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Cadmium in PDB 1gyn: Class II Fructose 1,6-Bisphosphate Aldolase with Cadmium (Not Zinc) in the Active Site

Enzymatic activity of Class II Fructose 1,6-Bisphosphate Aldolase with Cadmium (Not Zinc) in the Active Site

All present enzymatic activity of Class II Fructose 1,6-Bisphosphate Aldolase with Cadmium (Not Zinc) in the Active Site:
4.1.2.13;

Protein crystallography data

The structure of Class II Fructose 1,6-Bisphosphate Aldolase with Cadmium (Not Zinc) in the Active Site, PDB code: 1gyn was solved by D.R.Hall, L.E.Kemp, G.A.Leonard, A.Berry, W.N.Hunter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.35 / 2
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 77.331, 77.331, 290.851, 90.00, 90.00, 120.00
R / Rfree (%) 16.8 / 19.3

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Class II Fructose 1,6-Bisphosphate Aldolase with Cadmium (Not Zinc) in the Active Site (pdb code 1gyn). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 5 binding sites of Cadmium where determined in the Class II Fructose 1,6-Bisphosphate Aldolase with Cadmium (Not Zinc) in the Active Site, PDB code: 1gyn:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in 1gyn

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Cadmium binding site 1 out of 5 in the Class II Fructose 1,6-Bisphosphate Aldolase with Cadmium (Not Zinc) in the Active Site


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Class II Fructose 1,6-Bisphosphate Aldolase with Cadmium (Not Zinc) in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd401

b:28.6
occ:1.00
 ND1 A:HIS264 2.3 29.5 1.0
NE2 A:HIS110 2.3 20.8 1.0
O A:HOH2059 2.4 25.0 1.0
O A:HOH2055 2.5 17.1 1.0
O A:HOH2120 2.5 11.1 1.0
O A:HOH2060 2.6 31.0 1.0
CE1 A:HIS264 3.2 30.6 1.0
CD2 A:HIS110 3.2 19.6 1.0
CG A:HIS264 3.3 25.9 1.0
CE1 A:HIS110 3.4 27.4 1.0
CB A:HIS264 3.7 23.1 1.0
O A:HOH2094 3.7 14.4 1.0
ND2 A:ASN286 4.3 23.1 1.0
O A:HOH2019 4.3 37.7 1.0
NE2 A:HIS264 4.3 22.1 1.0
CD2 A:HIS264 4.4 27.1 1.0
CG A:HIS110 4.4 23.7 1.0
ND1 A:HIS110 4.5 25.6 1.0
OD1 A:ASP109 4.6 16.7 1.0
CA A:HIS264 4.6 24.1 1.0
OD2 A:ASP109 4.8 21.1 1.0
N A:GLY265 4.9 29.4 1.0

Cadmium binding site 2 out of 5 in 1gyn

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Cadmium binding site 2 out of 5 in the Class II Fructose 1,6-Bisphosphate Aldolase with Cadmium (Not Zinc) in the Active Site


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Class II Fructose 1,6-Bisphosphate Aldolase with Cadmium (Not Zinc) in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd402

b:48.7
occ:1.00
 O A:HOH2080 1.9 42.0 1.0
O A:HOH2079 2.1 45.3 1.0
OD2 A:ASP144 2.3 24.5 1.0
OE2 A:GLU174 2.4 33.1 1.0
OD1 A:ASP144 2.8 27.6 1.0
CG A:ASP144 2.9 25.2 1.0
CD A:GLU174 3.1 29.6 1.0
OE1 A:GLU174 3.1 32.5 1.0
OG A:SER146 3.2 30.4 1.0
O A:HOH2094 3.9 14.4 1.0
ND1 A:HIS110 4.0 25.6 1.0
CE1 A:HIS110 4.1 27.4 1.0
CB A:ASP144 4.4 21.5 1.0
CB A:SER146 4.4 30.9 1.0
CG A:GLU174 4.4 25.6 1.0
CB A:GLU174 4.9 21.6 1.0

