Zinc in PDB 6sj0: Amidohydrolase, Ahs
Protein crystallography data
The structure of Amidohydrolase, Ahs, PDB code: 6sj0
was solved by
J.H.Naismith,
H.Song,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
53.81 /
1.75
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
81.790,
82.750,
141.560,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
18.2 /
20.9
|
Zinc Binding Sites:
Zinc binding site 1 out
of 22 in 6sj0
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Zinc Binding Sites List in 6sj0
Zinc binding site 1 out
of 22 in the Amidohydrolase, Ahs
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Amidohydrolase, Ahs within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn504
b:22.5
occ:1.00
|
NE2
|
A:HIS75
|
2.0
|
22.6
|
1.0
|
NE2
|
A:HIS77
|
2.0
|
21.4
|
1.0
|
NE2
|
A:HIS253
|
2.0
|
22.2
|
1.0
|
O
|
A:HOH627
|
2.2
|
29.9
|
1.0
|
OD1
|
A:ASP345
|
2.6
|
34.2
|
1.0
|
CD2
|
A:HIS253
|
2.9
|
23.5
|
1.0
|
CE1
|
A:HIS75
|
3.0
|
34.2
|
1.0
|
CD2
|
A:HIS75
|
3.0
|
25.4
|
1.0
|
CE1
|
A:HIS77
|
3.0
|
27.6
|
1.0
|
CD2
|
A:HIS77
|
3.0
|
22.0
|
1.0
|
CE1
|
A:HIS253
|
3.1
|
24.9
|
1.0
|
CG
|
A:ASP345
|
3.5
|
33.6
|
1.0
|
OD2
|
A:ASP345
|
3.9
|
35.0
|
1.0
|
ND1
|
A:HIS75
|
4.1
|
31.1
|
1.0
|
NE2
|
A:HIS290
|
4.1
|
27.3
|
1.0
|
CG
|
A:HIS253
|
4.1
|
21.9
|
1.0
|
CG
|
A:HIS75
|
4.1
|
22.3
|
1.0
|
ND1
|
A:HIS77
|
4.1
|
24.8
|
1.0
|
ND1
|
A:HIS253
|
4.2
|
27.6
|
1.0
|
CG
|
A:HIS77
|
4.2
|
21.5
|
1.0
|
CB
|
A:ASP345
|
4.6
|
25.8
|
1.0
|
CA
|
A:ASP345
|
4.7
|
22.6
|
1.0
|
CE1
|
A:HIS290
|
4.8
|
25.0
|
1.0
|
CD2
|
A:HIS290
|
4.9
|
29.7
|
1.0
|
|
Zinc binding site 2 out
of 22 in 6sj0
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Zinc Binding Sites List in 6sj0
Zinc binding site 2 out
of 22 in the Amidohydrolase, Ahs
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Amidohydrolase, Ahs within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn505
b:0.2
occ:1.00
|
O
|
A:HOH763
|
3.1
|
46.0
|
1.0
|
OE2
|
A:GLU41
|
4.9
|
63.8
|
1.0
|
|
Zinc binding site 3 out
of 22 in 6sj0
Go back to
Zinc Binding Sites List in 6sj0
Zinc binding site 3 out
of 22 in the Amidohydrolase, Ahs
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Amidohydrolase, Ahs within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn506
b:56.6
occ:1.00
|
O
|
A:HOH777
|
2.4
|
49.1
|
1.0
|
O
|
A:HOH776
|
2.5
|
47.4
|
1.0
|
CD2
|
A:HIS246
|
2.6
|
43.3
|
1.0
|
CG
|
A:HIS246
|
3.3
|
45.2
|
1.0
|
CB
|
A:HIS246
|
3.4
|
37.5
|
1.0
|
NE2
|
A:HIS246
|
3.7
|
