Calcium in PDB 6q6j: Human Phosphoserine Phosphatase with Substrate Analogue Homo-Cysteic Acid
Enzymatic activity of Human Phosphoserine Phosphatase with Substrate Analogue Homo-Cysteic Acid
All present enzymatic activity of Human Phosphoserine Phosphatase with Substrate Analogue Homo-Cysteic Acid:
3.1.3.3;
Protein crystallography data
The structure of Human Phosphoserine Phosphatase with Substrate Analogue Homo-Cysteic Acid, PDB code: 6q6j
was solved by
J.Wouters,
M.Haufroid,
M.Mirgaux,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
40.94 /
1.99
|
Space group
|
C 2 2 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
49.230,
130.490,
157.760,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
19.8 /
24.7
|
Other elements in 6q6j:
The structure of Human Phosphoserine Phosphatase with Substrate Analogue Homo-Cysteic Acid also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Human Phosphoserine Phosphatase with Substrate Analogue Homo-Cysteic Acid
(pdb code 6q6j). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the
Human Phosphoserine Phosphatase with Substrate Analogue Homo-Cysteic Acid, PDB code: 6q6j:
Jump to Calcium binding site number:
1;
2;
3;
Calcium binding site 1 out
of 3 in 6q6j
Go back to
Calcium Binding Sites List in 6q6j
Calcium binding site 1 out
of 3 in the Human Phosphoserine Phosphatase with Substrate Analogue Homo-Cysteic Acid
 Mono view
 Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Human Phosphoserine Phosphatase with Substrate Analogue Homo-Cysteic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca301
b:31.9
occ:1.00
|
OD2
|
A:ASP20
|
2.2
|
36.9
|
1.0
|
OD2
|
A:ASP179
|
2.2
|
35.1
|
1.0
|
O
|
A:ASP22
|
2.3
|
29.8
|
1.0
|
O
|
A:HOH483
|
2.3
|
37.5
|
1.0
|
O
|
A:HOH473
|
2.3
|
43.5
|
1.0
|
O
|
A:HOH409
|
2.4
|
39.1
|
1.0
|
CG
|
A:ASP20
|
3.1
|
36.1
|
1.0
|
CG
|
A:ASP179
|
3.2
|
38.8
|
1.0
|
OD1
|
A:ASP20
|
3.3
|
35.6
|
1.0
|
C
|
A:ASP22
|
3.4
|
34.8
|
1.0
|
OD1
|
A:ASP179
|
3.5
|
46.0
|
1.0
|
CB
|
A:ASP22
|
4.1
|
35.9
|
1.0
|
OD2
|
A:ASP183
|
4.1
|
41.0
|
1.0
|
CA
|
A:ASP22
|
4.2
|
32.5
|
1.0
|
CB
|
A:SER23
|
4.3
|
39.4
|
1.0
|
N
|
A:ASP22
|
4.4
|
33.6
|
1.0
|
OG1
|
A:THR24
|
4.4
|
31.6
|
1.0
|
CB
|
A:ASP20
|
4.4
|
33.2
|
1.0
|
N
|
A:SER23
|
4.5
|
31.8
|
1.0
|
CB
|
A:ASP179
|
4.5
|
27.3
|
1.0
|
O
|
A:HOH439
|
4.6
|
35.7
|
1.0
|
N
|
A:ASP179
|
4.7
|
29.8
|
1.0
|
NZ
|
A:LYS158
|
4.7
|
40.6
|
1.0
|
CE
|
A:MET52
|
4.8
|
49.7
|
1.0
|
O
|
A:HOH464
|
4.8
|
35.2
|
1.0
|
O
|
A:HOH452
|
4.8
|
50.3
|
1.0
|
CA
|
A:SER23
|
4.8
|
31.3
|
1.0
|
OG
|
A:SER23
|
4.8
|
42.1
|
1.0
|
N
|
A:GLY180
|
4.8
|
31.7
|
1.0
|
O
|
A:HOH494
|
4.9
|
54.7
|
1.0
|
OE1
|
A:GLU29
|
4.9
|
58.2
|
1.0
|
O
|
A:HOH470
|
4.9
|
43.7
|
1.0
|
N
|
A:THR24
|
5.0
|
29.0
|
1.0
|
|
Calcium binding site 2 out
of 3 in 6q6j
Go back to
