Zinc in PDB 9f41: Crystal Structure of the Ntd Domain From S. Cerevisia Niemann-Pick Type C Protein NCR1 with Cholesterol Bound
Protein crystallography data
The structure of Crystal Structure of the Ntd Domain From S. Cerevisia Niemann-Pick Type C Protein NCR1 with Cholesterol Bound, PDB code: 9f41
was solved by
L.Nel,
E.Olesen,
K.M.Frain,
B.P.Pedersen,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
47.14 /
2.64
|
Space group
|
P 21 2 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
92.03,
109.78,
151.36,
90,
90,
90
|
R / Rfree (%)
|
22.6 /
26
|
Zinc Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
20;
Page 3, Binding sites: 21 -
26;
Binding sites:
The binding sites of Zinc atom in the Crystal Structure of the Ntd Domain From S. Cerevisia Niemann-Pick Type C Protein NCR1 with Cholesterol Bound
(pdb code 9f41). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 26 binding sites of Zinc where determined in the
Crystal Structure of the Ntd Domain From S. Cerevisia Niemann-Pick Type C Protein NCR1 with Cholesterol Bound, PDB code: 9f41:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Zinc binding site 1 out
of 26 in 9f41
Go back to
Zinc Binding Sites List in 9f41
Zinc binding site 1 out
of 26 in the Crystal Structure of the Ntd Domain From S. Cerevisia Niemann-Pick Type C Protein NCR1 with Cholesterol Bound
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 the Ntd Domain From S. Cerevisia Niemann-Pick Type C Protein NCR1 with Cholesterol Bound within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn302
b:85.3
occ:1.00
|
OD2
|
A:ASP218
|
1.9
|
78.8
|
1.0
|
OD1
|
A:ASN107
|
2.2
|
92.2
|
1.0
|
NE2
|
A:HIS111
|
2.3
|
75.9
|
1.0
|
OE1
|
A:GLU67
|
2.6
|
109.8
|
1.0
|
OE2
|
A:GLU67
|
2.7
|
126.8
|
1.0
|
CG
|
A:ASN107
|
2.9
|
76.5
|
1.0
|
ND2
|
A:ASN107
|
3.0
|
71.0
|
1.0
|
CD
|
A:GLU67
|
3.0
|
121.6
|
1.0
|
O
|
A:HOH403
|
3.1
|
86.2
|
1.0
|
CG
|
A:ASP218
|
3.1
|
81.8
|
1.0
|
CD2
|
A:HIS111
|
3.2
|
64.8
|
1.0
|
CE1
|
A:HIS111
|
3.3
|
78.3
|
1.0
|
OD1
|
A:ASP218
|
3.6
|
92.2
|
1.0
|
CB
|
A:ASP218
|
4.3
|
73.6
|
1.0
|
ND1
|
A:HIS111
|
4.3
|
71.5
|
1.0
|
CG
|
A:HIS111
|
4.3
|
67.9
|
1.0
|
CB
|
A:ASN107
|
4.4
|
65.6
|
1.0
|
CG
|
A:GLU67
|
4.5
|
114.4
|
1.0
|
NZ
|
A:LYS103
|
4.8
|
89.0
|
1.0
|
|
Zinc binding site 2 out
of 26 in 9f41
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Zinc Binding Sites List in 9f41
Zinc binding site 2 out
of 26 in the Crystal Structure of the Ntd Domain From S. Cerevisia Niemann-Pick Type C Protein NCR1 with Cholesterol Bound
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 the Ntd Domain From S. Cerevisia Niemann-Pick Type C Protein NCR1 with Cholesterol Bound within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn310
b:121.2
occ:1.00
|
OE2
|
A:GLU139
|
2.3
|
94.0
|
1.0
|
CD
|
A:GLU139
|
3.2
|
79.5
|
1.0
|
OE1
|
A:GLU139
|
3.4
|
91.3
|
1.0
|
ND2
|
A:ASN201
|
