Calcium in PDB 7nxv: Crystal Structure of the Complex of Dnase I/G-Actin/PPP1R15A_582-621

Enzymatic activity of Crystal Structure of the Complex of Dnase I/G-Actin/PPP1R15A_582-621

All present enzymatic activity of Crystal Structure of the Complex of Dnase I/G-Actin/PPP1R15A_582-621:
3.1.21.1;

Protein crystallography data

The structure of Crystal Structure of the Complex of Dnase I/G-Actin/PPP1R15A_582-621, PDB code: 7nxv was solved by Y.Yan, D.Ron, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 55.11 / 2.55
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 86.519, 107.807, 192.412, 90, 90, 90
R / Rfree (%) 21.6 / 24.8

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the Complex of Dnase I/G-Actin/PPP1R15A_582-621 (pdb code 7nxv). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of the Complex of Dnase I/G-Actin/PPP1R15A_582-621, PDB code: 7nxv:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 7nxv

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Calcium binding site 1 out of 6 in the Crystal Structure of the Complex of Dnase I/G-Actin/PPP1R15A_582-621


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 the Complex of Dnase I/G-Actin/PPP1R15A_582-621 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:26.4
occ:1.00
 O A:HOH507 2.2 21.6 1.0
O2B A:ATP401 2.3 25.7 1.0
O2G A:ATP401 2.3 26.6 1.0
O A:HOH502 2.4 20.7 1.0
O A:HOH506 2.4 26.0 1.0
O A:HOH501 2.5 21.9 1.0
PG A:ATP401 3.5 26.5 1.0
PB A:ATP401 3.6 26.3 1.0
O3B A:ATP401 3.9 26.4 1.0
O3G A:ATP401 4.0 26.7 1.0
O2A A:ATP401 4.1 26.5 1.0
OE1 A:GLN137 4.2 26.6 1.0
O3A A:ATP401 4.2 26.5 1.0
NZ A:LYS18 4.4 30.5 1.0
CA A:GLY13 4.5 31.9 1.0
CD A:GLN137 4.5 27.1 1.0
OD1 A:ASP154 4.5 37.7 1.0
OD2 A:ASP154 4.6 37.5 1.0
OD2 A:ASP11 4.6 30.6 1.0
OD1 A:ASP11 4.7 31.0 1.0
PA A:ATP401 4.7 26.6 1.0
O1G A:ATP401 4.8 26.9 1.0
O1B A:ATP401 4.8 25.7 1.0
CG A:ASP154 4.9 37.0 1.0
NE2 A:GLN137 4.9 26.8 1.0
CG A:GLN137 5.0 27.5 1.0

Calcium binding site 2 out of 6 in 7nxv

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Calcium binding site 2 out of 6 in the Crystal Structure of the Complex of Dnase I/G-Actin/PPP1R15A_582-621


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 the Complex of Dnase I/G-Actin/PPP1R15A_582-621 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca301

b:42.8
occ:1.00
 O B:PHE109 2.2 28.1 1.0
OE2 B:GLU112 2.4 38.6 1.0
OE1 B:GLU102 2.5 50.6 1.0
OD1 B:ASP107 2.7 31.0 1.0
OD1 B:ASP99 2.7 31.4 1.0
CD B:GLU112 3.4 35.6 1.0
C B:PHE109 3.5 28.6 1.0
CD B:GLU102 3.5 50.5 1.0
O B:SER110 3.6 30.0 1.0
CG B:ASP99 3.6 31.2 1.0
CG B:ASP107 3.7 30.5 1.0
CG B:GLU112 3.7 34.6 1.0
OD2 B:ASP99 3.8 31.1 1.0
CB B:ASP107 3.9 30.2 1.0
C B:SER110 4.0 29.3 1.0
CG B:GLU102 4.0 47.7 1.0
CA B:SER110 4.1 29.3 1.0
N B:SER110 4.2 28.6 1.0
CG B:ARG73 4.5 38.2 1.0
OE1 B:GLU112 4.5 36.1 1.0
CA B:PHE109 4.5 29.4 1.0
OE2 B:GLU102 4.6 54.0 1.0
NE B:ARG73 4.6 37.4 1.0
N B:PHE109 4.6 29.5 1.0
N B:GLU112 4.7 31.2 1.0
N B:ARG111 4.8 29.2 1.0
OD2 B:ASP107 4.8 30.9 1.0
CB B:PHE109 4.9 29.4 1.0
CZ B:ARG73 5.0 36.8 1.0

