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

Protein crystallography data

The structure of Crystal Structure of VIP36 Exoplasmic/Lumenal Domain, CA2+- Bound Form, PDB code: 2duo was solved by T.Satoh, N.P.Cowieson, 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 / 1.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 170.700, 45.400, 116.100, 90.00, 131.50, 90.00
R / Rfree (%) 20.5 / 24.1

Other elements in 2duo:

The structure of Crystal Structure of VIP36 Exoplasmic/Lumenal Domain, CA2+- Bound Form also contains other interesting chemical elements:

Chlorine (Cl) 11 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of VIP36 Exoplasmic/Lumenal Domain, CA2+- Bound Form (pdb code 2duo). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of VIP36 Exoplasmic/Lumenal Domain, CA2+- Bound Form, PDB code: 2duo:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 2duo

Go back to Calcium Binding Sites List in 2duo
Calcium binding site 1 out of 2 in the Crystal Structure of VIP36 Exoplasmic/Lumenal Domain, CA2+- 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+- Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1

b:19.1
occ:1.00
OD1 A:ASN166 2.3 20.7 1.0
O A:TYR164 2.4 18.2 1.0
OD2 A:ASP193 2.4 18.2 1.0
OD2 A:ASP162 2.4 14.8 1.0
O A:HOH319 2.5 14.6 1.0
O A:HOH336 2.5 16.1 1.0
OD1 A:ASP162 2.6 17.0 1.0
CG A:ASP162 2.9 17.6 1.0
CG A:ASN166 3.5 21.6 1.0
CG A:ASP193 3.5 17.4 1.0
C A:TYR164 3.6 19.9 1.0
N A:ASN166 4.0 20.3 1.0
CB A:ASP193 4.1 16.8 1.0
CB A:ASN166 4.2 20.8 1.0
N A:TYR164 4.3 19.6 1.0
CA A:TYR164 4.3 19.6 1.0
CA A:ASP193 4.4 16.9 1.0
CB A:ASP162 4.4 15.0 1.0
O A:HIS190 4.5 20.4 1.0
CE2 A:PHE174 4.5 20.0 1.0
CE1 A:HIS190 4.5 28.2 1.0
OD1 A:ASP193 4.5 17.4 1.0
OH A:TYR188 4.6 17.4 1.0
CB A:TYR164 4.6 20.7 1.0
ND2 A:ASN166 4.6 20.9 1.0
O A:HOH327 4.6 23.6 1.0
N A:PRO165 4.6 20.5 1.0
CA A:PRO165 4.7 20.7 1.0
CA A:ASN166 4.7 21.2 1.0
O A:ASP131 4.8 14.9 1.0
C A:PRO165 4.8 21.1 1.0
ND1 A:HIS190 4.8 26.8 1.0
CD2 A:TYR164 4.9 22.1 1.0
CZ A:PHE148 5.0 14.7 1.0
N A:ASP193 5.0 17.8 1.0

Calcium binding site 2 out of 2 in 2duo

Go back to Calcium Binding Sites List in 2duo
Calcium binding site 2 out of 2 in the Crystal Structure of VIP36 Exoplasmic/Lumenal Domain, CA2+- 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+- Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2

b:27.9
occ:1.00
O B:TYR164 2.3 27.4 1.0
OD2 B:ASP193 2.4 28.3 1.0
OD1 B:ASN166 2.5 33.3 1.0
O B:HOH370 2.5 28.1 1.0
OD2 B:ASP162 2.6 24.1 1.0
O B:HOH359 2.6 23.2 1.0
OD1 B:ASP162 2.6 23.0 1.0
CG B:ASP162 3.0 22.3 1.0
CG B:ASP193 3.5 30.5 1.0
C B:TYR164 3.6 28.6 1.0
CG B:ASN166 3.6 32.1 1.0
N B:ASN166 4.0 31.0 1.0
CB B:ASP193 4.1 32.4 1.0
CB B:ASN166 4.3 31.9 1.0
CA B:TYR164 4.4 28.3 1.0
N B:TYR164 4.4 26.8 1.0
CA B:ASP193 4.5 32.7 1.0
CB B:ASP162 4.5 21.6 1.0
OD1 B:ASP193 4.5 28.4 1.0
N B:PRO165 4.5 29.3 1.0
CE2 B:PHE174 4.6 23.9 1.0
CA B:PRO165 4.6 29.8 1.0
ND2 B:ASN166 4.6 32.0 1.0
OH B:TYR188 4.7 28.2 1.0
C B:PRO165 4.7 30.5 1.0
O B:HIS190 4.7 39.6 1.0
CA B:ASN166 4.7 32.0 1.0
CB B:TYR164 4.8 29.6 1.0
O B:ASP131 4.9 18.4 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: Sat Dec 12 03:35:26 2020

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