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Calcium in PDB 7pc8: The Pdz Domain of SNTG1 Complexed with the Phosphomimetic Mutant Pdz- Binding Motif of RSK1

Enzymatic activity of The Pdz Domain of SNTG1 Complexed with the Phosphomimetic Mutant Pdz- Binding Motif of RSK1

All present enzymatic activity of The Pdz Domain of SNTG1 Complexed with the Phosphomimetic Mutant Pdz- Binding Motif of RSK1:
2.7.11.1;

Protein crystallography data

The structure of The Pdz Domain of SNTG1 Complexed with the Phosphomimetic Mutant Pdz- Binding Motif of RSK1, PDB code: 7pc8 was solved by A.Cousido-Siah, G.Trave, G.Gogl, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.33 / 2.50
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 226.58, 59.82, 125.21, 90, 117.84, 90
R / Rfree (%) 20.2 / 23.2

Calcium Binding Sites:

The binding sites of Calcium atom in the The Pdz Domain of SNTG1 Complexed with the Phosphomimetic Mutant Pdz- Binding Motif of RSK1 (pdb code 7pc8). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the The Pdz Domain of SNTG1 Complexed with the Phosphomimetic Mutant Pdz- Binding Motif of RSK1, PDB code: 7pc8:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 7pc8

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Calcium binding site 1 out of 9 in the The Pdz Domain of SNTG1 Complexed with the Phosphomimetic Mutant Pdz- Binding Motif of RSK1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Pdz Domain of SNTG1 Complexed with the Phosphomimetic Mutant Pdz- Binding Motif of RSK1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:101.5
occ:1.00
 O A:GLY173 2.9 59.8 1.0
OE1 A:GLU176 3.0 62.5 1.0
OE2 A:GLU176 3.2 60.9 1.0
O A:VAL174 3.3 53.0 1.0
CD A:GLU176 3.5 58.5 1.0
C A:GLY173 3.8 50.9 1.0
CA A:GLY173 4.4 46.6 1.0
C A:VAL174 4.4 46.8 1.0
O A:HOH687 4.6 50.6 1.0
N A:VAL174 4.7 44.7 1.0

Calcium binding site 2 out of 9 in 7pc8

Go back to Calcium Binding Sites List in 7pc8
Calcium binding site 2 out of 9 in the The Pdz Domain of SNTG1 Complexed with the Phosphomimetic Mutant Pdz- Binding Motif of RSK1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Pdz Domain of SNTG1 Complexed with the Phosphomimetic Mutant Pdz- Binding Motif of RSK1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:90.5
occ:1.00
 OE1 A:GLU219 2.9 41.7 1.0
O A:LEU214 2.9 38.3 1.0
O A:LYS211 3.2 44.4 1.0
O A:HOH669 3.2 44.8 1.0
CA A:SER215 3.7 40.0 1.0
CB A:SER215 3.7 43.0 1.0
C A:LEU214 3.9 38.5 1.0
CD A:GLU219 4.1 44.8 1.0
N A:SER215 4.2 38.7 1.0
C A:LYS211 4.4 46.9 1.0
O A:SER212 4.9 54.9 1.0
OE2 A:GLU219 4.9 50.9 1.0
CA A:SER212 4.9 44.5 1.0
C A:SER215 5.0 38.3 1.0

Calcium binding site 3 out of 9 in 7pc8

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Calcium binding site 3 out of 9 in the The Pdz Domain of SNTG1 Complexed with the Phosphomimetic Mutant Pdz- Binding Motif of RSK1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The Pdz Domain of SNTG1 Complexed with the Phosphomimetic Mutant Pdz- Binding Motif of RSK1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:85.0
occ:1.00
 OD2 A:ASP285 2.2 106.8 1.0
O A:GLY243 2.4 74.4 1.0
O A:GLY245 2.7 80.9 1.0
CG A:ASP285 3.2 94.0 1.0
O A:MET241 3.4 72.1 1.0
N A:GLY245 3.4 82.7 1.0
C A:GLY245 3.5 77.7 1.0
C A:GLY243 3.5 76.4 1.0
OD1 A:ASP285 3.6 102.2 1.0
C A:LEU244 3.6 87.5 1.0
CA A:LEU244 3.8 87.0 1.0
OG1 A:THR246 3.9 75.0 1.0
CA A:GLY245 4.0 78.4 1.0
C A:MET241 4.2 67.0 1.0
N A:LEU244 4.2 83.3 1.0
O A:LEU244 4.3 90.5 1.0
CB A:ASP285 4.4 75.9 1.0
O A:LYS242 4.4 74.0 1.0
N A:THR246 4.5 74.6 1.0
C A:LYS242 4.6 74.5 1.0
CA A:MET241 4.7 60.5 1.0
CA A:GLY243 4.8 74.5 1.0
N A:GLY243 4.8 75.7 1.0
CA A:THR246 4.9 68.0 1.0
CA A:ASP285 4.9 67.0 1.0
CB A:THR246 5.0 66.7 1.0