54.5
|
1.0
|
CA
|
A:HIS246
|
3.9
|
33.0
|
1.0
|
O
|
A:HIS246
|
4.3
|
34.9
|
1.0
|
CD2
|
A:LEU208
|
4.3
|
39.9
|
1.0
|
ND1
|
A:HIS246
|
4.5
|
52.1
|
1.0
|
C
|
A:HIS246
|
4.6
|
32.1
|
1.0
|
CE1
|
A:HIS246
|
4.8
|
47.4
|
1.0
|
CG
|
A:LEU208
|
5.0
|
38.0
|
1.0
|
|
Zinc binding site 4 out
of 22 in 6sj0
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Zinc Binding Sites List in 6sj0
Zinc binding site 4 out
of 22 in the Amidohydrolase, Ahs
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Amidohydrolase, Ahs within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn507
b:64.2
occ:1.00
|
ND1
|
A:HIS110
|
2.2
|
45.8
|
1.0
|
O
|
A:HOH773
|
2.6
|
58.9
|
1.0
|
O
|
A:HOH768
|
2.6
|
50.9
|
1.0
|
O
|
A:HOH774
|
2.7
|
54.0
|
1.0
|
CE1
|
A:HIS110
|
3.0
|
43.0
|
1.0
|
O
|
A:HOH750
|
3.0
|
56.8
|
1.0
|
CG
|
A:HIS110
|
3.2
|
37.2
|
1.0
|
CB
|
A:HIS110
|
3.6
|
34.1
|
1.0
|
CB
|
A:PRO186
|
4.1
|
43.8
|
1.0
|
NE2
|
A:HIS110
|
4.2
|
42.6
|
1.0
|
CD2
|
A:HIS110
|
4.3
|
46.2
|
1.0
|
OD1
|
A:ASP108
|
4.4
|
33.0
|
1.0
|
CG
|
A:PRO186
|
4.8
|
39.2
|
1.0
|
O
|
A:HOH702
|
5.0
|
43.1
|
1.0
|
CA
|
A:HIS110
|
5.0
|
30.5
|
1.0
|
|
Zinc binding site 5 out
of 22 in 6sj0
Go back to
Zinc Binding Sites List in 6sj0
Zinc binding site 5 out
of 22 in the Amidohydrolase, Ahs
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of Amidohydrolase, Ahs within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn508
b:83.4
occ:1.00
|
OD1
|
A:ASP395
|
2.4
|
33.0
|
1.0
|
OD2
|
A:ASP395
|
3.0
|
34.9
|
1.0
|
CG
|
A:ASP395
|
3.0
|
31.7
|
1.0
|
CB
|
A:ASP395
|
4.5
|
27.7
|
1.0
|
CG
|
A:LYS390
|
4.5
|
32.1
|
1.0
|
O
|
A:LYS390
|
4.6
|
25.3
|
1.0
|
CA
|
A:ARG393
|
4.8
|
28.3
|
1.0
|
CA
|
A:LYS390
|
4.8
|
23.8
|
1.0
|
N
|
A:ASP395
|
4.9
|
24.4
|
1.0
|
|
Zinc binding site 6 out
of 22 in 6sj0
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Zinc Binding Sites List in 6sj0
Zinc binding site 6 out
of 22 in the Amidohydrolase, Ahs
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of Amidohydrolase, Ahs within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn509
b:0.3
occ:1.00
|
CE1
|
A:HIS21
|
2.9
|
41.2
|
1.0
|
O
|
A:HOH684
|
3.0
|
39.8
|
1.0
|
NE2
|
A:HIS21
|
3.3
|
41.9
|
1.0
|
ND1
|
A:HIS21
|
4.1
|
33.6
|
1.0
|
CD2
|
A:HIS21
|
4.6
|
37.9
|
1.0
|
CA
|
A:GLY37
|
4.6
|
30.6
|
1.0
|
CD
|
A:PRO38
|
4.7
|
37.4
|
1.0
|
O
|
A:VAL36
|
4.7
|
28.5
|
1.0
|
OE1
|
A:GLU41
|
4.8
|
51.6
|
1.0
|
OG
|
A:SER19
|
5.0
|
39.5
|
1.0
|
CG
|
A:HIS21
|
5.0
|
33.5
|
1.0
|
|
