Zinc in PDB 9h2a: Acmnpv Complete Basal Cap
Zinc Binding Sites:
The binding sites of Zinc atom in the Acmnpv Complete Basal Cap
(pdb code 9h2a). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the
Acmnpv Complete Basal Cap, PDB code: 9h2a:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Zinc binding site 1 out
of 8 in 9h2a
Go back to
Zinc Binding Sites List in 9h2a
Zinc binding site 1 out
of 8 in the Acmnpv Complete Basal Cap
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Acmnpv Complete Basal Cap within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Zn401
b:341.4
occ:1.00
|
NE2
|
G:HIS52
|
2.1
|
267.5
|
1.0
|
|
SG
|
G:CYS36
|
2.3
|
290.4
|
1.0
|
|
SG
|
G:CYS18
|
2.3
|
279.9
|
1.0
|
|
SG
|
G:CYS49
|
2.3
|
272.6
|
1.0
|
|
CB
|
G:CYS36
|
2.5
|
290.4
|
1.0
|
|
CD2
|
G:HIS52
|
2.8
|
267.5
|
1.0
|
|
CB
|
G:CYS49
|
3.0
|
272.6
|
1.0
|
|
CA
|
G:CYS36
|
3.0
|
290.4
|
1.0
|
|
CE1
|
G:HIS52
|
3.1
|
267.5
|
1.0
|
|
CB
|
G:CYS18
|
3.5
|
279.9
|
1.0
|
|
CG
|
G:HIS52
|
3.9
|
267.5
|
1.0
|
|
C
|
G:CYS36
|
3.9
|
290.4
|
1.0
|
|
N
|
G:SER37
|
3.9
|
270.0
|
1.0
|
|
ND1
|
G:HIS52
|
4.0
|
267.5
|
1.0
|
|
ND2
|
G:ASN16
|
4.2
|
269.4
|
1.0
|
|
CB
|
G:ALA40
|
4.2
|
274.5
|
1.0
|
|
N
|
G:CYS36
|
4.2
|
290.4
|
1.0
|
|
CA
|
G:CYS49
|
4.3
|
272.6
|
1.0
|
|
OD1
|
G:ASN16
|
4.3
|
269.4
|
1.0
|
|
O
|
G:PRO35
|
4.4
|
289.9
|
1.0
|
|
N
|
G:CYS49
|
4.4
|
272.6
|
1.0
|
|
CB
|
G:ALA21
|
4.4
|
284.1
|
1.0
|
|
N
|
G:ALA21
|
4.5
|
284.1
|
1.0
|
|
CA
|
G:ALA21
|
4.6
|
284.1
|
1.0
|
|
O
|
G:SER37
|
4.6
|
270.0
|
1.0
|
|
CG
|
G:ASN16
|
4.7
|
269.4
|
1.0
|
|
C
|
G:PRO35
|
4.7
|
289.9
|
1.0
|
|
CA
|
G:CYS18
|
4.9
|
279.9
|
1.0
|
|
O
|
G:CYS36
|
4.9
|
290.4
|
1.0
|
|
Zinc binding site 2 out
of 8 in 9h2a
Go back to
Zinc Binding Sites List in 9h2a
Zinc binding site 2 out
of 8 in the Acmnpv Complete Basal Cap
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Acmnpv Complete Basal Cap within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Zn401
b:277.5
occ:1.00
|
NE2
|
H:HIS52
|
2.0
|
205.5
|
1.0
|
|
SG
|
H:CYS49
|
2.3
|
204.3
|
1.0
|
|
SG
|
H:CYS18
|
2.3
|
208.3
|
1.0
|
|
SG
|
H:CYS36
|
2.3
|
216.4
|
1.0
|
|
CD2
|
H:HIS52
|
2.6
|
205.5
|
1.0
|
|
CB
|
H:CYS36
|
2.9
|
216.4
|
1.0
|
|
CB
|
H:CYS49
|
3.0
|
204.3
|
1.0
|
|
CE1
|
H:HIS52
|
3.1
|
205.5
|
1.0
|
|
CA
|
H:CYS36
|
3.2
|
216.4
|
1.0
|
|
CB
|
H:CYS18
|
3.5
|
208.3
