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Calcium in PDB 6bxu: Crystal Structure of Mouse Protocadherin-15 EC5-7 I582T

Protein crystallography data

The structure of Crystal Structure of Mouse Protocadherin-15 EC5-7 I582T, PDB code: 6bxu was solved by B.L.Neel, M.Sotomayor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 180.90 / 3.79
Space group P 42 2 2
Cell size a, b, c (Å), α, β, γ (°) 180.905, 180.905, 127.161, 90.00, 90.00, 90.00
R / Rfree (%) 24 / 28.3

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Mouse Protocadherin-15 EC5-7 I582T (pdb code 6bxu). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 10 binding sites of Calcium where determined in the Crystal Structure of Mouse Protocadherin-15 EC5-7 I582T, PDB code: 6bxu:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 10 in 6bxu

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Calcium binding site 1 out of 10 in the Crystal Structure of Mouse Protocadherin-15 EC5-7 I582T


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A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Mouse Protocadherin-15 EC5-7 I582T within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca901

b:0.6
occ:1.00
O A:SER591 2.2 0.9 1.0
OE1 A:GLN590 2.3 1.0 1.0
OD2 A:ASP621 2.6 0.8 1.0
OD1 A:ASP671 2.6 0.1 1.0
OE1 A:GLU623 2.7 1.0 1.0
CG A:ASP671 3.2 0.1 1.0
C A:SER591 3.3 0.7 1.0
CG A:ASP621 3.3 0.3 1.0
CD A:GLN590 3.3 0.1 1.0
OD1 A:ASP621 3.4 0.6 1.0
OD2 A:ASP625 3.6 0.2 1.0
OD2 A:ASP671 3.7 0.6 1.0
CG A:GLN590 3.8 0.8 1.0
CD A:GLU623 3.8 0.2 1.0
N A:SER591 3.9 0.8 1.0
O A:PRO592 3.9 0.9 1.0
C A:PRO592 3.9 0.3 1.0
CA A:PRO592 4.0 0.0 1.0
CB A:ASP671 4.1 0.1 1.0
N A:PRO592 4.1 0.9 1.0
C A:GLN590 4.2 0.3 1.0
CA A:SER591 4.2 0.0 1.0
CA A:GLN590 4.4 0.2 1.0
N A:PRO593 4.4 0.8 1.0
CB A:GLU623 4.5 0.8 1.0
OG A:SER591 4.5 0.6 1.0
CG A:GLU623 4.5 1.0 1.0
NE2 A:GLN590 4.5 0.1 1.0
N A:GLU623 4.6 0.3 1.0
CG A:ASP625 4.6 0.0 1.0
CB A:ASP621 4.7 1.0 1.0
OE2 A:GLU623 4.7 0.8 1.0
CB A:GLN590 4.7 1.0 1.0
O A:GLN590 4.7 0.9 1.0
CD A:PRO593 4.8 0.4 1.0
N A:ARG622 4.8 0.4 1.0
CB A:SER591 4.9 0.3 1.0
CA A:ASP671 4.9 0.2 1.0

Calcium binding site 2 out of 10 in 6bxu

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Calcium binding site 2 out of 10 in the Crystal Structure of Mouse Protocadherin-15 EC5-7 I582T


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Mouse Protocadherin-15 EC5-7 I582T within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca902

b:0.5
occ:1.00
OD1 A:ASP656 2.2 0.0 1.0
OE1 A:GLU606 2.4 0.7 1.0
OE1 A:GLU658 2.5 0.8 1.0
OD2 A:ASP691 2.8 0.4 1.0
OD1 A:ASP691 3.2 0.5 1.0
CG A:ASP656 3.2 0.7 1.0
CG A:ASP691 3.3 0.8 1.0
CA A:CA903 3.4 98.9 1.0
CD A:GLU606 3.4 0.4 1.0
CD A:GLU658 3.5 0.6 1.0
OD2 A:ASP656 3.6 0.7 1.0
OD1 A:ASN692 3.7 0.4 1.0
OE2 A:GLU606 3.7 1.0 1.0
N A:ARG657 4.0 0.8 1.0
OE2 A:GLU658 4.0 0.7 1.0
NE2 B:HIS776 4.3 0.5 1.0
CB A:ASP656 4.4 1.0 1.0
CA A:ASP656 4.4 0.9 1.0
N A:GLU658 4.5 0.9 1.0
CG A:ARG657 4.6 0.6 1.0
CG A:GLU658 4.6 0.8 1.0
C A:ASP656 4.7 0.7 1.0
CB A:GLU658 4.8 0.3 1.0
CB A:ASP691 4.8 0.3 1.0
CG A:GLU606 4.8 0.9 1.0
CD2 B:HIS776 4.8 0.9 1.0
CG A:ASN692 4.8 0.4 1.0
OD1 A:ASP724 4.9 0.6 1.0
CE1 B:HIS776 4.9 0.3 1.0
CA A:ARG657 5.0 0.8 1.0

