Zinc in PDB 2xyb: Crystal Structure of A Fully Functional Laccase From the Ligninolytic Fungus Pycnoporus Cinnabarinus
Enzymatic activity of Crystal Structure of A Fully Functional Laccase From the Ligninolytic Fungus Pycnoporus Cinnabarinus
All present enzymatic activity of Crystal Structure of A Fully Functional Laccase From the Ligninolytic Fungus Pycnoporus Cinnabarinus:
1.10.3.2;
Protein crystallography data
The structure of Crystal Structure of A Fully Functional Laccase From the Ligninolytic Fungus Pycnoporus Cinnabarinus, PDB code: 2xyb
was solved by
K.Piontek,
T.Choinowski,
M.Antorini,
I.Herpoel-Gimbert,
D.A.Plattner,
J.C.Sigoillot,
M.Asther,
K.Winterhalter,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
72.55 /
1.75
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
145.296,
62.902,
91.416,
90.00,
126.70,
90.00
|
R / Rfree (%)
|
16.4 /
20.8
|
Other elements in 2xyb:
The structure of Crystal Structure of A Fully Functional Laccase From the Ligninolytic Fungus Pycnoporus Cinnabarinus also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the Crystal Structure of A Fully Functional Laccase From the Ligninolytic Fungus Pycnoporus Cinnabarinus
(pdb code 2xyb). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the
Crystal Structure of A Fully Functional Laccase From the Ligninolytic Fungus Pycnoporus Cinnabarinus, PDB code: 2xyb:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Zinc binding site 1 out
of 8 in 2xyb
Go back to
Zinc Binding Sites List in 2xyb
Zinc binding site 1 out
of 8 in the Crystal Structure of A Fully Functional Laccase From the Ligninolytic Fungus Pycnoporus Cinnabarinus
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 A Fully Functional Laccase From the Ligninolytic Fungus Pycnoporus Cinnabarinus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn526
b:33.2
occ:1.00
|
OXT
|
A:ACT519
|
2.0
|
27.2
|
1.0
|
O
|
A:ACT519
|
2.1
|
33.9
|
1.0
|
OD1
|
A:ASN442
|
2.1
|
33.7
|
1.0
|
O
|
A:HOH706
|
2.1
|
29.9
|
1.0
|
O
|
A:HOH740
|
2.1
|
36.7
|
1.0
|
ND1
|
A:HIS402
|
2.2
|
31.6
|
1.0
|
C
|
A:ACT519
|
2.5
|
34.9
|
1.0
|
CG
|
A:ASN442
|
3.0
|
35.8
|
1.0
|
CE1
|
A:HIS402
|
3.0
|
26.2
|
1.0
|
ND2
|
A:ASN442
|
3.2
|
41.9
|
1.0
|
CG
|
A:HIS402
|
3.2
|
29.0
|
1.0
|
CB
|
A:HIS402
|
3.6
|
26.5
|
1.0
|
O
|
A:GLU440
|
3.9
|
34.0
|
1.0
|
CA
|
A:HIS402
|
3.9
|
25.6
|
1.0
|
O
|
A:GLY401
|
3.9
|
27.3
|
1.0
|
CH3
|
A:ACT519
|
4.0
|
35.8
|
1.0
|
NE2
|