Calcium binding site 4 out of 9 in 7pc8

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Calcium binding site 4 out of 9 in the The Pdz Domain of SNTG1 Complexed with the Phosphomimetic Mutant Pdz- Binding Motif of RSK1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of The Pdz Domain of SNTG1 Complexed with the Phosphomimetic Mutant Pdz- Binding Motif of RSK1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca504

b:79.3
occ:1.00
 O A:ARG328 2.3 75.2 1.0
O A:GLY325 2.5 64.5 1.0
OE1 A:GLU370 2.5 67.5 1.0
O A:GLY330 2.6 72.0 1.0
OE2 A:GLU370 2.7 69.7 1.0
O A:HOH713 2.8 60.3 1.0
CD A:GLU370 3.0 65.0 1.0
C A:ARG328 3.4 71.7 1.0
C A:GLY325 3.4 59.0 1.0
C A:GLY330 3.6 69.7 1.0
N A:GLY330 3.6 77.2 1.0
O A:HOH712 3.9 69.4 1.0
C A:LYS329 4.0 82.0 1.0
CA A:LYS329 4.1 80.0 1.0
CA A:GLY330 4.1 72.2 1.0
N A:LYS329 4.2 76.4 1.0
CA A:VAL326 4.3 55.4 1.0
N A:VAL326 4.3 56.5 1.0
CA A:GLY325 4.3 53.4 1.0
O A:VAL326 4.3 62.5 1.0
OG1 A:THR331 4.4 62.6 1.0
C A:VAL326 4.4 60.8 1.0
N A:ARG328 4.4 60.3 1.0
CG A:GLU370 4.5 57.7 1.0
CA A:ARG328 4.5 64.8 1.0
CG A:ARG328 4.6 65.9 1.0
N A:THR331 4.7 65.0 1.0
O A:LYS329 4.8 88.4 1.0

Calcium binding site 5 out of 9 in 7pc8

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Calcium binding site 5 out of 9 in the The Pdz Domain of SNTG1 Complexed with the Phosphomimetic Mutant Pdz- Binding Motif of RSK1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of The Pdz Domain of SNTG1 Complexed with the Phosphomimetic Mutant Pdz- Binding Motif of RSK1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca505

b:42.6
occ:1.00
 O A:MET401 2.3 38.9 1.0
O A:GLY405 2.3 42.4 1.0
O A:GLY403 2.4 43.7 1.0
OD2 A:ASP445 2.5 46.8 1.0
OD1 A:ASP445 2.6 43.4 1.0
CG A:ASP445 2.9 45.1 1.0
C A:MET401 3.3 37.6 1.0
C A:GLY405 3.4 42.9 1.0
C A:GLY403 3.6 40.2 1.0
CA A:MET401 3.9 35.8 1.0
N A:GLY405 3.9 47.1 1.0
N A:GLY403 4.1 42.0 1.0
CA A:GLY405 4.1 36.6 1.0
C A:LYS404 4.2 46.2 1.0
C A:LYS402 4.2 47.6 1.0
OG1 A:THR406 4.3 39.9 1.0
CB A:ASP445 4.4 43.0 1.0
N A:LYS402 4.4 38.7 1.0
O A:LYS402 4.4 54.3 1.0
CA A:GLY403 4.4 37.0 1.0
N A:THR406 4.5 45.0 1.0
N A:LYS404 4.6 45.6 1.0
CB A:MET401 4.6 33.6 1.0
O A:HOH706 4.6 53.3 1.0
O A:LYS404 4.6 44.6 1.0
CA A:LYS404 4.7 47.3 1.0
O A:HOH634 4.7 36.0 1.0
CA A:THR406 4.7 37.8 1.0
CA A:LYS402 4.8 44.6 1.0

Calcium binding site 6 out of 9 in 7pc8

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Calcium binding site 6 out of 9 in the The Pdz Domain of SNTG1 Complexed with the Phosphomimetic Mutant Pdz- Binding Motif of RSK1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of The Pdz Domain of SNTG1 Complexed with the Phosphomimetic Mutant Pdz- Binding Motif of RSK1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca501

b:104.9
occ:1.00
 O B:LYS211 3.0 60.1 1.0
OE1 B:GLU219 3.3 59.5 1.0
O B:LEU214 3.4 55.3 1.0
C B:LYS211 4.2 54.7 1.0
CA B:SER212 4.5 57.9 1.0
C B:LEU214 4.5 56.3 1.0
CD B:GLU219 4.5 57.7 1.0
CB B:SER215 4.6 54.7 1.0
CA B:SER215 4.6 57.1 1.0
O B:SER212 4.7 62.6 1.0
N B:SER212 4.8 53.1 1.0
C B:SER212 4.8 56.7 1.0

