Mercury in PDB 2xvb: Crystal Structure of Laccase From Thermus Thermophilus HB27 Complexed with Hg, Crystal of the Apoenzyme Soaked For 5 Min. in 5 Mm HGCL2 at 278 K.
Enzymatic activity of Crystal Structure of Laccase From Thermus Thermophilus HB27 Complexed with Hg, Crystal of the Apoenzyme Soaked For 5 Min. in 5 Mm HGCL2 at 278 K.
All present enzymatic activity of Crystal Structure of Laccase From Thermus Thermophilus HB27 Complexed with Hg, Crystal of the Apoenzyme Soaked For 5 Min. in 5 Mm HGCL2 at 278 K.:
1.10.3.2;
Protein crystallography data
The structure of Crystal Structure of Laccase From Thermus Thermophilus HB27 Complexed with Hg, Crystal of the Apoenzyme Soaked For 5 Min. in 5 Mm HGCL2 at 278 K., PDB code: 2xvb
was solved by
H.Serrano-Posada,
B.Valderrama,
E.Rudino-Pinera,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
19.689 /
1.70
|
Space group
|
C 2 2 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
93.456,
110.183,
96.343,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
15.28 /
17.78
|
Mercury Binding Sites:
The binding sites of Mercury atom in the Crystal Structure of Laccase From Thermus Thermophilus HB27 Complexed with Hg, Crystal of the Apoenzyme Soaked For 5 Min. in 5 Mm HGCL2 at 278 K.
(pdb code 2xvb). This binding sites where shown within
5.0 Angstroms radius around Mercury atom.
In total 5 binding sites of Mercury where determined in the
Crystal Structure of Laccase From Thermus Thermophilus HB27 Complexed with Hg, Crystal of the Apoenzyme Soaked For 5 Min. in 5 Mm HGCL2 at 278 K., PDB code: 2xvb:
Jump to Mercury binding site number:
1;
2;
3;
4;
5;
Mercury binding site 1 out
of 5 in 2xvb
Go back to
Mercury Binding Sites List in 2xvb
Mercury binding site 1 out
of 5 in the Crystal Structure of Laccase From Thermus Thermophilus HB27 Complexed with Hg, Crystal of the Apoenzyme Soaked For 5 Min. in 5 Mm HGCL2 at 278 K.
Mono view
Stereo pair view
|
A full contact list of Mercury with other atoms in the Hg binding
site number 1 of Crystal Structure of Laccase From Thermus Thermophilus HB27 Complexed with Hg, Crystal of the Apoenzyme Soaked For 5 Min. in 5 Mm HGCL2 at 278 K. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Hg1463
b:28.4
occ:0.19
|
ND1
|
A:HIS393
|
2.0
|
19.4
|
1.0
|
SG
|
A:CYS445
|
2.1
|
13.2
|
1.0
|
ND1
|
A:HIS450
|
2.2
|
15.6
|
1.0
|
CE1
|
A:HIS393
|
2.8
|
19.8
|
1.0
|
CG
|
A:HIS450
|
3.1
|
11.2
|
1.0
|
CG
|
A:HIS393
|
3.1
|
16.2
|
1.0
|
CB
|
A:CYS445
|
3.2
|
15.0
|
1.0
|
CB
|
A:HIS450
|
3.2
|
7.5
|
1.0
|
SD
|
A:MET455
|
3.3
|
11.2
|
0.3
|
CE1
|
A:HIS450
|
3.3
|
16.3
|
1.0
|
CB
|
A:HIS393
|
3.6
|
16.8
|
1.0
|
SD
|
A:MET455
|
3.8
|
14.8
|
0.7
|
NE2
|
A:HIS393
|
4.0
|
20.4
|
1.0
|
CA
|
A:HIS393
|
4.0
|
13.1
|
1.0
|
CD2
|
A:HIS393
|
4.2
|
14.4
|
1.0
|
CB
|
A:ILE447
|
4.2
|
8.5
|
1.0
|
CE
|
A:MET455
|
4.3
|
12.8
|
0.3
|
CE
|
A:MET455
|
4.3
|
13.0
|
0.7
|
CD2
|
A:HIS450
|
4.3
|
14.4
|
1.0
|
NE2
|
A:HIS450
|
4.4
|
12.6
|
1.0
|
CD1
|
A:ILE447
|
4.4
|
16.9
|
1.0
|
O
|
A:ASP392
|
4.6
|
11.2
|
1.0
|
CA
|
A:CYS445
|
4.6
|
12.1
|
1.0
|
CE
|
A:MET391
|
4.6
|
10.6
|
0.5
|
O
|
A:ILE447
|
4.6
|
11.4
|
1.0
|
CG1
|
A:ILE447
|
4.7
|
10.5
|
1.0
|
CA
|
A:HIS450
|
4.8
|
8.9
|
1.0
|
CD
|
A:PRO394
|
4.8
|
10.3
|
1.0
|
N
|
A:ILE447
|
4.8
|
9.3
|
1.0
|
CG
|
A:MET455
|
4.9
|
14.2
|
0.3
|
C
|
A:HIS393
|
5.0
|
12.5
|
1.0
|
CG2
|
A:ILE447
|
5.0
|
11.3
|
1.0
|
|
Mercury binding site 2 out
of 5 in 2xvb
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Mercury Binding Sites List in 2xvb
Mercury binding site 2 out
of 5 in the Crystal Structure of Laccase From Thermus Thermophilus HB27 Complexed with Hg, Crystal of the Apoenzyme Soaked For 5 Min. in 5 Mm HGCL2 at 278 K.