A:HIS402
|
4.2
|
27.6
|
1.0
|
O
|
A:HOH656
|
4.2
|
52.7
|
1.0
|
O
|
A:HOH1058
|
4.3
|
39.8
|
1.0
|
CD2
|
A:HIS402
|
4.3
|
28.8
|
1.0
|
O
|
A:HOH856
|
4.4
|
32.1
|
1.0
|
CB
|
A:ASN442
|
4.5
|
31.7
|
1.0
|
N
|
A:ASN442
|
4.7
|
28.8
|
1.0
|
CB
|
A:ASN443
|
4.7
|
29.7
|
1.0
|
N
|
A:ALA403
|
4.7
|
25.2
|
1.0
|
C
|
A:GLY401
|
4.8
|
25.8
|
1.0
|
N
|
A:HIS402
|
4.8
|
26.8
|
1.0
|
C
|
A:HIS402
|
4.9
|
25.9
|
1.0
|
CA
|
A:ASN442
|
5.0
|
25.4
|
1.0
|
O
|
A:ALA403
|
5.0
|
29.8
|
1.0
|
|
Zinc binding site 2 out
of 8 in 2xyb
Go back to
Zinc Binding Sites List in 2xyb
Zinc binding site 2 out
of 8 in the Crystal Structure of A Fully Functional Laccase From the Ligninolytic Fungus Pycnoporus Cinnabarinus
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 A Fully Functional Laccase From the Ligninolytic Fungus Pycnoporus Cinnabarinus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn527
b:38.2
occ:1.00
|
O
|
A:HOH639
|
2.0
|
34.8
|
1.0
|
OE2
|
A:GLU23
|
2.1
|
37.3
|
1.0
|
O
|
A:HOH633
|
2.3
|
28.4
|
1.0
|
CD
|
A:GLU23
|
3.1
|
31.8
|
1.0
|
OE1
|
A:GLU23
|
3.4
|
31.0
|
1.0
|
O
|
A:HOH946
|
4.3
|
30.2
|
1.0
|
O7
|
A:NAG506
|
4.4
|
37.9
|
1.0
|
CG
|
A:GLU23
|
4.4
|
33.0
|
1.0
|
CG
|
A:GLN14
|
4.5
|
37.4
|
1.0
|
O
|
A:HOH1250
|
4.6
|
63.3
|
1.0
|
N
|
A:GLN14
|
4.7
|
25.3
|
1.0
|
CB
|
A:GLN14
|
4.8
|
32.7
|
1.0
|
|
Zinc binding site 3 out
of 8 in 2xyb
Go back to
Zinc Binding Sites List in 2xyb
Zinc binding site 3 out
of 8 in the Crystal Structure of A Fully Functional Laccase From the Ligninolytic Fungus Pycnoporus Cinnabarinus
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 A Fully Functional Laccase From the Ligninolytic Fungus Pycnoporus Cinnabarinus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn528
b:42.3
occ:1.00
|
O3
|
A:SO4521
|
1.9
|
63.4
|
1.0
|
OD2
|
A:ASP471
|
2.0
|
36.2
|
1.0
|
OD2
|
A:ASP468
|
2.0
|
36.9
|
1.0
|
O
|
A:HOH1062
|
2.2
|
53.3
|
1.0
|
S
|
A:SO4521
|
2.9
|
70.2
|
1.0
|
CG
|
A:ASP468
|
2.9
|
38.6
|
1.0
|
CG
|
A:ASP471
|
2.9
|
36.2
|
1.0
|
OD1
|
A:ASP468
|
3.1
|
38.0
|
1.0
|
O1
|
A:SO4521
|
3.2
|
72.3
|
1.0
|
CB
|
A:ASP471
|
3.2
|
29.6
|
1.0
|
O4
|
A:SO4521
|
3.3
|
73.5
|
1.0
|
O
|
A:HOH670
|
4.0
|
51.4
|
1.0
|
OD1
|
A:ASP471
|
4.1
|
35.5
|
1.0
|
O2
|
A:SO4521
|
4.2
|
70.1
|
1.0
|
CB
|
A:SER376
|
4.2
|
41.0
|
1.0
|
CB
|
A:ASP468
|
4.3
|
35.8
|
1.0
|
OG
|
A:SER376
|
4.3
|
44.1
|
1.0
|
O
|
A:HOH1084
|
4.4
|
53.7
|
1.0
|
CG
|
A:PRO444
|
4.6
|
30.6
|
1.0
|
CA
|
