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Calcium in PDB 2e6v: Crystal Structure of VIP36 Exoplasmic/Lumenal Domain, CA2+/MAN3GLCNAC-Bound Form

Protein crystallography data

The structure of Crystal Structure of VIP36 Exoplasmic/Lumenal Domain, CA2+/MAN3GLCNAC-Bound Form, PDB code: 2e6v was solved by T.Satoh, R.Kato, S.Wakatsuki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 57.200, 151.200, 177.100, 90.00, 90.00, 90.00
R / Rfree (%) 22.1 / 27.9

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of VIP36 Exoplasmic/Lumenal Domain, CA2+/MAN3GLCNAC-Bound Form (pdb code 2e6v). 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 VIP36 Exoplasmic/Lumenal Domain, CA2+/MAN3GLCNAC-Bound Form, PDB code: 2e6v:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 2e6v

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Calcium binding site 1 out of 5 in the Crystal Structure of VIP36 Exoplasmic/Lumenal Domain, CA2+/MAN3GLCNAC-Bound Form


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 VIP36 Exoplasmic/Lumenal Domain, CA2+/MAN3GLCNAC-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca8

b:17.6
occ:1.00
 OD1 A:ASN166 2.2 22.1 1.0
O A:HOH321 2.2 17.8 1.0
O A:TYR164 2.2 18.9 1.0
OD2 A:ASP193 2.3 18.6 1.0
O A:HOH322 2.4 17.4 1.0
OD2 A:ASP162 2.4 15.9 1.0
OD1 A:ASP162 2.6 17.6 1.0
CG A:ASP162 2.9 15.3 1.0
CG A:ASN166 3.4 21.1 1.0
C A:TYR164 3.4 18.4 1.0
CG A:ASP193 3.5 19.4 1.0
N A:ASN166 3.9 22.2 1.0
CB A:ASN166 4.1 22.0 1.0
CB A:ASP193 4.1 19.8 1.0
CA A:TYR164 4.3 17.1 1.0
N A:TYR164 4.3 16.1 1.0
CA A:ASP193 4.3 19.9 1.0
ND2 A:ASN166 4.4 18.6 1.0
CB A:ASP162 4.4 13.3 1.0
N A:PRO165 4.4 19.7 1.0
O A:HIS190 4.4 23.9 1.0
CE2 A:PHE174 4.5 19.6 1.0
OD1 A:ASP193 4.5 16.9 1.0
CA A:PRO165 4.6 20.6 1.0
OH A:TYR188 4.6 15.4 1.0
O A:HOH311 4.6 8.9 1.0
CA A:ASN166 4.6 22.7 1.0
CB A:TYR164 4.7 16.7 1.0
C A:PRO165 4.7 21.9 1.0
CE1 A:HIS190 4.7 31.5 1.0
O A:ASP131 4.9 14.3 1.0
CD2 A:TYR164 4.9 17.6 1.0
OD2 A:ASP131 4.9 19.3 1.0
N A:ASP193 5.0 20.9 1.0

Calcium binding site 2 out of 5 in 2e6v

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Calcium binding site 2 out of 5 in the Crystal Structure of VIP36 Exoplasmic/Lumenal Domain, CA2+/MAN3GLCNAC-Bound Form


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 VIP36 Exoplasmic/Lumenal Domain, CA2+/MAN3GLCNAC-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca9

b:20.2
occ:1.00
 OD2 B:ASP193 2.3 22.3 1.0
O B:TYR164 2.3 23.3 1.0
OD1 B:ASN166 2.3 26.0 1.0
O B:HOH311 2.3 14.6 1.0
O B:HOH312 2.5 15.8 1.0
OD1 B:ASP162 2.5 24.7 1.0
OD2 B:ASP162 2.6 26.4 1.0
CG B:ASP162 2.9 23.2 1.0
CG B:ASP193 3.4 22.1 1.0
C B:TYR164 3.5 24.0 1.0
CG B:ASN166 3.5 27.8 1.0
N B:ASN166 3.9 27.6 1.0
CB B:ASP193 4.1 20.9 1.0
CB B:ASN166 4.3 28.3 1.0
CA B:ASP193 4.3 21.7 1.0
CA B:TYR164 4.4 23.9 1.0
N B:TYR164 4.4 23.3 1.0
OD1 B:ASP193 4.4 23.4 1.0
CB B:ASP162 4.4 20.4 1.0
N B:PRO165 4.5 24.6 1.0
ND2 B:ASN166 4.6 25.9 1.0
CE2 B:PHE174 4.6 25.2 1.0
CA B:PRO165 4.6 25.8 1.0
C B:PRO165 4.7 26.8 1.0
O B:HIS190 4.7 24.2 1.0
CB B:TYR164 4.7 24.0 1.0
CA B:ASN166 4.7 28.6 1.0
CD2 B:TYR164 4.8 24.3 1.0
OH B:TYR188 4.8 19.5 1.0
CE1 B:HIS190 5.0 33.1 1.0
N B:ASP193 5.0 22.3 1.0

Calcium binding site 3 out of 5 in 2e6v

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Calcium binding site 3 out of 5 in the Crystal Structure of VIP36 Exoplasmic/Lumenal Domain, CA2+/MAN3GLCNAC-Bound Form