|
1.0
|
|
CG
|
H:HIS52
|
3.8
|
205.5
|
1.0
|
|
ND1
|
H:HIS52
|
3.9
|
205.5
|
1.0
|
|
N
|
H:SER37
|
4.0
|
199.6
|
1.0
|
|
C
|
H:CYS36
|
4.1
|
216.4
|
1.0
|
|
CB
|
H:ALA40
|
4.2
|
201.1
|
1.0
|
|
O
|
H:PRO35
|
4.3
|
225.2
|
1.0
|
|
CA
|
H:CYS49
|
4.3
|
204.3
|
1.0
|
|
N
|
H:CYS36
|
4.4
|
216.4
|
1.0
|
|
N
|
H:CYS49
|
4.4
|
204.3
|
1.0
|
|
CB
|
H:ALA21
|
4.5
|
211.6
|
1.0
|
|
N
|
H:ALA21
|
4.6
|
211.6
|
1.0
|
|
O
|
H:SER37
|
4.7
|
199.6
|
1.0
|
|
CA
|
H:ALA21
|
4.7
|
211.6
|
1.0
|
|
C
|
H:PRO35
|
4.7
|
225.2
|
1.0
|
|
OD1
|
H:ASN16
|
4.8
|
203.8
|
1.0
|
|
ND2
|
H:ASN16
|
4.8
|
203.8
|
1.0
|
|
CA
|
H:CYS18
|
4.9
|
208.3
|
1.0
|
|
Zinc binding site 3 out
of 8 in 9h2a
Go back to
Zinc Binding Sites List in 9h2a
Zinc binding site 3 out
of 8 in the Acmnpv Complete Basal Cap
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Acmnpv Complete Basal Cap within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Zn401
b:367.2
occ:1.00
|
NE2
|
M:HIS52
|
2.1
|
288.1
|
1.0
|
|
SG
|
M:CYS18
|
2.3
|
291.2
|
1.0
|
|
SG
|
M:CYS49
|
2.3
|
290.6
|
1.0
|
|
SG
|
M:CYS36
|
2.3
|
307.7
|
1.0
|
|
CD2
|
M:HIS52
|
2.4
|
288.1
|
1.0
|
|
CB
|
M:CYS36
|
2.7
|
307.7
|
1.0
|
|
CA
|
M:CYS36
|
2.7
|
307.7
|
1.0
|
|
CB
|
M:CYS18
|
3.2
|
291.2
|
1.0
|
|
CE1
|
M:HIS52
|
3.2
|
288.1
|
1.0
|
|
N
|
M:SER37
|
3.4
|
290.0
|
1.0
|
|
C
|
M:CYS36
|
3.5
|
307.7
|
1.0
|
|
CG
|
M:HIS52
|
3.5
|
288.1
|
1.0
|
|
CB
|
M:CYS49
|
3.6
|
290.6
|
1.0
|
|
ND1
|
M:HIS52
|
3.9
|
288.1
|
1.0
|
|
O
|
M:PRO35
|
3.9
|
305.0
|
1.0
|
|
N
|
M:CYS36
|
3.9
|
307.7
|
1.0
|
|
C
|
M:PRO35
|
4.4
|
305.0
|
1.0
|
|
O
|
M:SER37
|
4.4
|
290.0
|
1.0
|
|
CB
|
M:ALA40
|
4.5
|
280.5
|
1.0
|
|
O
|
M:CYS36
|
4.5
|
307.7
|
1.0
|
|
CA
|
M:CYS18
|
4.6
|
291.2
|
1.0
|
|
CB
|
M:ALA21
|
4.6
|
294.5
|
1.0
|
|
CA
|
M:SER37
|
4.6
|
290.0
|
1.0
|
|
CA
|
M:CYS49
|
4.7
|
290.6
|
1.0
|
|
CB
|
M:HIS52
|
4.7
|
288.1
|
1.0
|
|
N
|
M:CYS49
|
4.7
|
290.6
|
1.0
|
|
N
|
M:HIS52
|
4.8
|
288.1
|
1.0
|
|
CB
|
M:ASN51
|
5.0
|
281.8
|
1.0
|
|
C
|
M:SER37
|
5.0
|
290.0
|
1.0
|
|
Zinc binding site 4 out
of 8 in 9h2a
Go back to
Zinc Binding Sites List in 9h2a
Zinc binding site 4 out
of 8 in the Acmnpv Complete Basal Cap
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Acmnpv Complete Basal Cap within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
N:Zn401
b:274.7
occ:1.00
|
CD2
|
N:HIS52
|
1.5
|