A:ASP471
|
4.7
|
32.0
|
1.0
|
|
Zinc binding site 4 out
of 8 in 2xyb
Go back to
Zinc Binding Sites List in 2xyb
Zinc binding site 4 out
of 8 in the Crystal Structure of A Fully Functional Laccase From the Ligninolytic Fungus Pycnoporus Cinnabarinus
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 A Fully Functional Laccase From the Ligninolytic Fungus Pycnoporus Cinnabarinus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn529
b:61.5
occ:1.00
|
OE1
|
A:GLU368
|
2.1
|
58.6
|
1.0
|
O
|
A:HOH1036
|
2.1
|
58.1
|
1.0
|
O
|
A:HOH624
|
2.2
|
48.2
|
1.0
|
NE2
|
A:HIS342
|
2.2
|
41.9
|
1.0
|
O
|
A:HOH1071
|
2.7
|
63.3
|
1.0
|
CD
|
A:GLU368
|
2.9
|
57.6
|
1.0
|
CD2
|
A:HIS342
|
3.0
|
38.0
|
1.0
|
OE2
|
A:GLU368
|
3.1
|
62.8
|
1.0
|
CE1
|
A:HIS342
|
3.2
|
40.7
|
1.0
|
CG
|
A:HIS342
|
4.2
|
37.5
|
1.0
|
O
|
A:GLU368
|
4.3
|
40.0
|
1.0
|
ND1
|
A:HIS342
|
4.3
|
39.2
|
1.0
|
CG
|
A:GLU368
|
4.4
|
52.0
|
1.0
|
C
|
A:GLU368
|
4.7
|
37.1
|
1.0
|
CA
|
A:GLY369
|
4.8
|
34.8
|
1.0
|
CB
|
A:GLU368
|
5.0
|
46.5
|
1.0
|
|
Zinc binding site 5 out
of 8 in 2xyb
Go back to
Zinc Binding Sites List in 2xyb
Zinc binding site 5 out
of 8 in the Crystal Structure of A Fully Functional Laccase From the Ligninolytic Fungus Pycnoporus Cinnabarinus
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 A Fully Functional Laccase From the Ligninolytic Fungus Pycnoporus Cinnabarinus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn530
b:53.4
occ:1.00
|
O
|
A:HOH817
|
2.1
|
49.3
|
1.0
|
NE2
|
A:HIS306
|
2.2
|
36.0
|
1.0
|
O
|
A:HOH1077
|
2.3
|
57.1
|
1.0
|
O
|
A:HOH1086
|
2.4
|
56.1
|
1.0
|
O
|
A:HOH1156
|
2.7
|
69.6
|
1.0
|
O
|
A:HOH664
|
2.9
|
41.9
|
1.0
|
CD2
|
A:HIS306
|
3.0
|
34.8
|
1.0
|
CE1
|
A:HIS306
|
3.2
|
33.8
|
1.0
|
CG
|
A:HIS306
|
4.2
|
35.1
|
1.0
|
O
|
A:VAL303
|
4.2
|
31.4
|
1.0
|
ND1
|
A:HIS306
|
4.3
|
36.7
|
1.0
|
O
|
A:ASP304
|
4.4
|
28.3
|
1.0
|
CA
|
A:ASP304
|
4.4
|
27.1
|
1.0
|
C
|
A:ASP304
|
4.7
|
29.4
|
1.0
|
O
|
A:HOH1239
|
4.9
|
57.9
|
1.0
|
OD1
|
A:ASP304
|
5.0
|
37.4
|
1.0
|
|
Zinc binding site 6 out
of 8 in 2xyb
Go back to
Zinc Binding Sites List in 2xyb
Zinc binding site 6 out
of 8 in the Crystal Structure of A Fully Functional Laccase From the Ligninolytic Fungus Pycnoporus Cinnabarinus
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 A Fully Functional Laccase From the Ligninolytic Fungus Pycnoporus Cinnabarinus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn531
