Calcium in PDB 7lpv: X-Ray Radiation Damage Series on Proteinase K at 277K, Multi-Conformer Model, Dataset 2
Enzymatic activity of X-Ray Radiation Damage Series on Proteinase K at 277K, Multi-Conformer Model, Dataset 2
All present enzymatic activity of X-Ray Radiation Damage Series on Proteinase K at 277K, Multi-Conformer Model, Dataset 2:
3.4.21.64;
Protein crystallography data
The structure of X-Ray Radiation Damage Series on Proteinase K at 277K, Multi-Conformer Model, Dataset 2, PDB code: 7lpv
was solved by
F.Yabukarski,
T.Doukov,
D.Herschlag,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
33.85 /
1.10
|
|
Space group
|
P 43 21 2
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
67.708,
67.708,
101.598,
90,
90,
90
|
|
R / Rfree (%)
|
12.3 /
14.6
|
Calcium Binding Sites:
The binding sites of Calcium atom in the X-Ray Radiation Damage Series on Proteinase K at 277K, Multi-Conformer Model, Dataset 2
(pdb code 7lpv). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the
X-Ray Radiation Damage Series on Proteinase K at 277K, Multi-Conformer Model, Dataset 2, PDB code: 7lpv:
Jump to Calcium binding site number:
1;
2;
Calcium binding site 1 out
of 2 in 7lpv
Go back to
Calcium Binding Sites List in 7lpv
Calcium binding site 1 out
of 2 in the X-Ray Radiation Damage Series on Proteinase K at 277K, Multi-Conformer Model, Dataset 2
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of X-Ray Radiation Damage Series on Proteinase K at 277K, Multi-Conformer Model, Dataset 2 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca304
b:10.4
occ:0.42
|
CA
|
A:CA304
|
0.0
|
10.4
|
0.4
|
|
CA
|
A:CA304
|
2.1
|
27.6
|
0.6
|
|
OD2
|
A:ASP200
|
2.2
|
7.9
|
0.3
|
|
O
|
A:VAL177
|
2.4
|
10.0
|
0.4
|
|
O
|
A:HOH522
|
2.4
|
26.2
|
1.0
|
|
O
|
A:PRO175
|
2.4
|
11.7
|
0.4
|
|
O
|
A:HOH467
|
2.4
|
14.1
|
1.0
|
|
O
|
A:VAL177
|
2.4
|
9.9
|
0.3
|
|
O
|
A:HOH600
|
2.5
|
26.4
|
1.0
|
|
O
|
A:PRO175
|
2.5
|
9.2
|
0.4
|
|
OD2
|
A:ASP200
|
2.5
|
7.0
|
0.3
|
|
O
|
A:VAL177
|
2.5
|
8.4
|
0.3
|
|
OD2
|
A:ASP200
|
2.6
|
8.9
|
0.4
|
|
O
|
A:PRO175
|
2.6
|
11.0
|
0.2
|
|
OD1
|
A:ASP200
|
2.7
|
9.2
|
0.4
|
|
OD1
|
A:ASP200
|
2.7
|
12.8
|
0.3
|
|
OD1
|
A:ASP200
|
2.8
|
10.5
|
0.3
|
|
CG
|
A:ASP200
|
2.8
|
11.9
|
0.3
|
|
CG
|
A:ASP200
|
3.0
|
6.4
|
0.3
|
|
CG
|
A:ASP200
|
3.0
|
6.7
|
0.4
|
|
HA
|
A:PRO175
|
