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Calcium in PDB 7pc9: The Pdz Domain of SYNJ2BP Complexed with the Pdz-Binding Motif of HTLV1-TAX1

Protein crystallography data

The structure of The Pdz Domain of SYNJ2BP Complexed with the Pdz-Binding Motif of HTLV1-TAX1, PDB code: 7pc9 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) 49.33 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.99, 99.85, 173.34, 90, 90, 90
R / Rfree (%) 20.3 / 24.3

Calcium Binding Sites:

The binding sites of Calcium atom in the The Pdz Domain of SYNJ2BP Complexed with the Pdz-Binding Motif of HTLV1-TAX1 (pdb code 7pc9). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 10 binding sites of Calcium where determined in the The Pdz Domain of SYNJ2BP Complexed with the Pdz-Binding Motif of HTLV1-TAX1, PDB code: 7pc9:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 10 in 7pc9

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Calcium binding site 1 out of 10 in the The Pdz Domain of SYNJ2BP Complexed with the Pdz-Binding Motif of HTLV1-TAX1


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 SYNJ2BP Complexed with the Pdz-Binding Motif of HTLV1-TAX1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca501

b:127.3
occ:1.00
 O B:GLY127 2.6 63.3 1.0
O B:VAL128 2.9 58.6 1.0
OE1 B:GLU130 3.0 88.5 1.0
O B:HOH638 3.1 61.5 1.0
C B:GLY127 3.5 61.4 1.0
CD B:GLU130 4.1 81.3 1.0
C B:VAL128 4.1 55.5 1.0
CA B:GLY127 4.2 60.0 1.0
N B:VAL128 4.4 60.5 1.0
O B:HOH707 4.4 59.0 1.0
OE2 B:GLU130 4.5 85.7 1.0
CA B:VAL128 4.7 57.3 1.0
CB B:VAL128 5.0 51.9 1.0

Calcium binding site 2 out of 10 in 7pc9

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Calcium binding site 2 out of 10 in the The Pdz Domain of SYNJ2BP Complexed with the Pdz-Binding Motif of HTLV1-TAX1


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 SYNJ2BP Complexed with the Pdz-Binding Motif of HTLV1-TAX1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca502

b:68.3
occ:1.00
 O B:LEU168 2.4 51.0 1.0
OE1 B:GLU173 2.5 54.7 1.0
O B:LYS165 2.5 43.7 1.0
CD B:GLU173 3.2 48.5 1.0
C B:LEU168 3.5 46.2 1.0
OE2 B:GLU173 3.6 53.6 1.0
C B:LYS165 3.7 41.8 1.0
CA B:SER169 3.8 45.6 1.0
CB B:SER169 4.1 43.5 1.0
N B:SER169 4.1 47.4 1.0
CG B:GLU173 4.4 38.4 1.0
O B:SER166 4.4 46.1 1.0
CA B:SER166 4.6 46.0 1.0
C B:SER166 4.6 44.1 1.0
CA B:LYS165 4.6 43.1 1.0
N B:SER166 4.6 40.0 1.0
N B:LEU168 4.7 42.4 1.0
CA B:LEU168 4.7 40.8 1.0
CG B:LYS165 4.8 48.1 1.0
CB B:GLU173 4.8 33.6 1.0

Calcium binding site 3 out of 10 in 7pc9

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Calcium binding site 3 out of 10 in the The Pdz Domain of SYNJ2BP Complexed with the Pdz-Binding Motif of HTLV1-TAX1


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 SYNJ2BP Complexed with the Pdz-Binding Motif of HTLV1-TAX1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca503