3.6
|
71.6
|
1.0
|
CG
|
A:ASN201
|
4.4
|
62.2
|
1.0
|
OD1
|
A:ASN201
|
4.5
|
63.9
|
1.0
|
CG
|
A:GLU139
|
4.5
|
71.7
|
1.0
|
CG
|
A:GLN199
|
4.8
|
59.5
|
1.0
|
|
Zinc binding site 3 out
of 26 in 9f41
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Zinc Binding Sites List in 9f41
Zinc binding site 3 out
of 26 in the Crystal Structure of the Ntd Domain From S. Cerevisia Niemann-Pick Type C Protein NCR1 with Cholesterol Bound
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 the Ntd Domain From S. Cerevisia Niemann-Pick Type C Protein NCR1 with Cholesterol Bound within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn311
b:178.1
occ:1.00
|
OE1
|
A:GLU70
|
3.6
|
165.1
|
1.0
|
CD
|
A:GLU70
|
3.7
|
146.8
|
1.0
|
OE2
|
A:GLU70
|
4.0
|
156.3
|
1.0
|
CG
|
A:GLU70
|
4.3
|
120.1
|
1.0
|
|
Zinc binding site 4 out
of 26 in 9f41
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Zinc Binding Sites List in 9f41
Zinc binding site 4 out
of 26 in the Crystal Structure of the Ntd Domain From S. Cerevisia Niemann-Pick Type C Protein NCR1 with Cholesterol Bound
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 the Ntd Domain From S. Cerevisia Niemann-Pick Type C Protein NCR1 with Cholesterol Bound within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn312
b:110.7
occ:1.00
|
OE2
|
A:GLU215
|
2.5
|
87.3
|
1.0
|
OE1
|
A:GLU215
|
2.9
|
70.7
|
1.0
|
CD
|
A:GLU215
|
3.1
|
73.0
|
1.0
|
O
|
A:TYR204
|
3.3
|
81.3
|
1.0
|
O2
|
A:SO4309
|
3.4
|
139.8
|
1.0
|
OG
|
A:SER146
|
3.9
|
82.4
|
1.0
|
O
|
A:MET144
|
3.9
|
63.0
|
1.0
|
N
|
A:SER146
|
3.9
|
76.5
|
1.0
|
C
|
A:TYR204
|
4.2
|
78.3
|
1.0
|
CA
|
A:ASN145
|
4.4
|
67.8
|
1.0
|
CB
|
A:SER146
|
4.5
|
70.7
|
1.0
|
CG
|
A:GLU215
|
4.6
|
67.9
|
1.0
|
S
|
A:SO4309
|
4.6
|
177.1
|
1.0
|
O1
|
A:SO4309
|
4.7
|
151.0
|
1.0
|
CA
|
A:TYR204
|
4.7
|
69.7
|
1.0
|
C
|
A:ASN145
|
4.7
|
69.4
|
1.0
|
C8
|
F:NAG1
|
4.8
|
100.3
|
1.0
|
CA
|
A:SER146
|
4.9
|
70.5
|
1.0
|
C
|
A:MET144
|
4.9
|
62.3
|
1.0
|
CB
|
A:TYR204
|
5.0
|
68.5
|
1.0
|
|
Zinc binding site 5 out
of 26 in 9f41
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Zinc Binding Sites List in 9f41
Zinc binding site 5 out
of 26 in the Crystal Structure of the Ntd Domain From S. Cerevisia Niemann-Pick Type C Protein NCR1 with Cholesterol Bound
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 the Ntd Domain From S. Cerevisia Niemann-Pick Type C Protein NCR1 with Cholesterol Bound within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn302
b:104.8
occ:1.00
|
OD2
|
B:ASP218
|
1.9
|
87.1
|
1.0
|
CE1
|
B:HIS111
|
2.1
|
105.7
|
1.0
|
NE2
|
B:HIS111
|
2.3
|
106.0
|
1.0
|
OD1
|
B:ASN107
|
2.4
|
98.6
|
1.0
|
OE2
|
B:GLU67
|
2.5
|
119.2
|
1.0
|
O
|
B:HOH401
|
2.7
|
93.0
|
1.0
|
ND2
|
B:ASN107
|
2.8
|
90.3
|
1.0
|
OE1
|
B:GLU67
|
3.0
|
104.8
|
1.0
|
CG
|
B:ASN107
|
3.0
|
92.7
|
1.0
|
CG
|
B:ASP218
|
3.0
|
95.9
|
1.0
|
CD
|
B:GLU67
|
