Manganese in PDB 6zei: Structure of PP1-IRSP53 S455E Chimera [PP1(7-304) + Linker (G/S)X9 + IRSP53(449-465)] Bound to PHACTR1 (516-580)
Enzymatic activity of Structure of PP1-IRSP53 S455E Chimera [PP1(7-304) + Linker (G/S)X9 + IRSP53(449-465)] Bound to PHACTR1 (516-580)
All present enzymatic activity of Structure of PP1-IRSP53 S455E Chimera [PP1(7-304) + Linker (G/S)X9 + IRSP53(449-465)] Bound to PHACTR1 (516-580):
3.1.3.16;
Protein crystallography data
The structure of Structure of PP1-IRSP53 S455E Chimera [PP1(7-304) + Linker (G/S)X9 + IRSP53(449-465)] Bound to PHACTR1 (516-580), PDB code: 6zei
was solved by
S.Mouilleron,
R.Treisman,
R.Fedoryshchak,
R.Lee,
A.M.Butler,
M.Prechova,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
69.37 /
1.39
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
48.795,
122.329,
69.424,
90.00,
92.27,
90.00
|
R / Rfree (%)
|
13 /
15.8
|
Manganese Binding Sites:
The binding sites of Manganese atom in the Structure of PP1-IRSP53 S455E Chimera [PP1(7-304) + Linker (G/S)X9 + IRSP53(449-465)] Bound to PHACTR1 (516-580)
(pdb code 6zei). This binding sites where shown within
5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the
Structure of PP1-IRSP53 S455E Chimera [PP1(7-304) + Linker (G/S)X9 + IRSP53(449-465)] Bound to PHACTR1 (516-580), PDB code: 6zei:
Jump to Manganese binding site number:
1;
2;
3;
4;
Manganese binding site 1 out
of 4 in 6zei
Go back to
Manganese Binding Sites List in 6zei
Manganese binding site 1 out
of 4 in the Structure of PP1-IRSP53 S455E Chimera [PP1(7-304) + Linker (G/S)X9 + IRSP53(449-465)] Bound to PHACTR1 (516-580)
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 1 of Structure of PP1-IRSP53 S455E Chimera [PP1(7-304) + Linker (G/S)X9 + IRSP53(449-465)] Bound to PHACTR1 (516-580) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn501
b:11.3
occ:1.00
|
OD1
|
A:ASN124
|
2.1
|
11.4
|
1.0
|
NE2
|
A:HIS173
|
2.2
|
10.7
|
1.0
|
ND1
|
A:HIS248
|
2.2
|
11.4
|
1.0
|
O4
|
A:PO4505
|
2.2
|
11.9
|
1.0
|
OD2
|
A:ASP92
|
2.3
|
11.3
|
1.0
|
O3
|
A:PO4505
|
2.3
|
13.2
|
1.0
|
P
|
A:PO4505
|
2.9
|
12.5
|
1.0
|
HA
|
A:HIS248
|
3.0
|
13.6
|
1.0
|
CE1
|
A:HIS248
|