b:77.9
occ:1.00
 OD1 B:ASP239 2.4 69.1 1.0
O B:HOH606 2.6 62.3 1.0
O B:GLY197 2.6 76.0 1.0
O B:MET195 2.8 61.8 1.0
OG1 B:THR200 3.0 71.4 1.0
O B:LEU198 3.0 76.3 1.0
C B:LEU198 3.2 75.4 1.0
C B:GLY197 3.3 76.9 1.0
N B:THR200 3.6 68.5 1.0
CA B:LEU198 3.6 80.2 1.0
CG B:ASP239 3.6 63.6 1.0
C B:GLY199 3.6 73.2 1.0
C B:MET195 3.8 59.2 1.0
N B:LEU198 3.8 81.7 1.0
N B:GLY199 3.8 71.9 1.0
CA B:THR200 3.9 62.3 1.0
O B:GLY199 3.9 74.5 1.0
CB B:THR200 4.0 62.6 1.0
CA B:GLY199 4.2 72.4 1.0
O B:LYS196 4.3 70.8 1.0
CA B:MET195 4.3 50.7 1.0
C B:LYS196 4.4 70.0 1.0
CA B:GLY197 4.4 72.8 1.0
OD2 B:ASP239 4.5 69.1 1.0
N B:GLY197 4.5 70.4 1.0
CB B:ASP239 4.5 51.8 1.0
N B:LYS196 4.8 64.1 1.0

Calcium binding site 4 out of 10 in 7pc9

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Calcium binding site 4 out of 10 in the The Pdz Domain of SYNJ2BP Complexed with the Pdz-Binding Motif of HTLV1-TAX1


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 SYNJ2BP Complexed with the Pdz-Binding Motif of HTLV1-TAX1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca504

b:50.5
occ:1.00
 O B:HOH651 2.3 59.9 1.0
O B:ARG282 2.4 50.5 1.0
OE2 B:GLU324 2.4 57.4 1.0
O B:HOH744 2.5 31.6 1.0
OE1 B:GLU324 2.5 53.2 1.0
O B:GLY279 2.5 42.8 1.0
O B:GLY284 2.6 43.5 1.0
CD B:GLU324 2.8 52.7 1.0
C B:GLY279 3.4 42.1 1.0
C B:ARG282 3.6 49.9 1.0
C B:GLY284 3.7 47.4 1.0
N B:GLY284 3.8 52.3 1.0
O B:HOH708 4.0 38.9 1.0
C B:LYS283 4.1 53.4 1.0
CA B:GLY279 4.1 46.1 1.0
N B:VAL280 4.2 41.9 1.0
CA B:LYS283 4.2 52.1 1.0
CA B:VAL280 4.2 43.8 1.0
CA B:GLY284 4.3 51.4 1.0
CG B:GLU324 4.3 44.9 1.0
OG1 B:THR285 4.3 55.1 1.0
N B:LYS283 4.3 49.9 1.0
O B:VAL280 4.4 50.3 1.0
C B:VAL280 4.4 46.6 1.0
N B:ARG282 4.5 54.3 1.0
CA B:ARG282 4.6 52.1 1.0
CG B:ARG282 4.7 45.2 1.0
N B:THR285 4.8 48.0 1.0
O B:LYS283 4.8 54.1 1.0

Calcium binding site 5 out of 10 in 7pc9

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Calcium binding site 5 out of 10 in the The Pdz Domain of SYNJ2BP Complexed with the Pdz-Binding Motif of HTLV1-TAX1


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 SYNJ2BP Complexed with the Pdz-Binding Motif of HTLV1-TAX1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca505

b:36.1
occ:1.00
 O B:GLY359 2.3 34.8 1.0
O B:GLY357 2.3 30.9 1.0
O B:MET355 2.4 30.6 1.0
OD1 B:ASP399 2.5 28.5 1.0
OD2 B:ASP399 2.7 37.4 1.0
CG B:ASP399 3.0 33.7 1.0
C B:MET355 3.3 30.2 1.0
C B:GLY359 3.5 34.0 1.0
C B:GLY357 3.5 30.3 1.0
CA B:MET355 3.9 29.2 1.0
N B:GLY357 3.9 36.1 1.0
N B:GLY359 3.9 34.4 1.0
C B:LYS356 4.1 31.8 1.0
CA B:GLY359 4.2 31.7 1.0
N B:LYS356 4.2 32.6 1.0
C B:LYS358 4.2 34.2 1.0
O B:HOH703 4.3 43.4 1.0
CA B:GLY357 4.3 29.6 1.0
OG1 B:THR360 4.4 37.0 1.0
O B:LYS356 4.4 32.6 1.0
CB B:ASP399 4.5 33.7 1.0
N B:THR360 4.5 34.5 1.0
N B:LYS358 4.5 30.7 1.0
CA B:LYS356 4.7 27.7 1.0
O B:LYS358 4.7 34.5 1.0
CA B:LYS358 4.7 31.1 1.0
CB B:MET355 4.7 27.3 1.0
CA B:THR360 4.7 35.5 1.0