Calcium binding site 3 out of 10 in 6bxu

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Calcium binding site 3 out of 10 in the Crystal Structure of Mouse Protocadherin-15 EC5-7 I582T


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 Mouse Protocadherin-15 EC5-7 I582T within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca903

b:98.9
occ:1.00
OD1 A:ASP724 2.2 0.6 1.0
OD1 A:ASP691 2.5 0.5 1.0
OE2 A:GLU606 2.5 1.0 1.0
O A:VAL689 2.6 0.6 1.0
OE2 A:GLU658 2.9 0.7 1.0
OD1 A:ASP688 3.0 0.4 1.0
OE1 A:GLU658 3.3 0.8 1.0
CA A:CA902 3.4 0.5 1.0
CG A:ASP724 3.4 0.9 1.0
CD A:GLU606 3.4 0.4 1.0
CD A:GLU658 3.5 0.6 1.0
CG A:ASP691 3.6 0.8 1.0
OE1 A:GLU606 3.6 0.7 1.0
CG A:ASP688 3.7 0.7 1.0
C A:VAL689 3.8 0.4 1.0
CG A:ARG657 3.9 0.6 1.0
N A:VAL689 3.9 1.0 1.0
OD1 A:ASN692 3.9 0.4 1.0
OD2 A:ASP691 4.0 0.4 1.0
OD2 A:ASP688 4.0 0.0 1.0
CD A:ARG657 4.2 0.6 1.0
CB A:ASP724 4.3 0.5 1.0
OD2 A:ASP724 4.3 0.4 1.0
NH1 A:ARG657 4.3 0.2 1.0
CA A:ASP724 4.4 0.1 1.0
N A:ASP691 4.4 0.3 1.0
CA A:VAL689 4.5 0.4 1.0
CG2 A:VAL689 4.5 0.0 1.0
CA A:ASP688 4.7 0.3 1.0
CB A:ASP688 4.8 0.2 1.0
C A:ASP688 4.8 0.4 1.0
CB A:ASP691 4.8 0.3 1.0
CG A:GLU606 4.8 0.9 1.0
N A:ASN690 4.9 0.1 1.0

Calcium binding site 4 out of 10 in 6bxu

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Calcium binding site 4 out of 10 in the Crystal Structure of Mouse Protocadherin-15 EC5-7 I582T


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 Mouse Protocadherin-15 EC5-7 I582T within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca904

b:0.6
occ:1.00
OD2 A:ASP722 2.4 0.7 1.0
O A:ASN692 2.4 0.8 1.0
OD1 A:ASN690 2.4 0.4 1.0
OD2 A:ASP724 2.5 0.4 1.0
OD2 A:ASP772 2.7 0.7 1.0
O A:ASN728 2.8 0.7 1.0
OD1 A:ASP722 2.9 0.6 1.0
CG A:ASP722 3.0 0.8 1.0
CG A:ASP772 3.3 0.0 1.0
CG A:ASN690 3.4 0.6 1.0
CG A:ASP724 3.5 0.9 1.0
C A:ASN692 3.6 1.0 1.0
CB A:ASP724 3.7 0.5 1.0
C A:ASN728 3.9 0.0 1.0
OD1 A:ASP772 4.0 0.8 1.0
CB A:ASP772 4.0 0.0 1.0
ND2 A:ASN690 4.0 0.4 1.0
N A:ASN692 4.2 0.8 1.0
CB A:ASN728 4.3 0.1 1.0
CA A:ASN692 4.3 0.4 1.0
CA A:ASN690 4.4 0.0 1.0
CB A:ASN690 4.4 0.5 1.0
CB A:ASP722 4.4 0.9 1.0
CA A:ASN728 4.5 0.5 1.0
N A:ALA693 4.5 0.4 1.0
OD1 A:ASP724 4.6 0.6 1.0
CB A:ASN692 4.7 0.6 1.0
C A:ASN690 4.7 0.4 1.0
CA A:ALA693 4.7 1.0 1.0
N A:ASP691 4.8 0.3 1.0
CD A:ARG778 4.8 0.9 1.0

