Zinc in PDB 3t3w: Crystal Structure of Probable Enoyl-Coa Hydratase From Mycobacterium Thermoresistibile
Enzymatic activity of Crystal Structure of Probable Enoyl-Coa Hydratase From Mycobacterium Thermoresistibile
All present enzymatic activity of Crystal Structure of Probable Enoyl-Coa Hydratase From Mycobacterium Thermoresistibile:
4.2.1.17;
Protein crystallography data
The structure of Crystal Structure of Probable Enoyl-Coa Hydratase From Mycobacterium Thermoresistibile, PDB code: 3t3w
was solved by
Seattle Structural Genomics Center For Infectious Disease (Ssgcid),
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
49.22 /
1.80
|
Space group
|
P 43 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
124.240,
124.240,
212.250,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
13.9 /
16.5
|
Other elements in 3t3w:
The structure of Crystal Structure of Probable Enoyl-Coa Hydratase From Mycobacterium Thermoresistibile also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the Crystal Structure of Probable Enoyl-Coa Hydratase From Mycobacterium Thermoresistibile
(pdb code 3t3w). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the
Crystal Structure of Probable Enoyl-Coa Hydratase From Mycobacterium Thermoresistibile, PDB code: 3t3w:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
Zinc binding site 1 out
of 6 in 3t3w
Go back to
Zinc Binding Sites List in 3t3w
Zinc binding site 1 out
of 6 in the Crystal Structure of Probable Enoyl-Coa Hydratase From Mycobacterium Thermoresistibile
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 Probable Enoyl-Coa Hydratase From Mycobacterium Thermoresistibile within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn301
b:18.6
occ:1.00
|
NE2
|
A:HIS249
|
2.0
|
14.3
|
1.0
|
NE2
|
A:HIS253
|
2.1
|
18.0
|
1.0
|
O
|
A:HOH280
|
2.1
|
16.4
|
1.0
|
OE2
|
A:GLU160
|
2.1
|
16.1
|
1.0
|
OE2
|
A:GLU99
|
2.1
|
16.5
|
1.0
|
OE1
|
A:GLU99
|
2.2
|
16.6
|
1.0
|
CD
|
A:GLU99
|
2.4
|
16.3
|
1.0
|
CE1
|
A:HIS249
|
3.0
|
15.1
|
1.0
|
CE1
|
A:HIS253
|
3.0
|
20.3
|
1.0
|
CD2
|
A:HIS249
|
3.1
|
14.1
|
1.0
|
CD2
|
A:HIS253
|
3.1
|
19.2
|
1.0
|
CD
|
A:GLU160
|
3.1
|
16.6
|
1.0
|
CG
|
A:GLU160
|
3.7
|
15.4
|
1.0
|
O
|
A:HOH718
|
3.9
|
28.4
|
1.0
|
CG
|
A:GLU99
|
3.9
|
16.8
|
1.0
|
O
|
A:HOH300
|
4.0
|
19.5
|
1.0
|
O
|
A:HOH631
|
4.1
|
36.0
|
1.0
|
OE1
|
A:GLU160
|
4.1
|
15.7
|
1.0
|
ND1
|
A:HIS253
|
4.2
|
20.6
|
1.0
|
ND1
|
A:HIS249
|
4.2
|
14.7
|
1.0
|
CG
|
A:HIS249
|
4.2
|
13.2
|
1.0
|
CG
|
A:HIS253
|
4.2
|
19.8
|
1.0
|
NE2
|
A:GLN250
|
4.4
|