Calcium binding site 6 out of 10 in 7pc9

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Calcium binding site 6 out of 10 in the The Pdz Domain of SYNJ2BP Complexed with the Pdz-Binding Motif of HTLV1-TAX1


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 SYNJ2BP Complexed with the Pdz-Binding Motif of HTLV1-TAX1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:64.2
occ:1.00
 O A:HOH717 2.3 44.8 1.0
O A:HOH624 2.3 58.8 1.0
O A:GLY127 2.4 63.6 1.0
O A:VAL128 2.4 57.6 1.0
OE1 A:GLU130 2.4 63.8 1.0
O A:HOH756 2.5 55.0 1.0
OE2 A:GLU130 2.8 62.2 1.0
CD A:GLU130 3.0 58.5 1.0
C A:GLY127 3.4 63.2 1.0
C A:VAL128 3.5 54.6 1.0
N A:VAL128 4.1 61.0 1.0
CA A:VAL128 4.2 56.2 1.0
CB A:VAL128 4.2 56.8 1.0
CA A:GLY127 4.3 64.8 1.0
CG A:GLU130 4.5 48.5 1.0
N A:GLU130 4.6 47.1 1.0
N A:ASP129 4.6 53.3 1.0
CG1 A:VAL128 4.9 48.2 1.0
CA A:ASP129 5.0 53.4 1.0

Calcium binding site 7 out of 10 in 7pc9

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Calcium binding site 7 out of 10 in the The Pdz Domain of SYNJ2BP Complexed with the Pdz-Binding Motif of HTLV1-TAX1


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 SYNJ2BP Complexed with the Pdz-Binding Motif of HTLV1-TAX1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:102.4
occ:1.00
 OE1 A:GLU173 2.6 49.3 1.0
O A:HOH657 2.7 51.4 1.0
O A:LEU168 2.8 56.4 1.0
O A:LYS165 2.8 59.6 1.0
CD A:GLU173 3.4 45.8 1.0
OE2 A:GLU173 3.7 48.6 1.0
C A:LEU168 3.9 50.1 1.0
C A:LYS165 4.0 52.5 1.0
CA A:SER169 4.2 50.7 1.0
CB A:SER169 4.5 52.6 1.0
N A:SER169 4.5 48.1 1.0
O A:SER166 4.6 55.2 1.0
CG A:GLU173 4.7 40.3 1.0
CA A:SER166 4.8 48.5 1.0
CG A:LYS165 4.9 55.5 1.0
C A:SER166 4.9 50.6 1.0
N A:SER166 4.9 47.3 1.0
CA A:LYS165 5.0 52.0 1.0

Calcium binding site 8 out of 10 in 7pc9

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Calcium binding site 8 out of 10 in the The Pdz Domain of SYNJ2BP Complexed with the Pdz-Binding Motif of HTLV1-TAX1


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 SYNJ2BP Complexed with the Pdz-Binding Motif of HTLV1-TAX1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:69.6
occ:1.00
 O A:GLY197 2.2 108.1 1.0
OD1 A:ASP239 2.2 77.9 1.0
O A:MET195 2.7 56.3 1.0
O A:LEU198 3.1 76.6 1.0
OG1 A:THR200 3.2 70.9 1.0
CG A:ASP239 3.2 70.3 1.0
C A:GLY197 3.4 97.6 1.0
C A:LEU198 3.4 80.7 1.0
CA A:LEU198 3.8 88.0 1.0
C A:MET195 3.8 55.9 1.0
OD2 A:ASP239 3.9 76.9 1.0
C A:GLY199 3.9 77.9 1.0
N A:THR200 3.9 68.6 1.0
O A:GLY199 4.0 82.4 1.0
N A:LEU198 4.0 95.5 1.0
N A:GLY199 4.1 79.9 1.0
CB A:ASP239 4.3 52.9 1.0
CA A:THR200 4.3 62.3 1.0
O A:LYS196 4.3 72.4 1.0
CB A:THR200 4.3 62.3 1.0
C A:LYS196 4.4 72.7 1.0
CA A:MET195 4.4 51.8 1.0
N A:GLY197 4.5 77.5 1.0
CA A:GLY197 4.5 85.8 1.0
CA A:GLY199 4.6 80.2 1.0
N A:LYS196 4.8 60.1 1.0
CA A:ASP239 5.0 46.1 1.0
CA A:LYS196 5.0 68.0 1.0

