Calcium in PDB 7p71: The Pdz Domain of MAGI1_2 Complexed with the Pdz-Binding Motif of HPV35-E6

Protein crystallography data

The structure of The Pdz Domain of MAGI1_2 Complexed with the Pdz-Binding Motif of HPV35-E6, PDB code: 7p71 was solved by G.Gogl, A.Cousido-Siah, G.Trave, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.64 / 2.60
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 192.13, 61.03, 98.99, 90, 97.33, 90
R / Rfree (%) 24.1 / 28.1

Calcium Binding Sites:

The binding sites of Calcium atom in the The Pdz Domain of MAGI1_2 Complexed with the Pdz-Binding Motif of HPV35-E6 (pdb code 7p71). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the The Pdz Domain of MAGI1_2 Complexed with the Pdz-Binding Motif of HPV35-E6, PDB code: 7p71:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 7p71

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Calcium binding site 1 out of 8 in the The Pdz Domain of MAGI1_2 Complexed with the Pdz-Binding Motif of HPV35-E6


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 MAGI1_2 Complexed with the Pdz-Binding Motif of HPV35-E6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca901

b:125.0
occ:1.00
 O A:GLY819 2.4 60.8 1.0
O A:GLY821 2.5 82.9 1.0
OD1 A:ASP861 2.5 118.1 1.0
O A:MET817 2.5 89.3 1.0
OD2 A:ASP861 2.6 111.7 1.0
CG A:ASP861 2.9 107.8 1.0
C A:MET817 3.5 76.5 1.0
C A:GLY821 3.6 75.9 1.0
C A:GLY819 3.7 60.0 1.0
N A:GLY821 3.9 66.3 1.0
CA A:MET817 3.9 71.9 1.0
OG1 A:THR822 4.2 77.8 1.0
C A:LYS820 4.2 68.6 1.0
CA A:GLY821 4.3 70.0 1.0
N A:GLY819 4.3 66.7 1.0
CB A:ASP861 4.4 94.9 1.0
C A:LYS818 4.4 75.1 1.0
N A:LYS818 4.5 73.8 1.0
CA A:LYS820 4.5 65.6 1.0
CB A:MET817 4.5 65.5 1.0
N A:LYS820 4.6 61.6 1.0
O A:LYS818 4.6 81.7 1.0
CA A:GLY819 4.6 61.1 1.0
N A:THR822 4.7 76.3 1.0
O A:LYS820 4.8 74.4 1.0
CA A:LYS818 4.9 74.3 1.0
CA A:THR822 4.9 73.0 1.0

Calcium binding site 2 out of 8 in 7p71

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Calcium binding site 2 out of 8 in the The Pdz Domain of MAGI1_2 Complexed with the Pdz-Binding Motif of HPV35-E6


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 MAGI1_2 Complexed with the Pdz-Binding Motif of HPV35-E6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca902

b:153.7
occ:1.00
 O A:ARG744 2.6 81.2 1.0
O A:GLY746 2.6 115.2 1.0
O A:GLY741 2.6 103.7 1.0
OE1 A:GLU786 2.7 88.4 1.0
OE2 A:GLU786 2.9 92.6 1.0
CD A:GLU786 3.2 89.0 1.0
N A:GLY746 3.3 103.7 1.0
CA A:LYS745 3.5 103.9 1.0
C A:GLY746 3.6 107.9 1.0
C A:ARG744 3.6 92.6 1.0
C A:LYS745 3.6 102.4 1.0
C A:GLY741 3.8 90.4 1.0
O A:HOH1005 3.9 69.2 1.0
CA A:GLY746 4.0 106.3 1.0
N A:LYS745 4.0 99.4 1.0
O A:VAL742 4.4 94.5 1.0
CA A:VAL742 4.5 80.2 1.0
OG1 A:THR747 4.6 87.2 1.0
O A:LYS745 4.6 102.0 1.0
N A:VAL742 4.6 83.3 1.0
C A:VAL742 4.6 88.0 1.0
CG A:GLU786 4.7 80.5 1.0
CA A:GLY741 4.7 88.3 1.0
CB A:LYS745 4.8 112.1 1.0
N A:THR747 4.8 99.9 1.0
CG A:LYS745 4.9 118.4 1.0
CA A:ARG744 5.0 101.2 1.0

