Zinc in PDB 5b2e: N,N'-Diacetylchitobiose Deacetylase From Pyrococcus Horikoshii Complexed with Its Inhibitor Mpg (Acetate-Containing Condition)
Protein crystallography data
The structure of N,N'-Diacetylchitobiose Deacetylase From Pyrococcus Horikoshii Complexed with Its Inhibitor Mpg (Acetate-Containing Condition), PDB code: 5b2e
was solved by
T.Nakamura,
M.Niiyama,
K.Ida,
K.Uegaki,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
37.89 /
1.80
|
Space group
|
P 32 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
77.435,
77.435,
229.573,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
18.4 /
22.1
|
Zinc Binding Sites:
The binding sites of Zinc atom in the N,N'-Diacetylchitobiose Deacetylase From Pyrococcus Horikoshii Complexed with Its Inhibitor Mpg (Acetate-Containing Condition)
(pdb code 5b2e). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the
N,N'-Diacetylchitobiose Deacetylase From Pyrococcus Horikoshii Complexed with Its Inhibitor Mpg (Acetate-Containing Condition), PDB code: 5b2e:
Jump to Zinc binding site number:
1;
2;
3;
Zinc binding site 1 out
of 3 in 5b2e
Go back to
Zinc Binding Sites List in 5b2e
Zinc binding site 1 out
of 3 in the N,N'-Diacetylchitobiose Deacetylase From Pyrococcus Horikoshii Complexed with Its Inhibitor Mpg (Acetate-Containing Condition)
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of N,N'-Diacetylchitobiose Deacetylase From Pyrococcus Horikoshii Complexed with Its Inhibitor Mpg (Acetate-Containing Condition) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn301
b:18.0
occ:1.00
|
O72
|
A:MQG302
|
1.9
|
19.9
|
1.0
|
NE2
|
A:HIS155
|
2.0
|
13.3
|
1.0
|
OD2
|
A:ASP47
|
2.0
|
13.3
|
1.0
|
ND1
|
A:HIS44
|
2.0
|
19.2
|
1.0
|
CG
|
A:ASP47
|
2.7
|
19.2
|
1.0
|
CE1
|
A:HIS155
|
2.9
|
20.2
|
1.0
|
OD1
|
A:ASP47
|
2.9
|
18.6
|
1.0
|
P7
|
A:MQG302
|
3.0
|
18.1
|
1.0
|
CE1
|
A:HIS44
|
3.0
|
17.1
|
1.0
|
O71
|
A:MQG302
|
3.0
|
18.3
|
1.0
|
CD2
|
A:HIS155
|
3.1
|
16.9
|
1.0
|
CG
|
A:HIS44
|
3.1
|
14.3
|
1.0
|
CB
|
A:HIS44
|
3.5
|
15.7
|
1.0
|
CB
|
A:PRO43
|
3.9
|
14.2
|
1.0
|
NE2
|
C:HIS264
|
4.0
|
18.7
|
1.0
|
N
|
A:HIS44
|
4.0
|
17.3
|
1.0
|
ND1
|
A:HIS155
|
4.0
|
16.2
|
1.0
|
NE2
|
A:HIS44
|
4.1
|
17.2
|
1.0
|
CG
|
A:HIS155
|
4.2
|
14.6
|
1.0
|
CB
|
A:ASP47
|
4.2
|
18.1
|
1.0
|
N2
|
A:MQG302
|
4.2
|
16.6
|
1.0
|
CD2
|
A:HIS44
|
4.2
|
16.8
|
1.0
|
C2
|
A:MQG302
|
4.2
|
19.6
|
1.0
|
C8
|
A:MQG302
|
4.3
|
18.4
|
1.0
|
CE1
|
C:HIS264
|
4.4
|
20.5
|
1.0
|
CA
|
A:HIS44
|
4.4
|
17.3
|
1.0
|
O3
|
A:MQG302
|
4.4
|
18.4
|
1.0
|
CG
|
A:PRO43
|
4.5
|
16.3
|
1.0
|
CD
|
A:PRO43
|
4.7
|
17.2
|
1.0
|
OD1
|
A:ASP46
|
4.7
|
20.3
|
1.0
|
C
|
A:PRO43
|
4.8
|
15.9
|
1.0
|
CA
|
A:PRO43
|
4.9
|
16.8
|
1.0
|
C3
|
A:MQG302
|
5.0
|
16.9
|
1.0
|
|
Zinc binding site 2 out
of 3 in 5b2e
Go back to
Zinc Binding Sites List in 5b2e
Zinc binding site 2 out
of 3 in the N,N'-Diacetylchitobiose Deacetylase From Pyrococcus Horikoshii Complexed with Its Inhibitor Mpg (Acetate-Containing Condition)
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of N,N'-Diacetylchitobiose Deacetylase From Pyrococcus Horikoshii Complexed with Its Inhibitor Mpg (Acetate-Containing Condition) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn301
