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Zinc in PDB 3gb6: Structure of Giardia Fructose-1,6-Biphosphate Aldolase D83A Mutant in Complex with Fructose-1,6-Bisphosphate

Enzymatic activity of Structure of Giardia Fructose-1,6-Biphosphate Aldolase D83A Mutant in Complex with Fructose-1,6-Bisphosphate

All present enzymatic activity of Structure of Giardia Fructose-1,6-Biphosphate Aldolase D83A Mutant in Complex with Fructose-1,6-Bisphosphate:
4.1.2.13;

Protein crystallography data

The structure of Structure of Giardia Fructose-1,6-Biphosphate Aldolase D83A Mutant in Complex with Fructose-1,6-Bisphosphate, PDB code: 3gb6 was solved by A.Galkin, O.Herzberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 56.500, 67.180, 172.180, 90.00, 90.00, 90.00
R / Rfree (%) 19.8 / 25.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Giardia Fructose-1,6-Biphosphate Aldolase D83A Mutant in Complex with Fructose-1,6-Bisphosphate (pdb code 3gb6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of Giardia Fructose-1,6-Biphosphate Aldolase D83A Mutant in Complex with Fructose-1,6-Bisphosphate, PDB code: 3gb6:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 3gb6

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Zinc binding site 1 out of 4 in the Structure of Giardia Fructose-1,6-Biphosphate Aldolase D83A Mutant in Complex with Fructose-1,6-Bisphosphate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Giardia Fructose-1,6-Biphosphate Aldolase D83A Mutant in Complex with Fructose-1,6-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn326

b:91.9
occ:0.50
 ZN A:ZN330 1.4 96.5 0.5
O3 A:P6F327 2.1 41.4 1.0
O4 A:P6F327 2.2 40.6 1.0
ND1 A:HIS84 3.0 57.1 1.0
O A:HOH553 3.2 53.0 1.0
C3 A:P6F327 3.2 43.6 1.0
C4 A:P6F327 3.2 45.6 1.0
ND1 A:HIS210 3.5 30.8 1.0
O A:ALA83 3.7 37.8 1.0
ND2 A:ASN253 3.7 34.4 1.0
O A:HOH471 3.7 41.9 1.0
CE1 A:HIS210 3.7 36.3 1.0
CE1 A:HIS84 4.0 49.5 1.0
CG A:HIS84 4.0 43.7 1.0
CB A:HIS84 4.1 39.0 1.0
O2 A:P6F327 4.2 37.3 1.0
C2 A:P6F327 4.2 34.4 1.0
C5 A:P6F327 4.2 47.2 1.0
NE2 A:GLN48 4.3 51.2 1.0
O A:HOH339 4.3 33.1 1.0
C A:ALA83 4.4 39.8 1.0
NE2 A:HIS178 4.4 37.5 1.0
CB A:ALA83 4.6 30.5 1.0
CG A:HIS210 4.7 23.9 1.0
O A:HOH525 4.8 44.8 1.0
CG A:ASN253 4.9 31.4 1.0
NE2 A:HIS210 4.9 32.0 1.0
C6 A:P6F327 4.9 42.4 1.0
CA A:HIS84 5.0 38.5 1.0
CE1 A:HIS178 5.0 41.0 1.0

Zinc binding site 2 out of 4 in 3gb6

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Zinc binding site 2 out of 4 in the Structure of Giardia Fructose-1,6-Biphosphate Aldolase D83A Mutant in Complex with Fructose-1,6-Bisphosphate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Giardia Fructose-1,6-Biphosphate Aldolase D83A Mutant in Complex with Fructose-1,6-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn330

b:96.5
occ:0.50
 ZN A:ZN326 1.4 91.9 0.5
O4 A:P6F327 2.1 40.6 1.0
O3 A:P6F327 2.2 41.4 1.0
C4 A:P6F327 2.9 45.6 1.0
ND1 A:HIS210 2.9 30.8 1.0
C3 A:P6F327 2.9 43.6 1.0
NE2 A:HIS178 3.1 37.5 1.0
O2 A:P6F327 3.2 37.3 1.0
ND1 A:HIS84 3.4 57.1 1.0
O A:HOH471 3.5 41.9 1.0
C2 A:P6F327 3.5 34.4 1.0
CE1 A:HIS210 3.6 36.3 1.0
CE1 A:HIS178 3.8 41.0 1.0
ND2 A:ASN253 3.9 34.4 1.0
CE1 A:HIS84 3.9 49.5 1.0
CG A:HIS210 3.9 23.9 1.0
CD2 A:HIS178 4.1 40.6 1.0
O A:HOH553 4.2 53.0 1.0
C5 A:P6F327 4.3 47.2 1.0
CB A:HIS210 4.3 29.0 1.0
CG A:HIS84 4.6 43.7 1.0
NE2 A:HIS210 4.8 32.0 1.0
O A:ALA83 4.9 37.8 1.0
CD2 A:HIS210 4.9 32.5 1.0
CG A:ASN253 4.9 31.4 1.0
C6 A:P6F327 5.0 42.4 1.0
C1 A:P6F327 5.0 33.7 1.0
ND1 A:HIS178 5.0 43.9 1.0