Calcium binding site 3 out of 8 in 7p71

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Calcium binding site 3 out of 8 in the The Pdz Domain of MAGI1_2 Complexed with the Pdz-Binding Motif of HPV35-E6


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 MAGI1_2 Complexed with the Pdz-Binding Motif of HPV35-E6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca903

b:254.8
occ:1.00
 O A:LYS627 2.5 115.7 1.0
O A:LEU630 2.5 110.3 1.0
OE1 A:GLU635 2.6 136.7 1.0
OE2 A:GLU635 2.7 136.7 1.0
CD A:GLU635 2.8 130.5 1.0
C A:LEU630 3.7 106.8 1.0
C A:LYS627 3.7 111.4 1.0
CG A:GLU635 4.1 116.0 1.0
CA A:SER631 4.2 108.2 1.0
N A:SER631 4.4 106.9 1.0
CA A:SER628 4.5 106.2 1.0
N A:SER628 4.5 106.3 1.0
CA A:LYS627 4.6 113.8 1.0
O A:SER628 4.6 117.0 1.0
C A:SER628 4.6 111.7 1.0
CB A:SER631 4.6 111.9 1.0
CB A:GLU635 4.7 104.4 1.0
N A:LEU630 4.7 106.7 1.0
CG A:LYS627 4.7 123.5 1.0
CA A:LEU630 4.8 101.5 1.0

Calcium binding site 4 out of 8 in 7p71

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Calcium binding site 4 out of 8 in the The Pdz Domain of MAGI1_2 Complexed with the Pdz-Binding Motif of HPV35-E6


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 MAGI1_2 Complexed with the Pdz-Binding Motif of HPV35-E6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca908

b:164.3
occ:1.00
 O6 A:CIT907 2.6 149.3 1.0
OD2 A:ASP824 2.6 85.2 1.0
O A:THR822 2.7 85.9 1.0
C6 A:CIT907 3.4 149.9 1.0
C4 A:CIT907 3.4 153.3 1.0
N A:THR822 3.7 76.3 1.0
C A:THR822 3.8 71.5 1.0
CG A:ASP824 3.8 78.9 1.0
C3 A:CIT907 4.1 151.1 1.0
CA A:THR822 4.1 73.0 1.0
O5 A:CIT907 4.1 149.6 1.0
CB A:THR822 4.2 72.8 1.0
OD1 A:ASP824 4.4 77.6 1.0
CE1 A:HIS633 4.5 93.2 1.0
C5 A:CIT907 4.7 155.2 1.0
C A:GLY821 4.8 75.9 1.0
O2 A:CIT907 4.8 143.4 1.0
CB A:ASP824 4.8 72.2 1.0
N A:ASP824 4.8 66.1 1.0
NE2 A:HIS633 4.9 89.8 1.0
O4 A:CIT907 4.9 155.1 1.0
C1 A:CIT907 4.9 144.6 1.0
CA A:GLY821 4.9 70.0 1.0
N A:ARG823 5.0 64.9 1.0

Calcium binding site 5 out of 8 in 7p71

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Calcium binding site 5 out of 8 in the The Pdz Domain of MAGI1_2 Complexed with the Pdz-Binding Motif of HPV35-E6


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 MAGI1_2 Complexed with the Pdz-Binding Motif of HPV35-E6 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca901

b:180.3
occ:1.00
 O B:HOH1001 2.4 69.5 1.0
O B:GLY821 2.4 110.3 1.0
OD2 B:ASP861 2.4 118.1 1.0
OD1 B:ASP861 2.4 123.7 1.0
CG B:ASP861 2.7 115.2 1.0
C B:GLY821 2.7 105.6 1.0
O B:GLY819 3.1 84.8 1.0
N B:GLY821 3.3 107.4 1.0
CA B:GLY821 3.3 108.4 1.0
N B:THR822 3.5 98.5 1.0
C B:LYS820 3.9 106.5 1.0
CA B:THR822 4.0 88.0 1.0
CB B:THR822 4.0 90.8 1.0
CB B:ASP861 4.2 103.5 1.0
C B:GLY819 4.3 91.2 1.0
O B:LYS820 4.5 111.6 1.0
CG2 B:THR822 4.5 105.5 1.0
CA B:LYS820 4.6 101.5 1.0
O B:ASP861 4.6 99.5 1.0
CA B:ASP861 4.7 95.8 1.0
CA B:MET817 4.8 71.5 1.0
O B:MET817 4.8 76.8 1.0
C B:MET817 5.0 77.1 1.0
N B:LYS820 5.0 102.4 1.0

