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Calcium in PDB 7qql: The Pdz Domain of SNTG2 Complexed with the Phosphorylated Pdz-Binding Motif of RSK1

Enzymatic activity of The Pdz Domain of SNTG2 Complexed with the Phosphorylated Pdz-Binding Motif of RSK1

All present enzymatic activity of The Pdz Domain of SNTG2 Complexed with the Phosphorylated Pdz-Binding Motif of RSK1:
2.7.11.1;

Protein crystallography data

The structure of The Pdz Domain of SNTG2 Complexed with the Phosphorylated Pdz-Binding Motif of RSK1, PDB code: 7qql 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) 48.42 / 2.44
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 97.46, 60.55, 135.21, 90, 92.42, 90
R / Rfree (%) 19.5 / 23

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Calcium atom in the The Pdz Domain of SNTG2 Complexed with the Phosphorylated Pdz-Binding Motif of RSK1 (pdb code 7qql). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 14 binding sites of Calcium where determined in the The Pdz Domain of SNTG2 Complexed with the Phosphorylated Pdz-Binding Motif of RSK1, PDB code: 7qql:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 14 in 7qql

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Calcium binding site 1 out of 14 in the The Pdz Domain of SNTG2 Complexed with the Phosphorylated 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 SNTG2 Complexed with the Phosphorylated Pdz-Binding Motif of RSK1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca501

b:76.3
occ:1.00
 O C:GLY183 2.4 81.5 1.0
OE2 C:GLU186 2.4 76.4 1.0
O C:HOH617 2.5 60.9 1.0
O C:HOH650 2.5 72.0 1.0
OE1 C:GLU186 2.6 78.1 1.0
O C:VAL184 2.6 77.2 1.0
CD C:GLU186 2.9 72.5 1.0
C C:GLY183 3.5 75.8 1.0
C C:VAL184 3.8 71.4 1.0
N C:VAL184 4.3 68.3 1.0
CA C:VAL184 4.3 63.3 1.0
CG C:GLU186 4.4 62.6 1.0
CB C:VAL184 4.4 61.1 1.0
CA C:GLY183 4.4 75.8 1.0
O C:HOH611 4.6 65.2 1.0
N C:GLU186 4.9 63.9 1.0
N C:ASP185 4.9 67.6 1.0

Calcium binding site 2 out of 14 in 7qql

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Calcium binding site 2 out of 14 in the The Pdz Domain of SNTG2 Complexed with the Phosphorylated 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 SNTG2 Complexed with the Phosphorylated Pdz-Binding Motif of RSK1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca502

b:96.8
occ:1.00
 O C:LYS221 2.8 75.6 1.0
O C:LEU224 2.8 74.3 1.0
OE1 C:GLU229 3.2 78.7 1.0
OE2 C:GLU229 3.5 76.4 1.0
CD C:GLU229 3.6 72.4 1.0
C C:LEU224 3.9 75.2 1.0
C C:LYS221 4.0 72.2 1.0
CA C:SER225 4.1 73.9 1.0
CB C:SER225 4.2 69.8 1.0
CA C:SER222 4.4 72.1 1.0
N C:SER225 4.5 85.0 1.0
O C:SER222 4.7 73.3 1.0
N C:SER222 4.7 72.2 1.0
CG C:GLU229 4.8 61.9 1.0
C C:SER222 4.8 70.0 1.0