b:54.5
occ:1.00
|
O
|
A:HOH1064
|
2.1
|
40.9
|
1.0
|
NE2
|
A:HIS91
|
2.2
|
42.6
|
1.0
|
O
|
A:HOH987
|
2.2
|
47.5
|
1.0
|
O
|
A:HOH1016
|
2.2
|
53.5
|
1.0
|
O
|
A:HOH1041
|
2.3
|
49.7
|
1.0
|
O
|
A:HOH1272
|
2.7
|
55.3
|
1.0
|
CE1
|
A:HIS91
|
3.1
|
37.2
|
1.0
|
CD2
|
A:HIS91
|
3.1
|
40.0
|
1.0
|
O
|
A:HOH1035
|
4.1
|
54.2
|
1.0
|
O
|
A:HOH846
|
4.2
|
42.4
|
1.0
|
ND1
|
A:HIS91
|
4.2
|
39.7
|
1.0
|
CG
|
A:HIS91
|
4.3
|
36.3
|
1.0
|
O
|
A:SER89
|
4.5
|
32.2
|
1.0
|
O
|
A:HOH826
|
4.8
|
38.2
|
1.0
|
CG2
|
A:ILE488
|
4.8
|
29.1
|
1.0
|
|
Zinc binding site 7 out
of 8 in 2xyb
Go back to
Zinc Binding Sites List in 2xyb
Zinc binding site 7 out
of 8 in the Crystal Structure of A Fully Functional Laccase From the Ligninolytic Fungus Pycnoporus Cinnabarinus
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 7 of Crystal Structure of A Fully Functional Laccase From the Ligninolytic Fungus Pycnoporus Cinnabarinus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn532
b:63.7
occ:1.00
|
NE2
|
A:HIS55
|
2.2
|
43.4
|
1.0
|
O
|
A:HOH1054
|
2.3
|
52.9
|
1.0
|
O
|
A:HOH1125
|
2.4
|
63.5
|
1.0
|
O
|
A:HOH1255
|
2.6
|
71.2
|
1.0
|
O
|
A:HOH849
|
2.7
|
48.9
|
1.0
|
CE1
|
A:HIS55
|
3.1
|
36.2
|
1.0
|
CD2
|
A:HIS55
|
3.2
|
36.2
|
1.0
|
O
|
A:HOH1117
|
4.0
|
63.0
|
1.0
|
O
|
A:PRO494
|
4.1
|
48.2
|
1.0
|
ND1
|
A:HIS55
|
4.2
|
33.6
|
1.0
|
CG
|
A:HIS55
|
4.3
|
33.6
|
1.0
|
O
|
A:HOH753
|
4.5
|
49.3
|
1.0
|
C
|
A:PRO494
|
4.9
|
49.0
|
1.0
|
O
|
A:HOH1261
|
5.0
|
61.0
|
1.0
|
|
Zinc binding site 8 out
of 8 in 2xyb
Go back to
Zinc Binding Sites List in 2xyb
Zinc binding site 8 out
of 8 in the Crystal Structure of A Fully Functional Laccase From the Ligninolytic Fungus Pycnoporus Cinnabarinus
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 8 of Crystal Structure of A Fully Functional Laccase From the Ligninolytic Fungus Pycnoporus Cinnabarinus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn533
b:84.9
occ:1.00
|
O
|
A:HOH1060
|
2.1
|
69.8
|
1.0
|
OD2
|
A:ASP418
|
2.1
|
60.6
|
1.0
|
O
|
A:HOH995
|
2.7
|
55.6
|
1.0
|
CG
|
A:ASP418
|
2.9
|
47.5
|
1.0
|
O
|
A:HOH1094
|
3.0
|
73.9
|
1.0
|
OD1
|
A:ASP418
|
3.0
|
47.3
|
1.0
|
O
|
A:HOH1099
|
4.2
|
47.4
|
1.0
|
CB
|
A:ASP418
|
4.3
|
41.7
|
1.0
|
|
Reference:
K.Piontek,
T.Choinowski,
M.Antorini,
I.Herpoel-Gimbert,
M.Asther,
D.A.Plattner.
Substrate Binding and Copper Geometry in Laccases To Be Published.
Page generated: Thu Oct 17 05:35:32 2024
|