Cadmium binding site 3 out of 5 in 1gyn

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Cadmium binding site 3 out of 5 in the Class II Fructose 1,6-Bisphosphate Aldolase with Cadmium (Not Zinc) in the Active Site


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Class II Fructose 1,6-Bisphosphate Aldolase with Cadmium (Not Zinc) in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd403

b:52.1
occ:1.00
 NE2 A:HIS91 2.4 25.4 1.0
O A:HOH2046 2.5 33.8 1.0
ND1 A:HIS129 2.5 33.8 1.0
O A:HOH2045 2.6 44.8 1.0
O A:HOH2043 2.6 44.7 1.0
CE1 A:HIS91 3.2 28.7 1.0
CE1 A:HIS129 3.4 31.2 1.0
CD2 A:HIS91 3.5 27.1 1.0
CG A:HIS129 3.6 35.0 1.0
CB A:HIS129 3.9 36.5 1.0
CD1 A:LEU137 4.3 25.5 1.0
ND1 A:HIS91 4.4 33.3 1.0
NE2 A:HIS129 4.6 35.9 1.0
CG A:HIS91 4.6 22.3 1.0
CA A:HIS129 4.6 35.8 1.0
CD2 A:HIS129 4.7 34.0 1.0

Cadmium binding site 4 out of 5 in 1gyn

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Cadmium binding site 4 out of 5 in the Class II Fructose 1,6-Bisphosphate Aldolase with Cadmium (Not Zinc) in the Active Site


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Class II Fructose 1,6-Bisphosphate Aldolase with Cadmium (Not Zinc) in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd404

b:27.9
occ:1.00
 OE2 A:GLU246 1.7 20.4 1.0
OE1 A:GLU246 2.4 38.0 1.0
ND1 A:HIS256 2.4 21.9 1.0
CD A:GLU246 2.4 30.9 1.0
CE1 A:HIS256 3.3 24.0 1.0
CG A:HIS256 3.4 23.7 1.0
O A:HOH2112 3.7 30.2 1.0
CB A:HIS256 3.7 24.6 1.0
CG A:GLU246 4.0 25.8 1.0
NE2 A:HIS256 4.4 23.8 1.0
CA A:HIS256 4.4 26.5 1.0
CD2 A:HIS256 4.5 23.6 1.0
O A:HOH2113 4.7 46.2 1.0

Cadmium binding site 5 out of 5 in 1gyn

Go back to Cadmium Binding Sites List in 1gyn
Cadmium binding site 5 out of 5 in the Class II Fructose 1,6-Bisphosphate Aldolase with Cadmium (Not Zinc) in the Active Site


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Class II Fructose 1,6-Bisphosphate Aldolase with Cadmium (Not Zinc) in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd405

b:56.7
occ:1.00
 O A:HOH2098 2.4 54.8 1.0
ND1 A:HIS252 2.5 27.5 1.0
O A:HOH2039 2.7 52.0 1.0
CG A:HIS252 3.4 34.3 1.0
CE1 A:HIS252 3.5 30.9 1.0
CB A:HIS252 3.6 35.1 1.0
CA A:HIS252 4.2 36.3 1.0
CD2 A:HIS252 4.6 31.2 1.0
NE2 A:HIS252 4.6 32.2 1.0
O A:HIS252 4.6 35.2 1.0
CE2 A:TYR206 4.8 30.5 1.0
C A:HIS252 4.9 36.5 1.0

Reference:

D.R.Hall, L.E.Kemp, G.A.Leonard, K.Marshall, A.Berry, W.N.Hunter. The Organization of Divalent Cations in the Active Site of Cadmium Escherichia Coli Fructose 1,6- Bisphosphate Aldolase Acta Crystallogr.,Sect.D V. 59 611 2003.
ISSN: ISSN 0907-4449
PubMed: 12595741
DOI: 10.1107/S0907444902023661
Page generated: Fri Jul 19 13:27:50 2024

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