Calcium binding site 3 out of 14 in 7qql

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Calcium binding site 3 out of 14 in the The Pdz Domain of SNTG2 Complexed with the Phosphorylated 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 SNTG2 Complexed with the Phosphorylated Pdz-Binding Motif of RSK1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca503

b:126.1
occ:1.00
 O C:LEU254 2.5 122.4 1.0
OD2 C:ASP295 2.6 115.3 1.0
O C:GLY253 2.7 130.9 1.0
OG1 C:THR256 2.7 112.0 1.0
C C:LEU254 3.1 127.3 1.0
CA C:LEU254 3.5 128.6 1.0
CG C:ASP295 3.5 111.3 1.0
C C:GLY253 3.7 132.7 1.0
N C:THR256 3.9 117.7 1.0
CB C:THR256 4.0 110.0 1.0
CB C:ASP295 4.0 98.1 1.0
O C:MET251 4.1 102.8 1.0
N C:LEU254 4.1 133.4 1.0
N C:GLY255 4.1 132.0 1.0
CA C:THR256 4.3 114.1 1.0
C C:GLY255 4.4 124.6 1.0
CA C:ASP295 4.5 89.8 1.0
OD1 C:ASP295 4.5 115.4 1.0
CA C:GLY255 4.7 129.2 1.0
O C:ASP295 4.7 91.5 1.0
CB C:LEU254 4.8 122.4 1.0
C C:MET251 5.0 100.0 1.0

Calcium binding site 4 out of 14 in 7qql

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Calcium binding site 4 out of 14 in the The Pdz Domain of SNTG2 Complexed with the Phosphorylated 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 SNTG2 Complexed with the Phosphorylated Pdz-Binding Motif of RSK1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca504

b:88.0
occ:1.00
 O C:ARG338 2.5 98.8 1.0
O C:HOH604 2.5 78.3 1.0
O C:GLY340 2.5 92.4 1.0
OE2 C:GLU380 2.6 96.2 1.0
O C:HOH642 2.7 65.2 1.0
O C:GLY335 2.8 97.0 1.0
OE1 C:GLU380 2.9 95.4 1.0
CD C:GLU380 3.1 93.7 1.0
N C:GLY340 3.3 87.3 1.0
C C:GLY340 3.4 90.6 1.0
C C:ARG338 3.6 92.4 1.0
NZ C:LYS379 3.8 97.1 1.0
C C:LYS339 3.8 86.9 1.0
C C:GLY335 3.9 87.2 1.0
CA C:GLY340 3.9 89.0 1.0
CA C:LYS339 4.0 89.5 1.0
N C:LYS339 4.3 90.8 1.0
OG1 C:THR341 4.4 93.5 1.0
CA C:VAL336 4.6 84.3 1.0
CG C:GLU380 4.6 87.7 1.0
N C:THR341 4.6 90.5 1.0
O C:LYS339 4.6 89.2 1.0
N C:VAL336 4.7 85.7 1.0
CA C:GLY335 4.7 76.7 1.0
O C:VAL336 4.7 91.2 1.0
C C:VAL336 4.7 88.6 1.0
N C:ARG338 4.8 85.2 1.0
CA C:ARG338 4.8 87.8 1.0
CE C:LYS379 4.8 96.7 1.0

Calcium binding site 5 out of 14 in 7qql

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Calcium binding site 5 out of 14 in the The Pdz Domain of SNTG2 Complexed with the Phosphorylated 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 SNTG2 Complexed with the Phosphorylated Pdz-Binding Motif of RSK1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca505

b:60.5
occ:1.00
 OD2 C:ASP455 2.3 64.8 1.0
O C:GLY415 2.4 57.1 1.0
O C:GLY413 2.5 70.7 1.0
O C:MET411 2.5 58.4 1.0
OD1 C:ASP455 2.9 62.9 1.0
CG C:ASP455 2.9 64.4 1.0
C C:MET411 3.4 58.8 1.0
C C:GLY415 3.6 63.0 1.0
C C:GLY413 3.7 62.8 1.0
CA C:MET411 3.8 50.5 1.0
N C:GLY413 4.1 58.5 1.0
N C:GLY415 4.1 67.2 1.0
OG1 C:THR416 4.2 60.8 1.0
C C:LYS412 4.3 59.3 1.0
CB C:ASP455 4.3 59.5 1.0
C C:LYS414 4.4 63.8 1.0
N C:LYS412 4.4 58.5 1.0
CA C:GLY415 4.4 63.5 1.0
CB C:MET411 4.5 49.1 1.0
CA C:GLY413 4.5 59.2 1.0
O C:HOH628 4.5 52.1 1.0
O C:LYS412 4.6 64.0 1.0
N C:THR416 4.6 66.0 1.0
N C:LYS414 4.7 69.1 1.0
CA C:LYS414 4.8 65.5 1.0
CA C:THR416 4.8 59.4 1.0
O C:LYS414 4.8 62.1 1.0
CA C:LYS412 4.9 55.9 1.0