3.1
|
12.2
|
1.0
|
HE1
|
A:HIS248
|
3.1
|
14.7
|
1.0
|
CG
|
A:ASN124
|
3.2
|
11.1
|
1.0
|
CG
|
A:ASP92
|
3.2
|
11.4
|
1.0
|
CD2
|
A:HIS173
|
3.2
|
11.3
|
1.0
|
CE1
|
A:HIS173
|
3.2
|
10.9
|
1.0
|
HD21
|
A:ASN124
|
3.2
|
13.8
|
1.0
|
HD2
|
A:HIS125
|
3.3
|
13.5
|
1.0
|
HD2
|
A:HIS173
|
3.4
|
13.6
|
1.0
|
CG
|
A:HIS248
|
3.4
|
11.1
|
1.0
|
HE1
|
A:HIS173
|
3.4
|
13.0
|
1.0
|
MN
|
A:MN502
|
3.4
|
11.4
|
1.0
|
OD1
|
A:ASP92
|
3.5
|
11.3
|
1.0
|
ND2
|
A:ASN124
|
3.6
|
11.5
|
1.0
|
HB2
|
A:HIS248
|
3.8
|
14.1
|
1.0
|
H
|
A:ASN124
|
3.8
|
12.9
|
1.0
|
CA
|
A:HIS248
|
3.8
|
11.3
|
1.0
|
CB
|
A:HIS248
|
3.9
|
11.7
|
1.0
|
O1
|
A:PO4505
|
3.9
|
14.6
|
1.0
|
O2
|
A:PO4505
|
4.0
|
12.4
|
1.0
|
CD2
|
A:HIS125
|
4.1
|
11.2
|
1.0
|
OD2
|
A:ASP64
|
4.2
|
11.9
|
1.0
|
HE2
|
A:HIS125
|
4.2
|
15.3
|
1.0
|
NE2
|
A:HIS248
|
4.3
|
13.1
|
1.0
|
O
|
A:HIS248
|
4.3
|
12.8
|
1.0
|
ND1
|
A:HIS173
|
4.3
|
10.0
|
1.0
|
CG
|
A:HIS173
|
4.4
|
11.2
|
1.0
|
CD2
|
A:HIS248
|
4.4
|
12.0
|
1.0
|
HD22
|
A:ASN124
|
4.4
|
13.8
|
1.0
|
CB
|
A:ASN124
|
4.5
|
11.3
|
1.0
|
CB
|
A:ASP92
|
4.5
|
10.2
|
1.0
|
NE2
|
A:HIS125
|
4.5
|
12.8
|
1.0
|
N
|
A:ASN124
|
4.6
|
10.7
|
1.0
|
HB2
|
A:ASP92
|
4.6
|
12.2
|
1.0
|
C
|
A:HIS248
|
4.6
|
12.1
|
1.0
|
HB3
|
A:ASN124
|
4.6
|
13.6
|
1.0
|
H
|
A:HIS125
|
4.6
|
12.3
|
1.0
|
HH12
|
A:ARG221
|
4.6
|
15.7
|
1.0
|
O
|
A:LEU205
|
4.7
|
11.5
|
1.0
|
HB3
|
A:HIS248
|
4.8
|
14.1
|
1.0
|
HB3
|
A:ASP92
|
4.8
|
12.2
|
1.0
|
H
|
A:HIS248
|
4.9
|
13.1
|
1.0
|
N
|
A:HIS248
|
4.9
|
10.9
|
1.0
|
HE2
|
A:HIS248
|
5.0
|
15.7
|
1.0
|
HH22
|
A:ARG221
|
5.0
|
15.4
|
1.0
|
|
Manganese binding site 2 out
of 4 in 6zei
Go back to
Manganese Binding Sites List in 6zei
Manganese binding site 2 out
of 4 in the Structure of PP1-IRSP53 S455E Chimera [PP1(7-304) + Linker (G/S)X9 + IRSP53(449-465)] Bound to PHACTR1 (516-580)
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 2 of Structure of PP1-IRSP53 S455E Chimera [PP1(7-304) + Linker (G/S)X9 + IRSP53(449-465)] Bound to PHACTR1 (516-580) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn502
b:11.4
occ:1.00
|
OD2
|
A:ASP64
|
2.0
|
11.9
|
1.0
|
O4
|
A:PO4505
|
2.0
|
11.9
|
1.0
|
NE2
|
A:HIS66
|
2.2