Zinc binding site 3 out of 4 in 3gb6

Go back to Zinc Binding Sites List in 3gb6
Zinc binding site 3 out of 4 in the Structure of Giardia Fructose-1,6-Biphosphate Aldolase D83A Mutant in Complex with Fructose-1,6-Bisphosphate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Giardia Fructose-1,6-Biphosphate Aldolase D83A Mutant in Complex with Fructose-1,6-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn328

b:76.5
occ:0.50
 ZN B:ZN331 1.7 83.4 0.5
O4 B:P6F329 2.2 32.1 1.0
O3 B:P6F329 2.3 30.0 1.0
ND1 B:HIS84 3.0 43.2 1.0
C4 B:P6F329 3.3 42.6 1.0
C3 B:P6F329 3.3 40.7 1.0
ND1 B:HIS210 3.4 27.8 1.0
O B:ALA83 3.4 37.0 1.0
CE1 B:HIS210 3.5 31.9 1.0
O B:HOH534 3.7 49.3 1.0
CG B:HIS84 3.8 37.6 1.0
CB B:HIS84 3.8 31.0 1.0
CE1 B:HIS84 4.0 46.2 1.0
ND2 B:ASN253 4.1 30.9 1.0
C B:ALA83 4.2 37.1 1.0
NE2 B:HIS178 4.2 32.0 1.0
O2 B:P6F329 4.3 31.6 1.0
C2 B:P6F329 4.3 35.9 1.0
O B:HOH344 4.3 32.2 1.0
C5 B:P6F329 4.4 36.0 1.0
CB B:ALA83 4.5 37.9 1.0
NE2 B:GLN48 4.6 31.4 1.0
CG B:HIS210 4.7 34.0 1.0
NE2 B:HIS210 4.7 38.6 1.0
CA B:HIS84 4.8 31.7 1.0
O B:HOH382 4.8 39.1 1.0
N B:HIS84 4.8 39.8 1.0
CE1 B:HIS178 4.9 30.9 1.0
CA B:ALA83 4.9 40.2 1.0
C6 B:P6F329 4.9 33.0 1.0
SD B:MET103 4.9 34.8 1.0

Zinc binding site 4 out of 4 in 3gb6

Go back to Zinc Binding Sites List in 3gb6
Zinc binding site 4 out of 4 in the Structure of Giardia Fructose-1,6-Biphosphate Aldolase D83A Mutant in Complex with Fructose-1,6-Bisphosphate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Giardia Fructose-1,6-Biphosphate Aldolase D83A Mutant in Complex with Fructose-1,6-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn331

b:83.4
occ:0.50
 ZN B:ZN328 1.7 76.5 0.5
O4 B:P6F329 2.1 32.1 1.0
O3 B:P6F329 2.3 30.0 1.0
NE2 B:HIS178 2.6 32.0 1.0
C4 B:P6F329 2.8 42.6 1.0
ND1 B:HIS210 3.0 27.8 1.0
C3 B:P6F329 3.0 40.7 1.0
O2 B:P6F329 3.2 31.6 1.0
CE1 B:HIS178 3.4 30.9 1.0
C2 B:P6F329 3.5 35.9 1.0
ND1 B:HIS84 3.5 43.2 1.0
O B:HOH534 3.6 49.3 1.0
CD2 B:HIS178 3.6 34.0 1.0
CE1 B:HIS210 3.6 31.9 1.0
CE1 B:HIS84 4.1 46.2 1.0
CG B:HIS210 4.1 34.0 1.0
C5 B:P6F329 4.3 36.0 1.0
CB B:HIS210 4.4 30.1 1.0
ND2 B:ASN253 4.5 30.9 1.0
ND1 B:HIS178 4.6 34.2 1.0
CG B:HIS84 4.6 37.6 1.0
CG B:HIS178 4.7 35.8 1.0
C6 B:P6F329 4.8 33.0 1.0
NE2 B:HIS210 4.9 38.6 1.0
C1 B:P6F329 4.9 47.0 1.0
CD1 B:LEU139 4.9 41.8 1.0

Reference:

A.Galkin, Z.Li, L.Li, L.Kulakova, L.R.Pal, D.Dunaway-Mariano, O.Herzberg. Structural Insights Into the Substrate Binding and Stereoselectivity of Giardia Fructose-1,6-Bisphosphate Aldolase. Biochemistry V. 48 3186 2009.
ISSN: ISSN 0006-2960
PubMed: 19236002
DOI: 10.1021/BI9001166
Page generated: Thu Oct 24 13:41:05 2024

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