Zinc in PDB 2y7f: Crystal Structure of the 3-Keto-5-Aminohexanoate Cleavage Enzyme (Kce)
Protein crystallography data
The structure of Crystal Structure of the 3-Keto-5-Aminohexanoate Cleavage Enzyme (Kce), PDB code: 2y7f
was solved by
M.Bellinzoni,
P.M.Alzari,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
33.50 /
1.75
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
98.500,
98.480,
103.180,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
14.97 /
17.36
|
Other elements in 2y7f:
The structure of Crystal Structure of the 3-Keto-5-Aminohexanoate Cleavage Enzyme (Kce) also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the Crystal Structure of the 3-Keto-5-Aminohexanoate Cleavage Enzyme (Kce)
(pdb code 2y7f). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the
Crystal Structure of the 3-Keto-5-Aminohexanoate Cleavage Enzyme (Kce), PDB code: 2y7f:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 2y7f
Go back to
Zinc Binding Sites List in 2y7f
Zinc binding site 1 out
of 4 in the Crystal Structure of the 3-Keto-5-Aminohexanoate Cleavage Enzyme (Kce)
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Crystal Structure of the 3-Keto-5-Aminohexanoate Cleavage Enzyme (Kce) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn301
b:15.9
occ:0.57
|
OF1
|
A:KMH1276
|
2.0
|
14.3
|
1.0
|
OE2
|
A:GLU230
|
2.1
|
16.1
|
1.0
|
O
|
A:HOH2236
|
2.2
|
18.7
|
1.0
|
O
|
A:KMH1276
|
2.2
|
19.0
|
1.0
|
NE2
|
A:HIS48
|
2.2
|
13.2
|
1.0
|
NE2
|
A:HIS46
|
2.3
|
15.5
|
1.0
|
CE
|
A:KMH1276
|
3.0
|
21.6
|
1.0
|
C
|
A:KMH1276
|
3.0
|
76.4
|
1.0
|
CD
|
A:GLU230
|
3.1
|
17.0
|
1.0
|
CD2
|
A:HIS48
|
3.2
|
14.7
|
1.0
|
CE1
|
A:HIS48
|
3.2
|
12.8
|
1.0
|
CE1
|
A:HIS46
|
3.2
|
15.8
|
1.0
|
C2
|
A:KMH1276
|
3.3
|
36.9
|
1.0
|
CD2
|
A:HIS46
|
3.3
|
15.5
|
1.0
|
OE1
|
A:GLU230
|
3.4
|
16.2
|
1.0
|
OG
|
A:SER82
|
3.9
|
17.6
|
1.0
|
O
|
A:HOH2237
|
3.9
|
40.8
|
1.0
|
O
|
A:HOH2007
|
4.1
|
17.2
|
1.0
|
NH2
|
A:ARG226
|
4.1
|
24.4
|
1.0
|
OF2
|
A:KMH1276
|
4.1
|
17.6
|
1.0
|
CB
|
A:SER82
|
4.2
|
14.9
|
1.0
|
CG
|
A:HIS48
|
4.3
|
13.0
|
1.0
|
NH1
|
A:ARG226
|
4.3
|
22.5
|
1.0
|
ND1
|
A:HIS48
|
4.3
|
14.1
|
1.0
|
ND1
|
A:HIS46
|
4.4
|
16.3
|
1.0
|
CG
|
A:GLU230
|
4.4
|
15.5
|
1.0
|
CG
|
A:HIS46
|
4.4
|
14.2
|
1.0
|
CA
|
A:KMH1276
|
4.4
|
48.6
|
1.0
|
CZ
|
A:ARG226
|
4.6
|
28.4
|
1.0
|
N
|
A:KMH1276