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 VIP36 Exoplasmic/Lumenal Domain, CA2+/MAN3GLCNAC-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca10

b:16.9
occ:1.00
 OD2 C:ASP193 2.2 16.6 1.0
O C:TYR164 2.4 18.0 1.0
OD1 C:ASN166 2.4 21.5 1.0
O C:HOH313 2.4 8.9 1.0
OD2 C:ASP162 2.5 14.9 1.0
OD1 C:ASP162 2.7 17.1 1.0
CG C:ASP162 2.9 15.1 1.0
CG C:ASP193 3.4 20.1 1.0
CG C:ASN166 3.6 22.2 1.0
C C:TYR164 3.6 18.0 1.0
N C:ASN166 4.0 21.5 1.0
CB C:ASP193 4.1 17.5 1.0
CB C:ASN166 4.3 22.5 1.0
OD1 C:ASP193 4.3 21.8 1.0
N C:TYR164 4.4 16.8 1.0
CA C:TYR164 4.4 17.7 1.0
CE2 C:PHE174 4.4 15.5 1.0
CA C:ASP193 4.4 18.1 1.0
CB C:ASP162 4.5 13.2 1.0
O C:HIS190 4.5 22.1 1.0
N C:PRO165 4.6 18.2 1.0
ND2 C:ASN166 4.6 21.1 1.0
CA C:PRO165 4.6 19.1 1.0
OH C:TYR188 4.7 16.6 1.0
CD2 C:TYR164 4.7 19.2 1.0
C C:PRO165 4.7 20.1 1.0
CA C:ASN166 4.8 23.1 1.0
OD2 C:ASP131 4.8 19.8 1.0
CB C:TYR164 4.8 17.9 1.0
CE1 C:HIS190 4.8 31.8 1.0
NE2 C:HIS190 4.9 30.2 1.0
O C:ASP131 5.0 15.2 1.0

Calcium binding site 4 out of 5 in 2e6v

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Calcium binding site 4 out of 5 in the Crystal Structure of VIP36 Exoplasmic/Lumenal Domain, CA2+/MAN3GLCNAC-Bound Form


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 VIP36 Exoplasmic/Lumenal Domain, CA2+/MAN3GLCNAC-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca11

b:18.0
occ:1.00
 OD2 D:ASP193 2.2 18.2 1.0
O D:TYR164 2.2 19.8 1.0
OD1 D:ASN166 2.3 17.7 1.0
OD1 D:ASP162 2.5 10.3 1.0
OD2 D:ASP162 2.5 16.3 1.0
CG D:ASP162 2.8 13.9 1.0
CG D:ASP193 3.4 18.7 1.0
C D:TYR164 3.4 20.6 1.0
CG D:ASN166 3.5 19.7 1.0
N D:ASN166 4.0 21.3 1.0
CB D:ASP193 4.0 17.6 1.0
CB D:ASN166 4.1 21.3 1.0
CA D:TYR164 4.3 20.7 1.0
N D:TYR164 4.3 20.3 1.0
CE2 D:PHE174 4.3 17.2 1.0
CB D:ASP162 4.3 15.1 1.0
CA D:ASP193 4.4 17.9 1.0
OD1 D:ASP193 4.4 19.4 1.0
N D:PRO165 4.4 20.7 1.0
ND2 D:ASN166 4.5 19.2 1.0
O D:HIS190 4.6 19.4 1.0
CB D:TYR164 4.6 21.0 1.0
OH D:TYR188 4.6 13.7 1.0
CE1 D:HIS190 4.7 24.0 1.0
CA D:PRO165 4.7 20.9 1.0
CA D:ASN166 4.7 22.1 1.0
C D:PRO165 4.8 21.1 1.0
CD2 D:TYR164 4.9 24.5 1.0
CZ D:PHE174 4.9 18.4 1.0

Calcium binding site 5 out of 5 in 2e6v

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Calcium binding site 5 out of 5 in the Crystal Structure of VIP36 Exoplasmic/Lumenal Domain, CA2+/MAN3GLCNAC-Bound Form


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 VIP36 Exoplasmic/Lumenal Domain, CA2+/MAN3GLCNAC-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca12

b:54.0
occ:1.00
 O E:TYR164 2.3 48.6 1.0
OD2 E:ASP193 2.3 58.0 1.0
OD2 E:ASP162 2.7 38.3 1.0
OD1 E:ASP162 2.9 37.1 1.0
CG E:ASP162 3.2 36.8 1.0
OD1 E:ASN166 3.4 61.1 1.0
C E:TYR164 3.5 48.9 1.0
CG E:ASP193 3.5 57.5 1.0
CG E:ASN166 3.7 60.4 1.0
N E:ASN166 3.9 57.3 1.0
CB E:ASP193 4.1 57.0 1.0
CB E:ASN166 4.2 59.6 1.0
CA E:ASP193 4.2 56.9 1.0
ND2 E:ASN166 4.4 60.8 1.0
OH E:TYR188 4.4 46.0 1.0
N E:PRO165 4.4 50.9 1.0
C E:PRO165 4.4 55.1 1.0
CA E:PRO165 4.4 53.1 1.0
CA E:TYR164 4.5 47.3 1.0
CE2 E:PHE174 4.5 37.5 1.0
OD1 E:ASP193 4.5 58.5 1.0
N E:TYR164 4.6 44.6 1.0
CA E:ASN166 4.7 59.5 1.0
CB E:ASP162 4.7 35.1 1.0
O E:HIS190 4.8 55.5 1.0
CB E:TYR164 4.8 47.8 1.0
N E:ASP193 4.9 57.0 1.0
CD2 E:TYR164 5.0 49.6 1.0

Reference:

T.Satoh, N.P.Cowieson, W.Hakamata, H.Ideo, K.Fukushima, M.Kurihara, R.Kato, K.Yamashita, S.Wakatsuki. Structural Basis For Recognition of High Mannose Type Glycoproteins By Mammalian Transport Lectin VIP36 J.Biol.Chem. V. 282 28246 2007.
ISSN: ISSN 0021-9258
PubMed: 17652092
DOI: 10.1074/JBC.M703064200
Page generated: Tue Jul 8 05:16:25 2025

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