Zinc binding site 7 out
of 22 in 6sj0
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Zinc Binding Sites List in 6sj0
Zinc binding site 7 out
of 22 in the Amidohydrolase, Ahs
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 7 of Amidohydrolase, Ahs within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn510
b:90.2
occ:1.00
|
OE2
|
A:GLU278
|
2.6
|
59.9
|
1.0
|
CD
|
A:GLU278
|
3.6
|
63.8
|
1.0
|
OE1
|
A:GLU278
|
4.0
|
63.6
|
1.0
|
CB
|
A:GLU270
|
4.9
|
34.0
|
1.0
|
CG
|
A:GLU278
|
4.9
|
53.6
|
1.0
|
CG
|
A:GLU270
|
4.9
|
36.9
|
1.0
|
OE1
|
A:GLU270
|
5.0
|
49.4
|
1.0
|
|
Zinc binding site 8 out
of 22 in 6sj0
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Zinc Binding Sites List in 6sj0
Zinc binding site 8 out
of 22 in the Amidohydrolase, Ahs
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 8 of Amidohydrolase, Ahs within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn511
b:85.0
occ:1.00
|
OD1
|
A:ASP296
|
2.6
|
55.2
|
1.0
|
CG
|
A:ASP296
|
3.5
|
50.8
|
1.0
|
OD2
|
A:ASP296
|
3.7
|
54.4
|
1.0
|
NE2
|
A:GLN299
|
4.3
|
27.6
|
1.0
|
OE1
|
A:GLN299
|
4.7
|
36.6
|
1.0
|
CD
|
A:GLN299
|
4.9
|
33.6
|
1.0
|
CB
|
A:ASP296
|
5.0
|
44.4
|
1.0
|
|
Zinc binding site 9 out
of 22 in 6sj0
Go back to
Zinc Binding Sites List in 6sj0
Zinc binding site 9 out
of 22 in the Amidohydrolase, Ahs
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 9 of Amidohydrolase, Ahs within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn512
b:0.8
occ:1.00
|
O
|
A:HOH741
|
3.7
|
36.2
|
1.0
|
O
|
A:HOH661
|
4.6
|
27.5
|
1.0
|
OG1
|
A:THR10
|
4.7
|
28.3
|
1.0
|
O
|
A:ASN422
|
4.7
|
24.1
|
1.0
|
OG1
|
A:THR414
|
4.8
|
26.9
|
1.0
|
O
|
A:HOH704
|
4.9
|
34.9
|
1.0
|
O
|
A:HOH609
|
4.9
|
30.7
|
1.0
|
|
Zinc binding site 10 out
of 22 in 6sj0
Go back to
Zinc Binding Sites List in 6sj0
Zinc binding site 10 out
of 22 in the Amidohydrolase, Ahs
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 10 of Amidohydrolase, Ahs within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn513
b:55.4
occ:1.00
|
OE2
|
A:GLU205
|
4.3
|
50.1
|
1.0
|
OE1
|
A:GLU205
|
4.3
|
46.9
|
1.0
|
CD
|
A:GLU205
|
4.8
|
49.8
|
1.0
|
O
|
A:HOH766
|
4.9
|
40.5
|
1.0
|
|
Reference:
H.Song,
C.Rao,
Z.Deng,
Y.Yi,
J.H.Naismith.
The Biosynthetic Pathway of the Benzoxazole in Nataxazole Proceeds Via An Unstable Ester and Has Synthetic Utility. Angew.Chem.Int.Ed.Engl. 2020.
ISSN: ESSN 1521-3773
PubMed: 31903677
DOI: 10.1002/ANIE.201915685
Page generated: Wed Dec 16 12:48:37 2020
|