Calcium in PDB 6p1h: Cryo-Em Structure of Dna Polymerase Delta Holoenzyme
Enzymatic activity of Cryo-Em Structure of Dna Polymerase Delta Holoenzyme
All present enzymatic activity of Cryo-Em Structure of Dna Polymerase Delta Holoenzyme:
2.7.7.7;
Other elements in 6p1h:
The structure of Cryo-Em Structure of Dna Polymerase Delta Holoenzyme also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Cryo-Em Structure of Dna Polymerase Delta Holoenzyme
(pdb code 6p1h). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the
Cryo-Em Structure of Dna Polymerase Delta Holoenzyme, PDB code: 6p1h:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
Calcium binding site 1 out
of 5 in 6p1h
Go back to
Calcium Binding Sites List in 6p1h
Calcium binding site 1 out
of 5 in the Cryo-Em Structure of Dna Polymerase Delta Holoenzyme
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 Dna Polymerase Delta Holoenzyme within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1103
b:65.0
occ:1.00
|
O1B
|
A:DCP1102
|
2.3
|
64.0
|
1.0
|
OD2
|
A:ASP764
|
2.4
|
67.2
|
1.0
|
O
|
A:PHE609
|
2.4
|
63.6
|
1.0
|
OD2
|
A:ASP608
|
2.6
|
66.8
|
1.0
|
O1G
|
A:DCP1102
|
2.8
|
64.0
|
1.0
|
O1A
|
A:DCP1102
|
3.1
|
64.0
|
1.0
|
CG
|
A:ASP608
|
3.3
|
66.8
|
1.0
|
CG
|
A:ASP764
|
3.5
|
67.2
|
1.0
|
C
|
A:PHE609
|
3.5
|
63.6
|
1.0
|
CB
|
A:ASP608
|
3.7
|
66.8
|
1.0
|
PB
|
A:DCP1102
|
3.8
|
64.0
|
1.0
|
N
|
A:PHE609
|
3.8
|
63.6
|
1.0
|
CA
|
A:CA1104
|
3.9
|
87.0
|
1.0
|
PG
|
A:DCP1102
|
3.9
|
64.0
|
1.0
|
O3G
|
A:DCP1102
|
4.0
|
64.0
|
1.0
|
OD1
|
A:ASP764
|
4.2
|
67.2
|
1.0
|
CA
|
A:PHE609
|
4.2
|
63.6
|
1.0
|
OD1
|
A:ASP608
|
4.3
|
66.8
|
1.0
|
C
|
A:ASP608
|
4.4
|
66.8
|
1.0
|
CB
|
A:ASP764
|
4.4
|
67.2
|
1.0
|
O3B
|
A:DCP1102
|
4.4
|
64.0
|
1.0
|
PA
|
A:DCP1102
|
4.4
|
64.0
|
1.0
|
N
|
A:ASN610
|
4.6
|
63.5
|
1.0
|
CA
|
A:ASP608
|
4.6
|
66.8
|
1.0
|
O3A
|
A:DCP1102
|
4.6
|
64.0
|
1.0
|
O2B
|
A:DCP1102
|
4.7
|
64.0
|
1.0
|
N
|
A:SER611
|
4.7
|
62.1
|
1.0
|
CA
|
A:ASN610
|
4.8
|
63.5
|
1.0
|
C5'
|
A:DCP1102
|
4.8
|
64.0
|
1.0
|
CB
|
A:PHE609
|
4.9
|
63.6
|
1.0
|
|
Calcium binding site 2 out
of 5 in 6p1h
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Calcium Binding Sites List in 6p1h
Calcium binding site 2 out
of 5 in the Cryo-Em Structure of Dna Polymerase Delta Holoenzyme
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 Dna Polymerase Delta Holoenzyme within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1104
b:87.0
occ:1.00
|
O
|
A:HOH1225
|
2.9
|
57.8
|
1.0
|
O1A
|
A:DCP1102
|
3.5
|
64.0
|
1.0
|
OD1
|
A:ASP764
|
3.6
|
67.2
|
1.0
|
OD2
|
A:ASP608
|
3.8
|
66.8
|
1.0
|
CA
|
A:CA1103
|
3.9
|
65.0
|
1.0
|
OD2
|
A:ASP764
|
3.9
|
67.2
|
1.0
|
CG
|
A:ASP764
|
4.1
|
67.2
|
1.0
|
C5'
|
P:DC30
|
4.1
|
65.4
|
1.0
|
CB
|
A:ASP608
|
4.1
|
66.8
|
1.0
|
OG
|
A:SER765
|
4.3
|
67.6
|
1.0
|
CB
|
A:SER765
|
4.3
|
67.6
|
1.0
|
CG
|
A:ASP608
|
4.4
|
66.8
|
1.0
|
C3'
|
P:DC30
|
4.4
|
65.4
|
1.0
|
OE2
|
A:GLU802
|
4.5
|
69.5
|
1.0
|
O5'
|
P:DC30
|
4.6
|
65.4
|
1.0
|
C4'
|
P:DC30
|
4.6
