Mercury in PDB 6pii: The Evolving Story of Atzt, A Periplasmic Binding Protein
Protein crystallography data
The structure of The Evolving Story of Atzt, A Periplasmic Binding Protein, PDB code: 6pii
was solved by
T.S.Peat,
J.Newman,
C.Scott,
L.Esquirol,
M.Dennis,
T.Nebl,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
49.40 /
1.87
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
98.920,
63.050,
120.436,
90.00,
93.49,
90.00
|
R / Rfree (%)
|
15.5 /
18.3
|
Other elements in 6pii:
The structure of The Evolving Story of Atzt, A Periplasmic Binding Protein also contains other interesting chemical elements:
Mercury Binding Sites:
The binding sites of Mercury atom in the The Evolving Story of Atzt, A Periplasmic Binding Protein
(pdb code 6pii). This binding sites where shown within
5.0 Angstroms radius around Mercury atom.
In total 4 binding sites of Mercury where determined in the
The Evolving Story of Atzt, A Periplasmic Binding Protein, PDB code: 6pii:
Jump to Mercury binding site number:
1;
2;
3;
4;
Mercury binding site 1 out
of 4 in 6pii
Go back to
Mercury Binding Sites List in 6pii
Mercury binding site 1 out
of 4 in the The Evolving Story of Atzt, A Periplasmic Binding Protein
Mono view
Stereo pair view
|
A full contact list of Mercury with other atoms in the Hg binding
site number 1 of The Evolving Story of Atzt, A Periplasmic Binding Protein within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Hg402
b:29.3
occ:0.90
|
HG
|
A:EMC402
|
0.0
|
29.3
|
0.9
|
C1
|
A:EMC402
|
2.3
|
30.7
|
0.9
|
SG
|
A:CYS238
|
2.4
|
35.3
|
1.0
|
O
|
A:GLN217
|
2.8
|
29.4
|
1.0
|
C2
|
A:EMC402
|
3.0
|
26.3
|
0.9
|
O
|
A:HOH629
|
3.2
|
35.7
|
1.0
|
CB
|
A:CYS238
|
3.2
|
27.6
|
1.0
|
OE1
|
A:GLN135
|
3.4
|
31.2
|
1.0
|
CD
|
A:GLN135
|
3.8
|
32.9
|
1.0
|
O
|
A:HOH525
|
4.0
|
29.7
|
1.0
|
NE2
|
A:GLN135
|
4.0
|
32.3
|
1.0
|
C
|
A:GLN217
|
4.0
|
27.8
|
1.0
|
O
|
A:HOH639
|
4.0
|
44.0
|
1.0
|
O
|
A:HOH535
|
4.1
|
32.4
|
1.0
|
CA
|
A:CYS238
|
4.1
|
24.0
|
1.0
|
CA
|
A:ASN218
|
4.2
|
23.4
|
1.0
|
N
|
A:ASN218
|
4.6
|
24.9
|
1.0
|
ND2
|
A:ASN218
|
4.6
|
26.6
|
1.0
|
O
|
A:HOH591
|
4.6
|
26.7
|
1.0
|
CG
|
A:ASN218
|
4.7
|
27.8
|
1.0
|
CG
|
A:GLN135
|
4.8
|
32.1
|
1.0
|
ND2
|
A:ASN169
|
5.0
|
23.6
|
1.0
|
C
|
A:CYS238
|
5.0
|
27.6
|
1.0
|
|
Mercury binding site 2 out
of 4 in 6pii
Go back to
Mercury Binding Sites List in 6pii
Mercury binding site 2 out
of 4 in the The Evolving Story of Atzt, A Periplasmic Binding Protein
Mono view
Stereo pair view
|
A full contact list of Mercury with other atoms in the Hg binding
site number 2 of The Evolving Story of Atzt, A Periplasmic Binding Protein within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Hg402
b:29.2
occ:0.90
|
HG
|
B:EMC402
|
0.0
|
29.2
|
0.9
|
SG
|
B:CYS238
|
2.3
|
29.6
|
1.0
|
C1
|
B:EMC402
|
2.3
|
17.6
|
0.9
|
O
|
B:GLN217
|
2.8
|
27.9
|
1.0
|
C2
|
B:EMC402
|
3.0
|
25.2
|
0.9
|
O
|
B:HOH628
|
3.2
|
30.4
|
1.0
|
OE1
|
B:GLN135
|
3.3
|
25.9
|
1.0
|
CB
|
B:CYS238
|
3.3
|
28.8
|
1.0
|
CD
|
B:GLN135
|
3.7
|
34.1
|
1.0
|
O
|
B:HOH560
|
3.8
|
26.6
|
1.0
|
C
|
B:GLN217
|
4.0
|
28.8
|
1.0
|
NE2
|
B:GLN135
|
4.1
|
31.6
|
1.0
|
CA
|