Mono view
Stereo pair view
|
A full contact list of Mercury with other atoms in the Hg binding
site number 2 of Crystal Structure of Laccase From Thermus Thermophilus HB27 Complexed with Hg, Crystal of the Apoenzyme Soaked For 5 Min. in 5 Mm HGCL2 at 278 K. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Hg1464
b:36.2
occ:0.23
|
ND1
|
A:HIS97
|
1.9
|
11.1
|
1.0
|
NE2
|
A:HIS135
|
2.0
|
8.2
|
0.9
|
NE2
|
A:HIS446
|
2.2
|
19.3
|
1.0
|
CE1
|
A:HIS97
|
2.5
|
12.8
|
1.0
|
NE2
|
A:HIS135
|
2.5
|
10.8
|
0.1
|
O
|
A:HOH2434
|
2.5
|
24.1
|
1.0
|
CE1
|
A:HIS135
|
2.7
|
9.7
|
0.9
|
CE1
|
A:HIS446
|
3.0
|
14.9
|
1.0
|
CG
|
A:HIS97
|
3.1
|
10.0
|
1.0
|
CD2
|
A:HIS135
|
3.1
|
10.2
|
0.1
|
CD2
|
A:HIS135
|
3.2
|
10.1
|
0.9
|
CD2
|
A:HIS446
|
3.3
|
16.1
|
1.0
|
CE1
|
A:HIS135
|
3.5
|
11.7
|
0.1
|
O
|
A:HOH2152
|
3.5
|
40.4
|
1.0
|
CZ2
|
A:TRP133
|
3.6
|
9.4
|
1.0
|
NE2
|
A:HIS97
|
3.7
|
9.7
|
1.0
|
CB
|
A:HIS97
|
3.7
|
7.3
|
1.0
|
HG
|
A:HG1465
|
3.8
|
32.8
|
0.2
|
CD2
|
A:HIS95
|
3.8
|
13.3
|
1.0
|
ND1
|
A:HIS135
|
3.9
|
10.9
|
0.9
|
CD2
|
A:HIS97
|
4.0
|
9.1
|
1.0
|
CE2
|
A:TRP133
|
4.0
|
8.8
|
1.0
|
ND1
|
A:HIS446
|
4.1
|
13.6
|
1.0
|
CG
|
A:HIS135
|
4.1
|
9.1
|
0.9
|
NE1
|
A:TRP133
|
4.2
|
9.0
|
1.0
|
CG
|
A:HIS135
|
4.2
|
10.6
|
0.1
|
CH2
|
A:TRP133
|
4.3
|
10.8
|
1.0
|
CG
|
A:HIS446
|
4.3
|
13.9
|
1.0
|
ND1
|
A:HIS135
|
4.3
|
11.3
|
0.1
|
CD2
|
A:HIS396
|
4.5
|
13.7
|
1.0
|
NE2
|
A:HIS396
|
4.5
|
14.3
|
1.0
|
NE2
|
A:HIS95
|
4.5
|
13.7
|
1.0
|
O
|
A:HOH2156
|
4.6
|
24.5
|
1.0
|
CG
|
A:HIS95
|
5.0
|
10.2
|
1.0
|
CA
|
A:HIS97
|
5.0
|
9.7
|
1.0
|
|
Mercury binding site 3 out
of 5 in 2xvb
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Mercury Binding Sites List in 2xvb
Mercury binding site 3 out
of 5 in the Crystal Structure of Laccase From Thermus Thermophilus HB27 Complexed with Hg, Crystal of the Apoenzyme Soaked For 5 Min. in 5 Mm HGCL2 at 278 K.