Calcium binding site 6 out of 14 in 7qql

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Calcium binding site 6 out of 14 in the The Pdz Domain of SNTG2 Complexed with the Phosphorylated 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 SNTG2 Complexed with the Phosphorylated Pdz-Binding Motif of RSK1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:74.8
occ:1.00
 O A:HOH673 2.2 70.0 1.0
O A:VAL184 2.4 64.5 1.0
O A:GLY183 2.4 72.0 1.0
O A:HOH672 2.5 56.3 1.0
OE1 A:GLU186 2.6 64.2 1.0
OE2 A:GLU186 2.7 66.2 1.0
CD A:GLU186 3.0 60.2 1.0
C A:GLY183 3.4 67.6 1.0
C A:VAL184 3.6 62.0 1.0
N A:VAL184 4.2 63.8 1.0
CA A:VAL184 4.2 61.1 1.0
CA A:GLY183 4.3 65.4 1.0
CB A:VAL184 4.4 53.9 1.0
CG A:GLU186 4.5 53.3 1.0
N A:ASP185 4.7 58.5 1.0
N A:GLU186 4.7 51.2 1.0
CA A:ASP185 4.9 51.1 1.0
CG1 A:VAL184 5.0 48.0 1.0

Calcium binding site 7 out of 14 in 7qql

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Calcium binding site 7 out of 14 in the The Pdz Domain of SNTG2 Complexed with the Phosphorylated 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 SNTG2 Complexed with the Phosphorylated Pdz-Binding Motif of RSK1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:93.7
occ:1.00
 O A:LEU224 2.5 59.5 1.0
O A:LYS221 2.5 60.9 1.0
OE1 A:GLU229 2.7 69.4 1.0
CD A:GLU229 3.3 61.1 1.0
C A:LEU224 3.5 52.1 1.0
OE2 A:GLU229 3.6 69.1 1.0
C A:LYS221 3.7 57.1 1.0
CA A:SER225 3.8 51.3 1.0
N A:SER225 4.1 51.7 1.0
CB A:SER225 4.2 49.1 1.0
CG A:GLU229 4.4 51.2 1.0
CA A:LYS221 4.6 51.9 1.0
CA A:SER222 4.6 60.3 1.0
N A:SER222 4.6 57.8 1.0
CG A:LYS221 4.7 61.0 1.0
O A:SER222 4.7 61.8 1.0
CA A:LEU224 4.7 47.2 1.0
N A:LEU224 4.7 48.0 1.0
C A:SER222 4.8 61.5 1.0
CB A:GLU229 4.8 50.2 1.0