|
11.6
|
1.0
|
O
|
A:HOH787
|
2.2
|
12.2
|
1.0
|
OD2
|
A:ASP92
|
2.2
|
11.3
|
1.0
|
O1
|
A:PO4505
|
2.9
|
14.6
|
1.0
|
P
|
A:PO4505
|
3.1
|
12.5
|
1.0
|
CD2
|
A:HIS66
|
3.1
|
12.2
|
1.0
|
CE1
|
A:HIS66
|
3.2
|
11.3
|
1.0
|
CG
|
A:ASP64
|
3.2
|
11.5
|
1.0
|
HB3
|
A:ASP92
|
3.3
|
12.2
|
1.0
|
CG
|
A:ASP92
|
3.3
|
11.4
|
1.0
|
HD2
|
A:HIS66
|
3.3
|
14.6
|
1.0
|
HE1
|
A:HIS66
|
3.3
|
13.5
|
1.0
|
MN
|
A:MN501
|
3.4
|
11.3
|
1.0
|
HB3
|
A:ASP64
|
3.5
|
13.6
|
1.0
|
HE1
|
A:PHE267
|
3.6
|
15.9
|
1.0
|
CB
|
A:ASP92
|
3.6
|
10.2
|
1.0
|
HA
|
A:HIS248
|
3.7
|
13.6
|
1.0
|
HB2
|
A:ASP92
|
3.7
|
12.2
|
1.0
|
HE1
|
A:HIS173
|
3.9
|
13.0
|
1.0
|
CB
|
A:ASP64
|
3.9
|
11.3
|
1.0
|
O3
|
A:PO4505
|
3.9
|
13.2
|
1.0
|
HD2
|
A:HIS125
|
4.0
|
13.5
|
1.0
|
O
|
A:HOH634
|
4.1
|
14.3
|
1.0
|
HE2
|
A:HIS125
|
4.1
|
15.3
|
1.0
|
O
|
A:HOH620
|
4.1
|
17.1
|
1.0
|
OD1
|
A:ASP64
|
4.1
|
11.4
|
1.0
|
O2
|
A:PO4505
|
4.1
|
12.4
|
1.0
|
HB2
|
A:ASP64
|
4.2
|
13.6
|
1.0
|
ND1
|
A:HIS66
|
4.3
|
11.8
|
1.0
|
CG
|
A:HIS66
|
4.3
|
12.9
|
1.0
|
CD2
|
A:HIS125
|
4.4
|
11.2
|
1.0
|
OD1
|
A:ASP92
|
4.4
|
11.3
|
1.0
|
CE1
|
A:PHE267
|
4.4
|
13.2
|
1.0
|
NE2
|
A:HIS125
|
4.4
|
12.8
|
1.0
|
CE1
|
A:HIS173
|
4.5
|
10.9
|
1.0
|
NE2
|
A:HIS173
|
4.5
|
10.7
|
1.0
|
CA
|
A:HIS248
|
4.6
|
11.3
|
1.0
|
O
|
A:HIS248
|
4.7
|
12.8
|
1.0
|
HH
|
A:TYR272
|
4.7
|
23.4
|
1.0
|
H
|
A:HIS248
|
4.7
|
13.1
|
1.0
|
OH
|
A:TYR272
|
4.8
|
19.5
|
1.0
|
C
|
A:HIS248
|
4.8
|
12.1
|
1.0
|
HZ
|
A:PHE267
|
4.9
|
16.0
|
1.0
|
|
Manganese binding site 3 out
of 4 in 6zei
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Manganese Binding Sites List in 6zei
Manganese binding site 3 out
of 4 in the Structure of PP1-IRSP53 S455E Chimera [PP1(7-304) + Linker (G/S)X9 + IRSP53(449-465)] Bound to PHACTR1 (516-580)
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 3 of Structure of PP1-IRSP53 S455E Chimera [PP1(7-304) + Linker (G/S)X9 + IRSP53(449-465)] Bound to PHACTR1 (516-580) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn501
b:12.1
occ:1.00
|
OD1
|
B:ASN124
|
2.1
|
11.7
|
1.0
|
ND1
|
B:HIS248
|
2.2
|
12.8
|
1.0
|
O1
|
B:PO4504
|
2.2
|
13.2
|
1.0
|
OD2
|
B:ASP92
|
2.2
|
11.4
|