Mono view
Stereo pair view
|
A full contact list of Mercury with other atoms in the Hg binding
site number 3 of Crystal Structure of Laccase From Thermus Thermophilus HB27 Complexed with Hg, Crystal of the Apoenzyme Soaked For 5 Min. in 5 Mm HGCL2 at 278 K. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Hg1465
b:32.8
occ:0.17
|
NE2
|
A:HIS396
|
1.6
|
14.3
|
1.0
|
NE2
|
A:HIS95
|
1.7
|
13.7
|
1.0
|
CD2
|
A:HIS95
|
2.4
|
13.3
|
1.0
|
CD2
|
A:HIS396
|
2.5
|
13.7
|
1.0
|
CE1
|
A:HIS396
|
2.8
|
11.1
|
1.0
|
CE1
|
A:HIS95
|
2.9
|
11.0
|
1.0
|
CD2
|
A:HIS398
|
3.2
|
10.1
|
1.0
|
NE2
|
A:HIS398
|
3.3
|
9.3
|
1.0
|
O
|
A:HOH2434
|
3.3
|
24.1
|
1.0
|
ND1
|
A:HIS97
|
3.4
|
11.1
|
1.0
|
CG
|
A:HIS97
|
3.5
|
10.0
|
1.0
|
O
|
A:HOH2102
|
3.6
|
11.2
|
1.0
|
CE1
|
A:HIS97
|
3.6
|
12.8
|
1.0
|
CG
|
A:HIS396
|
3.7
|
9.3
|
1.0
|
CG
|
A:HIS95
|
3.7
|
10.2
|
1.0
|
ND1
|
A:HIS396
|
3.7
|
10.8
|
1.0
|
ND1
|
A:HIS95
|
3.8
|
11.9
|
1.0
|
CD2
|
A:HIS97
|
3.8
|
9.1
|
1.0
|
CG
|
A:HIS398
|
3.8
|
8.4
|
1.0
|
HG
|
A:HG1464
|
3.8
|
36.2
|
0.2
|
NE2
|
A:HIS97
|
3.9
|
9.7
|
1.0
|
CE1
|
A:HIS398
|
4.0
|
9.5
|
1.0
|
CA
|
A:HIS97
|
4.0
|
9.7
|
1.0
|
CB
|
A:HIS97
|
4.0
|
7.3
|
1.0
|
HG
|
A:HG1466
|
4.2
|
50.0
|
0.1
|
ND1
|
A:HIS398
|
4.3
|
7.9
|
1.0
|
N
|
A:GLY98
|
4.5
|
10.2
|
1.0
|
CA
|
A:HIS398
|
4.5
|
6.3
|
1.0
|
NE2
|
A:HIS444
|
4.7
|
11.9
|
1.0
|
CB
|
A:HIS398
|
4.7
|
9.1
|
1.0
|
C
|
A:HIS97
|
4.8
|
11.8
|
1.0
|
N
|
A:HIS398
|
4.9
|
5.3
|
1.0
|
NE2
|
A:HIS446
|
4.9
|
19.3
|
1.0
|
NE2
|
A:HIS135
|
5.0
|
8.2
|
0.9
|
|
Mercury binding site 4 out
of 5 in 2xvb
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Mercury Binding Sites List in 2xvb
Mercury binding site 4 out
of 5 in the Crystal Structure of Laccase From Thermus Thermophilus HB27 Complexed with Hg, Crystal of the Apoenzyme Soaked For 5 Min. in 5 Mm HGCL2 at 278 K.