16.7
|
1.0
|
O
|
A:HOH453
|
4.5
|
27.1
|
1.0
|
CB
|
A:GLU99
|
4.7
|
16.2
|
1.0
|
CE2
|
A:TYR103
|
4.9
|
18.3
|
1.0
|
CD2
|
A:TYR103
|
4.9
|
17.4
|
1.0
|
|
Zinc binding site 2 out
of 6 in 3t3w
Go back to
Zinc Binding Sites List in 3t3w
Zinc binding site 2 out
of 6 in the Crystal Structure of Probable Enoyl-Coa Hydratase From Mycobacterium Thermoresistibile
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 Probable Enoyl-Coa Hydratase From Mycobacterium Thermoresistibile within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn301
b:18.3
occ:1.00
|
NE2
|
B:HIS249
|
2.0
|
14.1
|
1.0
|
NE2
|
B:HIS253
|
2.1
|
18.4
|
1.0
|
OE2
|
B:GLU160
|
2.1
|
17.1
|
1.0
|
OE2
|
B:GLU99
|
2.1
|
16.4
|
1.0
|
O
|
B:HOH277
|
2.2
|
16.3
|
1.0
|
OE1
|
B:GLU99
|
2.2
|
17.3
|
1.0
|
CD
|
B:GLU99
|
2.5
|
15.9
|
1.0
|
CE1
|
B:HIS249
|
3.0
|
14.9
|
1.0
|
CD2
|
B:HIS249
|
3.0
|
14.7
|
1.0
|
CE1
|
B:HIS253
|
3.0
|
20.5
|
1.0
|
CD2
|
B:HIS253
|
3.1
|
19.6
|
1.0
|
CD
|
B:GLU160
|
3.1
|
17.0
|
1.0
|
CG
|
B:GLU160
|
3.6
|
16.4
|
1.0
|
O
|
B:HOH766
|
3.9
|
25.5
|
1.0
|
CG
|
B:GLU99
|
4.0
|
15.7
|
1.0
|
O
|
B:HOH423
|
4.1
|
22.6
|
1.0
|
OE1
|
B:GLU160
|
4.1
|
16.5
|
1.0
|
O
|
B:HOH1283
|
4.1
|
37.0
|
1.0
|
ND1
|
B:HIS249
|
4.2
|
14.9
|
1.0
|
ND1
|
B:HIS253
|
4.2
|
20.2
|
1.0
|
CG
|
B:HIS249
|
4.2
|
14.3
|
1.0
|
CG
|
B:HIS253
|
4.2
|
19.5
|
1.0
|
NE2
|
B:GLN250
|
4.4
|
17.3
|
1.0
|
O
|
B:HOH389
|
4.5
|
26.6
|
1.0
|
CB
|
B:GLU99
|
4.7
|
15.3
|
1.0
|
CD2
|
B:TYR103
|
4.9
|
19.6
|
1.0
|
CE2
|
B:TYR103
|
4.9
|
20.3
|
1.0
|
|
Zinc binding site 3 out
of 6 in 3t3w
Go back to
Zinc Binding Sites List in 3t3w
Zinc binding site 3 out
of 6 in the Crystal Structure of Probable Enoyl-Coa Hydratase From Mycobacterium Thermoresistibile
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 Probable Enoyl-Coa Hydratase From Mycobacterium Thermoresistibile within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn301
b:11.8
occ:1.00
|
NE2
|
C:HIS253
|
2.1
|
11.1
|
1.0
|
NE2
|
C:HIS249
|
2.1
|
9.1
|
1.0
|
OE2
|
C:GLU160
|
2.1
|
9.7
|
1.0
|
OE2
|
C:GLU99
|
2.2
|
10.9
|
1.0
|
O
|
C:HOH277
|
2.2
|
12.3
|
1.0
|
OE1
|
C:GLU99
|
2.2
|
10.0
|
1.0
|
CD
|
C:GLU99
|
2.5
|
10.6
|
1.0
|
CE1
|
C:HIS253
|
3.0
|
12.4
|
1.0
|
CD2
|
C:HIS249
|
3.1
|
8.7
|
1.0
|
CD
|
C:GLU160
|
3.1
|
10.0
|
1.0
|
CE1
|
C:HIS249
|
3.1
|
8.9
|
1.0
|
CD2
|
C:HIS253
|
3.1
|
11.1
|
1.0
|
CG
|
C:GLU160
|
3.6
|
10.1
|
1.0
|
O
|
C:HOH329
|
3.8
|
19.7
|
1.0
|
CG
|
C:GLU99
|
4.0
|
10.4
|
1.0
|
O
|
C:HOH284
|
4.0
|
13.2
|
1.0
|
OE1
|
C:GLU160
|
4.1
|
10.7
|
1.0
|
O
|
C:HOH536
