Calcium in PDB 8fn3: Crystal Structure of Human Dna Polymerase Eta Incorporating Ditp Across Dc
Enzymatic activity of Crystal Structure of Human Dna Polymerase Eta Incorporating Ditp Across Dc
All present enzymatic activity of Crystal Structure of Human Dna Polymerase Eta Incorporating Ditp Across Dc:
2.7.7.7;
Protein crystallography data
The structure of Crystal Structure of Human Dna Polymerase Eta Incorporating Ditp Across Dc, PDB code: 8fn3
was solved by
H.Jung,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
37.81 /
2.17
|
Space group
|
P 61
|
Cell size a, b, c (Å), α, β, γ (°)
|
98.595,
98.595,
81.376,
90,
90,
120
|
R / Rfree (%)
|
20.7 /
25.3
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Crystal Structure of Human Dna Polymerase Eta Incorporating Ditp Across Dc
(pdb code 8fn3). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the
Crystal Structure of Human Dna Polymerase Eta Incorporating Ditp Across Dc, PDB code: 8fn3:
Jump to Calcium binding site number:
1;
2;
Calcium binding site 1 out
of 2 in 8fn3
Go back to
Calcium Binding Sites List in 8fn3
Calcium binding site 1 out
of 2 in the Crystal Structure of Human Dna Polymerase Eta Incorporating Ditp Across Dc
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Crystal Structure of Human Dna Polymerase Eta Incorporating Ditp Across Dc within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca502
b:39.7
occ:1.00
|
OD1
|
A:ASP13
|
2.2
|
37.9
|
1.0
|
OD2
|
A:ASP115
|
2.2
|
34.6
|
1.0
|
O
|
A:MET14
|
2.3
|
28.6
|
1.0
|
OAR
|
A:Y43501
|
2.4
|
38.0
|
1.0
|
OAN
|
A:Y43501
|
2.4
|
34.4
|
1.0
|
OAK
|
A:Y43501
|
2.6
|
42.5
|
1.0
|
CA
|
A:CA503
|
3.1
|
64.0
|
1.0
|
CG
|
A:ASP13
|
3.3
|
40.4
|
1.0
|
CG
|
A:ASP115
|
3.3
|
39.0
|
1.0
|
C
|
A:MET14
|
3.5
|
31.2
|
1.0
|
PAM
|
A:Y43501
|
3.5
|
38.7
|
1.0
|
PAI
|
A:Y43501
|
3.6
|
47.3
|
1.0
|
PAQ
|
A:Y43501
|
3.7
|
53.5
|
1.0
|
OD1
|
A:ASP115
|
3.7
|
39.4
|
1.0
|
OD2
|
A:ASP13
|
3.7
|
49.5
|
1.0
|
OAL
|
A:Y43501
|
3.8
|
42.2
|
1.0
|
OAP
|
A:Y43501
|
3.9
|
40.4
|
1.0
|
N
|
A:MET14
|
4.0
|
29.1
|
1.0
|
CAG
|
A:Y43501
|
4.2
|
37.2
|
1.0
|
OAS
|
A:Y43501
|
4.2
|
34.5
|
1.0
|
CA
|
A:MET14
|
4.3
|
30.6
|
1.0
|
C
|
A:ASP13
|
4.3
|
33.3
|
1.0
|
OAH
|