3.5
|
10.8
|
0.2
|
|
C
|
A:PRO175
|
3.5
|
9.1
|
0.2
|
|
C
|
A:PRO175
|
3.6
|
8.9
|
0.4
|
|
C
|
A:VAL177
|
3.6
|
9.7
|
0.4
|
|
C
|
A:PRO175
|
3.6
|
10.0
|
0.4
|
|
HA
|
A:CYS178
|
3.7
|
9.2
|
0.4
|
|
C
|
A:VAL177
|
3.7
|
8.6
|
0.3
|
|
HA
|
A:CYS178
|
3.7
|
9.0
|
0.3
|
|
C
|
A:VAL177
|
3.7
|
7.1
|
0.3
|
|
HA
|
A:CYS178
|
3.7
|
9.2
|
0.3
|
|
H
|
A:THR179
|
3.8
|
8.2
|
0.3
|
|
HA
|
A:PRO175
|
3.8
|
11.8
|
0.4
|
|
H
|
A:THR179
|
3.9
|
8.8
|
0.4
|
|
HA
|
A:PRO175
|
3.9
|
9.9
|
0.4
|
|
H
|
A:VAL177
|
4.0
|
11.9
|
0.4
|
|
CA
|
A:PRO175
|
4.1
|
9.0
|
0.2
|
|
O
|
A:VAL198
|
4.1
|
8.9
|
0.3
|
|
H
|
A:THR179
|
4.1
|
9.4
|
0.3
|
|
N
|
A:VAL177
|
4.1
|
9.9
|
0.4
|
|
H
|
A:VAL177
|
4.2
|
9.7
|
0.4
|
|
N
|
A:VAL177
|
4.2
|
8.1
|
0.3
|
|
CB
|
A:ASP200
|
4.2
|
8.7
|
0.3
|
|
CA
|
A:PRO175
|
4.3
|
9.8
|
0.4
|
|
HA
|
A:SER176
|
4.3
|
9.2
|
0.4
|
|
O
|
A:VAL198
|
4.3
|
11.3
|
0.3
|
|
O
|
A:GLU174
|
4.3
|
9.2
|
0.3
|
|
CA
|
A:PRO175
|
4.3
|
8.3
|
0.4
|
|
N
|
A:VAL177
|
4.4
|
8.4
|
0.3
|
|
O
|
A:GLU174
|
4.4
|
9.2
|
0.3
|
|
CB
|
A:ASP200
|
4.4
|
9.5
|
0.3
|
|
O
|
A:HOH643
|
4.4
|
27.7
|
0.6
|
|
C
|
A:SER176
|
4.4
|
11.3
|
0.2
|
|
CA
|
A:CYS178
|
4.5
|
7.5
|
0.3
|
|
H
|
A:VAL177
|
4.5
|
10.0
|
0.2
|
|
CA
|
A:CYS178
|
4.5
|
7.6
|
0.4
|
|
HG1
|
A:THR179
|
4.5
|
9.9
|
0.4
|
|
CB
|
A:ASP200
|
4.5
|
10.2
|
0.4
|
|
O
|
A:HOH449
|
4.5
|
22.8
|
0.5
|
|
N
|
A:SER176
|
4.5
|
9.0
|
0.4
|
|
N
|
A:SER176
|
4.5
|
10.1
|
0.4
|
|
N
|
A:CYS178
|
4.5
|
8.2
|
0.3
|
|
N
|
A:THR179
|
4.5
|
6.8
|
0.4
|
|
N
|
A:CYS178
|
4.5
|
8.1
|
0.3
|
|
HB2
|
A:ASP200
|
4.5
|
10.5
|
0.3
|
|
CA
|
A:CYS178
|
4.5
|
7.7
|
0.3
|
|
C
|
A:SER176
|
4.5
|
11.0
|
0.4
|
|
N
|
A:CYS178
|
4.5
|
7.3
|
0.4
|
|
C
|
A:SER176
|
4.5
|
8.4
|
0.4
|
|
CA
|
A:VAL177
|
4.5
|
8.9
|
0.4
|
|
O
|
A:VAL198
|
4.5
|
10.2
|
0.4
|
|
HB
|
A:THR179
|
4.6
|
11.1
|
0.4
|
|
HG22
|
A:VAL198
|
4.6
|
11.2
|
0.3
|
|
HA
|
A:SER176
|
4.6
|
11.6
|
0.4
|
|
O
|
A:GLU174
|
4.6
|
8.7
|
0.4
|
|
N
|
A:SER176
|
4.6
|
9.0
|
0.2
|
|
HB3
|
A:ASP200
|
4.6
|
10.5
|
0.3
|
|
N
|
A:THR179
|
4.6
|
7.3
|
0.1
|
|
OG1
|
A:THR179
|
4.6
|
8.3
|
0.4
|
|
CA
|
A:VAL177
|
4.6
|
7.9
|
0.3
|
|
HB3
|
A:ASP200
|
4.7
|
11.4
|
0.3
|
|
CA
|
A:SER176
|
4.7
|
7.7
|
0.4
|
|
CA
|
A:VAL177
|
4.7
|
8.0
|
0.3
|
|
O
|
A:SER176
|
4.7
|
12.1
|
0.2
|
|
HB2
|
A:ASP200
|
4.7
|
11.4
|
0.3
|
|
HA
|
A:SER176
|
4.7
|
11.1
|
0.2
|
|
O
|
