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Sodium in PDB 1b57: Class II Fructose-1,6-Bisphosphate Aldolase in Complex with Phosphoglycolohydroxamate

Enzymatic activity of Class II Fructose-1,6-Bisphosphate Aldolase in Complex with Phosphoglycolohydroxamate

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

Protein crystallography data

The structure of Class II Fructose-1,6-Bisphosphate Aldolase in Complex with Phosphoglycolohydroxamate, PDB code: 1b57 was solved by D.R.Hall, W.N.Hunter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.00
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 78.237, 78.237, 289.687, 90.00, 90.00, 120.00
R / Rfree (%) 19.2 / 23

Other elements in 1b57:

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

Zinc (Zn) 7 atoms
Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Class II Fructose-1,6-Bisphosphate Aldolase in Complex with Phosphoglycolohydroxamate (pdb code 1b57). 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 in Complex with Phosphoglycolohydroxamate, PDB code: 1b57:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 1b57

Go back to Sodium Binding Sites List in 1b57
Sodium binding site 1 out of 2 in the Class II Fructose-1,6-Bisphosphate Aldolase in Complex with Phosphoglycolohydroxamate


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 in Complex with Phosphoglycolohydroxamate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na364

b:22.8
occ:1.00
O A:SER267 2.4 25.6 1.0
O A:GLY227 2.5 23.4 1.0
O A:GLY265 2.5 20.3 1.0
O A:VAL225 2.6 26.4 1.0
O A:HOH390 2.7 42.3 1.0
O4P A:PGH359 2.7 22.5 1.0
C A:GLY265 3.3 20.0 1.0
C A:SER267 3.5 22.8 1.0
N A:GLY227 3.5 23.2 1.0
CA A:GLY265 3.6 16.2 1.0
C A:GLY227 3.6 23.8 1.0
O A:HOH389 3.7 35.7 1.0
N A:SER267 3.7 14.6 1.0
C A:VAL225 3.8 27.8 1.0
CA A:SER267 3.9 18.3 1.0
C A:HIS226 4.1 26.5 1.0
CB A:SER267 4.2 16.8 1.0
P A:PGH359 4.2 18.8 1.0
CA A:GLY227 4.2 19.8 1.0
C A:GLY266 4.2 19.0 1.0
O A:HOH388 4.3 36.8 1.0
N A:GLY266 4.3 19.1 1.0
CA A:HIS226 4.3 25.4 1.0
N A:HIS226 4.5 23.6 1.0
O3P A:PGH359 4.6 20.5 1.0
N A:GLY268 4.6 24.9 1.0
N A:VAL228 4.7 25.0 1.0
CA A:GLY266 4.8 14.2 1.0
CG2 A:VAL225 4.8 37.2 1.0
O A:GLY266 4.8 20.3 1.0
O1P A:PGH359 4.9 18.4 1.0
O A:HIS226 4.9 27.9 1.0
CG2 A:VAL228 5.0 28.0 1.0

Sodium binding site 2 out of 2 in 1b57

Go back to Sodium Binding Sites List in 1b57
Sodium binding site 2 out of 2 in the Class II Fructose-1,6-Bisphosphate Aldolase in Complex with Phosphoglycolohydroxamate


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 in Complex with Phosphoglycolohydroxamate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na364

b:21.4
occ:1.00
O B:GLY227 2.5 24.2 1.0
O B:SER267 2.5 24.9 1.0
O B:GLY265 2.6 21.1 1.0
O B:VAL225 2.6 26.0 1.0
O4P B:PGH359 2.7 20.3 1.0
O B:HOH414 3.1 34.5 1.0
C B:GLY265 3.3 19.8 1.0
N B:GLY227 3.5 23.2 1.0
O B:HOH413 3.5 31.1 1.0
C B:SER267 3.6 22.0 1.0
C B:GLY227 3.6 23.7 1.0
CA B:GLY265 3.6 16.7 1.0
N B:SER267 3.7 15.1 1.0
C B:VAL225 3.8 27.9 1.0
CA B:SER267 4.0 17.4 1.0
C B:HIS226 4.0 25.7 1.0
CB B:SER267 4.1 14.7 1.0
P B:PGH359 4.2 17.2 1.0
CA B:GLY227 4.2 19.3 1.0
C B:GLY266 4.2 19.3 1.0
CA B:HIS226 4.2 24.9 1.0
N B:GLY266 4.3 19.6 1.0
N B:HIS226 4.5 22.6 1.0
CG2 B:VAL225 4.5 36.9 1.0
O3P B:PGH359 4.6 17.5 1.0
O B:HOH412 4.6 36.1 1.0
N B:VAL228 4.7 24.8 1.0
N B:GLY268 4.7 24.6 1.0
O B:GLY266 4.8 20.8 1.0
O B:HIS226 4.8 26.4 1.0
CA B:GLY266 4.8 14.2 1.0
O1P B:PGH359 4.9 16.5 1.0
CA B:VAL225 4.9 32.3 1.0
CG2 B:VAL228 5.0 27.7 1.0
N B:VAL225 5.0 33.2 1.0
CA B:VAL228 5.0 26.8 1.0

Reference:

D.R.Hall, G.A.Leonard, C.D.Reed, C.I.Watt, A.Berry, W.N.Hunter. The Crystal Structure of Escherichia Coli Class II Fructose-1, 6-Bisphosphate Aldolase in Complex with Phosphoglycolohydroxamate Reveals Details of Mechanism and Specificity. J.Mol.Biol. V. 287 383 1999.
ISSN: ISSN 0022-2836
PubMed: 10080900
DOI: 10.1006/JMBI.1999.2609
Page generated: Tue Dec 15 05:21:54 2020

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