Calcium binding site 3 out of 6 in 7nxv

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Calcium binding site 3 out of 6 in the Crystal Structure of the Complex of Dnase I/G-Actin/PPP1R15A_582-621


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of the Complex of Dnase I/G-Actin/PPP1R15A_582-621 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca302

b:52.5
occ:1.00
 O B:THR207 2.4 37.6 1.0
O B:THR205 2.5 39.8 1.0
O B:THR203 2.5 37.9 1.0
OD2 B:ASP201 2.5 38.4 1.0
OG1 B:THR203 2.6 39.2 1.0
OD1 B:ASP201 2.9 37.4 1.0
CG B:ASP201 3.1 37.0 1.0
C B:THR203 3.4 38.2 1.0
C B:THR205 3.6 39.6 1.0
C B:THR207 3.7 36.9 1.0
CB B:THR203 3.8 38.6 1.0
CA B:THR203 4.0 38.2 1.0
N B:THR207 4.1 38.1 1.0
C B:SER206 4.2 39.0 1.0
N B:THR205 4.3 39.7 1.0
N B:THR203 4.4 37.4 1.0
N B:SER206 4.4 39.6 1.0
CA B:SER206 4.4 39.7 1.0
N B:ALA204 4.4 38.3 1.0
C B:ALA204 4.4 38.8 1.0
CA B:THR207 4.5 37.6 1.0
CB B:ASP201 4.6 36.4 1.0
CA B:THR205 4.6 39.5 1.0
OG1 B:THR207 4.6 37.9 1.0
N B:ASN208 4.6 35.9 1.0
O B:SER206 4.7 39.2 1.0
CA B:ALA204 4.8 38.4 1.0
O B:ALA204 4.8 40.0 1.0
CA B:ASN208 4.8 35.9 1.0
CE2 B:TYR253 4.8 33.3 1.0
OG1 B:THR205 4.9 39.7 1.0
OH B:TYR253 4.9 33.6 1.0
CG2 B:THR203 5.0 38.9 1.0

Calcium binding site 4 out of 6 in 7nxv

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Calcium binding site 4 out of 6 in the Crystal Structure of the Complex of Dnase I/G-Actin/PPP1R15A_582-621


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of the Complex of Dnase I/G-Actin/PPP1R15A_582-621 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca402

b:27.1
occ:1.00
 O2G D:ATP401 2.2 29.1 1.0
O2B D:ATP401 2.3 27.8 1.0
O D:HOH507 2.3 17.3 1.0
O D:HOH504 2.4 17.8 1.0
O D:HOH508 2.4 12.3 1.0
O D:HOH505 2.5 26.5 1.0
O D:HOH501 2.7 24.3 1.0
PG D:ATP401 3.4 28.9 1.0
PB D:ATP401 3.5 27.6 1.0
O3B D:ATP401 3.8 28.3 1.0
O3G D:ATP401 3.9 29.0 1.0
O2A D:ATP401 4.2 27.5 1.0
O3A D:ATP401 4.2 27.6 1.0
OE1 D:GLN137 4.2 28.0 1.0
CA D:GLY13 4.3 30.7 1.0
NZ D:LYS18 4.5 30.8 1.0
CD D:GLN137 4.5 28.2 1.0
OD2 D:ASP154 4.6 31.1 1.0
OD1 D:ASP11 4.6 31.1 1.0
OD1 D:ASP154 4.6 31.1 1.0
O1G D:ATP401 4.7 28.5 1.0
OD2 D:ASP11 4.7 32.0 1.0
PA D:ATP401 4.7 27.4 1.0
O1B D:ATP401 4.8 27.7 1.0
CG D:GLN137 4.8 28.6 1.0
NE2 D:GLN137 5.0 28.3 1.0

Calcium binding site 5 out of 6 in 7nxv

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Calcium binding site 5 out of 6 in the Crystal Structure of the Complex of Dnase I/G-Actin/PPP1R15A_582-621


