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Calcium in PDB 6a48: Crystal Structure of Reelin N-Terminal Region

Protein crystallography data

The structure of Crystal Structure of Reelin N-Terminal Region, PDB code: 6a48 was solved by M.Nagae, J.Takagi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.27 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.753, 90.999, 90.535, 90.00, 90.00, 90.00
R / Rfree (%) 21.5 / 25.7

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Reelin N-Terminal Region (pdb code 6a48). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Crystal Structure of Reelin N-Terminal Region, PDB code: 6a48:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 6a48

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Calcium binding site 1 out of 5 in the Crystal Structure of Reelin N-Terminal Region


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Reelin N-Terminal Region within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca901

b:26.6
occ:1.00
 O A:ASN390 2.3 25.0 1.0
O A:ASN364 2.3 24.7 1.0
O A:HOH1031 2.4 27.5 1.0
O A:ASP388 2.4 30.0 1.0
OD2 A:ASP366 2.4 29.8 1.0
OD2 A:ASP667 2.5 22.8 1.0
OD1 A:ASP667 2.6 22.4 1.0
CG A:ASP667 2.9 26.5 1.0
CG A:ASP366 3.4 31.3 1.0
C A:ASN364 3.5 24.0 1.0
C A:ASN390 3.5 29.8 1.0
C A:ASP388 3.7 30.0 1.0
N A:ASN390 3.8 30.9 1.0
OD1 A:ASP366 3.9 34.1 1.0
CB A:ASN364 4.1 24.8 1.0
C A:GLY389 4.2 30.5 1.0
CA A:ASN364 4.2 25.4 1.0
CA A:ASN390 4.2 30.4 1.0
OD1 A:ASN668 4.3 25.3 1.0
CA A:GLY389 4.4 26.6 1.0
CB A:ASP667 4.4 20.1 1.0
CB A:LEU365 4.5 25.9 1.0
N A:GLY389 4.5 30.2 1.0
N A:LEU365 4.5 27.1 1.0
N A:SER391 4.6 29.1 1.0
CB A:ASP366 4.6 29.3 1.0
CA A:ASP388 4.6 31.1 1.0
CB A:ASP388 4.6 38.5 1.0
CG A:ASN364 4.7 26.4 1.0
OD2 A:ASP388 4.7 48.2 1.0
C A:LEU365 4.8 30.6 1.0
N A:ASP366 4.8 27.9 1.0
O A:HOH1025 4.8 27.2 1.0
CA A:LEU365 4.8 26.0 1.0
CD2 A:LEU365 4.8 21.8 1.0
O A:GLY389 4.8 31.0 1.0
CA A:SER391 4.9 27.0 1.0
CG A:ASP388 4.9 39.8 1.0
CB A:ASN390 4.9 30.6 1.0
N A:ASP388 4.9 36.3 1.0

Calcium binding site 2 out of 5 in 6a48

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Calcium binding site 2 out of 5 in the Crystal Structure of Reelin N-Terminal Region


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Reelin N-Terminal Region within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca902

b:35.5
occ:1.00
 O A:SER744 2.3 34.5 1.0
O A:LYS746 2.3 26.3 1.0
O A:SER715 2.4 28.9 1.0
O A:HOH1010 2.5 33.2 1.0
OD2 A:ASP858 2.6 27.8 1.0
OD1 A:ASP858 2.6 30.6 1.0
O A:HOH1099 2.6 35.5 1.0
CG A:ASP858 2.9 29.9 1.0
C A:LYS746 3.5 29.1 1.0
C A:SER744 3.5 36.8 1.0
C A:SER715 3.5 30.9 1.0
N A:LYS746 3.9 28.2 1.0
O A:HOH1049 4.0 34.4 1.0
C A:GLY745 4.0 36.2 1.0
CA A:SER715 4.1 29.0 1.0
N A:SER744 4.2 35.0 1.0
CB A:SER715 4.3 32.3 1.0
CA A:LYS746 4.3 29.2 1.0
CB A:ASP858 4.4 31.3 1.0
OG A:SER744 4.4 37.1 1.0
CA A:GLY745 4.4 31.3 1.0
N A:GLY745 4.4 34.9 1.0
O A:GLY745 4.4 34.5 1.0
CA A:SER744 4.4 33.1 1.0
N A:ALA747 4.5 27.6 1.0
N A:PHE716 4.6 26.1 1.0
CB A:PHE716 4.6 27.5 1.0
OE2 A:GLU859 4.6 33.2 1.0
CA A:ALA747 4.7 29.2 1.0
O A:PHE716 4.7 28.2 1.0
C A:PHE716 4.8 28.4 1.0
CA A:PHE716 4.9 24.8 1.0

Calcium binding site 3 out of 5 in 6a48

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Calcium binding site 3 out of 5 in the Crystal Structure of Reelin N-Terminal Region


