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
Go back to
Zinc Binding Sites List in 3gb6
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
Go back to
Zinc Binding Sites List in 3gb6
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
|