3.1
|
113.5
|
1.0
|
ND1
|
B:HIS111
|
3.3
|
98.6
|
1.0
|
CD2
|
B:HIS111
|
3.6
|
88.6
|
1.0
|
OD1
|
B:ASP218
|
3.6
|
97.3
|
1.0
|
CG
|
B:HIS111
|
4.1
|
89.0
|
1.0
|
CB
|
B:ASP218
|
4.2
|
88.0
|
1.0
|
CB
|
B:ASN107
|
4.5
|
83.3
|
1.0
|
CG
|
B:GLU67
|
4.5
|
104.9
|
1.0
|
O
|
B:HOH426
|
4.6
|
88.2
|
1.0
|
NZ
|
B:LYS103
|
4.9
|
96.2
|
1.0
|
O
|
B:ASN107
|
5.0
|
85.6
|
1.0
|
|
Zinc binding site 6 out
of 26 in 9f41
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Zinc Binding Sites List in 9f41
Zinc binding site 6 out
of 26 in the Crystal Structure of the Ntd Domain From S. Cerevisia Niemann-Pick Type C Protein NCR1 with Cholesterol Bound
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 the Ntd Domain From S. Cerevisia Niemann-Pick Type C Protein NCR1 with Cholesterol Bound within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn303
b:66.8
occ:1.00
|
OE1
|
B:GLU210
|
2.0
|
73.8
|
1.0
|
OE2
|
B:GLU212
|
2.0
|
68.7
|
1.0
|
OE2
|
A:GLU212
|
2.0
|
72.8
|
1.0
|
OE1
|
A:GLU210
|
2.1
|
77.3
|
1.0
|
CD
|
B:GLU210
|
2.7
|
73.8
|
1.0
|
CD
|
A:GLU210
|
2.8
|
79.0
|
1.0
|
OE2
|
B:GLU210
|
2.8
|
75.4
|
1.0
|
OE2
|
A:GLU210
|
2.8
|
83.6
|
1.0
|
CD
|
B:GLU212
|
3.0
|
65.0
|
1.0
|
CD
|
A:GLU212
|
3.1
|
71.2
|
1.0
|
CG
|
B:GLU212
|
3.3
|
64.8
|
1.0
|
CG
|
A:GLU212
|
3.5
|
66.7
|
1.0
|
CD1
|
B:TRP213
|
3.9
|
65.0
|
1.0
|
NE1
|
B:TRP213
|
3.9
|
65.1
|
1.0
|
NE1
|
A:TRP213
|
4.0
|
62.0
|
1.0
|
OE1
|
B:GLU212
|
4.1
|
64.9
|
1.0
|
CD1
|
A:TRP213
|
4.1
|
61.5
|
1.0
|
OE1
|
A:GLU212
|
4.2
|
75.8
|
1.0
|
CG
|
B:GLU210
|
4.2
|
78.1
|
1.0
|
CG
|
A:GLU210
|
4.3
|
74.9
|
1.0
|
CB
|
B:GLU210
|
4.7
|
78.2
|
1.0
|
CB
|
A:GLU210
|
4.8
|
73.8
|
1.0
|
CB
|
B:GLU212
|
4.8
|
64.2
|
1.0
|
CA
|
B:GLU210
|
4.9
|
84.7
|
1.0
|
|
Zinc binding site 7 out
of 26 in 9f41
Go back to
Zinc Binding Sites List in 9f41
Zinc binding site 7 out
of 26 in the Crystal Structure of the Ntd Domain From S. Cerevisia Niemann-Pick Type C Protein NCR1 with Cholesterol Bound
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 the Ntd Domain From S. Cerevisia Niemann-Pick Type C Protein NCR1 with Cholesterol Bound within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn304
b:100.0
occ:1.00
|
OE2
|
B:GLU151
|
2.1
|
82.4
|
1.0
|
OD2
|
B:ASP154
|
2.6
|
120.2
|
1.0
|
OE1
|
B:GLU151
|
2.7
|
87.8
|
1.0
|
CD
|
B:GLU151
|
2.7
|
92.7
|
1.0
|
CG
|
B:ASP154
|
3.4
|
110.4
|
1.0
|
OE2
|
B:GLU237
|
3.8
|
101.5
|
1.0
|
ZN
|
B:ZN305
|
4.1
|
100.0
|
1.0
|
OD1
|
B:ASP154
|
4.1
|
117.5
|
1.0
|
CG
|
B:GLU151
|
4.2
|
90.5
|
1.0
|
CB
|
B:ASP154
|
4.2
|
97.0
|
1.0
|
CB
|
B:ALA222
|
4.4
|
88.1
|
1.0
|
CD
|
B:GLU237
|
4.8
|
106.7
|
1.0
|
|
Zinc binding site 8 out
of 26 in 9f41
Go back to
Zinc Binding Sites List in 9f41
Zinc binding site 8 out
of 26 in the Crystal Structure of the Ntd Domain From S. Cerevisia Niemann-Pick Type C Protein NCR1 with Cholesterol Bound