A:HOH417
|
4.7
|
20.8
|
0.8
|
|
N
|
A:THR179
|
4.7
|
7.8
|
0.5
|
|
O
|
A:HOH666
|
4.8
|
42.5
|
1.0
|
|
HB3
|
A:PRO175
|
4.8
|
7.5
|
0.2
|
|
CA
|
A:SER176
|
4.8
|
9.7
|
0.4
|
|
SG
|
A:CYS249
|
4.8
|
7.8
|
0.4
|
|
OG1
|
A:THR179
|
4.8
|
8.2
|
0.1
|
|
HG23
|
A:VAL198
|
4.8
|
11.2
|
0.3
|
|
HG1
|
A:THR179
|
4.8
|
9.8
|
0.1
|
|
HB2
|
A:ASP200
|
4.8
|
12.3
|
0.4
|
|
HG22
|
A:VAL177
|
4.8
|
11.0
|
0.3
|
|
HB3
|
A:ASP200
|
4.9
|
12.3
|
0.4
|
|
CA
|
A:SER176
|
4.9
|
9.2
|
0.2
|
|
HB
|
A:THR179
|
4.9
|
7.8
|
0.1
|
|
SG
|
A:CYS249
|
5.0
|
10.8
|
0.4
|
|
HG22
|
A:VAL198
|
5.0
|
14.1
|
0.3
|
|
Calcium binding site 2 out
of 2 in 7lpv
Go back to
Calcium Binding Sites List in 7lpv
Calcium binding site 2 out
of 2 in the X-Ray Radiation Damage Series on Proteinase K at 277K, Multi-Conformer Model, Dataset 2
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of X-Ray Radiation Damage Series on Proteinase K at 277K, Multi-Conformer Model, Dataset 2 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca304
b:27.6
occ:0.58
|
CA
|
A:CA304
|
0.0
|
27.6
|
0.6
|
|
CA
|
A:CA304
|
2.1
|
10.4
|
0.4
|
|
O
|
A:HOH600
|
2.7
|
26.4
|
1.0
|
|
O
|
A:VAL177
|
2.7
|
10.0
|
0.4
|
|
O
|
A:VAL177
|
2.7
|
9.9
|
0.3
|
|
O
|
A:HOH643
|
2.9
|
27.7
|
0.6
|
|
OD1
|
A:ASP200
|
3.0
|
9.2
|
0.4
|
|
O
|
A:PRO175
|
3.1
|
11.0
|
0.2
|
|
O
|
A:PRO175
|
3.1
|
9.2
|
0.4
|
|
O
|
A:HOH417
|
3.1
|
20.8
|
0.8
|
|
O
|
A:VAL177
|
3.2
|
8.4
|
0.3
|
|
OD2
|
A:ASP200
|
3.2
|
7.9
|
0.3
|
|
O
|
A:PRO175
|
3.3
|
11.7
|
0.4
|
|
OD1
|
A:ASP200
|
3.4
|
12.8
|
0.3
|
|
O
|
A:HOH661
|
3.4
|
42.1
|
1.0
|
|
CG
|
A:ASP200
|
3.5
|
11.9
|
0.3
|
|
CG
|
A:ASP200
|
3.6
|
6.7
|
0.4
|
|
OD1
|
A:ASP200
|
3.6
|
10.5
|
0.3
|
|
C
|
A:VAL177
|
3.6
|
9.7
|
0.4
|
|
OD2
|
A:ASP200
|
3.7
|
8.9
|
0.4
|
|
O
|
A:SER176
|
3.7
|
12.1
|
0.2
|
|
HA
|
A:CYS178
|
3.7
|
9.0
|
0.3
|
|
SG
|
A:CYS249
|
3.7
|
7.8
|
0.4
|
|
C
|
A:VAL177
|
3.8
|
8.6
|
0.3
|
|
HA
|
A:CYS178
|
3.8
|
9.2
|
0.4
|
|
OD2
|
A:ASP200
|
3.8
|
7.0
|
0.3
|
|
C
|
A:VAL177
|
3.9
|
7.1
|
0.3
|
|
CG
|
A:ASP200
|
3.9
|
6.4
|
0.3
|
|
HA
|
A:CYS178
|
3.9
|
9.2
|
0.3
|
|
HA
|
A:SER176
|
3.9
|
9.2
|
0.4
|
|
HB3
|
A:CYS249
|
3.9
|
11.7
|
0.4
|
|
C
|
A:SER176
|
4.0
|
11.3
|
0.2
|
|
C
|
A:SER176
|
4.0
|
11.0
|
0.4
|
|
HB3
|
A:CYS249
|
4.0
|
11.6
|
0.4
|
|
SG
|
A:CYS249
|
4.0
|
10.8
|
0.4
|
|
HA
|
A:SER176
|
4.0
|
11.6
|
0.4
|
