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Zinc 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:

Chlorine (Cl) 1 atom
Sodium (Na) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 7 binding sites of Zinc where determined in the Class II Fructose-1,6-Bisphosphate Aldolase in Complex with Phosphoglycolohydroxamate, PDB code: 1b57:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 1b57

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Zinc binding site 1 out of 7 in the Class II Fructose-1,6-Bisphosphate Aldolase in Complex with Phosphoglycolohydroxamate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn360

b:18.8
occ:1.00
 NE2 A:HIS226 1.9 24.6 1.0
ND1 A:HIS264 1.9 12.0 1.0
NE2 A:HIS110 2.1 16.0 1.0
O1 A:PGH359 2.2 20.4 1.0
O2 A:PGH359 2.3 18.3 1.0
CE1 A:HIS226 2.6 30.6 1.0
N2 A:PGH359 2.9 20.5 1.0
C1 A:PGH359 2.9 19.4 1.0
CE1 A:HIS264 2.9 16.1 1.0
CG A:HIS264 3.0 14.1 1.0
CE1 A:HIS110 3.1 17.4 1.0
CD2 A:HIS226 3.1 28.6 1.0
CD2 A:HIS110 3.2 17.0 1.0
CB A:HIS264 3.4 11.8 1.0
ND1 A:HIS226 3.9 31.2 1.0
ND2 A:ASN286 4.1 13.7 1.0
NE2 A:HIS264 4.1 15.0 1.0
CD2 A:HIS264 4.1 12.5 1.0
CG A:HIS226 4.1 28.7 1.0
OD1 A:ASP109 4.2 14.8 1.0
ND1 A:HIS110 4.2 17.7 1.0
OD2 A:ASP109 4.2 11.9 1.0
CG A:HIS110 4.3 18.7 1.0
CA A:HIS264 4.3 15.9 1.0
C2 A:PGH359 4.4 20.6 1.0
N A:GLY265 4.5 16.6 1.0
CG A:ASP109 4.6 13.7 1.0
O A:HOH395 4.7 18.6 1.0
O1P A:PGH359 4.9 18.4 1.0
C A:HIS264 4.9 18.9 1.0
CB A:ASN286 4.9 11.9 1.0
OG1 A:THR178 4.9 53.6 1.0
CG A:ASN286 5.0 14.6 1.0

Zinc binding site 2 out of 7 in 1b57

Go back to Zinc Binding Sites List in 1b57
Zinc binding site 2 out of 7 in the Class II Fructose-1,6-Bisphosphate Aldolase in Complex with Phosphoglycolohydroxamate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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
A:Zn361

b:30.9
occ:1.00
 OE2 A:GLU181 1.9 31.1 1.0
OE2 A:GLU174 2.0 26.4 1.0
OD2 A:ASP144 2.0 21.2 1.0
O A:HOH448 2.1 36.7 1.0
CD A:GLU181 2.6 40.5 1.0
OE1 A:GLU181 2.7 40.3 1.0
CG A:ASP144 2.8 25.2 1.0
OD1 A:ASP144 2.8 23.6 1.0
CD A:GLU174 2.9 26.1 1.0
OE1 A:GLU174 3.1 28.2 1.0
OG A:SER146 3.6 28.8 1.0
ND1 A:HIS110 3.8 17.7 1.0
CE1 A:HIS110 4.1 17.4 1.0
CG A:GLU181 4.1 43.2 1.0
CB A:ASP144 4.2 18.9 1.0
CG A:GLU174 4.2 21.0 1.0
OG1 A:THR178 4.3 53.6 1.0
N A:THR178 4.5 57.6 1.0
CB A:GLU174 4.7 16.7 1.0
CB A:SER146 4.7 26.7 1.0
CA A:CYS177 4.8 53.3 1.0
CG A:HIS110 5.0 18.7 1.0
CB A:THR178 5.0 58.4 1.0

Zinc binding site 3 out of 7 in 1b57

Go back to Zinc Binding Sites List in 1b57
Zinc binding site 3 out of 7 in the Class II Fructose-1,6-Bisphosphate Aldolase in Complex with Phosphoglycolohydroxamate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Class II Fructose-1,6-Bisphosphate Aldolase in Complex with Phosphoglycolohydroxamate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn362

b:49.5
occ:1.00
 O A:HOH437 2.0 31.0 1.0
NE2 A:HIS91 2.2 29.1 1.0
ND1 A:HIS129 2.3 38.7 1.0
O A:HOH439 2.5 37.9 1.0
CE1 A:HIS129 3.0 41.6 1.0
CE1 A:HIS91 3.1 27.1 1.0
CD2 A:HIS91 3.2 27.2 1.0
O A:HOH438 3.2 67.7 1.0
CG A:HIS129 3.4 38.1 1.0
CB A:HIS129 3.9 37.6 1.0
NE2 A:HIS129 4.2 42.2 1.0
CD1 A:LEU137 4.2 22.4 1.0
ND1 A:HIS91 4.2 30.6 1.0
CG A:HIS91 4.3 24.5 1.0
CD2 A:HIS129 4.4 39.6 1.0
O A:HOH436 4.5 47.8 1.0
CA A:HIS129 4.8 38.3 1.0

