Calcium in PDB 6pqx: Cryo-Em Structure of Hztransib/Nicked Tir Substrate Dna Hairpin Forming Complex (Hfc)
Calcium Binding Sites:
The binding sites of Calcium atom in the Cryo-Em Structure of Hztransib/Nicked Tir Substrate Dna Hairpin Forming Complex (Hfc)
(pdb code 6pqx). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the
Cryo-Em Structure of Hztransib/Nicked Tir Substrate Dna Hairpin Forming Complex (Hfc), PDB code: 6pqx:
Jump to Calcium binding site number:
1;
2;
3;
4;
Calcium binding site 1 out
of 4 in 6pqx
Go back to
Calcium Binding Sites List in 6pqx
Calcium binding site 1 out
of 4 in the Cryo-Em Structure of Hztransib/Nicked Tir Substrate Dna Hairpin Forming Complex (Hfc)
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Cryo-Em Structure of Hztransib/Nicked Tir Substrate Dna Hairpin Forming Complex (Hfc) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca601
b:0.9
occ:1.00
|
O
|
A:GLY126
|
2.3
|
75.6
|
1.0
|
OP2
|
D:DA17
|
2.3
|
0.3
|
1.0
|
OE2
|
A:GLU435
|
2.3
|
75.8
|
1.0
|
OD2
|
A:ASP125
|
2.4
|
74.2
|
1.0
|
OD1
|
A:ASP125
|
2.4
|
74.2
|
1.0
|
CG
|
A:ASP125
|
2.7
|
74.2
|
1.0
|
O3'
|
D:DG16
|
2.7
|
82.8
|
1.0
|
P
|
D:DA17
|
3.1
|
0.3
|
1.0
|
C
|
A:GLY126
|
3.3
|
75.6
|
1.0
|
CD
|
A:GLU435
|
3.5
|
75.8
|
1.0
|
N
|
A:ALA127
|
4.0
|
76.8
|
1.0
|
CA
|
A:ALA127
|
4.0
|
76.8
|
1.0
|
C3'
|
D:DG16
|
4.1
|
82.8
|
1.0
|
O5'
|
D:DA17
|
4.1
|
0.3
|
1.0
|
N
|
A:GLY126
|
4.2
|
75.6
|
1.0
|
OP1
|
D:DA17
|
4.2
|
0.3
|
1.0
|
C5'
|
D:DA17
|
4.2
|
0.3
|
1.0
|
CB
|
A:ASP125
|
4.2
|
74.2
|
1.0
|
OE1
|
A:GLU435
|
4.3
|
75.8
|
1.0
|
CG
|
A:GLU435
|
4.3
|
75.8
|
1.0
|
CB
|
A:ALA127
|
4.3
|
76.8
|
1.0
|
CA
|
A:GLY126
|
4.4
|
75.6
|
1.0
|
C4'
|
D:DG16
|
4.4
|
82.8
|
1.0
|
ND2
|
A:ASN438
|
4.5
|
63.3
|
1.0
|
OP1
|
D:DG16
|
4.6
|
82.8
|
1.0
|
CA
|
A:CA602
|
4.7
|
66.0
|
1.0
|
C
|
A:ASP125
|
4.9
|
74.2
|
1.0
|
C2'
|
D:DG16
|
4.9
|
82.8
|
1.0
|
CA
|
A:ASP125
|
5.0
|
74.2
|
1.0
|
|
Calcium binding site 2 out
of 4 in 6pqx
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Calcium Binding Sites List in 6pqx
Calcium binding site 2 out
of 4 in the Cryo-Em Structure of Hztransib/Nicked Tir Substrate Dna Hairpin Forming Complex (Hfc)
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Cryo-Em Structure of Hztransib/Nicked Tir Substrate Dna Hairpin Forming Complex (Hfc) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca602
b:66.0
occ:1.00
|
OD2
|
A:ASP224
|
2.5
|
84.2
|
1.0
|
OP1
|
D:DA17
|
2.6
|
0.3
|
1.0
|
OP2
|
D:DA17
|
2.7
|
0.3
|
1.0
|
O3'
|
B:DT16
|
2.8
|
0.7
|
1.0
|
P
|
D:DA17
|
3.1
|
0.3
|
1.0
|
CG
|
A:ASP224
|
3.7
|
84.2
|
1.0
|
C3'
|
B:DT16
|
3.9
|
0.7
|
1.0
|
O5'
|
D:DA17
|
4.0
|
0.3
|
1.0
|
NE2
|
A:HIS274
|
4.1
|
82.8
|
1.0
|
CB
|
A:LYS226
|
4.1
|
86.3
|
1.0
|
CG
|
A:LYS226
|
4.2
|
86.3
|
1.0
|
CE1
|
A:HIS274
|
4.2
|
82.8
|
1.0
|
C4'
|
B:DT16
|
4.4
|
0.7
|
1.0
|
O3'
|
D:DG16
|
4.5
|
82.8
|
1.0
|
CB
|
A:ASP224
|
4.5
|
84.2
|
1.0
|
OD1
|
A:ASP224
|
4.6
|
84.2
|
1.0
|
CA
|