Calcium binding site 5 out of 10 in 6bxu

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Calcium binding site 5 out of 10 in the Crystal Structure of Mouse Protocadherin-15 EC5-7 I582T


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 Mouse Protocadherin-15 EC5-7 I582T within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca905

b:0.8
occ:1.00
OD1 A:ASN482 2.4 0.7 1.0
O A:ASN484 2.5 0.2 1.0
OD2 A:ASP566 2.6 0.2 1.0
O A:ASN520 2.8 0.5 1.0
OD1 A:ASP514 2.8 0.8 1.0
OD2 A:ASP514 2.9 0.6 1.0
CG A:ASP514 3.2 0.8 1.0
CG A:ASP566 3.5 0.0 1.0
OD2 A:ASP516 3.5 0.6 1.0
CG A:ASN482 3.5 0.6 1.0
C A:ASN520 3.7 0.0 1.0
C A:ASN484 3.7 0.3 1.0
CB A:ASP566 3.8 0.1 1.0
CB A:ASP516 3.9 0.2 1.0
CB A:ASN520 4.1 0.1 1.0
ND2 A:ASN482 4.1 0.3 1.0
CG A:ASP516 4.1 0.3 1.0
N A:ASN484 4.2 0.7 1.0
CA A:ASN520 4.4 0.6 1.0
CA A:ASN484 4.4 0.5 1.0
OD1 A:ASP566 4.4 0.4 1.0
N A:GLY521 4.6 0.6 1.0
CB A:ASP514 4.7 0.6 1.0
CB A:ASN484 4.7 0.6 1.0
CB A:ASN482 4.8 0.4 1.0
N A:THR485 4.8 0.6 1.0
O A:ASP516 4.9 0.9 1.0
N A:ASP483 4.9 0.0 1.0
CA A:GLY521 4.9 0.1 1.0
NH2 A:ARG574 5.0 0.8 1.0
CA A:ASN482 5.0 0.6 1.0

Calcium binding site 6 out of 10 in 6bxu

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Calcium binding site 6 out of 10 in the Crystal Structure of Mouse Protocadherin-15 EC5-7 I582T


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 Mouse Protocadherin-15 EC5-7 I582T within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca901

b:0.7
occ:1.00
O B:SER591 2.4 0.4 1.0
OE1 B:GLN590 2.4 0.3 1.0
OD2 B:ASP671 2.5 0.9 1.0
OD1 B:ASP621 2.7 0.3 1.0
OE1 B:GLU623 2.7 0.5 1.0
OD2 B:ASP625 2.8 0.9 1.0
CG B:ASP671 3.2 0.9 1.0
OD1 B:ASP671 3.2 0.6 1.0
OD2 B:ASP621 3.4 0.7 1.0
CG B:ASP621 3.4 0.5 1.0
CD B:GLU623 3.4 1.0 1.0
C B:SER591 3.5 1.0 1.0
CD B:GLN590 3.6 0.6 1.0
N B:SER591 3.8 0.6 1.0
CG B:ASP625 4.0 0.3 1.0
OE2 B:GLU623 4.0 0.9 1.0
CA B:GLN590 4.0 0.0 1.0
CB B:GLU623 4.1 0.6 1.0
OG B:SER591 4.2 0.4 1.0
CG B:GLU623 4.2 0.5 1.0
C B:GLN590 4.2 0.1 1.0
CA B:SER591 4.2 0.6 1.0
NE2 B:GLN590 4.4 0.1 1.0
CB B:GLN590 4.5 0.1 1.0
N B:GLU623 4.5 0.8 1.0
NH1 B:ARG673 4.5 0.8 1.0
N B:PRO592 4.5 0.7 1.0
CB B:ASP671 4.6 0.4 1.0
CB B:ASP625 4.6 0.8 1.0
O B:PRO592 4.6 0.3 1.0
CG B:GLN590 4.7 0.7 1.0
C B:PRO592 4.7 0.8 1.0
CA B:PRO592 4.7 0.8 1.0
CB B:ASP621 4.9 0.7 1.0
NE B:ARG673 4.9 0.8 1.0
CB B:SER591 4.9 0.1 1.0
OD1 B:ASP625 4.9 0.5 1.0
CA B:GLU623 4.9 0.9 1.0