Calcium binding site 6 out of 8 in 7p71

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Calcium binding site 6 out of 8 in the The Pdz Domain of MAGI1_2 Complexed with the Pdz-Binding Motif of HPV35-E6


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 MAGI1_2 Complexed with the Pdz-Binding Motif of HPV35-E6 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca902

b:151.5
occ:1.00
 O B:GLY741 2.4 107.7 1.0
O B:ARG744 2.5 122.0 1.0
OE2 B:GLU786 2.6 144.0 1.0
OE1 B:GLU786 2.6 146.6 1.0
O B:GLY746 2.7 87.6 1.0
CD B:GLU786 3.0 137.6 1.0
N B:GLY746 3.4 99.2 1.0
C B:GLY741 3.6 88.2 1.0
C B:ARG744 3.6 120.0 1.0
C B:GLY746 3.7 93.0 1.0
CA B:LYS745 3.8 107.7 1.0
C B:LYS745 4.0 100.3 1.0
CA B:GLY746 4.1 98.3 1.0
O B:VAL742 4.2 107.8 1.0
CA B:VAL742 4.2 94.1 1.0
N B:LYS745 4.2 115.6 1.0
C B:VAL742 4.3 102.1 1.0
N B:VAL742 4.3 93.1 1.0
CG B:GLU786 4.5 121.1 1.0
OG1 B:THR747 4.5 99.3 1.0
CA B:GLY741 4.6 76.2 1.0
N B:THR747 4.9 97.2 1.0
CA B:ARG744 4.9 121.0 1.0
N B:ARG744 4.9 109.6 1.0
O B:LYS745 5.0 98.3 1.0

Calcium binding site 7 out of 8 in 7p71

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Calcium binding site 7 out of 8 in the The Pdz Domain of MAGI1_2 Complexed with the Pdz-Binding Motif of HPV35-E6


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 MAGI1_2 Complexed with the Pdz-Binding Motif of HPV35-E6 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca903

b:152.2
occ:1.00
 O B:LEU630 2.7 83.9 1.0
OE1 B:GLU635 2.7 96.4 1.0
O B:LYS627 2.8 119.9 1.0
CD B:GLU635 3.3 95.5 1.0
OE2 B:GLU635 3.3 98.1 1.0
C B:LEU630 3.8 88.2 1.0
C B:LYS627 4.0 114.4 1.0
CA B:SER631 4.1 98.0 1.0
CB B:SER631 4.4 106.0 1.0
N B:SER631 4.4 94.6 1.0
CG B:GLU635 4.6 91.0 1.0
CG B:LYS627 4.7 113.8 1.0
CA B:LYS627 4.9 111.1 1.0
N B:LEU630 4.9 95.9 1.0
CA B:SER628 4.9 104.9 1.0
N B:SER628 4.9 108.7 1.0
CA B:LEU630 5.0 91.6 1.0

Calcium binding site 8 out of 8 in 7p71

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Calcium binding site 8 out of 8 in the The Pdz Domain of MAGI1_2 Complexed with the Pdz-Binding Motif of HPV35-E6


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 MAGI1_2 Complexed with the Pdz-Binding Motif of HPV35-E6 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca906

b:122.0
occ:1.00
 O B:THR822 2.6 83.9 1.0
OD2 B:ASP824 3.0 89.4 1.0
C B:THR822 3.8 77.9 1.0
CG B:ASP824 4.0 84.1 1.0
N B:ASP824 4.4 82.8 1.0
CG2 B:THR822 4.4 105.5 1.0
N B:THR822 4.5 98.5 1.0
NE2 B:HIS633 4.6 82.5 1.0
CB B:ASP824 4.7 82.2 1.0
CA B:THR822 4.7 88.0 1.0
CE1 B:HIS633 4.7 84.3 1.0
N B:ARG823 4.8 73.9 1.0
CA B:ARG823 4.9 79.6 1.0
OD1 B:ASP824 4.9 85.8 1.0

Reference:

G.Gogl, A.Cousido-Siah, G.Trave. The Pdz Domain of MAGI1_2 Complexed with the Pdz-Binding Motif of HPV35-E6 To Be Published.
Page generated: Fri Jul 19 02:44:47 2024

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