Calcium binding site 9 out of 10 in 7pc9

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Calcium binding site 9 out of 10 in the The Pdz Domain of SYNJ2BP Complexed with the Pdz-Binding Motif of HTLV1-TAX1


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 SYNJ2BP Complexed with the Pdz-Binding Motif of HTLV1-TAX1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca504

b:41.7
occ:1.00
 O A:GLY284 2.4 47.1 1.0
O A:HOH623 2.4 41.6 1.0
O A:ARG282 2.5 41.5 1.0
OE1 A:GLU324 2.5 42.0 1.0
O A:GLY279 2.5 33.8 1.0
OE2 A:GLU324 2.6 43.4 1.0
CD A:GLU324 2.9 41.1 1.0
O A:HOH757 3.0 59.7 1.0
C A:GLY279 3.3 33.8 1.0
C A:GLY284 3.5 44.8 1.0
C A:ARG282 3.6 41.2 1.0
N A:GLY284 3.7 46.1 1.0
CA A:GLY279 4.0 30.8 1.0
O A:HOH627 4.1 52.0 1.0
C A:LYS283 4.1 47.3 1.0
N A:VAL280 4.2 34.3 1.0
CA A:GLY284 4.2 42.7 1.0
OG1 A:THR285 4.2 45.6 1.0
O A:HOH720 4.3 55.0 1.0
CA A:VAL280 4.3 34.3 1.0
CG A:GLU324 4.4 34.4 1.0
CA A:LYS283 4.4 50.9 1.0
N A:ARG282 4.5 36.9 1.0
N A:LYS283 4.5 47.0 1.0
C A:VAL280 4.6 38.7 1.0
CG A:ARG282 4.6 38.4 1.0
CA A:ARG282 4.6 36.2 1.0
N A:THR285 4.6 43.5 1.0
O A:VAL280 4.7 43.8 1.0
O A:LYS283 4.8 45.2 1.0
CA A:THR285 4.9 39.0 1.0

Calcium binding site 10 out of 10 in 7pc9

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Calcium binding site 10 out of 10 in the The Pdz Domain of SYNJ2BP Complexed with the Pdz-Binding Motif of HTLV1-TAX1


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 SYNJ2BP Complexed with the Pdz-Binding Motif of HTLV1-TAX1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca505

b:35.4
occ:1.00
 O A:MET355 2.4 32.2 1.0
O A:GLY357 2.4 39.1 1.0
O A:GLY359 2.4 28.6 1.0
OD1 A:ASP399 2.5 36.3 1.0
OD2 A:ASP399 2.7 39.3 1.0
CG A:ASP399 2.9 35.8 1.0
C A:MET355 3.4 29.6 1.0
C A:GLY359 3.5 31.6 1.0
C A:GLY357 3.6 38.2 1.0
CA A:MET355 3.9 27.3 1.0
N A:GLY359 3.9 34.8 1.0
N A:GLY357 4.1 36.7 1.0
C A:LYS356 4.2 34.3 1.0
CA A:GLY359 4.2 31.7 1.0
C A:LYS358 4.3 36.8 1.0
N A:LYS356 4.4 29.2 1.0
CA A:GLY357 4.4 33.9 1.0
OG1 A:THR360 4.4 44.9 1.0
CB A:ASP399 4.4 30.3 1.0
O A:LYS356 4.4 36.7 1.0
N A:THR360 4.6 36.2 1.0
N A:LYS358 4.6 37.9 1.0
O A:HOH641 4.6 36.5 1.0
CB A:MET355 4.6 30.2 1.0
CA A:LYS358 4.7 34.9 1.0
O A:HOH701 4.7 32.6 1.0
O A:LYS358 4.7 36.4 1.0
CA A:LYS356 4.8 30.5 1.0
CA A:THR360 4.8 35.5 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 02:52:05 2024

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