Calcium binding site 7 out of 10 in 6bxu

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Calcium binding site 7 out of 10 in the Crystal Structure of Mouse Protocadherin-15 EC5-7 I582T


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Mouse Protocadherin-15 EC5-7 I582T within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca902

b:0.1
occ:1.00
O B:ASN692 2.3 0.6 1.0
OD2 B:ASP722 2.5 0.5 1.0
OD1 B:ASN690 2.6 0.1 1.0
OD2 B:ASP724 2.6 0.5 1.0
O B:ASN728 3.0 0.6 1.0
OD1 B:ASP722 3.1 0.0 1.0
CG B:ASP722 3.1 0.3 1.0
OD2 B:ASP772 3.2 0.5 1.0
CG B:ASP772 3.3 0.4 1.0
CG B:ASN690 3.4 0.2 1.0
C B:ASN692 3.5 0.8 1.0
CB B:ASP772 3.6 0.4 1.0
CG B:ASP724 3.7 0.5 1.0
ND2 B:ASN690 3.8 0.1 1.0
OD1 B:ASP772 3.8 0.5 1.0
CB B:ASP724 4.0 0.6 1.0
C B:ASN728 4.1 0.8 1.0
N B:ASN692 4.3 0.7 1.0
CA B:ASN692 4.3 0.4 1.0
N B:ALA693 4.5 0.4 1.0
CB B:ASN692 4.6 0.5 1.0
CB B:ASN728 4.6 0.8 1.0
CB B:ASN690 4.6 0.1 1.0
CA B:ALA693 4.6 0.8 1.0
CA B:ASN728 4.6 0.5 1.0
CA B:ASN690 4.6 0.7 1.0
CB B:ASP722 4.6 0.1 1.0
CD B:PRO694 4.7 0.3 1.0
OD1 B:ASP724 4.8 0.8 1.0
CB B:ARG778 4.9 0.2 1.0
N B:PRO694 4.9 0.2 1.0
C B:ALA693 4.9 0.6 1.0

Calcium binding site 8 out of 10 in 6bxu

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Calcium binding site 8 out of 10 in the Crystal Structure of Mouse Protocadherin-15 EC5-7 I582T


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Mouse Protocadherin-15 EC5-7 I582T within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca903

b:0.8
occ:1.00
OE1 B:GLU606 2.3 0.3 1.0
OD1 B:ASP691 2.6 0.7 1.0
CG B:ASP691 2.9 0.9 1.0
OD2 B:ASP691 3.0 0.7 1.0
OE1 B:GLU658 3.0 0.8 1.0
OD2 B:ASP656 3.1 0.7 1.0
CG B:ASP656 3.2 0.5 1.0
OD1 B:ASP656 3.4 0.1 1.0
OE2 B:GLU658 3.4 0.3 1.0
CD B:GLU606 3.5 0.1 1.0
CD B:GLU658 3.5 0.8 1.0
CA B:CA904 3.9 0.9 1.0
CA B:ASP656 4.0 0.6 1.0
CB B:ASP656 4.0 0.4 1.0
OE2 B:GLU606 4.0 0.1 1.0
CB B:ASP691 4.0 0.9 1.0
N B:ARG657 4.2 0.3 1.0
NE2 A:HIS776 4.4 0.2 1.0
C B:ASP656 4.6 0.4 1.0
CE1 A:HIS776 4.7 0.6 1.0
CG B:GLU606 4.7 0.5 1.0
ND2 B:ASN692 4.7 0.6 1.0
CG B:GLU658 4.9 0.9 1.0
O B:LEU655 4.9 0.1 1.0
N B:GLU658 5.0 0.8 1.0

Calcium binding site 9 out of 10 in 6bxu

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Calcium binding site 9 out of 10 in the Crystal Structure of Mouse Protocadherin-15 EC5-7 I582T