|
N
|
A:VAL177
|
4.1
|
9.9
|
0.4
|
|
HB3
|
A:CYS249
|
4.1
|
11.5
|
0.2
|
|
HA
|
A:SER176
|
4.1
|
11.1
|
0.2
|
|
O
|
A:HOH522
|
4.2
|
26.2
|
1.0
|
|
O
|
A:SER176
|
4.2
|
11.2
|
0.4
|
|
C
|
A:SER176
|
4.2
|
8.4
|
0.4
|
|
SG
|
A:CYS249
|
4.2
|
8.3
|
0.2
|
|
C
|
A:PRO175
|
4.2
|
9.1
|
0.2
|
|
O
|
A:SER176
|
4.2
|
10.0
|
0.4
|
|
C
|
A:PRO175
|
4.3
|
10.0
|
0.4
|
|
H
|
A:VAL177
|
4.4
|
11.9
|
0.4
|
|
N
|
A:VAL177
|
4.4
|
8.1
|
0.3
|
|
O
|
A:HOH467
|
4.4
|
14.1
|
1.0
|
|
CA
|
A:VAL177
|
4.4
|
8.9
|
0.4
|
|
N
|
A:VAL177
|
4.4
|
8.4
|
0.3
|
|
N
|
A:CYS178
|
4.4
|
8.1
|
0.3
|
|
CB
|
A:CYS249
|
4.4
|
9.7
|
0.4
|
|
C
|
A:PRO175
|
4.4
|
8.9
|
0.4
|
|
CB
|
A:CYS249
|
4.5
|
9.7
|
0.4
|
|
CA
|
A:CYS178
|
4.5
|
7.5
|
0.3
|
|
CA
|
A:SER176
|
4.5
|
9.7
|
0.4
|
|
N
|
A:CYS178
|
4.5
|
8.2
|
0.3
|
|
CA
|
A:SER176
|
4.5
|
7.7
|
0.4
|
|
HA
|
A:VAL177
|
4.5
|
10.6
|
0.4
|
|
CA
|
A:SER176
|
4.5
|
9.2
|
0.2
|
|
CA
|
A:CYS178
|
4.6
|
7.6
|
0.4
|
|
N
|
A:CYS178
|
4.6
|
7.3
|
0.4
|
|
O
|
A:HOH470
|
4.6
|
9.3
|
0.2
|
|
CA
|
A:CYS178
|
4.6
|
7.7
|
0.3
|
|
CA
|
A:VAL177
|
4.6
|
7.9
|
0.3
|
|
CA
|
A:VAL177
|
4.7
|
8.0
|
0.3
|
|
HB3
|
A:ASP200
|
4.7
|
10.5
|
0.3
|
|
CB
|
A:CYS249
|
4.7
|
9.6
|
0.2
|
|
H
|
A:VAL177
|
4.7
|
9.7
|
0.4
|
|
HB2
|
A:CYS249
|
4.7
|
11.7
|
0.4
|
|
CB
|
A:ASP200
|
4.7
|
8.7
|
0.3
|
|
O
|
A:HOH643
|
4.7
|
23.8
|
0.4
|
|
HB2
|
A:CYS249
|
4.7
|
11.6
|
0.4
|
|
N
|
A:SER176
|
4.8
|
10.1
|
0.4
|
|
HB3
|
A:ASP200
|
4.8
|
11.4
|
0.3
|
|
HA
|
A:VAL177
|
4.8
|
9.6
|
0.3
|
|
H
|
A:THR179
|
4.8
|
8.2
|
0.3
|
|
HB3
|
A:ASP200
|
4.8
|
12.3
|
0.4
|
|
CB
|
A:ASP200
|
4.8
|
10.2
|
0.4
|
|
H
|
A:VAL177
|
4.9
|
10.0
|
0.2
|
|
HA
|
A:VAL177
|
4.9
|
9.5
|
0.3
|
|
N
|
A:SER176
|
4.9
|
9.0
|
0.2
|
|
N
|
A:SER176
|
4.9
|
9.0
|
0.4
|
|
CB
|
A:ASP200
|
5.0
|
9.5
|
0.3
|
|
O
|
A:HOH511
|
5.0
|
27.9
|
1.0
|
|
HB2
|
A:CYS178
|
5.0
|
9.9
|
0.4
|
|
HB2
|
A:CYS249
|
5.0
|
11.5
|
0.2
|
|
H
|
A:THR179
|
5.0
|
8.8
|
0.4
|
|
Reference:
F.Yabukarski,
T.Doukov,
D.A.Mokhtari,
S.Du,
D.Herschlag.
Evaluating the Impact of X-Ray Damage on Conformational Heterogeneity in Room-Temperature (277 K) and Cryo-Cooled Protein Crystals. Acta Crystallogr D Struct V. 78 945 2022BIOL.
ISSN: ISSN 2059-7983
PubMed: 35916220
DOI: 10.1107/S2059798322005939
Page generated: Fri Jul 19 01:41:22 2024
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