|
4.1
|
26.4
|
1.0
|
ND1
|
C:HIS253
|
4.2
|
11.7
|
1.0
|
CG
|
C:HIS249
|
4.2
|
8.2
|
1.0
|
ND1
|
C:HIS249
|
4.2
|
8.4
|
1.0
|
CG
|
C:HIS253
|
4.3
|
10.8
|
1.0
|
NE2
|
C:GLN250
|
4.4
|
10.3
|
1.0
|
O
|
C:HOH321
|
4.6
|
19.0
|
1.0
|
CB
|
C:GLU99
|
4.7
|
10.3
|
1.0
|
CD2
|
C:TYR103
|
4.9
|
12.5
|
1.0
|
CE2
|
C:TYR103
|
4.9
|
13.1
|
1.0
|
|
Zinc binding site 4 out
of 6 in 3t3w
Go back to
Zinc Binding Sites List in 3t3w
Zinc binding site 4 out
of 6 in the Crystal Structure of Probable Enoyl-Coa Hydratase From Mycobacterium Thermoresistibile
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 Probable Enoyl-Coa Hydratase From Mycobacterium Thermoresistibile within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn301
b:10.6
occ:1.00
|
NE2
|
D:HIS249
|
2.1
|
7.7
|
1.0
|
OE2
|
D:GLU160
|
2.1
|
9.0
|
1.0
|
NE2
|
D:HIS253
|
2.1
|
8.9
|
1.0
|
OE2
|
D:GLU99
|
2.1
|
8.6
|
1.0
|
O
|
D:HOH871
|
2.1
|
8.3
|
1.0
|
OE1
|
D:GLU99
|
2.2
|
9.0
|
1.0
|
CD
|
D:GLU99
|
2.4
|
9.0
|
1.0
|
CE1
|
D:HIS253
|
3.0
|
9.3
|
1.0
|
CD2
|
D:HIS249
|
3.1
|
7.6
|
1.0
|
CE1
|
D:HIS249
|
3.1
|
8.1
|
1.0
|
CD
|
D:GLU160
|
3.1
|
9.0
|
1.0
|
CD2
|
D:HIS253
|
3.1
|
8.7
|
1.0
|
CG
|
D:GLU160
|
3.6
|
8.7
|
1.0
|
O
|
D:HOH320
|
3.8
|
13.6
|
1.0
|
CG
|
D:GLU99
|
4.0
|
9.3
|
1.0
|
O
|
D:HOH290
|
4.0
|
9.8
|
1.0
|
O
|
D:HOH817
|
4.0
|
21.8
|
1.0
|
OE1
|
D:GLU160
|
4.1
|
9.2
|
1.0
|
ND1
|
D:HIS249
|
4.2
|
7.8
|
1.0
|
ND1
|
D:HIS253
|
4.2
|
9.4
|
1.0
|
CG
|
D:HIS249
|
4.2
|
7.7
|
1.0
|
CG
|
D:HIS253
|
4.3
|
9.2
|
1.0
|
NE2
|
D:GLN250
|
4.4
|
9.9
|
1.0
|
O
|
D:HOH321
|
4.5
|
24.6
|
1.0
|
CB
|
D:GLU99
|
4.7
|
9.2
|
1.0
|
CD2
|
D:TYR103
|
4.9
|
11.0
|
1.0
|
CE2
|
D:TYR103
|
4.9
|
11.5
|
1.0
|
|
Zinc binding site 5 out
of 6 in 3t3w
Go back to
Zinc Binding Sites List in 3t3w
Zinc binding site 5 out
of 6 in the Crystal Structure of Probable Enoyl-Coa Hydratase From Mycobacterium Thermoresistibile
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of Crystal Structure of Probable Enoyl-Coa Hydratase From Mycobacterium Thermoresistibile within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Zn301
b:10.3
occ:1.00
|
NE2
|
E:HIS249
|
2.1
|
7.2
|
1.0
|
NE2
|
E:HIS253
|
2.1
|
10.1
|
1.0
|
OE2
|
E:GLU160
|
2.1
|
8.6
|
1.0
|
OE2
|
E:GLU99
|
2.1
|
8.7
|
1.0
|
O
|
E:HOH872
|
2.1
|
9.0
|
1.0
|
OE1
|
E:GLU99
|
2.2
|
9.4
|
1.0
|
CD
|
E:GLU99
|
2.4
|
9.0
|
1.0
|
CE1
|
E:HIS249
|
3.0
|
7.3
|
1.0
|
CD2
|
E:HIS249
|
3.1
|
7.2
|
1.0
|
CE1
|
E:HIS253
|
3.1
|
10.3
|
1.0
|
CD2
|
E:HIS253
|
3.1
|
9.8
|
1.0
|
CD
|
E:GLU160
|
3.1
|
8.0
|
1.0
|
CG
