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Calcium in PDB 4gej: N-Terminal Domain of Vdup-1

Protein crystallography data

The structure of N-Terminal Domain of Vdup-1, PDB code: 4gej was solved by G.Polekhina, S.F.Kok, D.B.Ascher, M.Waltham, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.00 / 2.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 79.740, 178.810, 81.890, 90.00, 113.32, 90.00
R / Rfree (%) 21.2 / 29.4

Calcium Binding Sites:

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

Calcium binding site 1 out of 5 in 4gej

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Calcium binding site 1 out of 5 in the N-Terminal Domain of Vdup-1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of N-Terminal Domain of Vdup-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca201

b:99.3
occ:1.00
 O A:THR75 2.2 98.7 1.0
O F:THR75 2.5 94.6 1.0
OD1 F:ASP74 2.7 0.3 1.0
OD2 A:ASP74 2.8 93.3 1.0
OD2 F:ASP74 3.3 0.5 1.0
CG F:ASP74 3.3 0.6 1.0
C A:THR75 3.4 98.1 1.0
CG A:ASP74 3.4 90.6 1.0
OD1 A:ASP74 3.5 89.9 1.0
C F:THR75 3.6 95.1 1.0
N A:THR75 3.9 90.4 1.0
CA A:THR75 4.1 95.2 1.0
N F:THR75 4.1 93.7 1.0
CA F:THR75 4.3 93.5 1.0
CB A:THR75 4.4 98.7 1.0
N A:LEU76 4.4 98.1 1.0
CA A:LEU76 4.6 0.6 1.0
CB A:ASP74 4.6 85.5 1.0
N F:LEU76 4.7 95.2 1.0
CB F:THR75 4.7 94.0 1.0
C A:ASP74 4.7 86.8 1.0
CB F:ASP74 4.8 1.0 1.0
CD1 A:LEU77 4.8 0.6 1.0
CA A:ASP74 4.9 83.9 1.0
CA F:LEU76 4.9 0.0 1.0
C F:ASP74 5.0 94.8 1.0

Calcium binding site 2 out of 5 in 4gej

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Calcium binding site 2 out of 5 in the N-Terminal Domain of Vdup-1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of N-Terminal Domain of Vdup-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca201

b:74.3
occ:1.00
 O J:THR75 2.2 71.8 1.0
O C:THR75 2.3 70.6 1.0
OD1 C:ASP74 2.5 75.5 1.0
OD1 J:ASP74 2.6 80.0 1.0
C J:THR75 3.4 69.4 1.0
C C:THR75 3.5 66.9 1.0
CG C:ASP74 3.5 70.0 1.0
CG J:ASP74 3.6 78.6 1.0
N C:THR75 3.7 61.4 1.0
OD2 J:ASP74 3.9 79.6 1.0
N J:THR75 3.9 65.3 1.0
OD2 C:ASP74 4.0 75.1 1.0
CA C:THR75 4.0 65.1 1.0
CA J:THR75 4.2 66.8 1.0
CB C:THR75 4.2 70.1 1.0
N J:LEU76 4.5 67.9 1.0
N C:LEU76 4.6 64.1 1.0
C C:ASP74 4.6 58.5 1.0
CB J:THR75 4.6 67.5 1.0
CA J:LEU76 4.7 72.0 1.0
CB C:ASP74 4.7 61.9 1.0
CA C:LEU76 4.8 67.4 1.0
CA C:ASP74 4.8 58.9 1.0
C J:ASP74 4.8 64.7 1.0
CB J:ASP74 4.9 73.3 1.0
OG1 C:THR75 5.0 71.3 1.0