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 the Ntd Domain From S. Cerevisia Niemann-Pick Type C Protein NCR1 with Cholesterol Bound within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn305
b:100.0
occ:1.00
|
OE2
|
B:GLU237
|
2.0
|
101.5
|
1.0
|
OD1
|
B:ASP154
|
2.3
|
117.5
|
1.0
|
OD2
|
B:ASP154
|
2.7
|
120.2
|
1.0
|
CG
|
B:ASP154
|
2.8
|
110.4
|
1.0
|
CD
|
B:GLU237
|
2.9
|
106.7
|
1.0
|
OE1
|
B:GLU237
|
3.3
|
107.6
|
1.0
|
NZ
|
B:LYS157
|
4.0
|
88.0
|
1.0
|
CE
|
B:LYS157
|
4.1
|
81.7
|
1.0
|
O
|
B:ASP154
|
4.1
|
105.4
|
1.0
|
ZN
|
B:ZN304
|
4.1
|
100.0
|
1.0
|
CG
|
B:GLU237
|
4.3
|
104.6
|
1.0
|
CB
|
B:ASP154
|
4.3
|
97.0
|
1.0
|
C
|
B:ASP154
|
4.9
|
95.2
|
1.0
|
CA
|
B:ASP154
|
4.9
|
95.0
|
1.0
|
|
Zinc binding site 9 out
of 26 in 9f41
Go back to
Zinc Binding Sites List in 9f41
Zinc binding site 9 out
of 26 in the Crystal Structure of the Ntd Domain From S. Cerevisia Niemann-Pick Type C Protein NCR1 with Cholesterol Bound
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 9 of Crystal Structure of the Ntd Domain From S. Cerevisia Niemann-Pick Type C Protein NCR1 with Cholesterol Bound within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn306
b:82.3
occ:1.00
|
O2
|
B:SO4307
|
2.0
|
85.3
|
1.0
|
OD2
|
B:ASP79
|
2.0
|
82.7
|
1.0
|
OE2
|
B:GLU38
|
2.3
|
93.4
|
1.0
|
OE1
|
B:GLU38
|
2.4
|
80.9
|
1.0
|
CD
|
B:GLU38
|
2.7
|
87.2
|
1.0
|
CG
|
B:ASP79
|
3.0
|
79.7
|
1.0
|
S
|
B:SO4307
|
3.1
|
79.7
|
1.0
|
O1
|
B:SO4307
|
3.3
|
83.8
|
1.0
|
CB
|
B:ASP79
|
3.4
|
72.4
|
1.0
|
O4
|
B:SO4307
|
3.9
|
83.6
|
1.0
|
ND2
|
B:ASN28
|
3.9
|
78.1
|
1.0
|
OD1
|
B:ASP79
|
4.1
|
78.7
|
1.0
|
CG
|
B:GLU38
|
4.2
|
87.2
|
1.0
|
O3
|
B:SO4307
|
4.2
|
85.4
|
1.0
|
CB
|
B:ASN28
|
4.4
|
75.2
|
1.0
|
CG
|
B:ASN28
|
4.6
|
77.3
|
1.0
|
CA
|
B:ASP79
|
4.9
|
69.8
|
1.0
|
|
Zinc binding site 10 out
of 26 in 9f41
Go back to
Zinc Binding Sites List in 9f41
Zinc binding site 10 out
of 26 in the Crystal Structure of the Ntd Domain From S. Cerevisia Niemann-Pick Type C Protein NCR1 with Cholesterol Bound
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 10 of Crystal Structure of the Ntd Domain From S. Cerevisia Niemann-Pick Type C Protein NCR1 with Cholesterol Bound within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn309
b:135.8
occ:1.00
|
OE2
|
B:GLU139
|
2.4
|
106.3
|
1.0
|
CD
|
B:GLU139
|
3.2
|
86.7
|
1.0
|
OE1
|
B:GLU139
|
3.4
|
96.0
|
1.0
|
ND2
|
B:ASN201
|
3.7
|
92.4
|
1.0
|
OD1
|
B:ASN201
|
4.5
|
75.2
|
1.0
|
CG
|
B:ASN201
|
4.5
|
70.3
|
1.0
|
CG
|
B:GLU139
|
4.6
|
75.3
|
1.0
|
CG
|
B:GLN199
|
4.6
|
67.7
|
1.0
|
|
Reference:
D.Jamecna,
K.Thaysen,
L.Nel,
E.Olesen,
M.Szomek,
K.M.Frain,
J.Langer,
B.P.Pedersen,
D.Wustner,
D.Hoglinger.
Structural and Biochemical Analysis of Ligand Binding in Yeast Niemann-Pick Type C 1-Related Protein To Be Published.
Page generated: Thu Oct 31 15:31:12 2024
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