|
E:GLU160
|
3.6
|
7.9
|
1.0
|
O
|
E:HOH421
|
3.8
|
17.8
|
1.0
|
CG
|
E:GLU99
|
3.9
|
9.2
|
1.0
|
O
|
E:HOH307
|
4.0
|
10.9
|
1.0
|
OE1
|
E:GLU160
|
4.1
|
8.1
|
1.0
|
ND1
|
E:HIS249
|
4.2
|
7.1
|
1.0
|
O
|
E:HOH711
|
4.2
|
32.8
|
1.0
|
CG
|
E:HIS249
|
4.2
|
7.0
|
1.0
|
ND1
|
E:HIS253
|
4.2
|
10.6
|
1.0
|
CG
|
E:HIS253
|
4.2
|
9.8
|
1.0
|
NE2
|
E:GLN250
|
4.4
|
9.0
|
1.0
|
O
|
E:HOH328
|
4.6
|
19.5
|
1.0
|
CB
|
E:GLU99
|
4.7
|
8.8
|
1.0
|
CD2
|
E:TYR103
|
4.9
|
9.4
|
1.0
|
CE2
|
E:TYR103
|
5.0
|
9.8
|
1.0
|
|
Zinc binding site 6 out
of 6 in 3t3w
Go back to
Zinc Binding Sites List in 3t3w
Zinc binding site 6 out
of 6 in the Crystal Structure of Probable Enoyl-Coa Hydratase From Mycobacterium Thermoresistibile
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of Crystal Structure of Probable Enoyl-Coa Hydratase From Mycobacterium Thermoresistibile within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Zn301
b:11.0
occ:1.00
|
NE2
|
F:HIS249
|
2.1
|
8.1
|
1.0
|
NE2
|
F:HIS253
|
2.1
|
10.7
|
1.0
|
O
|
F:HOH277
|
2.1
|
11.4
|
1.0
|
OE2
|
F:GLU99
|
2.1
|
9.1
|
1.0
|
OE2
|
F:GLU160
|
2.1
|
9.2
|
1.0
|
OE1
|
F:GLU99
|
2.2
|
9.3
|
1.0
|
CD
|
F:GLU99
|
2.5
|
9.4
|
1.0
|
CE1
|
F:HIS253
|
3.0
|
12.1
|
1.0
|
CD2
|
F:HIS249
|
3.0
|
8.0
|
1.0
|
CE1
|
F:HIS249
|
3.1
|
8.2
|
1.0
|
CD
|
F:GLU160
|
3.1
|
9.2
|
1.0
|
CD2
|
F:HIS253
|
3.2
|
10.4
|
1.0
|
CG
|
F:GLU160
|
3.6
|
8.8
|
1.0
|
O
|
F:HOH282
|
3.8
|
16.6
|
1.0
|
CG
|
F:GLU99
|
4.0
|
9.6
|
1.0
|
O
|
F:HOH284
|
4.0
|
11.6
|
1.0
|
O
|
F:HOH658
|
4.1
|
32.7
|
1.0
|
OE1
|
F:GLU160
|
4.1
|
9.6
|
1.0
|
ND1
|
F:HIS253
|
4.2
|
11.8
|
1.0
|
ND1
|
F:HIS249
|
4.2
|
7.9
|
1.0
|
CG
|
F:HIS249
|
4.2
|
7.9
|
1.0
|
CG
|
F:HIS253
|
4.3
|
10.9
|
1.0
|
NE2
|
F:GLN250
|
4.4
|
10.4
|
1.0
|
O
|
F:HOH398
|
4.5
|
17.9
|
1.0
|
CB
|
F:GLU99
|
4.7
|
9.8
|
1.0
|
CD2
|
F:TYR103
|
4.9
|
10.7
|
1.0
|
CE2
|
F:TYR103
|
4.9
|
11.2
|
1.0
|
|
Reference:
L.Baugh,
I.Phan,
D.W.Begley,
M.C.Clifton,
B.Armour,
D.M.Dranow,
B.M.Taylor,
M.M.Muruthi,
J.Abendroth,
J.W.Fairman,
D.Fox,
S.H.Dieterich,
B.L.Staker,
A.S.Gardberg,
R.Choi,
S.N.Hewitt,
A.J.Napuli,
J.Myers,
L.K.Barrett,
Y.Zhang,
M.Ferrell,
E.Mundt,
K.Thompkins,
N.Tran,
S.Lyons-Abbott,
A.Abramov,
A.Sekar,
D.Serbzhinskiy,
D.Lorimer,
G.W.Buchko,
R.Stacy,
L.J.Stewart,
T.E.Edwards,
W.C.Van Voorhis,
P.J.Myler.
Increasing the Structural Coverage of Tuberculosis Drug Targets. Tuberculosis (Edinb) V. 95 142 2015.
ISSN: ISSN 1472-9792
PubMed: 25613812
DOI: 10.1016/J.TUBE.2014.12.003
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