Calcium binding site 3 out of 5 in 4gej

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Calcium binding site 3 out of 5 in the N-Terminal Domain of Vdup-1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of N-Terminal Domain of Vdup-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca201

b:77.0
occ:1.00
 O D:THR75 2.2 70.9 1.0
O B:THR75 2.3 58.4 1.0
OD1 D:ASP74 2.4 76.0 1.0
OD1 B:ASP74 2.6 70.9 1.0
CG D:ASP74 3.2 73.9 1.0
C D:THR75 3.4 72.2 1.0
OD2 D:ASP74 3.4 75.8 1.0
C B:THR75 3.5 56.8 1.0
CG B:ASP74 3.5 68.0 1.0
OD2 B:ASP74 3.7 73.5 1.0
N D:THR75 4.0 68.5 1.0
N B:THR75 4.1 58.6 1.0
CA D:THR75 4.2 71.2 1.0
CA B:THR75 4.2 56.0 1.0
CB B:THR75 4.4 56.2 1.0
N D:LEU76 4.4 75.8 1.0
N B:LEU76 4.5 58.1 1.0
CB D:ASP74 4.6 66.4 1.0
CA D:LEU76 4.6 81.7 1.0
CD2 D:LEU77 4.6 95.5 1.0
CB D:THR75 4.6 73.0 1.0
CA B:LEU76 4.7 61.8 1.0
C D:ASP74 4.7 64.8 1.0
CA D:ASP74 4.8 64.5 1.0
CB B:ASP74 4.9 61.0 1.0
C B:ASP74 5.0 59.6 1.0

Calcium binding site 4 out of 5 in 4gej

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Calcium binding site 4 out of 5 in the N-Terminal Domain of Vdup-1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of N-Terminal Domain of Vdup-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca201

b:64.7
occ:1.00
 O E:THR75 2.2 55.8 1.0
OD1 E:ASP74 2.3 54.4 1.0
O H:THR75 2.3 51.2 1.0
OD1 H:ASP74 2.5 62.4 1.0
CG H:ASP74 3.3 58.0 1.0
CG E:ASP74 3.4 55.3 1.0
OD2 H:ASP74 3.4 67.2 1.0
C E:THR75 3.4 49.4 1.0
C H:THR75 3.4 50.9 1.0
N E:THR75 3.9 46.5 1.0
N H:THR75 3.9 50.0 1.0
OD2 E:ASP74 3.9 58.7 1.0
CA H:THR75 4.1 51.5 1.0
CA E:THR75 4.2 46.5 1.0
CB H:THR75 4.4 55.4 1.0
CB E:THR75 4.5 46.6 1.0
N E:LEU76 4.5 46.5 1.0
N H:LEU76 4.5 52.2 1.0
CB E:ASP74 4.7 49.6 1.0
C E:ASP74 4.7 45.2 1.0
CB H:ASP74 4.7 52.2 1.0
CA E:LEU76 4.8 47.7 1.0
CA E:ASP74 4.8 47.5 1.0
C H:ASP74 4.9 50.3 1.0
CA H:LEU76 4.9 52.2 1.0

Calcium binding site 5 out of 5 in 4gej

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Calcium binding site 5 out of 5 in the N-Terminal Domain of Vdup-1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of N-Terminal Domain of Vdup-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ca201

b:69.0
occ:1.00
 O I:THR75 2.4 60.7 1.0
OD1 I:ASP74 2.5 69.3 1.0
CG I:ASP74 3.5 70.1 1.0
C I:THR75 3.5 60.3 1.0
OD2 I:ASP74 3.8 72.0 1.0
N I:THR75 3.9 62.1 1.0
CA I:THR75 4.2 62.3 1.0
CB I:THR75 4.4 66.4 1.0
N I:LEU76 4.6 59.3 1.0
CB I:ASP74 4.8 66.0 1.0
C I:ASP74 4.8 64.3 1.0
CA I:LEU76 4.8 59.6 1.0

Reference:

G.Polekhina, D.B.Ascher, S.F.Kok, S.Beckham, M.Wilce, M.Waltham. Structure of the N-Terminal Domain of Human Thioredoxin-Interacting Protein. Acta Crystallogr.,Sect.D V. 69 333 2013.
ISSN: ISSN 0907-4449
PubMed: 23519408
DOI: 10.1107/S0907444912047099
Page generated: Tue Jul 8 20:16:49 2025

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