Calcium binding site 8 out of 14 in 7qql

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Calcium binding site 8 out of 14 in the The Pdz Domain of SNTG2 Complexed with the Phosphorylated 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 SNTG2 Complexed with the Phosphorylated Pdz-Binding Motif of RSK1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:53.4
occ:1.00
 O A:GLY340 2.4 53.3 1.0
OE1 A:GLU380 2.4 55.4 1.0
O A:GLY335 2.4 48.6 1.0
O A:ARG338 2.5 52.2 1.0
OE2 A:GLU380 2.6 53.2 1.0
CD A:GLU380 2.8 49.9 1.0
O A:HOH680 3.1 53.8 1.0
C A:GLY335 3.4 43.1 1.0
C A:GLY340 3.4 45.8 1.0
N A:GLY340 3.6 47.1 1.0
C A:ARG338 3.7 50.3 1.0
OG1 A:THR341 4.0 47.2 1.0
CA A:GLY340 4.1 39.0 1.0
C A:LYS339 4.1 48.5 1.0
CA A:GLY335 4.2 38.0 1.0
NZ A:LYS379 4.2 71.9 1.0
N A:VAL336 4.3 41.9 1.0
CA A:LYS339 4.3 50.2 1.0
CG A:GLU380 4.4 39.9 1.0
CA A:VAL336 4.4 46.6 1.0
N A:LYS339 4.5 54.7 1.0
N A:THR341 4.5 44.3 1.0
N A:ARG338 4.6 52.1 1.0
C A:VAL336 4.6 44.0 1.0
O A:VAL336 4.6 47.4 1.0
CA A:ARG338 4.7 49.6 1.0
CG A:ARG338 4.7 43.0 1.0
O A:LYS339 4.8 50.1 1.0
CA A:THR341 4.8 41.2 1.0

Calcium binding site 9 out of 14 in 7qql

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Calcium binding site 9 out of 14 in the The Pdz Domain of SNTG2 Complexed with the Phosphorylated 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 SNTG2 Complexed with the Phosphorylated Pdz-Binding Motif of RSK1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca504

b:47.0
occ:1.00
 O A:GLY415 2.4 48.4 1.0
O A:MET411 2.5 37.1 1.0
O A:GLY413 2.5 40.1 1.0
OD1 A:ASP455 2.5 42.6 1.0
OD2 A:ASP455 2.5 47.6 1.0
CG A:ASP455 2.8 49.8 1.0
C A:MET411 3.5 39.1 1.0
C A:GLY415 3.6 45.4 1.0
C A:GLY413 3.7 39.9 1.0
CA A:MET411 4.0 39.8 1.0
OG1 A:THR416 4.0 43.2 1.0
N A:GLY415 4.1 44.5 1.0
N A:GLY413 4.2 37.2 1.0
CB A:ASP455 4.3 48.9 1.0
C A:LYS414 4.3 40.2 1.0
C A:LYS412 4.3 40.2 1.0
CA A:GLY415 4.4 42.5 1.0
N A:LYS412 4.5 37.0 1.0
CA A:GLY413 4.5 35.7 1.0
O A:LYS412 4.6 40.4 1.0
N A:THR416 4.6 40.3 1.0
CB A:MET411 4.6 37.8 1.0
N A:LYS414 4.7 41.7 1.0
O A:HOH619 4.7 36.5 1.0
CA A:LYS414 4.7 39.6 1.0
CA A:THR416 4.8 39.0 1.0
O A:LYS414 4.8 43.1 1.0
CA A:LYS412 4.9 37.7 1.0
CA A:ASP455 5.0 43.9 1.0
CB A:THR416 5.0 40.5 1.0

Calcium binding site 10 out of 14 in 7qql

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Calcium binding site 10 out of 14 in the The Pdz Domain of SNTG2 Complexed with the Phosphorylated 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 10 of The Pdz Domain of SNTG2 Complexed with the Phosphorylated Pdz-Binding Motif of RSK1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca501

b:73.0
occ:1.00
 O B:GLY183 2.5 63.2 1.0
O B:HOH667 2.5 69.3 1.0
O B:HOH657 2.5 53.3 1.0
OE2 B:GLU186 2.5 66.3 1.0
O B:HOH671 2.5 46.4 1.0
OE1 B:GLU186 2.8 66.2 1.0
O B:HOH668 2.8 65.8 1.0
O B:VAL184 2.9 66.6 1.0
CD B:GLU186 3.0 64.9 1.0
C B:GLY183 3.5 64.4 1.0
C B:VAL184 4.0 60.2 1.0
CA B:GLY183 4.3 69.7 1.0
N B:VAL184 4.4 62.1 1.0
CG B:GLU186 4.5 56.5 1.0
CA B:VAL184 4.6 58.8 1.0
CB B:VAL184 4.7 53.5 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 03:30:04 2024

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