b:20.4
occ:1.00
|
O72
|
B:MQG302
|
1.7
|
21.4
|
1.0
|
OD2
|
B:ASP47
|
1.9
|
17.9
|
1.0
|
ND1
|
B:HIS44
|
2.1
|
21.4
|
1.0
|
NE2
|
B:HIS155
|
2.1
|
21.6
|
1.0
|
CG
|
B:ASP47
|
2.7
|
15.5
|
1.0
|
OD1
|
B:ASP47
|
2.8
|
18.2
|
1.0
|
P7
|
B:MQG302
|
2.8
|
20.8
|
1.0
|
O71
|
B:MQG302
|
2.9
|
18.6
|
1.0
|
CE1
|
B:HIS44
|
3.0
|
22.0
|
1.0
|
CE1
|
B:HIS155
|
3.1
|
17.6
|
1.0
|
CD2
|
B:HIS155
|
3.1
|
21.6
|
1.0
|
CG
|
B:HIS44
|
3.2
|
22.5
|
1.0
|
CB
|
B:HIS44
|
3.5
|
18.8
|
1.0
|
NE2
|
A:HIS264
|
4.0
|
23.5
|
1.0
|
N
|
B:HIS44
|
4.0
|
19.9
|
1.0
|
CB
|
B:PRO43
|
4.1
|
16.9
|
1.0
|
N2
|
B:MQG302
|
4.1
|
17.8
|
1.0
|
CB
|
B:ASP47
|
4.2
|
17.6
|
1.0
|
C2
|
B:MQG302
|
4.2
|
22.8
|
1.0
|
NE2
|
B:HIS44
|
4.2
|
19.6
|
1.0
|
C8
|
B:MQG302
|
4.2
|
20.8
|
1.0
|
ND1
|
B:HIS155
|
4.2
|
22.1
|
1.0
|
CG
|
B:HIS155
|
4.3
|
19.6
|
1.0
|
CD2
|
B:HIS44
|
4.3
|
22.6
|
1.0
|
CE1
|
A:HIS264
|
4.3
|
25.6
|
1.0
|
CG
|
B:PRO43
|
4.3
|
20.6
|
1.0
|
CA
|
B:HIS44
|
4.4
|
20.6
|
1.0
|
O3
|
B:MQG302
|
4.4
|
19.4
|
1.0
|
OD1
|
B:ASP46
|
4.8
|
23.5
|
1.0
|
CD
|
B:PRO43
|
4.8
|
17.1
|
1.0
|
C
|
B:PRO43
|
4.8
|
21.0
|
1.0
|
CA
|
B:PRO43
|
5.0
|
19.4
|
1.0
|
|
Zinc binding site 3 out
of 3 in 5b2e
Go back to
Zinc Binding Sites List in 5b2e
Zinc binding site 3 out
of 3 in the N,N'-Diacetylchitobiose Deacetylase From Pyrococcus Horikoshii Complexed with Its Inhibitor Mpg (Acetate-Containing Condition)
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of N,N'-Diacetylchitobiose Deacetylase From Pyrococcus Horikoshii Complexed with Its Inhibitor Mpg (Acetate-Containing Condition) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn301
b:22.7
occ:1.00
|
ND1
|
C:HIS44
|
1.9
|
16.1
|
1.0
|
NE2
|
C:HIS155
|
2.0
|
17.8
|
1.0
|
O72
|
C:MQG302
|
2.0
|
21.0
|
1.0
|
OD2
|
C:ASP47
|
2.1
|
23.1
|
1.0
|
CG
|
C:ASP47
|
2.8
|
22.8
|
1.0
|
CE1
|
C:HIS44
|
2.9
|
19.9
|
1.0
|
CE1
|
C:HIS155
|
2.9
|
19.9
|
1.0
|
O71
|
C:MQG302
|
2.9
|
22.1
|
1.0
|
OD1
|
C:ASP47
|
2.9
|
19.1
|
1.0
|
P7
|
C:MQG302
|
3.0
|
23.5
|
1.0
|
CG
|
C:HIS44
|
3.0
|
17.2
|
1.0
|
CD2
|
C:HIS155
|
3.0
|
22.2
|
1.0
|
CB
|
C:HIS44
|
3.4
|
19.2
|
1.0
|
CB
|
C:PRO43
|
3.9
|
18.0
|
1.0
|
NE2
|
B:HIS264
|
4.0
|
25.4
|
1.0
|
N
|
C:HIS44
|
4.0
|
17.9
|
1.0
|
NE2
|
C:HIS44
|
4.0
|
19.9
|
1.0
|
ND1
|
C:HIS155
|
4.1
|
19.9
|
1.0
|
CD2
|
C:HIS44
|
4.1
|
20.0
|
1.0
|
CG
|
C:HIS155
|
4.1
|
14.9
|
1.0
|
N2
|
C:MQG302
|
4.2
|
20.2
|
1.0
|
CB
|
C:ASP47
|
4.2
|
20.4
|
1.0
|
C2
|
C:MQG302
|
4.3
|
23.1
|
1.0
|
CA
|
C:HIS44
|
4.3
|
19.3
|
1.0
|
C8
|
C:MQG302
|
4.3
|
20.5
|
1.0
|
CE1
|
B:HIS264
|
4.4
|
21.4
|
1.0
|
CG
|
C:PRO43
|
4.4
|
16.9
|
1.0
|
O3
|
C:MQG302
|
4.5
|
26.1
|
1.0
|
CD
|
C:PRO43
|
4.7
|
18.0
|
1.0
|
C
|
C:PRO43
|
4.7
|
18.0
|
1.0
|
OD1
|
C:ASP46
|
4.8
|
24.8
|
1.0
|
CA
|
C:PRO43
|
4.9
|
17.9
|
1.0
|
C3
|
C:MQG302
|
4.9
|
21.1
|
1.0
|
|
Reference:
T.Nakamura,
Y.Yonezawa,
Y.Tsuchiya,
M.Niiyama,
K.Ida,
M.Oshima,
J.Morita,
K.Uegaki.
Substrate Recognition of N,N'-Diacetylchitobiose Deacetylase From Pyrococcus Horikoshii J.Struct.Biol. V. 195 286 2016.
ISSN: ESSN 1095-8657
PubMed: 27456364
DOI: 10.1016/J.JSB.2016.07.015
Page generated: Sun Oct 27 13:18:19 2024
|