Calcium binding site 7 out of 9 in 7pc8

Go back to Calcium Binding Sites List in 7pc8
Calcium binding site 7 out of 9 in the The Pdz Domain of SNTG1 Complexed with the Phosphomimetic Mutant Pdz- Binding Motif of RSK1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of The Pdz Domain of SNTG1 Complexed with the Phosphomimetic Mutant Pdz- Binding Motif of RSK1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca502

b:109.9
occ:1.00
 O B:GLY243 2.3 98.7 1.0
OD2 B:ASP285 2.5 89.3 1.0
O B:GLY245 2.8 96.6 1.0
CG B:ASP285 3.3 86.1 1.0
OD1 B:ASP285 3.5 90.5 1.0
C B:GLY243 3.5 95.8 1.0
O B:MET241 3.7 85.5 1.0
N B:GLY245 3.8 94.7 1.0
C B:GLY245 3.8 91.2 1.0
C B:LEU244 4.0 96.8 1.0
CA B:LEU244 4.0 98.4 1.0
OG1 B:THR246 4.1 78.5 1.0
C B:MET241 4.2 77.4 1.0
N B:LEU244 4.2 98.3 1.0
CA B:GLY245 4.4 91.8 1.0
C B:LYS242 4.5 89.3 1.0
O B:LYS242 4.6 92.4 1.0
CB B:ASP285 4.6 77.0 1.0
N B:GLY243 4.6 89.6 1.0
CA B:GLY243 4.7 91.5 1.0
O B:LEU244 4.7 96.6 1.0
CA B:MET241 4.7 69.8 1.0
N B:LYS242 4.8 78.2 1.0
N B:THR246 4.8 82.1 1.0

Calcium binding site 8 out of 9 in 7pc8

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Calcium binding site 8 out of 9 in the The Pdz Domain of SNTG1 Complexed with the Phosphomimetic Mutant Pdz- Binding Motif of RSK1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of The Pdz Domain of SNTG1 Complexed with the Phosphomimetic Mutant Pdz- Binding Motif of RSK1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca503

b:86.8
occ:1.00
 OE1 B:GLU370 2.5 74.6 1.0
O B:ARG328 2.5 74.9 1.0
O B:HOH677 2.6 57.6 1.0
O B:GLY325 2.7 71.3 1.0
OE2 B:GLU370 2.7 74.1 1.0
O B:GLY330 2.9 73.1 1.0
CD B:GLU370 3.0 70.8 1.0
N B:GLY330 3.5 76.5 1.0
C B:ARG328 3.7 73.2 1.0
C B:GLY325 3.7 66.3 1.0
C B:GLY330 3.8 72.5 1.0
C B:LYS329 4.1 82.7 1.0
CA B:GLY330 4.1 73.6 1.0
CA B:LYS329 4.2 78.6 1.0
CA B:VAL326 4.4 63.4 1.0
N B:LYS329 4.4 77.2 1.0
O B:VAL326 4.4 71.6 1.0
CG B:GLU370 4.5 65.7 1.0
N B:VAL326 4.5 62.2 1.0
C B:VAL326 4.6 65.4 1.0
OG1 B:THR331 4.6 78.3 1.0
CA B:GLY325 4.7 62.0 1.0
N B:ARG328 4.8 69.2 1.0
CA B:ARG328 4.9 70.5 1.0

Calcium binding site 9 out of 9 in 7pc8

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Calcium binding site 9 out of 9 in the The Pdz Domain of SNTG1 Complexed with the Phosphomimetic Mutant Pdz- Binding Motif of RSK1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of The Pdz Domain of SNTG1 Complexed with the Phosphomimetic Mutant Pdz- Binding Motif of RSK1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca504

b:49.8
occ:1.00
 OD2 B:ASP445 2.2 69.6 1.0
O B:GLY403 2.4 45.2 1.0
O B:GLY405 2.4 50.9 1.0
O B:MET401 2.5 48.5 1.0
CG B:ASP445 2.9 67.2 1.0
OD1 B:ASP445 3.0 72.7 1.0
C B:GLY405 3.5 45.0 1.0
C B:MET401 3.5 46.0 1.0
C B:GLY403 3.6 45.4 1.0
N B:GLY405 3.9 45.0 1.0
CA B:MET401 4.1 41.5 1.0
C B:LYS404 4.2 48.4 1.0
N B:GLY403 4.2 51.9 1.0
CA B:GLY405 4.2 44.5 1.0
OG1 B:THR406 4.3 42.5 1.0
CB B:ASP445 4.4 56.5 1.0
C B:LYS402 4.4 55.5 1.0
CA B:GLY403 4.5 46.2 1.0
N B:LYS404 4.5 46.5 1.0
N B:THR406 4.6 46.1 1.0
O B:LYS404 4.6 54.3 1.0
CA B:LYS404 4.6 46.9 1.0
N B:LYS402 4.6 46.6 1.0
O B:LYS402 4.6 63.9 1.0
CB B:MET401 4.7 40.3 1.0
CA B:THR406 4.8 41.9 1.0
CA B:LYS402 5.0 49.9 1.0

Reference:

A.Cousido-Siah, L.Carneiro, C.Kostmann, P.Ecsedi, L.Nyitray, G.Trave, G.Gogl. A Scalable Strategy to Solve Structures of Pdz Domains and Their Complexes. Acta Crystallogr D Struct V. 78 509 2022BIOL.
ISSN: ISSN 2059-7983
PubMed: 35362473
DOI: 10.1107/S2059798322001784
Page generated: Fri Jul 19 02:51:32 2024

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