Zinc in PDB 6gf7: Molecular Basis of Egg Coat Filament Cross-Linking: Zn-Sad Structure of the Partially Deglycosylated ZP1 Zp-N1 Domain Homodimer
Protein crystallography data
The structure of Molecular Basis of Egg Coat Filament Cross-Linking: Zn-Sad Structure of the Partially Deglycosylated ZP1 Zp-N1 Domain Homodimer, PDB code: 6gf7
was solved by
K.Nishimura,
L.Jovine,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
53.32 /
2.70
|
Space group
|
P 41 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
75.410,
75.410,
100.780,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
22.2 /
27.2
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Molecular Basis of Egg Coat Filament Cross-Linking: Zn-Sad Structure of the Partially Deglycosylated ZP1 Zp-N1 Domain Homodimer
(pdb code 6gf7). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the
Molecular Basis of Egg Coat Filament Cross-Linking: Zn-Sad Structure of the Partially Deglycosylated ZP1 Zp-N1 Domain Homodimer, PDB code: 6gf7:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
Zinc binding site 1 out
of 9 in 6gf7
Go back to
Zinc Binding Sites List in 6gf7
Zinc binding site 1 out
of 9 in the Molecular Basis of Egg Coat Filament Cross-Linking: Zn-Sad Structure of the Partially Deglycosylated ZP1 Zp-N1 Domain Homodimer
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Molecular Basis of Egg Coat Filament Cross-Linking: Zn-Sad Structure of the Partially Deglycosylated ZP1 Zp-N1 Domain Homodimer within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn202
b:84.4
occ:0.88
|
O
|
A:HOH305
|
2.2
|
70.1
|
0.4
|
O
|
A:HOH312
|
2.2
|
84.4
|
0.9
|
NE2
|
A:HIS91
|
2.2
|
70.5
|
0.6
|
NE2
|
A:HIS71
|
2.3
|
72.7
|
1.0
|
CE1
|
A:HIS71
|
3.0
|
71.6
|
1.0
|
CE1
|
A:HIS91
|
3.0
|
55.5
|
0.6
|
CD2
|
A:HIS91
|
3.3
|
66.0
|
0.6
|
O
|
A:HOH313
|
3.5
|
51.3
|
1.0
|
CD2
|
A:HIS71
|
3.5
|
50.4
|
1.0
|
SG
|
A:CYS69
|
3.7
|
85.0
|
0.6
|
CB
|
A:CYS69
|
4.0
|
68.4
|
0.6
|
CB
|
A:CYS69
|
4.0
|
68.8
|
0.4
|
NE1
|
B:TRP72
|
4.0
|
64.2
|
1.0
|
SG
|
A:CYS69
|
4.1
|
81.3
|
0.4
|
ND1
|
A:HIS91
|
4.2
|
59.0
|
0.6
|
ND1
|
A:HIS71
|
4.2
|
70.5
|
1.0
|
CG
|
A:HIS91
|
4.4
|
59.9
|
0.6
|
CG
|
A:HIS71
|
4.5
|
58.8
|
1.0
|
ND1
|
A:HIS91
|
4.6
|
57.4
|
0.4
|
CD1
|
B:TRP72
|
4.7
|
61.1
|
1.0
|
CB
|
A:CYS90
|
4.9
|
68.2
|
0.4
|
O
|
B:ASN65
|
4.9
|
100.0
|
1.0
|
|
Zinc binding site 2 out
of 9 in 6gf7
Go back to
Zinc Binding Sites List in 6gf7
Zinc binding site 2 out
of 9 in the Molecular Basis of Egg Coat Filament Cross-Linking: Zn-Sad Structure of the Partially Deglycosylated ZP1 Zp-N1 Domain Homodimer