|
65.4
|
1.0
|
PA
|
A:DCP1102
|
4.8
|
64.0
|
1.0
|
O2A
|
A:DCP1102
|
4.9
|
64.0
|
1.0
|
|
Calcium binding site 3 out
of 5 in 6p1h
Go back to
Calcium Binding Sites List in 6p1h
Calcium binding site 3 out
of 5 in the Cryo-Em Structure of Dna Polymerase Delta Holoenzyme
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 Dna Polymerase Delta Holoenzyme within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1105
b:90.2
occ:1.00
|
OE1
|
A:GLU800
|
2.3
|
71.0
|
1.0
|
OD1
|
A:ASP608
|
3.1
|
66.8
|
1.0
|
OD2
|
A:ASP608
|
3.3
|
66.8
|
1.0
|
OD1
|
A:ASN610
|
3.4
|
63.5
|
1.0
|
CD
|
A:GLU800
|
3.4
|
71.0
|
1.0
|
CG
|
A:ASP608
|
3.6
|
66.8
|
1.0
|
CG
|
A:GLU802
|
3.8
|
69.5
|
1.0
|
CG
|
A:GLU800
|
3.8
|
71.0
|
1.0
|
CB
|
A:GLU802
|
4.2
|
69.5
|
1.0
|
CD
|
A:GLU802
|
4.5
|
69.5
|
1.0
|
OE2
|
A:GLU800
|
4.5
|
71.0
|
1.0
|
O1G
|
A:DCP1102
|
4.6
|
64.0
|
1.0
|
CG
|
A:ASN610
|
4.6
|
63.5
|
1.0
|
O3G
|
A:DCP1102
|
4.6
|
64.0
|
1.0
|
CA
|
A:GLU802
|
4.7
|
69.5
|
1.0
|
OE1
|
A:GLU802
|
4.8
|
69.5
|
1.0
|
|
Calcium binding site 4 out
of 5 in 6p1h
Go back to
Calcium Binding Sites List in 6p1h
Calcium binding site 4 out
of 5 in the Cryo-Em Structure of Dna Polymerase Delta Holoenzyme
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 Dna Polymerase Delta Holoenzyme within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1106
b:95.6
occ:1.00
|
OD2
|
A:ASP321
|
1.9
|
74.1
|
1.0
|
CG
|
A:ASP321
|
2.6
|
74.1
|
1.0
|
OD1
|
A:ASP321
|
2.6
|
74.1
|
1.0
|
O
|
A:ILE322
|
3.3
|
74.7
|
1.0
|
OD2
|
A:ASP520
|
4.0
|
77.5
|
1.0
|
CB
|
A:ASP321
|
4.1
|
74.1
|
1.0
|
OE2
|
A:GLU323
|
4.2
|
81.8
|
1.0
|
CD
|
A:GLU323
|
4.3
|
81.8
|
1.0
|
N
|
A:ILE322
|
4.3
|
74.7
|
1.0
|
C
|
A:ILE322
|
4.4
|
74.7
|
1.0
|
O
|
A:HOH1211
|
4.4
|
77.3
|
1.0
|
CB
|
A:ASP520
|
4.5
|
77.5
|
1.0
|
OE1
|
A:GLU323
|
4.6
|
81.8
|
1.0
|
CG
|
A:ASP520
|
4.6
|
77.5
|
1.0
|
OD1
|
A:ASP407
|
4.7
|
77.2
|
1.0
|
CG
|
A:GLU323
|
4.8
|
81.8
|
1.0
|
CA
|
A:ASP321
|
4.8
|
74.1
|
1.0
|
C
|
A:ASP321
|
5.0
|
74.1
|
1.0
|
|
Calcium binding site 5 out
of 5 in 6p1h
Go back to
Calcium Binding Sites List in 6p1h
Calcium binding site 5 out
of 5 in the Cryo-Em Structure of Dna Polymerase Delta Holoenzyme
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Cryo-Em Structure of Dna Polymerase Delta Holoenzyme within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
T:Ca101
b:0.9
occ:1.00
|
O
|
T:HOH201
|
3.2
|
81.7
|
1.0
|
OP2
|
T:DG10
|
3.2
|
72.6
|
1.0
|
C8
|
T:DG10
|
4.0
|
72.6
|
1.0
|
N7
|
T:DG10
|
4.2
|
72.6
|
1.0
|
N7
|
T:DG11
|
4.3
|
78.3
|
1.0
|
P
|
T:DG10
|
4.6
|
72.6
|
1.0
|
C2'
|
T:DG9
|
4.9
|
68.7
|
1.0
|
O5'
|
T:DG10
|
4.9
|
72.6
|
1.0
|
C8
|
T:DG11
|
4.9
|
78.3
|
1.0
|
|
Reference:
R.Jain,
W.J.Rice,
R.Malik,
R.E.Johnson,
L.Prakash,
S.Prakash,
I.Ubarretxena-Belandia,
A.K.Aggarwal.
Cryo-Em Structure and Dynamics of Eukaryotic Dna Polymerase Delta Holoenzyme. Nat.Struct.Mol.Biol. V. 26 955 2019.
ISSN: ESSN 1545-9985
PubMed: 31582849
DOI: 10.1038/S41594-019-0305-Z
Page generated: Tue Jul 16 12:43:16 2024
|