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Calcium in PDB 2vme: Structure of the Wild-Type Discoidin II From Dictyostelium Discoideum

Protein crystallography data

The structure of Structure of the Wild-Type Discoidin II From Dictyostelium Discoideum, PDB code: 2vme was solved by K.S.Aragao, M.Satre, A.Imberty, A.Varrot, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.80 / 2.45
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 287.885, 56.281, 123.674, 90.00, 109.10, 90.00
R / Rfree (%) 18.1 / 23.8

Other elements in 2vme:

The structure of Structure of the Wild-Type Discoidin II From Dictyostelium Discoideum also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Zinc (Zn) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of the Wild-Type Discoidin II From Dictyostelium Discoideum (pdb code 2vme). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Structure of the Wild-Type Discoidin II From Dictyostelium Discoideum, PDB code: 2vme:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 2vme

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Calcium binding site 1 out of 6 in the Structure of the Wild-Type Discoidin II From Dictyostelium Discoideum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of the Wild-Type Discoidin II From Dictyostelium Discoideum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca500

b:25.7
occ:1.00
 O A:HOH2023 2.1 22.9 1.0
O A:SER40 2.3 34.9 1.0
OD1 A:ASP47 2.4 25.9 1.0
OD1 A:ASN39 2.4 29.9 1.0
O A:HOH2024 2.8 21.1 1.0
CG A:ASN39 3.4 27.6 1.0
CG A:ASP47 3.4 25.9 1.0
C A:SER40 3.5 35.1 1.0
OD2 A:ASP47 3.7 25.1 1.0
ND2 A:ASN39 3.8 24.1 1.0
N A:SER40 3.9 31.7 1.0
CA A:SER40 4.2 33.6 1.0
C A:ASN39 4.4 30.0 1.0
O A:GLY48 4.4 23.6 1.0
CB A:SER40 4.5 33.5 1.0
CB A:ASN39 4.6 28.0 1.0
N A:ASP47 4.6 28.9 1.0
N A:LYS41 4.6 36.6 1.0
O A:ARG45 4.7 36.6 1.0
CB A:ASP47 4.8 26.8 1.0
OE2 A:GLU50 4.8 30.8 1.0
O A:ASN39 4.9 29.0 1.0
CA A:ASN39 4.9 28.7 1.0
CA A:LYS41 4.9 38.4 1.0
O A:ASP42 5.0 43.7 1.0

Calcium binding site 2 out of 6 in 2vme

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Calcium binding site 2 out of 6 in the Structure of the Wild-Type Discoidin II From Dictyostelium Discoideum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of the Wild-Type Discoidin II From Dictyostelium Discoideum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca500

b:19.8
occ:1.00
 O B:HOH2025 1.9 24.7 1.0
O B:SER40 2.2 23.9 1.0
O B:HOH2021 2.3 24.9 1.0
OD1 B:ASP47 2.3 24.1 1.0
OD1 B:ASN39 2.6 24.3 1.0
O B:HOH2022 2.8 27.9 1.0
CG B:ASP47 3.2 23.4 1.0
C B:SER40 3.3 24.9 1.0
CG B:ASN39 3.4 22.7 1.0
OD2 B:ASP47 3.5 21.7 1.0
N B:SER40 3.7 23.8 1.0
ND2 B:ASN39 3.9 20.9 1.0
CA B:SER40 4.0 23.8 1.0
C B:ASN39 4.2 22.6 1.0
CB B:SER40 4.3 23.2 1.0
CB B:ASN39 4.3 21.8 1.0
O B:GLY48 4.4 21.9 1.0
N B:LYS41 4.4 26.6 1.0
O B:HOH2034 4.4 21.1 1.0
N B:ASP47 4.6 25.8 1.0
CB B:ASP47 4.6 24.5 1.0
OE2 B:GLU50 4.7 26.8 1.0
CA B:ASN39 4.7 22.3 1.0
CA B:LYS41 4.7 28.4 1.0
O B:ASN39 4.7 21.8 1.0
O B:ASP42 4.8 30.2 1.0
OG B:SER40 5.0 23.2 1.0
N B:ASP42 5.0 30.1 1.0

Calcium binding site 3 out of 6 in 2vme

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Calcium binding site 3 out of 6 in the Structure of the Wild-Type Discoidin II From Dictyostelium Discoideum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of the Wild-Type Discoidin II From Dictyostelium Discoideum within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca500

b:21.2
occ:1.00
 OD1 C:ASP47 2.3 21.7 1.0
O C:SER40 2.3 34.0 1.0
O C:HOH2022 2.5 22.2 1.0
O C:HOH2020 2.5 18.3 1.0
OD1 C:ASN39 2.6 26.1 1.0
CG C:ASP47 3.3 26.6 1.0
CG C:ASN39 3.4 25.4 1.0
C C:SER40 3.5 34.0 1.0
OD2 C:ASP47 3.7 28.3 1.0
ND2 C:ASN39 3.8 23.6 1.0
N C:SER40 4.0 30.0 1.0
CA C:SER40 4.1 32.7 1.0
O C:GLY48 4.3 22.6 1.0
C C:ASN39 4.4 28.7 1.0
CB C:SER40 4.4 32.4 1.0
N C:ASP47 4.5 27.2 1.0
CB C:ASN39 4.5 26.9 1.0
N C:LYS41 4.6 35.4 1.0
CB C:ASP47 4.7 26.4 1.0
O C:ASN39 4.8 28.9 1.0
CA C:LYS41 4.9 37.1 1.0
OE2 C:GLU50 4.9 31.0 1.0
CA C:ASN39 4.9 27.3 1.0