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Molecular Basis of Egg Coat Filament Cross-Linking: Zn-Sad Structure of the Partially Deglycosylated ZP1 Zp-N1 Domain Homodimer within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn203
b:65.1
occ:1.00
|
OD2
|
A:ASP31
|
2.0
|
67.1
|
1.0
|
NE2
|
A:HIS29
|
2.0
|
56.5
|
1.0
|
O
|
A:HOH315
|
2.2
|
65.1
|
1.0
|
O
|
A:HOH314
|
2.2
|
65.1
|
1.0
|
CG
|
A:ASP31
|
2.7
|
67.3
|
1.0
|
OD1
|
A:ASP31
|
2.8
|
57.5
|
1.0
|
CD2
|
A:HIS29
|
3.0
|
53.1
|
1.0
|
CE1
|
A:HIS29
|
3.0
|
57.0
|
1.0
|
CD1
|
A:LEU40
|
3.7
|
80.3
|
1.0
|
ND1
|
A:HIS29
|
4.1
|
58.3
|
1.0
|
CG
|
A:HIS29
|
4.1
|
43.6
|
1.0
|
CB
|
A:ASP31
|
4.2
|
49.7
|
1.0
|
CG
|
A:LEU40
|
4.7
|
50.8
|
1.0
|
|
Zinc binding site 3 out
of 9 in 6gf7
Go back to
Zinc Binding Sites List in 6gf7
Zinc binding site 3 out
of 9 in the Molecular Basis of Egg Coat Filament Cross-Linking: Zn-Sad Structure of the Partially Deglycosylated ZP1 Zp-N1 Domain Homodimer
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Molecular Basis of Egg Coat Filament Cross-Linking: Zn-Sad Structure of the Partially Deglycosylated ZP1 Zp-N1 Domain Homodimer within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn204
b:65.1
occ:0.88
|
ND1
|
A:HIS50
|
2.1
|
65.2
|
1.0
|
OE2
|
A:GLU62
|
2.1
|
82.1
|
1.0
|
O
|
A:HOH306
|
2.2
|
65.1
|
0.7
|
O
|
A:HOH304
|
2.2
|
65.1
|
0.9
|
CD
|
A:GLU62
|
2.7
|
69.4
|
1.0
|
OE1
|
A:GLU62
|
2.8
|
86.2
|
1.0
|
CE1
|
A:HIS50
|
3.0
|
56.1
|
1.0
|
CG
|
A:HIS50
|
3.1
|
56.7
|
1.0
|
O
|
A:HOH306
|
3.3
|
96.2
|
0.3
|
CB
|
A:HIS50
|
3.4
|
54.6
|
1.0
|
CG
|
A:GLU62
|
4.0
|
53.6
|
1.0
|
NE2
|
A:HIS50
|
4.2
|
55.5
|
1.0
|
CD2
|
A:HIS50
|
4.2
|
61.6
|
1.0
|
SD
|
A:MET108
|
4.3
|
81.2
|
1.0
|
OE1
|
A:GLU106
|
4.7
|
96.2
|
1.0
|
CA
|
A:HIS50
|
4.9
|
59.9
|
1.0
|
CE
|
A:LYS52
|
5.0
|
56.4
|
1.0
|
|
Zinc binding site 4 out
of 9 in 6gf7
Go back to
Zinc Binding Sites List in 6gf7
Zinc binding site 4 out
of 9 in the Molecular Basis of Egg Coat Filament Cross-Linking: Zn-Sad Structure of the Partially Deglycosylated ZP1 Zp-N1 Domain Homodimer
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Molecular Basis of Egg Coat Filament Cross-Linking: Zn-Sad Structure of the Partially Deglycosylated ZP1 Zp-N1 Domain Homodimer within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn205
b:0.3
occ:0.70
|
OE1
|
A:GLU106
|
2.2
|
96.2
|
1.0
|
OE2
|
A:GLU106
|
2.2
|
0.0
|
1.0
|
O
|
A:HOH306
|
2.2
|
96.2
|
0.3
|
O
|
A:HOH303
|
2.2
|
0.0
|
0.7
|
NZ
|
A:LYS52
|
2.3
|
91.7
|
1.0
|
CD
|
A:GLU106
|
2.5
|
89.9
|
1.0
|
CE
|
A:LYS52
|
3.2
|
56.4
|
1.0
|
O
|
A:HOH306
|
3.3
|
65.1
|
0.7
|
CG
|
A:GLU106
|
4.0
|
63.3
|
1.0
|
CG2
|
A:VAL114
|
4.1
|
62.3
|
1.0
|
CD
|
A:LYS52
|
4.3
|
67.7
|
1.0
|
CB
|
A:GLU106
|
4.8
|
64.1
|
1.0
|
|
Zinc binding site 5 out
of 9 in 6gf7
Go back to
Zinc Binding Sites List in 6gf7
Zinc binding site 5 out
of 9 in the Molecular Basis of Egg Coat Filament Cross-Linking: Zn-Sad Structure of the Partially Deglycosylated ZP1 Zp-N1 Domain Homodimer
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of Molecular Basis of Egg Coat Filament Cross-Linking: Zn-Sad Structure of the Partially Deglycosylated ZP1 Zp-N1 Domain Homodimer within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn206
b:0.1
occ:0.91
|
O
|
A:HOH308
|
2.2
|
0.1
|
0.9
|
O
|
A:HOH309
|
2.2
|
0.1
|
0.9
|
O
|
A:HOH316
|
2.2
|
0.1
|
0.9
|
OD2
|
A:ASP34
|
2.4
|
99.6
|
1.0
|
CG
|
A:ASP34
|
3.1
|
89.5
|
1.0
|
OD1
|
A:ASP34
|
3.2
|
84.5
|
1.0
|
CB
|
A:ASP34
|
4.4
|
81.8
|
1.0
|
|
Zinc binding site 6 out
of 9 in 6gf7
Go back to
Zinc Binding Sites List in 6gf7
Zinc binding site 6 out
of 9 in the Molecular Basis of Egg Coat Filament Cross-Linking: Zn-Sad Structure of the Partially Deglycosylated ZP1 Zp-N1 Domain Homodimer
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of Molecular Basis of Egg Coat Filament Cross-Linking: Zn-Sad Structure of the Partially Deglycosylated ZP1 Zp-N1 Domain Homodimer within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn202
b:85.5
occ:0.54
|
ND1
|
B:HIS71
|
2.2
|
68.3
|
1.0
|
CE1
|
B:HIS71
|
3.1
|
79.9
|
1.0
|
CG
|
B:HIS71
|
3.2
|
56.5
|
1.0
|
CD2
|
B:HIS91
|
3.3
|
85.8
|
1.0
|
O
|
B:CYS69
|
3.3
|
79.9
|
1.0
|
CB
|
B:HIS71
|
3.5
|
55.7
|
1.0
|
CB
|
B:CYS69
|
3.9
|
67.7
|
1.0
|
N
|
B:CYS90
|
4.0
|
85.2
|
1.0
|
NE2
|
B:HIS91
|
4.1
|
78.8
|
1.0
|
N
|
B:HIS91
|
4.2
|
61.5
|
1.0
|
C
|
B:CYS69
|
4.2
|
61.2
|
1.0
|
CB
|
B:CYS90
|
4.2
|
93.3
|
1.0
|
NE2
|
B:HIS71
|
4.2
|
72.7
|
1.0
|
CD2
|
B:HIS71
|
4.3
|
62.3
|
1.0
|
CG
|
B:HIS91
|
4.3
|
93.4
|
1.0
|
N
|
B:HIS71
|
4.5
|
54.3
|
1.0
|
CA
|
B:CYS90
|
4.6
|
88.7
|
1.0
|
O
|
B:MET70
|
4.6
|
64.3
|
1.0
|
CA
|
B:HIS71
|
4.6
|
57.1
|
1.0
|
C
|
B:MET70
|
4.6
|
59.7
|
1.0
|
CA
|
B:CYS69
|
4.7
|
64.8
|
1.0
|
CB
|
B:HIS91
|
4.8
|
86.9
|
1.0
|
SG
|
B:CYS69
|
4.8
|
0.3
|
1.0
|
C
|
B:GLY89
|
4.9
|
71.4
|
1.0
|
CG2
|
B:VAL53
|
4.9
|
52.6
|
1.0
|
CA
|
B:GLY89
|
4.9
|
61.2
|
1.0
|
C
|
B:CYS90
|
4.9
|
78.5
|
1.0
|
|
Zinc binding site 7 out
of 9 in 6gf7
Go back to
Zinc Binding Sites List in 6gf7
Zinc binding site 7 out
of 9 in the Molecular Basis of Egg Coat Filament Cross-Linking: Zn-Sad Structure of the Partially Deglycosylated ZP1 Zp-N1 Domain Homodimer
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 7 of Molecular Basis of Egg Coat Filament Cross-Linking: Zn-Sad Structure of the Partially Deglycosylated ZP1 Zp-N1 Domain Homodimer within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn203
b:79.5
occ:0.73
|
OD1
|
B:ASP31
|
1.9
|
79.0
|
1.0
|
O
|
B:HOH306
|
2.2
|
79.5
|
1.0
|
NE2
|
B:HIS29
|
2.2
|
77.8
|
1.0
|
CE1
|
B:HIS29
|
2.6
|
82.6
|
1.0
|
CG
|
B:ASP31
|
2.7
|
68.2
|
1.0
|
OD2
|
B:ASP31
|
2.9
|
73.0
|
1.0
|
CD2
|
B:HIS29
|
3.5
|
71.2
|
1.0
|
ZN
|
B:ZN204
|
3.8
|
0.1
|
0.9
|
ND1
|
B:HIS29
|
3.9
|
83.9
|
1.0
|
CB
|
B:ASP31
|
4.1
|
54.6
|
1.0
|
CG
|
B:HIS29
|
4.4
|
76.0
|
1.0
|
O
|
B:TYR30
|
4.5
|
61.9
|
1.0
|
CA
|
B:ASP31
|
4.7
|
66.6
|
1.0
|
|
Zinc binding site 8 out
of 9 in 6gf7
Go back to
Zinc Binding Sites List in 6gf7
Zinc binding site 8 out
of 9 in the Molecular Basis of Egg Coat Filament Cross-Linking: Zn-Sad Structure of the Partially Deglycosylated ZP1 Zp-N1 Domain Homodimer
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 8 of Molecular Basis of Egg Coat Filament Cross-Linking: Zn-Sad Structure of the Partially Deglycosylated ZP1 Zp-N1 Domain Homodimer within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn204
b:0.1
occ:0.85
|
O
|
B:HOH306
|
2.2
|
79.5
|
1.0
|
ZN
|
B:ZN203
|
3.8
|
79.5
|
0.7
|
|
Zinc binding site 9 out
of 9 in 6gf7
Go back to
Zinc Binding Sites List in 6gf7
Zinc binding site 9 out
of 9 in the Molecular Basis of Egg Coat Filament Cross-Linking: Zn-Sad Structure of the Partially Deglycosylated ZP1 Zp-N1 Domain Homodimer
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 9 of Molecular Basis of Egg Coat Filament Cross-Linking: Zn-Sad Structure of the Partially Deglycosylated ZP1 Zp-N1 Domain Homodimer within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn205
b:1.0
occ:1.00
|
O
|
B:HOH303
|
2.2
|
85.7
|
1.0
|
OE1
|
B:GLU106
|
2.2
|
0.3
|
1.0
|
ND1
|
B:HIS50
|
2.4
|
85.7
|
1.0
|
CG
|
B:HIS50
|
3.3
|
77.7
|
1.0
|
CD
|
B:GLU106
|
3.3
|
0.5
|
1.0
|
CE1
|
B:HIS50
|
3.3
|
0.4
|
1.0
|
CB
|
B:HIS50
|
3.5
|
73.2
|
1.0
|
OE2
|
B:GLU106
|
3.8
|
0.1
|
1.0
|
SD
|
B:MET108
|
4.2
|
95.4
|
1.0
|
CD2
|
B:HIS50
|
4.4
|
67.7
|
1.0
|
NE2
|
B:HIS50
|
4.4
|
93.7
|
1.0
|
CG
|
B:GLU106
|
4.5
|
0.0
|
1.0
|
CE
|
B:LYS52
|
4.6
|
0.6
|
1.0
|
CB
|
B:GLU106
|
4.7
|
0.7
|
1.0
|
NZ
|
B:LYS52
|
4.8
|
81.3
|
1.0
|
CD
|
B:LYS52
|
5.0
|
98.8
|
1.0
|
|
Reference:
K.Nishimura,
E.Dioguardi,
S.Nishio,
A.Villa,
L.Han,
T.Matsuda,
L.Jovine.
Molecular Basis of Egg Coat Cross-Linking Sheds Light on ZP1-Associated Female Infertility. Nat Commun V. 10 3086 2019.
ISSN: ESSN 2041-1723
PubMed: 31300655
DOI: 10.1038/S41467-019-10931-5
Page generated: Mon Oct 28 21:48:07 2024
|