A:Y43501
|
4.4
|
41.8
|
1.0
|
CB
|
A:ASP13
|
4.5
|
38.8
|
1.0
|
N
|
A:CYS16
|
4.5
|
32.0
|
1.0
|
N
|
A:ASP15
|
4.5
|
30.4
|
1.0
|
CB
|
A:ASP115
|
4.6
|
33.5
|
1.0
|
N
|
A:PHE17
|
4.7
|
27.4
|
1.0
|
CA
|
A:ASP15
|
4.7
|
32.6
|
1.0
|
CA
|
A:ASP13
|
4.8
|
29.9
|
1.0
|
O
|
A:ASP115
|
4.8
|
34.0
|
1.0
|
O
|
A:ASP13
|
4.8
|
33.7
|
1.0
|
C
|
A:ASP15
|
4.8
|
34.7
|
1.0
|
OAO
|
A:Y43501
|
4.8
|
38.5
|
1.0
|
CB
|
A:MET14
|
4.8
|
34.1
|
1.0
|
CB
|
A:PHE17
|
4.8
|
29.2
|
1.0
|
OAT
|
A:Y43501
|
4.9
|
43.4
|
1.0
|
NZ
|
A:LYS231
|
4.9
|
49.7
|
1.0
|
OAJ
|
A:Y43501
|
5.0
|
34.1
|
1.0
|
|
Calcium binding site 2 out
of 2 in 8fn3
Go back to
Calcium Binding Sites List in 8fn3
Calcium binding site 2 out
of 2 in the Crystal Structure of Human Dna Polymerase Eta Incorporating Ditp Across Dc
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Crystal Structure of Human Dna Polymerase Eta Incorporating Ditp Across Dc within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca503
b:64.0
occ:1.00
|
OAK
|
A:Y43501
|
2.3
|
42.5
|
1.0
|
OE1
|
A:GLU116
|
2.4
|
40.2
|
1.0
|
OD1
|
A:ASP13
|
2.6
|
37.9
|
1.0
|
OD2
|
A:ASP13
|
2.7
|
49.5
|
1.0
|
OD1
|
A:ASP115
|
2.8
|
39.4
|
1.0
|
CG
|
A:ASP13
|
2.9
|
40.4
|
1.0
|
CA
|
A:CA502
|
3.1
|
39.7
|
1.0
|
O3'
|
P:DG8
|
3.2
|
46.6
|
1.0
|
CD
|
A:GLU116
|
3.3
|
41.1
|
1.0
|
OD2
|
A:ASP115
|
3.5
|
34.6
|
1.0
|
CG
|
A:ASP115
|
3.5
|
39.0
|
1.0
|
PAI
|
A:Y43501
|
3.7
|
47.3
|
1.0
|
C3'
|
P:DG8
|
3.7
|
41.7
|
1.0
|
OE2
|
A:GLU116
|
4.0
|
43.1
|
1.0
|
CB
|
A:GLU116
|
4.1
|
32.6
|
1.0
|
OAR
|
A:Y43501
|
4.2
|
38.0
|
1.0
|
CG
|
A:GLU116
|
4.2
|
35.4
|
1.0
|
CB
|
A:ASP13
|
4.3
|
38.8
|
1.0
|
OAJ
|
A:Y43501
|
4.3
|
34.1
|
1.0
|
OAH
|
A:Y43501
|
4.4
|
41.8
|
1.0
|
C4'
|
P:DG8
|
4.5
|
41.3
|
1.0
|
OG
|
A:SER113
|
4.5
|
38.6
|
1.0
|
O
|
A:ASP115
|
4.6
|
34.0
|
1.0
|
CAG
|
A:Y43501
|
4.7
|
37.2
|
1.0
|
C5'
|
P:DG8
|
4.7
|
42.9
|
1.0
|
C
|
A:ASP115
|
4.7
|
36.8
|
1.0
|
CA
|
A:ASP13
|
4.8
|
29.9
|
1.0
|
OAL
|
A:Y43501
|
4.8
|
42.2
|
1.0
|
OAN
|
A:Y43501
|
4.9
|
34.4
|
1.0
|
NZ
|
A:LYS224
|
4.9
|
43.1
|
1.0
|
N
|
A:GLU116
|
5.0
|
34.2
|
1.0
|
CB
|
A:ASP115
|
5.0
|
33.5
|
1.0
|
|
Reference:
H.Jung,
H.Jung.
N/A N/A.
Page generated: Wed Jul 26 13:19:02 2023
|