Calcium binding site 4 out of 6 in 2vme

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Calcium binding site 4 out of 6 in the Structure of the Wild-Type Discoidin II From Dictyostelium Discoideum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of the Wild-Type Discoidin II From Dictyostelium Discoideum within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca500

b:26.5
occ:1.00
 O D:SER40 2.3 32.5 1.0
OD1 D:ASP47 2.3 25.0 1.0
OD1 D:ASN39 2.4 28.9 1.0
O D:HOH2016 2.6 27.5 1.0
O D:HOH2017 2.8 25.0 1.0
CG D:ASN39 3.3 28.3 1.0
CG D:ASP47 3.3 25.7 1.0
C D:SER40 3.5 32.7 1.0
OD2 D:ASP47 3.6 25.4 1.0
ND2 D:ASN39 3.8 25.5 1.0
N D:SER40 4.0 31.2 1.0
CA D:SER40 4.2 32.1 1.0
C D:ASN39 4.2 30.4 1.0
O D:GLY48 4.3 21.0 1.0
CB D:ASN39 4.3 29.1 1.0
N D:ASP47 4.6 26.0 1.0
N D:LYS41 4.6 33.3 1.0
O D:ASN39 4.6 30.7 1.0
CB D:SER40 4.6 31.6 1.0
OE2 D:GLU50 4.6 28.9 1.0
CB D:ASP47 4.7 24.7 1.0
CA D:ASN39 4.7 29.7 1.0
CA D:LYS41 4.9 34.4 1.0
O D:ARG45 5.0 32.4 1.0

Calcium binding site 5 out of 6 in 2vme

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Calcium binding site 5 out of 6 in the Structure of the Wild-Type Discoidin II From Dictyostelium Discoideum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of the Wild-Type Discoidin II From Dictyostelium Discoideum within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca500

b:31.4
occ:1.00
 OD1 E:ASP47 2.3 36.7 1.0
O E:HOH2017 2.4 24.2 1.0
O E:SER40 2.4 39.3 1.0
OD1 E:ASN39 2.4 37.7 1.0
CG E:ASP47 3.2 36.3 1.0
CG E:ASN39 3.2 36.4 1.0
OD2 E:ASP47 3.4 36.0 1.0
C E:SER40 3.5 39.4 1.0
ND2 E:ASN39 3.8 37.3 1.0
N E:SER40 3.9 37.0 1.0
CA E:SER40 4.2 38.0 1.0
C E:ASN39 4.3 36.4 1.0
CB E:ASN39 4.3 36.0 1.0
O E:GLY48 4.4 29.8 1.0
CB E:SER40 4.4 37.6 1.0
OE2 E:GLU50 4.5 27.8 1.0
CB E:ASP47 4.6 34.7 1.0
N E:LYS41 4.6 40.7 1.0
N E:ASP47 4.7 35.7 1.0
CA E:ASN39 4.8 35.7 1.0
O E:ASN39 4.8 36.5 1.0
O E:ASP42 4.8 48.3 1.0
O E:ARG45 4.9 40.1 1.0
CA E:LYS41 4.9 42.6 1.0

Calcium binding site 6 out of 6 in 2vme

Go back to Calcium Binding Sites List in 2vme
Calcium binding site 6 out of 6 in the Structure of the Wild-Type Discoidin II From Dictyostelium Discoideum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of the Wild-Type Discoidin II From Dictyostelium Discoideum within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca500

b:25.2
occ:1.00
 O F:HOH2013 2.3 20.8 1.0
O F:SER40 2.4 35.2 1.0
OD1 F:ASP47 2.4 27.6 1.0
OD1 F:ASN39 2.5 37.0 1.0
CG F:ASP47 3.4 28.0 1.0
CG F:ASN39 3.4 33.6 1.0
C F:SER40 3.5 36.1 1.0
OD2 F:ASP47 3.7 27.8 1.0
ND2 F:ASN39 3.8 30.1 1.0
N F:SER40 4.0 36.2 1.0
CA F:SER40 4.2 36.4 1.0
O F:GLY48 4.3 24.7 1.0
O F:HOH2015 4.4 38.8 1.0
C F:ASN39 4.4 35.5 1.0
CB F:SER40 4.5 36.6 1.0
CB F:ASN39 4.5 34.1 1.0
N F:ASP47 4.5 29.0 1.0
N F:LYS41 4.6 36.6 1.0
CB F:ASP47 4.7 27.8 1.0
O F:ARG45 4.7 35.1 1.0
O F:ASP42 4.8 37.1 1.0
O F:ASN39 4.9 35.6 1.0
OE2 F:GLU50 5.0 33.4 1.0
CA F:ASN39 5.0 34.9 1.0

Reference:

K.S.Aragao, M.Satre, A.Imberty, A.Varrot. Structure Determination of Discoidin II From Dictyostelium Discoideum and Carbohydrate Binding Properties of the Lectin Domain. Proteins V. 73 43 2008.
ISSN: ISSN 0887-3585
PubMed: 18384150
DOI: 10.1002/PROT.22038
Page generated: Tue Jul 8 08:40:33 2025

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