216.1
|
1.0
|
|
NE2
|
N:HIS52
|
2.1
|
216.1
|
1.0
|
|
SG
|
N:CYS36
|
2.3
|
225.7
|
1.0
|
|
SG
|
N:CYS49
|
2.3
|
221.8
|
1.0
|
|
SG
|
N:CYS18
|
2.3
|
222.4
|
1.0
|
|
CG
|
N:HIS52
|
2.5
|
216.1
|
1.0
|
|
CE1
|
N:HIS52
|
3.0
|
216.1
|
1.0
|
|
ND1
|
N:HIS52
|
3.2
|
216.1
|
1.0
|
|
CB
|
N:HIS52
|
3.4
|
216.1
|
1.0
|
|
CB
|
N:CYS36
|
3.5
|
225.7
|
1.0
|
|
CB
|
N:CYS49
|
3.6
|
221.8
|
1.0
|
|
N
|
N:HIS52
|
3.7
|
216.1
|
1.0
|
|
CB
|
N:CYS18
|
3.7
|
222.4
|
1.0
|
|
N
|
N:CYS49
|
3.9
|
221.8
|
1.0
|
|
O
|
N:CYS49
|
4.0
|
221.8
|
1.0
|
|
CA
|
N:CYS49
|
4.0
|
221.8
|
1.0
|
|
CA
|
N:CYS18
|
4.1
|
222.4
|
1.0
|
|
C
|
N:CYS49
|
4.1
|
221.8
|
1.0
|
|
CA
|
N:HIS52
|
4.1
|
216.1
|
1.0
|
|
N
|
N:SER37
|
4.2
|
211.8
|
1.0
|
|
OG
|
N:SER37
|
4.2
|
211.8
|
1.0
|
|
O
|
N:ILE19
|
4.3
|
211.5
|
1.0
|
|
C
|
N:CYS18
|
4.6
|
222.4
|
1.0
|
|
CA
|
N:CYS36
|
4.6
|
225.7
|
1.0
|
|
O
|
N:SER37
|
4.7
|
211.8
|
1.0
|
|
N
|
N:ASN51
|
4.7
|
205.8
|
1.0
|
|
C
|
N:CYS36
|
4.7
|
225.7
|
1.0
|
|
C
|
N:ASN51
|
4.7
|
205.8
|
1.0
|
|
N
|
N:ASN50
|
4.8
|
211.3
|
1.0
|
|
CB
|
N:ASN51
|
4.9
|
205.8
|
1.0
|
|
O
|
N:CYS18
|
5.0
|
222.4
|
1.0
|
|
CB
|
N:ALA40
|
5.0
|
209.7
|
1.0
|
|
Zinc binding site 5 out
of 8 in 9h2a
Go back to
Zinc Binding Sites List in 9h2a
Zinc binding site 5 out
of 8 in the Acmnpv Complete Basal Cap
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of Acmnpv Complete Basal Cap within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
Y:Zn401
b:341.4
occ:1.00
|
NE2
|
Y:HIS52
|
2.1
|
267.5
|
1.0
|
|
SG
|
Y:CYS36
|
2.3
|
290.4
|
1.0
|
|
SG
|
Y:CYS18
|
2.3
|
279.9
|
1.0
|
|
SG
|
Y:CYS49
|
2.3
|
272.6
|
1.0
|
|
CB
|
Y:CYS36
|
2.5
|
290.4
|
1.0
|
|
CD2
|
Y:HIS52
|
2.8
|
267.5
|
1.0
|
|
CB
|
Y:CYS49
|
3.0
|
272.6
|
1.0
|
|
CA
|
Y:CYS36
|
3.0
|
290.4
|
1.0
|
|
CE1
|
Y:HIS52
|
3.1
|
267.5
|
1.0
|
|
CB
|
Y:CYS18
|
3.5
|
279.9
|
1.0
|
|
C
|
Y:CYS36
|
3.9
|
290.4
|
1.0
|
|
CG
|
Y:HIS52
|
3.9
|
267.5
|
1.0
|
|
N
|
Y:SER37
|
3.9
|
270.0
|
1.0
|
|
ND1
|
Y:HIS52
|
4.0
|
267.5
|
1.0
|
|
ND2
|
Y:ASN16
|
4.2
|
269.4
|
1.0
|
|
CB
|
Y:ALA40
|
4.2
|
274.5
|
1.0
|
|
N
|
Y:CYS36
|
4.2
|
290.4
|
1.0
|
|
CA
|
Y:CYS49
|
4.3
|
272.6
|
1.0
|
|
OD1
|
Y:ASN16
|
4.3
|
269.4
|
1.0
|
|
O
|
Y:PRO35
|
4.4
|
289.9
|
1.0
|
|
N
|
Y:CYS49
|
4.4
|
272.6
|
1.0
|
|
CB
|
Y:ALA21
|
4.4
|
284.1
|
1.0
|
|
N
|
Y:ALA21
|
4.5
|
284.1
|
1.0
|
|
CA
|
Y:ALA21
|
4.6
|
284.1