|
4.9
|
27.6
|
1.0
|
|
Zinc binding site 2 out
of 4 in 2y7f
Go back to
Zinc Binding Sites List in 2y7f
Zinc binding site 2 out
of 4 in the Crystal Structure of the 3-Keto-5-Aminohexanoate Cleavage Enzyme (Kce)
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Crystal Structure of the 3-Keto-5-Aminohexanoate Cleavage Enzyme (Kce) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn301
b:15.3
occ:0.52
|
OE2
|
B:GLU230
|
2.1
|
17.0
|
1.0
|
OF2
|
B:KMH1276
|
2.1
|
16.1
|
1.0
|
O
|
B:HOH2228
|
2.1
|
15.9
|
1.0
|
NE2
|
B:HIS48
|
2.2
|
14.9
|
1.0
|
O
|
B:KMH1276
|
2.2
|
18.8
|
1.0
|
NE2
|
B:HIS46
|
2.3
|
14.9
|
1.0
|
CD
|
B:GLU230
|
3.0
|
16.6
|
1.0
|
C
|
B:KMH1276
|
3.1
|
38.8
|
1.0
|
CE
|
B:KMH1276
|
3.1
|
30.5
|
1.0
|
CD2
|
B:HIS48
|
3.1
|
15.4
|
1.0
|
CE1
|
B:HIS46
|
3.2
|
15.2
|
1.0
|
CE1
|
B:HIS48
|
3.2
|
14.4
|
1.0
|
CD2
|
B:HIS46
|
3.3
|
15.2
|
1.0
|
OE1
|
B:GLU230
|
3.3
|
15.8
|
1.0
|
C2
|
B:KMH1276
|
3.4
|
33.4
|
1.0
|
OG
|
B:SER82
|
3.9
|
16.1
|
1.0
|
NH2
|
B:ARG226
|
4.1
|
20.4
|
1.0
|
O
|
B:HOH2011
|
4.1
|
16.1
|
1.0
|
CB
|
B:SER82
|
4.2
|
16.4
|
1.0
|
OF1
|
B:KMH1276
|
4.2
|
17.9
|
1.0
|
CG
|
B:HIS48
|
4.3
|
14.1
|
1.0
|
ND1
|
B:HIS48
|
4.3
|
15.5
|
1.0
|
NH1
|
B:ARG226
|
4.3
|
18.3
|
1.0
|
ND1
|
B:HIS46
|
4.4
|
15.7
|
1.0
|
CG
|
B:GLU230
|
4.4
|
16.0
|
1.0
|
CG
|
B:HIS46
|
4.4
|
13.8
|
1.0
|
CA
|
B:KMH1276
|
4.5
|
33.0
|
1.0
|
CZ
|
B:ARG226
|
4.7
|
27.0
|
1.0
|
N
|
B:KMH1276
|
5.0
|
21.0
|
1.0
|
|
Zinc binding site 3 out
of 4 in 2y7f
Go back to
Zinc Binding Sites List in 2y7f
Zinc binding site 3 out
of 4 in the Crystal Structure of the 3-Keto-5-Aminohexanoate Cleavage Enzyme (Kce)
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Crystal Structure of the 3-Keto-5-Aminohexanoate Cleavage Enzyme (Kce) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn301
b:14.8
occ:0.52
|
OF1
|
C:KMH1276
|
2.1
|
18.0
|
1.0
|
OE2
|
C:GLU230
|
2.1
|
14.3
|
1.0
|
O
|
C:HOH2198
|
2.1
|
15.7
|
1.0
|
O
|
C:KMH1276
|
2.2
|
19.9
|
1.0
|
NE2
|
C:HIS46
|
2.2
|
16.2
|
1.0
|
NE2
|
C:HIS48
|
2.2
|
16.4
|
1.0
|
C
|
C:KMH1276
|
3.0
|
0.1
|
1.0
|
CE
|
C:KMH1276
|
3.0
|
25.5
|
1.0
|
CD
|
C:GLU230
|
3.0
|
21.1
|
1.0
|
CE1
|
C:HIS46
|
3.2
|
16.5
|
1.0
|
CD2
|
C:HIS48
|
3.2
|
17.4
|
1.0
|
CE1
|
C:HIS48
|
3.3
|
16.5
|
1.0
|
C2
|
C:KMH1276
|
3.3
|
55.9
|
1.0
|
CD2
|
C:HIS46
|
3.3
|
16.9
|
1.0
|