A:CA601
|
4.7
|
0.9
|
1.0
|
C5'
|
D:DA17
|
4.8
|
0.3
|
1.0
|
OE2
|
A:GLU185
|
4.9
|
98.6
|
1.0
|
OD2
|
A:ASP125
|
4.9
|
74.2
|
1.0
|
|
Calcium binding site 3 out
of 4 in 6pqx
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Calcium Binding Sites List in 6pqx
Calcium binding site 3 out
of 4 in the Cryo-Em Structure of Hztransib/Nicked Tir Substrate Dna Hairpin Forming Complex (Hfc)
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Cryo-Em Structure of Hztransib/Nicked Tir Substrate Dna Hairpin Forming Complex (Hfc) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca601
b:96.1
occ:1.00
|
O
|
E:GLY126
|
2.3
|
72.0
|
1.0
|
OE2
|
E:GLU435
|
2.3
|
72.7
|
1.0
|
OD2
|
E:ASP125
|
2.4
|
68.8
|
1.0
|
OD1
|
E:ASP125
|
2.4
|
68.8
|
1.0
|
OP2
|
H:DA17
|
2.5
|
0.2
|
1.0
|
CG
|
E:ASP125
|
2.8
|
68.8
|
1.0
|
O3'
|
H:DG16
|
3.0
|
82.9
|
1.0
|
P
|
H:DA17
|
3.3
|
0.2
|
1.0
|
C
|
E:GLY126
|
3.3
|
72.0
|
1.0
|
CD
|
E:GLU435
|
3.5
|
72.7
|
1.0
|
OP1
|
H:DA17
|
4.0
|
0.2
|
1.0
|
N
|
E:ALA127
|
4.0
|
69.8
|
1.0
|
CA
|
E:ALA127
|
4.1
|
69.8
|
1.0
|
CA
|
E:CA602
|
4.2
|
61.9
|
1.0
|
N
|
E:GLY126
|
4.2
|
72.0
|
1.0
|
OE1
|
E:GLU435
|
4.3
|
72.7
|
1.0
|
C3'
|
H:DG16
|
4.3
|
82.9
|
1.0
|
CB
|
E:ASP125
|
4.3
|
68.8
|
1.0
|
CG
|
E:GLU435
|
4.3
|
72.7
|
1.0
|
CB
|
E:ALA127
|
4.4
|
69.8
|
1.0
|
CA
|
E:GLY126
|
4.4
|
72.0
|
1.0
|
ND2
|
E:ASN438
|
4.6
|
63.0
|
1.0
|
O5'
|
H:DA17
|
4.6
|
0.2
|
1.0
|
C4'
|
H:DG16
|
4.7
|
82.9
|
1.0
|
C2'
|
H:DG16
|
4.7
|
82.9
|
1.0
|
C
|
E:ASP125
|
4.9
|
68.8
|
1.0
|
C5'
|
H:DA17
|
5.0
|
0.2
|
1.0
|
CA
|
E:ASP125
|
5.0
|
68.8
|
1.0
|
|
Calcium binding site 4 out
of 4 in 6pqx
Go back to
Calcium Binding Sites List in 6pqx
Calcium binding site 4 out
of 4 in the Cryo-Em Structure of Hztransib/Nicked Tir Substrate Dna Hairpin Forming Complex (Hfc)
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Cryo-Em Structure of Hztransib/Nicked Tir Substrate Dna Hairpin Forming Complex (Hfc) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca602
b:61.9
occ:1.00
|
OD2
|
E:ASP224
|
2.5
|
78.8
|
1.0
|
OP1
|
H:DA17
|
2.9
|
0.2
|
1.0
|
OP2
|
H:DA17
|
3.3
|
0.2
|
1.0
|
P
|
H:DA17
|
3.6
|
0.2
|
1.0
|
O3'
|
F:DT16
|
3.6
|
0.8
|
1.0
|
CG
|
E:ASP224
|
3.7
|
78.8
|
1.0
|
NE2
|
E:HIS274
|
4.2
|
79.6
|
1.0
|
CA
|
E:CA601
|
4.2
|
96.1
|
1.0
|
C3'
|
F:DT16
|
4.3
|
0.8
|
1.0
|
CE1
|
E:HIS274
|
4.4
|
79.6
|
1.0
|
CB
|
E:LYS226
|
4.5
|
84.0
|
1.0
|
CB
|
E:ASP224
|
4.5
|
78.8
|
1.0
|
C4'
|
F:DT16
|
4.5
|
0.8
|
1.0
|
OD2
|
E:ASP125
|
4.5
|
68.8
|
1.0
|
CG
|
E:LYS226
|
4.5
|
84.0
|
1.0
|
OD1
|
E:ASP224
|
4.6
|
78.8
|
1.0
|
O3'
|
H:DG16
|
4.7
|
82.9
|
1.0
|
O5'
|
H:DA17
|
4.7
|
0.2
|
1.0
|
OE2
|
E:GLU185
|
4.9
|
88.9
|
1.0
|
OE2
|
E:GLU435
|
4.9
|
72.7
|
1.0
|
|
Reference:
C.Liu,
Y.Yang,
D.G.Schatz.
Structures of A Rag-Like Transposase During Cut-and-Paste Transposition. Nature V. 575 540 2019.
ISSN: ESSN 1476-4687
PubMed: 31723264
DOI: 10.1038/S41586-019-1753-7
Page generated: Tue Jul 16 12:58:32 2024
|