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of Mouse Protocadherin-15 EC5-7 I582T within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca904

b:0.9
occ:1.00
OD2 B:ASP691 2.2 0.7 1.0
OD1 B:ASP688 2.3 0.9 1.0
OD1 B:ASP724 2.4 0.8 1.0
OE2 B:GLU606 2.4 0.1 1.0
O B:VAL689 2.8 0.1 1.0
OE2 B:GLU658 3.0 0.3 1.0
OE1 B:GLU658 3.1 0.8 1.0
CG B:ASP691 3.3 0.9 1.0
CD B:GLU658 3.3 0.8 1.0
NH1 B:ARG657 3.3 0.9 1.0
CD B:GLU606 3.4 0.1 1.0
CG B:ASP688 3.5 0.2 1.0
OE1 B:GLU606 3.5 0.3 1.0
CG B:ASP724 3.6 0.5 1.0
OD1 B:ASP691 3.7 0.7 1.0
N B:VAL689 3.9 0.3 1.0
CA B:CA903 3.9 0.8 1.0
C B:VAL689 3.9 1.0 1.0
OD2 B:ASP688 4.2 0.1 1.0
CA B:ASP724 4.2 0.3 1.0
CB B:ASP724 4.3 0.6 1.0
N B:ASP691 4.4 0.8 1.0
CB B:ASP691 4.5 0.9 1.0
CG B:GLU658 4.5 0.9 1.0
OD2 B:ASP724 4.5 0.5 1.0
CG2 B:VAL689 4.6 0.1 1.0
CA B:VAL689 4.6 0.9 1.0
CB B:ASP688 4.6 0.2 1.0
CZ B:ARG657 4.6 0.0 1.0
CA B:ASP688 4.6 0.8 1.0
CG B:GLU606 4.7 0.5 1.0
C B:ASP688 4.8 0.3 1.0
CB B:ARG657 4.8 0.1 1.0
ND2 B:ASN692 4.9 0.6 1.0
N B:ASP724 5.0 0.4 1.0

Calcium binding site 10 out of 10 in 6bxu

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Calcium binding site 10 out of 10 in the Crystal Structure of Mouse Protocadherin-15 EC5-7 I582T


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure of Mouse Protocadherin-15 EC5-7 I582T within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca905

b:0.7
occ:1.00
OD1 B:ASN482 2.3 0.8 1.0
O B:ASN484 2.5 0.8 1.0
OD1 B:ASP514 2.5 0.7 1.0
OD2 B:ASP566 2.5 0.5 1.0
O B:ASN520 2.5 1.0 1.0
OD2 B:ASP514 2.7 0.1 1.0
OD1 B:ASP516 2.8 0.3 1.0
CG B:ASP514 2.9 1.0 1.0
CG B:ASN482 3.2 0.7 1.0
CG B:ASP566 3.4 0.7 1.0
ND2 B:ASN482 3.5 0.1 1.0
CG B:ASP516 3.6 0.4 1.0
OD1 B:ASP566 3.6 0.8 1.0
C B:ASN484 3.7 0.4 1.0
OD2 B:ASP516 3.7 0.3 1.0
C B:ASN520 3.7 0.8 1.0
N B:ASN484 4.0 0.0 1.0
CB B:ASN520 4.2 0.2 1.0
CA B:ASN484 4.3 0.8 1.0
CB B:ASP514 4.4 0.2 1.0
CA B:ASN520 4.5 0.3 1.0
CB B:ASN482 4.5 0.2 1.0
ND2 B:ASN520 4.6 0.1 1.0
CB B:ASN484 4.6 0.1 1.0
N B:GLY521 4.7 0.7 1.0
CD B:PRO486 4.7 0.3 1.0
N B:THR485 4.7 0.5 1.0
N B:ASP483 4.7 0.9 1.0
CB B:ASP566 4.8 0.7 1.0
O B:ASP516 4.8 0.1 1.0
CG B:ASN520 4.8 0.9 1.0
CA B:ASN482 4.9 0.6 1.0
CA B:GLY521 4.9 0.8 1.0
CB B:ASP516 5.0 0.6 1.0

Reference:

B.L.Neel, M.Sotomayor. Crystal Structure of Mouse Protocadherin-15 EC5-7 I582T To Be Published.
Page generated: Mon Jul 15 17:12:30 2024

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