OE1
|
C:GLU230
|
3.4
|
15.8
|
1.0
|
OG
|
C:SER82
|
3.9
|
18.5
|
1.0
|
NH2
|
C:ARG226
|
4.0
|
22.8
|
1.0
|
OF2
|
C:KMH1276
|
4.2
|
18.4
|
1.0
|
CB
|
C:SER82
|
4.2
|
17.1
|
1.0
|
O
|
C:HOH2007
|
4.2
|
19.6
|
1.0
|
NH1
|
C:ARG226
|
4.3
|
18.7
|
1.0
|
ND1
|
C:HIS46
|
4.3
|
17.6
|
1.0
|
CG
|
C:HIS48
|
4.3
|
16.3
|
1.0
|
CA
|
C:KMH1276
|
4.4
|
32.3
|
1.0
|
CG
|
C:HIS46
|
4.4
|
15.7
|
1.0
|
ND1
|
C:HIS48
|
4.4
|
17.4
|
1.0
|
CG
|
C:GLU230
|
4.4
|
14.2
|
1.0
|
CZ
|
C:ARG226
|
4.6
|
26.8
|
1.0
|
|
Zinc binding site 4 out
of 4 in 2y7f
Go back to
Zinc Binding Sites List in 2y7f
Zinc binding site 4 out
of 4 in the Crystal Structure of the 3-Keto-5-Aminohexanoate Cleavage Enzyme (Kce)
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Crystal Structure of the 3-Keto-5-Aminohexanoate Cleavage Enzyme (Kce) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn301
b:17.6
occ:0.56
|
OE2
|
D:GLU230
|
2.0
|
16.9
|
1.0
|
OF2
|
D:KMH1276
|
2.0
|
16.2
|
1.0
|
NE2
|
D:HIS48
|
2.1
|
14.8
|
1.0
|
O
|
D:KMH1276
|
2.2
|
18.3
|
1.0
|
O
|
D:HOH2209
|
2.2
|
16.5
|
1.0
|
NE2
|
D:HIS46
|
2.3
|
14.8
|
1.0
|
CE
|
D:KMH1276
|
3.0
|
19.4
|
1.0
|
C
|
D:KMH1276
|
3.0
|
52.1
|
1.0
|
CD
|
D:GLU230
|
3.0
|
17.3
|
1.0
|
CD2
|
D:HIS48
|
3.1
|
15.9
|
1.0
|
CE1
|
D:HIS48
|
3.2
|
15.3
|
1.0
|
CE1
|
D:HIS46
|
3.2
|
14.9
|
1.0
|
C2
|
D:KMH1276
|
3.2
|
39.3
|
1.0
|
CD2
|
D:HIS46
|
3.3
|
15.3
|
1.0
|
OE1
|
D:GLU230
|
3.3
|
13.1
|
1.0
|
OG
|
D:SER82
|
3.9
|
16.1
|
1.0
|
O
|
D:HOH2008
|
4.1
|
15.6
|
1.0
|
NH2
|
D:ARG226
|
4.1
|
20.1
|
1.0
|
OF1
|
D:KMH1276
|
4.1
|
18.2
|
1.0
|
CB
|
D:SER82
|
4.2
|
17.1
|
1.0
|
CG
|
D:HIS48
|
4.3
|
15.8
|
1.0
|
ND1
|
D:HIS48
|
4.3
|
16.7
|
1.0
|
NH1
|
D:ARG226
|
4.3
|
16.7
|
1.0
|
CG
|
D:GLU230
|
4.4
|
16.9
|
1.0
|
ND1
|
D:HIS46
|
4.4
|
15.6
|
1.0
|
CA
|
D:KMH1276
|
4.4
|
38.1
|
1.0
|
CG
|
D:HIS46
|
4.4
|
13.6
|
1.0
|
CZ
|
D:ARG226
|
4.7
|
26.4
|
1.0
|
N
|
D:KMH1276
|
5.0
|
26.2
|
1.0
|
|
Reference:
M.Bellinzoni,
K.Bastard,
A.Perret,
A.Zaparucha,
N.Perchat,
C.Vergne,
T.Wagner,
R.C.De Melo-Minardi,
F.Artiguenave,
G.N.Cohen,
J.Weissenbach,
M.Salanoubat,
P.M.Alzari.
3-Keto-5-Aminohexanoate Cleavage Enzyme: A Common Fold For An Uncommon Claisen-Type Condensation. J.Biol.Chem. V. 286 27399 2011.
ISSN: ISSN 0021-9258
PubMed: 21632536
DOI: 10.1074/JBC.M111.253260
Page generated: Thu Oct 17 05:46:09 2024
|