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 Reelin N-Terminal Region within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca903

b:31.4
occ:1.00
 O A:ASP206 2.3 30.2 1.0
O A:HIS237 2.3 32.0 1.0
O A:HOH1070 2.4 26.6 1.0
OD2 A:ASP208 2.4 33.1 1.0
O A:ASN239 2.4 32.6 1.0
OD1 A:ASP347 2.5 26.1 1.0
OD2 A:ASP347 2.9 25.1 1.0
CG A:ASP347 3.1 29.8 1.0
CG A:ASP208 3.4 37.3 1.0
C A:ASP206 3.5 34.2 1.0
C A:ASN239 3.5 32.5 1.0
C A:HIS237 3.6 32.8 1.0
N A:ASN239 3.7 32.5 1.0
OD1 A:ASP208 4.0 39.5 1.0
C A:GLY238 4.1 34.2 1.0
CA A:ASN239 4.2 32.1 1.0
CB A:ASP206 4.2 32.1 1.0
OD1 A:ASN348 4.2 28.0 1.0
CA A:ASP206 4.2 27.9 1.0
N A:HIS237 4.3 31.9 1.0
O A:HOH1043 4.3 31.3 1.0
CA A:HIS237 4.5 36.5 1.0
CA A:GLY238 4.5 34.3 1.0
N A:GLY238 4.5 34.2 1.0
N A:PHE207 4.6 28.0 1.0
CB A:ASP347 4.6 28.5 1.0
CB A:ASP208 4.6 31.9 1.0
CB A:PHE207 4.6 34.4 1.0
N A:ASP208 4.6 37.0 1.0
N A:ALA240 4.6 33.3 1.0
C A:PHE207 4.7 33.9 1.0
O A:GLY238 4.7 31.5 1.0
CA A:PHE207 4.9 26.9 1.0
CB A:ASN239 4.9 34.2 1.0
CB A:HIS237 5.0 31.0 1.0
CA A:ALA240 5.0 34.2 1.0
CG A:ASP206 5.0 37.6 1.0

Calcium binding site 4 out of 5 in 6a48

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Calcium binding site 4 out of 5 in the Crystal Structure of Reelin N-Terminal Region


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 Reelin N-Terminal Region within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca904

b:23.7
occ:1.00
 O A:SER448 2.4 27.8 1.0
O A:LEU450 2.4 25.0 1.0
O A:GLU424 2.4 22.8 1.0
O A:HOH1038 2.4 26.5 1.0
OD1 A:ASP557 2.5 23.3 1.0
OE2 A:GLU426 2.6 33.2 1.0
OD2 A:ASP557 2.7 28.7 1.0
CG A:ASP557 2.9 24.0 1.0
C A:GLU424 3.5 25.9 1.0
C A:LEU450 3.6 28.3 1.0
C A:SER448 3.6 28.4 1.0
CD A:GLU426 3.7 29.0 1.0
N A:LEU450 3.8 26.1 1.0
C A:GLY449 4.0 25.8 1.0
CA A:GLU424 4.1 23.3 1.0
CB A:GLU424 4.2 29.2 1.0
CA A:GLY449 4.3 26.4 1.0
CA A:LEU450 4.3 26.2 1.0
O A:HOH1066 4.4 27.3 1.0
OE1 A:GLU426 4.4 30.6 1.0
N A:GLY449 4.4 22.0 1.0
N A:SER448 4.4 26.8 1.0
CB A:ASP557 4.4 25.7 1.0
OE1 A:GLU424 4.5 43.2 1.0
CG A:GLU426 4.5 29.9 1.0
O A:GLY449 4.5 25.5 1.0
N A:SER451 4.6 24.1 1.0
CA A:SER448 4.6 28.2 1.0
C A:PHE425 4.6 27.6 1.0
N A:PHE425 4.6 25.7 1.0
OG A:SER448 4.6 37.9 1.0
OE1 A:GLU447 4.8 25.6 1.0
O A:PHE425 4.8 28.1 1.0
N A:GLU426 4.8 26.8 1.0
CA A:SER451 4.8 25.4 1.0
CB A:PHE425 4.9 23.2 1.0
CA A:PHE425 4.9 25.8 1.0

Calcium binding site 5 out of 5 in 6a48

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Calcium binding site 5 out of 5 in the Crystal Structure of Reelin N-Terminal Region


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 Reelin N-Terminal Region within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca905

b:46.6
occ:1.00
 OD2 A:ASP790 2.4 49.3 1.0
OE1 A:GLU794 2.4 47.0 1.0
OG A:SER848 2.4 46.8 1.0
OE2 A:GLU794 2.5 48.9 1.0
OD1 A:ASP853 2.8 44.1 1.0
OD2 A:ASP853 2.8 46.0 1.0
CD A:GLU794 2.8 47.1 1.0
CG A:ASP853 3.1 47.3 1.0
CG A:ASP790 3.3 48.4 1.0
OD1 A:ASP790 3.6 52.5 1.0
CB A:SER848 3.7 48.9 1.0
N A:SER848 4.2 51.3 1.0
N A:ASP790 4.3 47.0 1.0
CG A:GLN791 4.3 57.6 1.0
N A:GLN791 4.3 51.7 1.0
CG A:GLU794 4.3 45.8 1.0
CB A:GLN791 4.4 54.3 1.0
CA A:SER848 4.5 51.3 1.0
CB A:ASP853 4.6 41.0 1.0
CB A:ASP790 4.6 50.5 1.0
CA A:ASP790 4.8 52.9 1.0
C A:ASP790 4.9 52.0 1.0

Reference:

M.Nagae, J.Takagi. Crystal Structure of Reelin N-Terminal Region To Be Published.
Page generated: Wed Jul 9 12:20:04 2025

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