Mono view
Stereo pair view
|
A full contact list of Mercury with other atoms in the Hg binding
site number 4 of Crystal Structure of Laccase From Thermus Thermophilus HB27 Complexed with Hg, Crystal of the Apoenzyme Soaked For 5 Min. in 5 Mm HGCL2 at 278 K. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Hg1466
b:50.0
occ:0.15
|
NE2
|
A:HIS444
|
2.0
|
11.9
|
1.0
|
NE2
|
A:HIS398
|
2.2
|
9.3
|
1.0
|
ND1
|
A:HIS137
|
2.2
|
17.0
|
1.0
|
CE1
|
A:HIS137
|
2.5
|
14.5
|
1.0
|
O
|
A:HOH2434
|
2.6
|
24.1
|
1.0
|
CE1
|
A:HIS398
|
2.8
|
9.5
|
1.0
|
CE1
|
A:HIS444
|
2.9
|
14.5
|
1.0
|
CD2
|
A:HIS444
|
3.0
|
10.0
|
1.0
|
O
|
A:HOH2156
|
3.1
|
24.5
|
1.0
|
CG
|
A:HIS137
|
3.3
|
15.7
|
1.0
|
CD2
|
A:HIS398
|
3.4
|
10.1
|
1.0
|
NE2
|
A:HIS137
|
3.6
|
21.7
|
1.0
|
ND1
|
A:HIS444
|
3.9
|
12.1
|
1.0
|
CD2
|
A:HIS137
|
3.9
|
20.2
|
1.0
|
CG
|
A:HIS444
|
4.0
|
11.4
|
1.0
|
CD2
|
A:HIS95
|
4.0
|
13.3
|
1.0
|
ND1
|
A:HIS398
|
4.0
|
7.9
|
1.0
|
CB
|
A:HIS137
|
4.1
|
14.1
|
1.0
|
HG
|
A:HG1465
|
4.2
|
32.8
|
0.2
|
CD2
|
A:HIS396
|
4.3
|
13.7
|
1.0
|
CG
|
A:HIS398
|
4.4
|
8.4
|
1.0
|
NE2
|
A:HIS95
|
4.4
|
13.7
|
1.0
|
O
|
A:HOH2435
|
4.4
|
31.0
|
1.0
|
CG2
|
A:VAL442
|
4.5
|
10.0
|
1.0
|
CG
|
A:HIS95
|
4.6
|
10.2
|
1.0
|
NE2
|
A:HIS396
|
4.8
|
14.3
|
1.0
|
NE2
|
A:HIS135
|
4.9
|
10.8
|
0.1
|
|
Mercury binding site 5 out
of 5 in 2xvb
Go back to
Mercury Binding Sites List in 2xvb
Mercury binding site 5 out
of 5 in the Crystal Structure of Laccase From Thermus Thermophilus HB27 Complexed with Hg, Crystal of the Apoenzyme Soaked For 5 Min. in 5 Mm HGCL2 at 278 K.
Mono view
Stereo pair view
|
A full contact list of Mercury with other atoms in the Hg binding
site number 5 of Crystal Structure of Laccase From Thermus Thermophilus HB27 Complexed with Hg, Crystal of the Apoenzyme Soaked For 5 Min. in 5 Mm HGCL2 at 278 K. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Hg1467
b:83.4
occ:0.10
|
NE2
|
A:HIS303
|
1.2
|
64.2
|
1.0
|
SD
|
A:MET296
|
1.4
|
90.4
|
1.0
|
CD2
|
A:HIS303
|
2.0
|
80.6
|
1.0
|
CE1
|
A:HIS303
|
2.3
|
66.5
|
1.0
|
SD
|
A:MET301
|
2.4
|
0.6
|
1.0
|
CE
|
A:MET301
|
2.8
|
82.5
|
1.0
|
CG
|
A:MET296
|
2.9
|
58.0
|
1.0
|
CG
|
A:HIS303
|
3.1
|
85.7
|
1.0
|
ND1
|
A:HIS303
|
3.2
|
85.1
|
1.0
|
SD
|
A:MET305
|
3.3
|
44.5
|
1.0
|
CG
|
A:MET305
|
3.6
|
43.6
|
1.0
|
CE
|
A:MET296
|
3.9
|
56.0
|
1.0
|
CB
|
A:MET296
|
3.9
|
34.7
|
1.0
|
CG
|
A:MET301
|
4.2
|
90.9
|
1.0
|
CE
|
A:MET305
|
4.2
|
31.7
|
1.0
|
CB
|
A:HIS303
|
4.5
|
83.2
|
1.0
|
O
|
A:HIS303
|
4.6
|
44.2
|
1.0
|
CB
|
A:MET298
|
4.8
|
48.5
|
1.0
|
C
|
A:MET296
|
4.8
|
46.1
|
1.0
|
CA
|
A:MET296
|
4.9
|
38.8
|
1.0
|
O
|
A:MET296
|
4.9
|
44.1
|
1.0
|
C
|
A:HIS303
|
4.9
|
60.4
|
1.0
|
CA
|
A:HIS303
|
5.0
|
74.8
|
1.0
|
|
Reference:
H.Serrano-Posada,
S.Centeno-Leija,
S.P.Rojas-Trejo,
C.Rodriguez-Almazan,
V.Stojanoff,
E.Rudino-Pinera.
X-Ray-Induced Catalytic Active-Site Reduction of A Multicopper Oxidase: Structural Insights Into the Proton- Relay Mechanism and O2-Reduction States. Acta Crystallogr.,Sect.D V. 71 2396 2015.
ISSN: ISSN 0907-4449
PubMed: 26627648
DOI: 10.1107/S1399004715018714
Page generated: Sun Aug 11 03:06:03 2024
|