List in 5vjd
Sodium binding site 3 out of 4 in the Class II Fructose-1,6-Bisphosphate Aldolase of Escherichia Coli with Dhap


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 of Escherichia Coli with Dhap within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na401

b:21.9
occ:1.00
 O B:GLY227 2.3 28.4 1.0
O3P B:13P404 2.4 20.2 1.0
O B:SER267 2.5 20.1 1.0
O B:VAL225 2.5 28.3 1.0
O B:HOH515 2.7 33.9 1.0
O B:GLY265 2.8 20.5 1.0
HA2 B:GLY265 3.1 23.1 1.0
H B:GLY227 3.1 35.7 1.0
HB2 B:SER267 3.3 21.8 1.0
C B:GLY265 3.3 19.7 1.0
C B:GLY227 3.4 28.7 1.0
N B:GLY227 3.4 29.8 1.0
HA3 B:GLY265 3.5 23.1 1.0
CA B:GLY265 3.5 19.3 1.0
C B:SER267 3.5 19.8 1.0
HA B:HIS226 3.6 39.9 1.0
H B:SER267 3.6 22.5 1.0
C B:VAL225 3.7 30.2 1.0
N B:SER267 3.7 18.7 1.0
P B:13P404 3.9 20.5 1.0
C B:HIS226 3.9 33.2 1.0
CA B:SER267 3.9 19.1 1.0
O B:HOH636 4.0 26.6 1.0
CA B:GLY227 4.0 29.5 1.0
CB B:SER267 4.0 18.1 1.0
CA B:HIS226 4.1 33.3 1.0
N B:GLY266 4.2 17.8 1.0
HA B:VAL228 4.3 35.8 1.0
C B:GLY266 4.3 18.3 1.0
H B:VAL225 4.4 38.2 1.0
N B:HIS226 4.4 32.5 1.0
HB3 B:SER267 4.4 21.8 1.0
HG12 B:VAL228 4.5 30.4 1.0
HA2 B:GLY227 4.5 35.5 1.0
O2P B:13P404 4.5 20.4 1.0
O B:HOH690 4.5 25.5 1.0
N B:VAL228 4.5 28.7 1.0
HA3 B:GLY268 4.6 26.7 1.0
HB B:VAL225 4.6 44.3 1.0
O1 B:13P404 4.6 20.5 1.0
N B:GLY268 4.7 20.2 1.0
O B:HIS226 4.7 36.6 1.0
HA3 B:GLY227 4.7 35.5 1.0
HG B:SER269 4.8 29.9 1.0
H B:GLY266 4.8 21.4 1.0
HG13 B:VAL228 4.8 30.4 1.0
CA B:GLY266 4.8 17.8 1.0
O1P B:13P404 4.9 19.0 1.0
O B:GLY266 4.9 18.4 1.0
CA B:VAL225 4.9 32.1 1.0
HA B:SER267 4.9 22.9 1.0
HE1 B:TYR229 4.9 61.4 1.0
CA B:VAL228 4.9 29.9 1.0
N B:GLY265 4.9 16.6 1.0
HG21 B:VAL234 5.0 50.5 1.0

Sodium binding site 4 out of 4 in 5vjd

Go back to Sodium Binding Sites List in 5vjd
Sodium binding site 4 out of 4 in the Class II Fructose-1,6-Bisphosphate Aldolase of Escherichia Coli with Dhap


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 of Escherichia Coli with Dhap within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na403

b:21.4
occ:1.00
 HE2 B:HIS107 2.1 13.9 1.0
HD21 B:ASN286 2.2 16.3 1.0
HZ2 B:LYS284 2.5 12.8 1.0
HZ3 B:LYS284 2.7 12.8 1.0
OD1 B:ASP109 2.7 15.4 1.0
OE2 B:GLU172 2.8 12.7 1.0
NE2 B:HIS107 2.9 11.6 1.0
NZ B:LYS284 2.9 10.7 1.0
ND2 B:ASN286 3.1 13.6 1.0
HE1 B:HIS264 3.1 23.6 1.0
HA B:ASP109 3.1 16.8 1.0
OE1 B:GLU172 3.1 12.0 1.0
HZ1 B:LYS284 3.2 12.8 1.0
CD B:GLU172 3.3 12.3 1.0
HB2 B:MET142 3.3 15.9 1.0
HE2 B:HIS264 3.4 22.9 1.0
HD22 B:ASN286 3.4 16.3 1.0
HD2 B:HIS107 3.5 13.3 1.0
HE22 B:GLN59 3.5 18.2 1.0
CE1 B:HIS264 3.6 19.7 1.0
CD2 B:HIS107 3.6 11.1 1.0
SD B:MET142 3.7 19.5 1.0
NE2 B:HIS264 3.7 19.0 1.0
OE1 B:GLN59 3.7 11.6 1.0
CG B:ASP109 3.7 15.7 1.0
HG11 B:VAL262 4.0 15.4 1.0
CB B:MET142 4.0 13.3 1.0
CG B:ASN286 4.0 13.2 1.0
CA B:ASP109 4.0 14.0 1.0
CE1 B:HIS107 4.1 11.9 1.0
HB3 B:MET142 4.1 15.9 1.0
NE2 B:GLN59 4.1 15.2 1.0
OD1 B:ASN286 4.2 13.7 1.0
CG B:MET142 4.2 15.3 1.0
CD B:GLN59 4.3 12.6 1.0
HG3 B:MET142 4.3 18.3 1.0
CE B:LYS284 4.3 10.3 1.0
HE1 B:HIS107 4.3 14.3 1.0
H B:HIS110 4.3 17.2 0.5
H B:HIS110 4.3 17.2 0.5
CB B:ASP109 4.4 15.1 1.0
HE3 B:LYS284 4.4 12.4 1.0
O B:THR108 4.4 12.2 1.0
HO3 B:13P404 4.5 27.8 1.0
HE3 B:MET142 4.6 22.8 1.0
HB2 B:ASP109 4.6 18.2 1.0
CG B:GLU172 4.6 12.7 1.0
OD2 B:ASP109 4.7 15.7 1.0
ND1 B:HIS264 4.7 18.6 1.0
HB3 B:GLU172 4.7 15.9 1.0
CE B:MET142 4.7 19.0 1.0
N B:HIS110 4.8 14.3 1.0
HE21 B:GLN59 4.8 18.2 1.0
HE2 B:LYS284 4.8 12.4 1.0
C B:ASP109 4.8 15.3 1.0
HG2 B:GLU172 4.8 15.2 1.0
CG B:HIS107 4.9 11.3 1.0
CG1 B:VAL262 4.9 12.8 1.0
O3 B:13P404 4.9 23.1 1.0
CD2 B:HIS264 4.9 18.6 1.0
N B:ASP109 4.9 14.1 1.0
HE1 B:MET142 4.9 22.8 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 00:50:43 2024

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