B:ASN218
|
4.2
|
22.9
|
1.0
|
CA
|
B:CYS238
|
4.2
|
26.8
|
1.0
|
O
|
B:HOH568
|
4.3
|
47.7
|
1.0
|
O
|
B:HOH504
|
4.3
|
32.4
|
1.0
|
ND2
|
B:ASN218
|
4.5
|
24.7
|
1.0
|
N
|
B:ASN218
|
4.6
|
24.9
|
1.0
|
CG
|
B:ASN218
|
4.7
|
28.2
|
1.0
|
O
|
B:HOH537
|
4.7
|
30.2
|
1.0
|
CG
|
B:GLN135
|
4.7
|
28.3
|
1.0
|
ND2
|
B:ASN169
|
5.0
|
23.9
|
1.0
|
|
Mercury binding site 3 out
of 4 in 6pii
Go back to
Mercury Binding Sites List in 6pii
Mercury binding site 3 out
of 4 in the The Evolving Story of Atzt, A Periplasmic Binding Protein
Mono view
Stereo pair view
|
A full contact list of Mercury with other atoms in the Hg binding
site number 3 of The Evolving Story of Atzt, A Periplasmic Binding Protein within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Hg402
b:29.0
occ:0.80
|
HG
|
C:EMC402
|
0.0
|
29.0
|
0.8
|
C1
|
C:EMC402
|
2.3
|
26.1
|
0.8
|
SG
|
C:CYS238
|
2.4
|
36.4
|
1.0
|
O
|
C:GLN217
|
2.9
|
33.0
|
1.0
|
O
|
C:HOH631
|
3.0
|
38.3
|
1.0
|
C2
|
C:EMC402
|
3.2
|
26.4
|
0.8
|
CB
|
C:CYS238
|
3.3
|
34.2
|
1.0
|
OE1
|
C:GLN135
|
3.5
|
30.6
|
1.0
|
O
|
C:HOH545
|
3.9
|
33.5
|
1.0
|
CD
|
C:GLN135
|
3.9
|
31.8
|
1.0
|
O
|
C:HOH543
|
3.9
|
48.8
|
1.0
|
O
|
C:HOH535
|
4.0
|
38.4
|
1.0
|
C
|
C:GLN217
|
4.1
|
28.7
|
1.0
|
NE2
|
C:GLN135
|
4.1
|
34.0
|
1.0
|
CA
|
C:CYS238
|
4.2
|
29.8
|
1.0
|
CA
|
C:ASN218
|
4.3
|
25.8
|
1.0
|
ND2
|
C:ASN218
|
4.5
|
30.2
|
1.0
|
CA
|
C:CA403
|
4.5
|
55.6
|
1.0
|
CG
|
C:ASN218
|
4.6
|
30.5
|
1.0
|
N
|
C:ASN218
|
4.7
|
25.8
|
1.0
|
CG
|
C:GLN135
|
4.8
|
27.7
|
1.0
|
OD1
|
C:ASN218
|
4.9
|
28.2
|
1.0
|
ND2
|
C:ASN169
|
4.9
|
24.6
|
1.0
|
CB
|
C:ASN218
|
5.0
|
28.1
|
1.0
|
|
Mercury binding site 4 out
of 4 in 6pii
Go back to
Mercury Binding Sites List in 6pii
Mercury binding site 4 out
of 4 in the The Evolving Story of Atzt, A Periplasmic Binding Protein
Mono view
Stereo pair view
|
A full contact list of Mercury with other atoms in the Hg binding
site number 4 of The Evolving Story of Atzt, A Periplasmic Binding Protein within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Hg402
b:31.6
occ:0.80
|
HG
|
D:EMC402
|
0.0
|
31.6
|
0.8
|
SG
|
D:CYS238
|
2.3
|
41.5
|
1.0
|
C1
|
D:EMC402
|
2.3
|
30.5
|
0.8
|
O
|
D:GLN217
|
2.9
|
30.6
|
1.0
|
C2
|
D:EMC402
|
3.0
|
25.9
|
0.8
|
CB
|
D:CYS238
|
3.2
|
36.4
|
1.0
|
O
|
D:HOH579
|
3.3
|
35.8
|
1.0
|
OE1
|
D:GLN135
|
3.5
|
31.2
|
1.0
|
O
|
D:HOH551
|
3.8
|
34.7
|
1.0
|
CD
|
D:GLN135
|
3.8
|
41.5
|
1.0
|
NE2
|
D:GLN135
|
4.0
|
40.2
|
1.0
|
C
|
D:GLN217
|
4.1
|
29.6
|
1.0
|
CA
|
D:CYS238
|
4.1
|
32.1
|
1.0
|
O
|
D:HOH537
|
4.3
|
38.2
|
1.0
|
CA
|
D:ASN218
|
4.3
|
27.6
|
1.0
|
ND2
|
D:ASN218
|
4.5
|
29.6
|
1.0
|
N
|
D:ASN218
|
4.6
|
29.2
|
1.0
|
CG
|
D:ASN218
|
4.6
|
29.4
|
1.0
|
O
|
D:HOH563
|
4.7
|
35.4
|
1.0
|
CG
|
D:GLN135
|
4.8
|
36.5
|
1.0
|
OD1
|
D:ASN218
|
5.0
|
28.8
|
1.0
|
ND2
|
D:ASN169
|
5.0
|
24.8
|
1.0
|
C
|
D:CYS238
|
5.0
|
30.6
|
1.0
|
|
Reference:
M.Dennis,
L.Esquirol,
T.Nebl,
J.Newman,
C.Scott,
T.S.Peat.
The Evolving Story of Atzt, A Periplasmic Binding Protein Acta Crystallogr.,Sect.D V. 75 995 2019.
ISSN: ESSN 1399-0047
DOI: 10.1107/S2059798319013883
Page generated: Sun Aug 11 07:33:15 2024
|