1.0
|
NE2
|
B:HIS173
|
2.3
|
11.8
|
1.0
|
O4
|
B:PO4504
|
2.3
|
13.4
|
1.0
|
P
|
B:PO4504
|
2.8
|
13.3
|
1.0
|
CE1
|
B:HIS248
|
3.1
|
12.3
|
1.0
|
HA
|
B:HIS248
|
3.1
|
14.9
|
1.0
|
HE1
|
B:HIS248
|
3.1
|
14.8
|
1.0
|
CG
|
B:ASN124
|
3.1
|
11.7
|
1.0
|
CG
|
B:ASP92
|
3.2
|
10.2
|
1.0
|
HD21
|
B:ASN124
|
3.2
|
16.1
|
1.0
|
CD2
|
B:HIS173
|
3.2
|
11.7
|
1.0
|
HD2
|
B:HIS125
|
3.2
|
15.6
|
1.0
|
CE1
|
B:HIS173
|
3.3
|
11.4
|
1.0
|
HD2
|
B:HIS173
|
3.3
|
14.1
|
1.0
|
CG
|
B:HIS248
|
3.4
|
12.8
|
1.0
|
MN
|
B:MN502
|
3.4
|
12.7
|
1.0
|
HE1
|
B:HIS173
|
3.4
|
13.7
|
1.0
|
OD1
|
B:ASP92
|
3.5
|
11.6
|
1.0
|
ND2
|
B:ASN124
|
3.5
|
13.4
|
1.0
|
HB2
|
B:HIS248
|
3.7
|
14.4
|
1.0
|
H
|
B:ASN124
|
3.8
|
14.0
|
1.0
|
CB
|
B:HIS248
|
3.8
|
12.0
|
1.0
|
O3
|
B:PO4504
|
3.8
|
14.3
|
1.0
|
CA
|
B:HIS248
|
3.8
|
12.4
|
1.0
|
O2
|
B:PO4504
|
4.0
|
14.4
|
1.0
|
CD2
|
B:HIS125
|
4.1
|
13.0
|
1.0
|
OD2
|
B:ASP64
|
4.2
|
11.8
|
1.0
|
NE2
|
B:HIS248
|
4.2
|
12.4
|
1.0
|
HE2
|
B:HIS125
|
4.3
|
16.6
|
1.0
|
O
|
B:HIS248
|
4.3
|
13.4
|
1.0
|
ND1
|
B:HIS173
|
4.4
|
10.7
|
1.0
|
CG
|
B:HIS173
|
4.4
|
10.4
|
1.0
|
HD22
|
B:ASN124
|
4.4
|
16.1
|
1.0
|
CD2
|
B:HIS248
|
4.4
|
11.8
|
1.0
|
CB
|
B:ASP92
|
4.5
|
10.8
|
1.0
|
CB
|
B:ASN124
|
4.5
|
11.5
|
1.0
|
HB2
|
B:ASP92
|
4.5
|
13.0
|
1.0
|
NE2
|
B:HIS125
|
4.6
|
13.9
|
1.0
|
HH12
|
B:ARG221
|
4.6
|
16.3
|
1.0
|
N
|
B:ASN124
|
4.6
|
11.7
|
1.0
|
C
|
B:HIS248
|
4.6
|
12.7
|
1.0
|
H
|
B:HIS125
|
4.6
|
15.4
|
1.0
|
HB3
|
B:ASN124
|
4.7
|
13.8
|
1.0
|
O
|
B:LEU205
|
4.7
|
12.3
|
1.0
|
HB3
|
B:HIS248
|
4.8
|
14.4
|
1.0
|
HB3
|
B:ASP92
|
4.8
|
13.0
|
1.0
|
H
|
B:HIS248
|
4.8
|
13.7
|
1.0
|
N
|
B:HIS248
|
4.9
|
11.4
|
1.0
|
HH22
|
B:ARG221
|
4.9
|
17.0
|
1.0
|
HB
|
B:THR330
|
5.0
|
22.3
|
1.0
|
HE1
|
B:HIS66
|
5.0
|
16.0
|
1.0
|
HE2
|
B:HIS248
|
5.0
|
14.8
|
1.0
|
|
Manganese binding site 4 out
of 4 in 6zei
Go back to
Manganese Binding Sites List in 6zei
Manganese binding site 4 out
of 4 in the Structure of PP1-IRSP53 S455E Chimera [PP1(7-304) + Linker (G/S)X9 + IRSP53(449-465)] Bound to PHACTR1 (516-580)