Zinc binding site 4 out of 7 in 1b57

Go back to Zinc Binding Sites List in 1b57
Zinc binding site 4 out of 7 in the Class II Fructose-1,6-Bisphosphate Aldolase in Complex with Phosphoglycolohydroxamate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Class II Fructose-1,6-Bisphosphate Aldolase in Complex with Phosphoglycolohydroxamate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn363

b:28.4
occ:1.00
 CL A:CL365 1.9 22.4 1.0
N A:SER1 2.3 34.7 1.0
CA A:SER1 2.9 32.3 1.0
CB A:SER1 3.2 31.4 1.0
O A:HOH470 3.3 26.0 1.0
OG A:SER1 3.7 33.9 1.0
O A:HOH469 3.7 51.3 1.0
C A:SER1 4.3 33.5 1.0
OE2 A:GLU26 4.7 44.5 1.0
O A:SER1 4.8 31.7 1.0

Zinc binding site 5 out of 7 in 1b57

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Zinc binding site 5 out of 7 in the Class II Fructose-1,6-Bisphosphate Aldolase in Complex with Phosphoglycolohydroxamate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Class II Fructose-1,6-Bisphosphate Aldolase in Complex with Phosphoglycolohydroxamate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn360

b:17.8
occ:1.00
 ND1 B:HIS264 1.9 10.7 1.0
NE2 B:HIS226 1.9 26.6 1.0
NE2 B:HIS110 2.2 17.9 1.0
O1 B:PGH359 2.3 14.8 1.0
O2 B:PGH359 2.3 15.9 1.0
CE1 B:HIS226 2.8 29.9 1.0
CE1 B:HIS264 2.9 15.6 1.0
N2 B:PGH359 2.9 16.0 1.0
CG B:HIS264 3.0 14.7 1.0
C1 B:PGH359 3.0 16.7 1.0
CD2 B:HIS226 3.1 26.3 1.0
CE1 B:HIS110 3.1 18.5 1.0
CD2 B:HIS110 3.2 15.4 1.0
CB B:HIS264 3.4 15.5 1.0
ND1 B:HIS226 4.0 29.0 1.0
NE2 B:HIS264 4.0 15.5 1.0
CD2 B:HIS264 4.1 14.0 1.0
ND2 B:ASN286 4.1 17.3 1.0
CG B:HIS226 4.1 26.8 1.0
OD1 B:ASP109 4.1 13.7 1.0
OD2 B:ASP109 4.2 13.1 1.0
ND1 B:HIS110 4.3 16.9 1.0
CG B:HIS110 4.3 19.4 1.0
CA B:HIS264 4.3 16.0 1.0
C2 B:PGH359 4.4 17.4 1.0
N B:GLY265 4.6 17.1 1.0
CG B:ASP109 4.6 12.1 1.0
O B:HOH384 4.8 17.1 1.0
O1P B:PGH359 4.9 16.5 1.0
CG B:ASN286 5.0 15.3 1.0
CB B:ASN286 5.0 16.2 1.0
C B:HIS264 5.0 19.1 1.0

Zinc binding site 6 out of 7 in 1b57

Go back to Zinc Binding Sites List in 1b57
Zinc binding site 6 out of 7 in the Class II Fructose-1,6-Bisphosphate Aldolase in Complex with Phosphoglycolohydroxamate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Class II Fructose-1,6-Bisphosphate Aldolase in Complex with Phosphoglycolohydroxamate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn361

b:28.8
occ:1.00
 OE2 B:GLU181 2.0 32.3 1.0
OD2 B:ASP144 2.0 24.4 1.0
O B:HOH392 2.0 37.4 1.0
OE2 B:GLU174 2.1 26.9 1.0
OE1 B:GLU181 2.6 42.3 1.0
CD B:GLU181 2.7 40.7 1.0
CG B:ASP144 2.8 26.4 1.0
CD B:GLU174 2.9 24.4 1.0
OD1 B:ASP144 2.9 26.3 1.0
OE1 B:GLU174 3.1 24.0 1.0
OG B:SER146 3.5 27.5 1.0
O B:HOH393 3.7 41.7 1.0
ND1 B:HIS110 3.9 16.9 1.0
CE1 B:HIS110 4.2 18.5 1.0
CG B:GLU181 4.2 41.4 1.0
CB B:ASP144 4.2 21.0 1.0
CG B:GLU174 4.3 19.5 1.0
CA B:CYS177 4.4 54.5 1.0
OG1 B:THR178 4.6 52.0 1.0
N B:THR178 4.6 56.3 1.0
CB B:CYS177 4.7 59.2 1.0
CB B:SER146 4.8 24.1 1.0
CB B:GLU174 4.8 15.3 1.0

Zinc binding site 7 out of 7 in 1b57

Go back to Zinc Binding Sites List in 1b57
Zinc binding site 7 out of 7 in the Class II Fructose-1,6-Bisphosphate Aldolase in Complex with Phosphoglycolohydroxamate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Class II Fructose-1,6-Bisphosphate Aldolase in Complex with Phosphoglycolohydroxamate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn362

b:47.8
occ:1.00
 NE2 B:HIS91 2.2 26.2 1.0
ND1 B:HIS129 2.3 36.2 1.0
O B:HOH423 2.3 46.5 1.0
O B:HOH424 2.6 40.2 1.0
CE1 B:HIS91 3.0 26.5 1.0
CE1 B:HIS129 3.0 41.3 1.0
CD2 B:HIS91 3.2 21.5 1.0
CG B:HIS129 3.4 36.5 1.0
CB B:HIS129 3.9 38.0 1.0
CD1 B:LEU137 4.0 22.6 1.0
ND1 B:HIS91 4.2 28.5 1.0
NE2 B:HIS129 4.3 40.0 1.0
CG B:HIS91 4.3 21.0 1.0
CD2 B:HIS129 4.4 38.7 1.0
CA B:HIS129 4.6 38.0 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: Sat Oct 12 22:23:57 2024

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