|
1.0
|
|
O
|
Y:SER37
|
4.6
|
270.0
|
1.0
|
|
CG
|
Y:ASN16
|
4.7
|
269.4
|
1.0
|
|
C
|
Y:PRO35
|
4.7
|
289.9
|
1.0
|
|
CA
|
Y:CYS18
|
4.9
|
279.9
|
1.0
|
|
O
|
Y:CYS36
|
4.9
|
290.4
|
1.0
|
|
Zinc binding site 6 out
of 8 in 9h2a
Go back to
Zinc Binding Sites List in 9h2a
Zinc binding site 6 out
of 8 in the Acmnpv Complete Basal Cap
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of Acmnpv Complete Basal Cap within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
Z:Zn401
b:277.5
occ:1.00
|
NE2
|
Z:HIS52
|
2.0
|
205.5
|
1.0
|
|
SG
|
Z:CYS49
|
2.3
|
204.3
|
1.0
|
|
SG
|
Z:CYS18
|
2.3
|
208.3
|
1.0
|
|
SG
|
Z:CYS36
|
2.3
|
216.4
|
1.0
|
|
CD2
|
Z:HIS52
|
2.6
|
205.5
|
1.0
|
|
CB
|
Z:CYS36
|
2.9
|
216.4
|
1.0
|
|
CB
|
Z:CYS49
|
3.0
|
204.3
|
1.0
|
|
CE1
|
Z:HIS52
|
3.1
|
205.5
|
1.0
|
|
CA
|
Z:CYS36
|
3.2
|
216.4
|
1.0
|
|
CB
|
Z:CYS18
|
3.5
|
208.3
|
1.0
|
|
CG
|
Z:HIS52
|
3.8
|
205.5
|
1.0
|
|
ND1
|
Z:HIS52
|
3.9
|
205.5
|
1.0
|
|
N
|
Z:SER37
|
4.0
|
199.6
|
1.0
|
|
C
|
Z:CYS36
|
4.1
|
216.4
|
1.0
|
|
CB
|
Z:ALA40
|
4.2
|
201.1
|
1.0
|
|
O
|
Z:PRO35
|
4.3
|
225.2
|
1.0
|
|
CA
|
Z:CYS49
|
4.3
|
204.3
|
1.0
|
|
N
|
Z:CYS36
|
4.4
|
216.4
|
1.0
|
|
N
|
Z:CYS49
|
4.4
|
204.3
|
1.0
|
|
CB
|
Z:ALA21
|
4.5
|
211.6
|
1.0
|
|
N
|
Z:ALA21
|
4.6
|
211.6
|
1.0
|
|
O
|
Z:SER37
|
4.7
|
199.6
|
1.0
|
|
CA
|
Z:ALA21
|
4.7
|
211.6
|
1.0
|
|
C
|
Z:PRO35
|
4.7
|
225.2
|
1.0
|
|
OD1
|
Z:ASN16
|
4.8
|
203.8
|
1.0
|
|
ND2
|
Z:ASN16
|
4.8
|
203.8
|
1.0
|
|
CA
|
Z:CYS18
|
4.9
|
208.3
|
1.0
|
|
Zinc binding site 7 out
of 8 in 9h2a
Go back to
Zinc Binding Sites List in 9h2a
Zinc binding site 7 out
of 8 in the Acmnpv Complete Basal Cap
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 7 of Acmnpv Complete Basal Cap within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
e:Zn401
b:367.2
occ:1.00
|
NE2
|
e:HIS52
|
2.1
|
288.1
|
1.0
|
|
SG
|
e:CYS18
|
2.3
|
291.2
|
1.0
|
|
SG
|
e:CYS49
|
2.3
|
290.6
|
1.0
|
|
SG
|
e:CYS36
|
2.3
|
307.7
|
1.0
|
|
CD2
|
e:HIS52
|
2.4
|
288.1
|
1.0
|
|
CB
|
e:CYS36
|
2.7
|
307.7
|
1.0
|
|
CA
|
e:CYS36
|
2.7
|
307.7
|
1.0
|
|
CB
|
e:CYS18
|
3.2
|
291.2
|
1.0
|
|
CE1
|
e:HIS52
|
3.2
|
288.1
|
1.0
|
|
N
|
e:SER37
|
3.4
|
290.0
|
1.0
|
|
C
|
e:CYS36
|
3.5
|
307.7
|
1.0
|
|
CG
|
e:HIS52
|
3.5
|
288.1
|
1.0
|
|
CB
|
e:CYS49
|
3.6
|
290.6
|
1.0
|
|
ND1
|
e:HIS52
|
3.9
|
288.1
|
1.0
|
|
O
|