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 4 of Structure of PP1-IRSP53 S455E Chimera [PP1(7-304) + Linker (G/S)X9 + IRSP53(449-465)] Bound to PHACTR1 (516-580) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn502
b:12.7
occ:1.00
|
O1
|
B:PO4504
|
2.0
|
13.2
|
1.0
|
OD2
|
B:ASP64
|
2.0
|
11.8
|
1.0
|
NE2
|
B:HIS66
|
2.1
|
12.6
|
1.0
|
OD2
|
B:ASP92
|
2.2
|
11.4
|
1.0
|
O
|
B:HOH769
|
2.2
|
13.7
|
1.0
|
O3
|
B:PO4504
|
2.9
|
14.3
|
1.0
|
P
|
B:PO4504
|
3.0
|
13.3
|
1.0
|
CE1
|
B:HIS66
|
3.1
|
13.3
|
1.0
|
CD2
|
B:HIS66
|
3.1
|
13.1
|
1.0
|
CG
|
B:ASP64
|
3.2
|
11.4
|
1.0
|
HB3
|
B:ASP92
|
3.2
|
13.0
|
1.0
|
CG
|
B:ASP92
|
3.3
|
10.2
|
1.0
|
HE1
|
B:HIS66
|
3.3
|
16.0
|
1.0
|
HD2
|
B:HIS66
|
3.3
|
15.7
|
1.0
|
MN
|
B:MN501
|
3.4
|
12.1
|
1.0
|
HB3
|
B:ASP64
|
3.5
|
14.6
|
1.0
|
HE1
|
B:PHE267
|
3.6
|
18.7
|
1.0
|
CB
|
B:ASP92
|
3.6
|
10.8
|
1.0
|
HA
|
B:HIS248
|
3.7
|
14.9
|
1.0
|
HB2
|
B:ASP92
|
3.7
|
13.0
|
1.0
|
CB
|
B:ASP64
|
3.9
|
12.1
|
1.0
|
HE1
|
B:HIS173
|
3.9
|
13.7
|
1.0
|
O4
|
B:PO4504
|
4.0
|
13.4
|
1.0
|
HD2
|
B:HIS125
|
4.0
|
15.6
|
1.0
|
O
|
B:HOH617
|
4.0
|
16.9
|
1.0
|
O
|
B:HOH643
|
4.1
|
15.1
|
1.0
|
OD1
|
B:ASP64
|
4.1
|
12.4
|
1.0
|
O2
|
B:PO4504
|
4.1
|
14.4
|
1.0
|
HE2
|
B:HIS125
|
4.2
|
16.6
|
1.0
|
ND1
|
B:HIS66
|
4.2
|
12.5
|
1.0
|
HB2
|
B:ASP64
|
4.2
|
14.6
|
1.0
|
CG
|
B:HIS66
|
4.3
|
12.9
|
1.0
|
CD2
|
B:HIS125
|
4.4
|
13.0
|
1.0
|
OD1
|
B:ASP92
|
4.4
|
11.6
|
1.0
|
CE1
|
B:PHE267
|
4.5
|
15.6
|
1.0
|
NE2
|
B:HIS125
|
4.5
|
13.9
|
1.0
|
CE1
|
B:HIS173
|
4.5
|
11.4
|
1.0
|
NE2
|
B:HIS173
|
4.5
|
11.8
|
1.0
|
CA
|
B:HIS248
|
4.6
|
12.4
|
1.0
|
H
|
B:HIS248
|
4.7
|
13.7
|
1.0
|
O
|
B:HIS248
|
4.7
|
13.4
|
1.0
|
HH
|
B:TYR272
|
4.7
|
21.5
|
1.0
|
C
|
B:HIS248
|
4.8
|
12.7
|
1.0
|
OH
|
B:TYR272
|
4.9
|
17.9
|
1.0
|
HZ
|
B:PHE267
|
5.0
|
18.0
|
1.0
|
HD1
|
B:HIS66
|
5.0
|
15.0
|
1.0
|
|
Reference:
R.O.Fedoryshchak,
M.Prechova,
A.Butler,
R.Lee,
N.O'reilly,
H.R.Flynn,
A.P.Snijders,
N.Eder,
S.Ultanir,
S.Mouilleron,
R.Treisman.
Molecular Basis For Substrate Specificity of the PHACTR1/PP1 Phosphatase Holoenzyme. Elife V. 9 2020.
ISSN: ESSN 2050-084X
PubMed: 32975518
DOI: 10.7554/ELIFE.61509
Page generated: Sun Oct 6 07:58:10 2024
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