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of the Complex of Dnase I/G-Actin/PPP1R15A_582-621 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca301

b:33.7
occ:1.00
 O F:PHE109 2.3 31.4 1.0
OD1 F:ASP99 2.4 34.1 1.0
O F:HOH406 2.5 15.0 1.0
OD1 F:ASP107 2.5 38.3 1.0
OE2 F:GLU112 2.7 33.9 1.0
OE1 F:GLU102 2.7 45.3 1.0
CG F:ASP99 3.2 35.0 1.0
CD F:GLU112 3.4 32.6 1.0
OD2 F:ASP99 3.5 35.0 1.0
CG F:ASP107 3.5 38.8 1.0
C F:PHE109 3.5 31.0 1.0
CD F:GLU102 3.6 45.8 1.0
CG F:GLU112 3.6 32.6 1.0
CG F:GLU102 3.7 44.8 1.0
CB F:ASP107 3.7 39.3 1.0
O F:SER110 4.1 30.2 1.0
O F:HOH412 4.3 23.0 1.0
N F:PHE109 4.3 31.9 1.0
CA F:PHE109 4.4 31.4 1.0
C F:SER110 4.4 30.4 1.0
N F:SER110 4.5 30.4 1.0
OE1 F:GLU112 4.5 33.4 1.0
OD2 F:ASP107 4.6 39.9 1.0
CB F:PHE109 4.6 31.1 1.0
CA F:SER110 4.6 30.2 1.0
CB F:ASP99 4.6 35.4 1.0
N F:GLU112 4.6 31.6 1.0
O F:HOH402 4.7 25.4 1.0
OE2 F:GLU102 4.7 46.5 1.0
NH1 F:ARG73 4.9 41.4 1.0
NE F:ARG73 4.9 42.1 1.0
CB F:GLU112 4.9 32.0 1.0
CA F:ASP107 5.0 39.3 1.0
CG F:ARG73 5.0 41.8 1.0

Calcium binding site 6 out of 6 in 7nxv

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Calcium binding site 6 out of 6 in the Crystal Structure of the Complex of Dnase I/G-Actin/PPP1R15A_582-621


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of the Complex of Dnase I/G-Actin/PPP1R15A_582-621 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca302

b:61.8
occ:1.00
 O F:THR205 2.3 35.3 1.0
O F:THR207 2.4 37.0 1.0
O F:THR203 2.5 30.4 1.0
OD2 F:ASP201 2.6 34.2 1.0
OG1 F:THR203 2.7 32.1 1.0
O F:HOH416 2.8 26.0 1.0
OD1 F:ASP201 2.9 34.2 1.0
CG F:ASP201 3.1 33.9 1.0
C F:THR203 3.4 31.2 1.0
C F:THR205 3.5 35.4 1.0
C F:THR207 3.6 36.2 1.0
CB F:THR203 3.9 31.6 1.0
C F:SER206 4.0 36.4 1.0
N F:THR207 4.0 36.0 1.0
CA F:THR203 4.1 31.4 1.0
N F:THR205 4.3 34.4 1.0
N F:SER206 4.3 35.7 1.0
CA F:SER206 4.3 36.0 1.0
C F:ALA204 4.3 33.4 1.0
N F:ALA204 4.4 32.0 1.0
O F:SER206 4.4 37.1 1.0
N F:THR203 4.4 31.4 1.0
OG1 F:THR207 4.4 37.0 1.0
CA F:THR207 4.4 36.1 1.0
CA F:THR205 4.5 34.7 1.0
CB F:ASP201 4.6 33.1 1.0
N F:ASN208 4.6 35.7 1.0
CA F:ALA204 4.7 32.4 1.0
O F:ALA204 4.7 33.9 1.0
CA F:ASN208 4.8 35.5 1.0
CE2 F:TYR253 4.9 30.2 1.0
OG1 F:THR205 5.0 34.2 1.0

Reference:

Y.Yan, H.Harding, D.Ron. Higher Order Phosphatase-Substrate Contacts Terminate the Integrated Stress Response To Be Published.
Page generated: Fri Nov 5 11:39:46 2021

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