Calcium Binding Sites List in 6q6j
Calcium binding site 2 out
of 3 in the Human Phosphoserine Phosphatase with Substrate Analogue Homo-Cysteic Acid
 Mono view
 Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Human Phosphoserine Phosphatase with Substrate Analogue Homo-Cysteic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca302
b:58.5
occ:1.00
|
O
|
A:HOH458
|
2.3
|
45.4
|
1.0
|
O
|
A:GLU185
|
2.5
|
40.7
|
1.0
|
O
|
A:PRO188
|
2.5
|
32.5
|
1.0
|
C
|
A:PRO188
|
3.7
|
31.9
|
1.0
|
C
|
A:GLU185
|
3.7
|
44.1
|
1.0
|
CD
|
A:PRO189
|
4.1
|
30.0
|
1.0
|
N
|
A:PRO189
|
4.4
|
30.6
|
1.0
|
CA
|
A:ALA186
|
4.4
|
37.2
|
1.0
|
N
|
A:PRO188
|
4.5
|
34.8
|
1.0
|
N
|
A:ALA186
|
4.5
|
35.8
|
1.0
|
C
|
A:ALA186
|
4.5
|
30.4
|
1.0
|
CG
|
A:PRO188
|
4.5
|
34.8
|
1.0
|
CD
|
A:PRO188
|
4.6
|
32.5
|
1.0
|
CA
|
A:GLU185
|
4.6
|
40.2
|
1.0
|
CA
|
A:PRO188
|
4.7
|
29.0
|
1.0
|
N
|
A:CYS187
|
4.7
|
31.6
|
1.0
|
C
|
A:CYS187
|
4.8
|
36.2
|
1.0
|
O
|
A:ALA186
|
5.0
|
30.1
|
1.0
|
CB
|
A:GLU185
|
5.0
|
44.0
|
1.0
|
|
Calcium binding site 3 out
of 3 in 6q6j
Go back to
Calcium Binding Sites List in 6q6j
Calcium binding site 3 out
of 3 in the Human Phosphoserine Phosphatase with Substrate Analogue Homo-Cysteic Acid
 Mono view
 Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Human Phosphoserine Phosphatase with Substrate Analogue Homo-Cysteic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca301
b:34.2
occ:1.00
|
O
|
B:HOH438
|
2.3
|
36.9
|
1.0
|
OD1
|
B:ASP179
|
2.3
|
35.6
|
1.0
|
O
|
B:ASP22
|
2.3
|
32.7
|
1.0
|
OD2
|
B:ASP20
|
2.4
|
38.4
|
1.0
|
O
|
B:HOH463
|
2.5
|
44.4
|
1.0
|
O
|
B:HOH414
|
2.6
|
39.9
|
1.0
|
CG
|
B:ASP20
|
3.1
|
38.3
|
1.0
|
OD1
|
B:ASP20
|
3.2
|
42.9
|
1.0
|
CG
|
B:ASP179
|
3.3
|
35.1
|
1.0
|
C
|
B:ASP22
|
3.5
|
33.7
|
1.0
|
OD2
|
B:ASP179
|
3.5
|
41.9
|
1.0
|
CB
|
B:ASP22
|
4.1
|
37.2
|
1.0
|
O1S
|
B:HJT302
|
4.1
|
32.0
|
0.4
|
CA
|
B:ASP22
|
4.2
|
32.1
|
1.0
|
CB
|
B:SER23
|
4.2
|
34.6
|
1.0
|
OD2
|
B:ASP183
|
4.3
|
37.7
|
1.0
|
OG
|
B:SER23
|
4.4
|
37.5
|
1.0
|
N
|
B:ASP22
|
4.4
|
29.2
|
1.0
|
N
|
B:SER23
|
4.5
|
31.9
|
1.0
|
CB
|
B:ASP20
|
4.5
|
31.6
|
1.0
|
OG1
|
B:THR24
|
4.5
|
34.0
|
1.0
|
CG
|
B:HJT302
|
4.6
|
40.6
|
0.4
|
CB
|
B:ASP179
|
4.6
|
32.1
|
1.0
|
S
|
B:HJT302
|
4.7
|
51.4
|
0.4
|
O2S
|
B:HJT302
|
4.7
|
43.0
|
0.4
|
CA
|
B:SER23
|
4.8
|
32.4
|
1.0
|
N
|
B:ASP179
|
4.8
|
35.3
|
1.0
|
O
|
B:HOH410
|
4.9
|
48.9
|
1.0
|
N
|
B:GLY180
|
4.9
|
31.3
|
1.0
|
OXT
|
B:HJT302
|
5.0
|
51.4
|
0.4
|
NH2
|
B:ARG202
|
5.0
|
43.1
|
1.0
|
|
Reference:
M.Haufroid,
M.Mirgaux,
L.Leherte,
J.Wouters.
Crystal Structures and Snapshots Along the Reaction Pathway of Human Phosphoserine Phosphatase. Acta Crystallogr D Struct V. 75 592 2019BIOL.
ISSN: ISSN 2059-7983
PubMed: 31205021
DOI: 10.1107/S2059798319006867
Page generated: Sat Dec 12 07:26:57 2020
|