e:PRO35
|
3.9
|
305.0
|
1.0
|
|
N
|
e:CYS36
|
3.9
|
307.7
|
1.0
|
|
C
|
e:PRO35
|
4.4
|
305.0
|
1.0
|
|
O
|
e:SER37
|
4.4
|
290.0
|
1.0
|
|
CB
|
e:ALA40
|
4.5
|
280.5
|
1.0
|
|
O
|
e:CYS36
|
4.5
|
307.7
|
1.0
|
|
CA
|
e:CYS18
|
4.6
|
291.2
|
1.0
|
|
CB
|
e:ALA21
|
4.6
|
294.5
|
1.0
|
|
CA
|
e:SER37
|
4.6
|
290.0
|
1.0
|
|
CA
|
e:CYS49
|
4.7
|
290.6
|
1.0
|
|
CB
|
e:HIS52
|
4.7
|
288.1
|
1.0
|
|
N
|
e:CYS49
|
4.7
|
290.6
|
1.0
|
|
N
|
e:HIS52
|
4.8
|
288.1
|
1.0
|
|
CB
|
e:ASN51
|
5.0
|
281.8
|
1.0
|
|
C
|
e:SER37
|
5.0
|
290.0
|
1.0
|
|
Zinc binding site 8 out
of 8 in 9h2a
Go back to
Zinc Binding Sites List in 9h2a
Zinc binding site 8 out
of 8 in the Acmnpv Complete Basal Cap
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 8 of Acmnpv Complete Basal Cap within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
f:Zn401
b:274.7
occ:1.00
|
CD2
|
f:HIS52
|
1.5
|
216.1
|
1.0
|
|
NE2
|
f:HIS52
|
2.1
|
216.1
|
1.0
|
|
SG
|
f:CYS49
|
2.3
|
221.8
|
1.0
|
|
SG
|
f:CYS36
|
2.3
|
225.7
|
1.0
|
|
SG
|
f:CYS18
|
2.3
|
222.4
|
1.0
|
|
CG
|
f:HIS52
|
2.5
|
216.1
|
1.0
|
|
CE1
|
f:HIS52
|
3.0
|
216.1
|
1.0
|
|
ND1
|
f:HIS52
|
3.2
|
216.1
|
1.0
|
|
CB
|
f:HIS52
|
3.4
|
216.1
|
1.0
|
|
CB
|
f:CYS36
|
3.5
|
225.7
|
1.0
|
|
CB
|
f:CYS49
|
3.6
|
221.8
|
1.0
|
|
N
|
f:HIS52
|
3.7
|
216.1
|
1.0
|
|
CB
|
f:CYS18
|
3.7
|
222.4
|
1.0
|
|
N
|
f:CYS49
|
3.9
|
221.8
|
1.0
|
|
O
|
f:CYS49
|
4.0
|
221.8
|
1.0
|
|
CA
|
f:CYS49
|
4.0
|
221.8
|
1.0
|
|
CA
|
f:CYS18
|
4.1
|
222.4
|
1.0
|
|
C
|
f:CYS49
|
4.1
|
221.8
|
1.0
|
|
CA
|
f:HIS52
|
4.1
|
216.1
|
1.0
|
|
N
|
f:SER37
|
4.2
|
211.8
|
1.0
|
|
OG
|
f:SER37
|
4.2
|
211.8
|
1.0
|
|
O
|
f:ILE19
|
4.3
|
211.5
|
1.0
|
|
C
|
f:CYS18
|
4.6
|
222.4
|
1.0
|
|
CA
|
f:CYS36
|
4.6
|
225.7
|
1.0
|
|
N
|
f:ASN51
|
4.7
|
205.8
|
1.0
|
|
O
|
f:SER37
|
4.7
|
211.8
|
1.0
|
|
C
|
f:CYS36
|
4.7
|
225.7
|
1.0
|
|
C
|
f:ASN51
|
4.7
|
205.8
|
1.0
|
|
N
|
f:ASN50
|
4.8
|
211.3
|
1.0
|
|
CB
|
f:ASN51
|
4.9
|
205.8
|
1.0
|
|
O
|
f:CYS18
|
5.0
|
222.4
|
1.0
|
|
CB
|
f:ALA40
|
5.0
|
209.7
|
1.0
|
|
Reference:
G.Effantin,
E.Kandiah,
M.Pelosse.
Structure of Acmnpv Nucleocapsid Reveals Dna Portal Organization and Packaging Apparatus of Circular Dsdna Baculovirus. Nat Commun V. 16 4844 2025.
ISSN: ESSN 2041-1723
PubMed: 40413174
DOI: 10.1038/S41467-025-60152-2
Page generated: Fri Aug 22 18:01:11 2025
|
