Atomistry » Calcium » PDB 2dw1-2eek » 2e6v
Atomistry »
  Calcium »
    PDB 2dw1-2eek »
      2e6v »

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

Go back to Calcium Binding Sites List in 2e6v
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

Go back to Calcium Binding Sites List in 2e6v
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

Go back to Calcium Binding Sites List in 2e6v
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

Go back to Calcium Binding Sites List in 2e6v
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

Go back to Calcium Binding Sites List in 2e6v
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: Fri Jul 12 10:05:53 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy