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Calcium in PDB 2ox8: Human Scavenger Receptor C-Type Lectin Carbohydrate- Recognition Domain.

Protein crystallography data

The structure of Human Scavenger Receptor C-Type Lectin Carbohydrate- Recognition Domain., PDB code: 2ox8 was solved by W.I.Weis, H.Feinberg, K.Drickamer, M.E.Taylor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.92 / 2.50
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 80.422, 80.422, 67.159, 90.00, 90.00, 120.00
R / Rfree (%) 23.3 / 30.8

Other elements in 2ox8:

The structure of Human Scavenger Receptor C-Type Lectin Carbohydrate- Recognition Domain. also contains other interesting chemical elements:

Chlorine (Cl) 12 atoms
Zinc (Zn) 16 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Human Scavenger Receptor C-Type Lectin Carbohydrate- Recognition Domain. (pdb code 2ox8). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Human Scavenger Receptor C-Type Lectin Carbohydrate- Recognition Domain., PDB code: 2ox8:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 2ox8

Go back to Calcium Binding Sites List in 2ox8
Calcium binding site 1 out of 6 in the Human Scavenger Receptor C-Type Lectin Carbohydrate- Recognition Domain.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Human Scavenger Receptor C-Type Lectin Carbohydrate- Recognition Domain. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca6

b:26.9
occ:0.50
OE2 C:GLU674 2.2 35.0 0.5
O C:GLU706 2.3 30.4 0.5
OD1 C:ASN697 2.5 37.3 0.5
OD1 C:ASP707 2.6 29.9 0.5
OD2 C:ASP670 3.0 28.5 0.5
OD1 C:ASP670 3.1 28.7 0.5
CG C:ASN697 3.3 37.6 0.5
C C:GLU706 3.3 29.4 0.5
CG C:ASP670 3.4 28.7 0.5
CD C:GLU674 3.4 35.5 0.5
CB C:ASN697 3.7 37.2 0.5
CG C:ASP707 3.7 29.4 0.5
CA C:ASP707 4.0 29.3 0.5
OE1 C:GLU674 4.0 35.4 0.5
N C:ASP707 4.1 28.7 0.5
CZ2 C:TRP677 4.1 22.7 0.5
CA C:ASN697 4.2 37.9 0.5
N C:GLU706 4.3 32.2 0.5
ND2 C:ASN697 4.3 37.9 0.5
CA C:GLU706 4.3 30.9 0.5
CB C:ASP707 4.4 29.2 0.5
OD2 C:ASP719 4.4 34.4 0.5
CG C:GLU674 4.6 35.6 0.5
CH2 C:TRP677 4.6 21.1 0.5
OD2 C:ASP707 4.6 28.9 0.5
CB C:GLU706 4.8 29.7 0.5
CB C:ASP670 4.8 26.8 0.5
CE2 C:TRP677 5.0 22.9 0.5

Calcium binding site 2 out of 6 in 2ox8

Go back to Calcium Binding Sites List in 2ox8
Calcium binding site 2 out of 6 in the Human Scavenger Receptor C-Type Lectin Carbohydrate- Recognition Domain.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Human Scavenger Receptor C-Type Lectin Carbohydrate- Recognition Domain. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca7

b:49.0
occ:0.50
OD1 C:ASP696 2.3 38.3 0.5
OD1 C:ASN718 2.5 28.6 0.5
O C:ASP719 2.7 32.5 0.5
OE1 C:GLU706 2.7 25.0 0.5
OD1 C:ASP719 2.9 35.7 0.5
OE1 C:GLN694 3.0 32.8 0.5
CG C:ASP719 3.1 35.1 0.5
OD2 C:ASP719 3.2 34.4 0.5
CD C:GLU706 3.4 27.4 0.5
CG C:ASP696 3.4 38.6 0.5
CG C:ASN718 3.5 30.9 0.5
OE2 C:GLU706 3.5 27.4 0.5
C C:ASP719 3.6 33.6 0.5
N C:ASP719 3.7 34.1 0.5
OD2 C:ASP696 3.8 40.2 0.5
ND2 C:ASN718 4.0 30.9 0.5
CA C:ASP719 4.0 34.1 0.5
CB C:ASP719 4.0 34.8 0.5
CD C:GLN694 4.1 32.4 0.5
N C:ASP696 4.4 36.1 0.5
N C:ASN697 4.5 38.1 0.5
CG C:GLU706 4.6 28.3 0.5
CB C:ASP696 4.7 38.1 0.5
C C:ASN718 4.7 34.0 0.5
CB C:GLU706 4.7 29.7 0.5
N C:TRP698 4.8 38.8 0.5
NE2 C:GLN694 4.8 33.2 0.5
N C:PHE720 4.8 34.3 0.5
CB C:ASN718 4.8 32.6 0.5
CB C:TRP698 5.0 38.5 0.5
CA C:ASP696 5.0 37.4 0.5

Calcium binding site 3 out of 6 in 2ox8

Go back to Calcium Binding Sites List in 2ox8
Calcium binding site 3 out of 6 in the Human Scavenger Receptor C-Type Lectin Carbohydrate- Recognition Domain.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Human Scavenger Receptor C-Type Lectin Carbohydrate- Recognition Domain. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca8

b:37.4
occ:0.50
OD2 C:ASP707 2.2 28.9 0.5
OE1 C:GLU674 2.6 35.4 0.5
CG C:ASP707 3.2 29.4 0.5
OD1 C:ASP707 3.5 29.9 0.5
O C:PRO704 3.6 40.3 0.5
CD C:GLU674 3.8 35.5 0.5
OE2 C:GLU674 4.4 35.0 0.5
CB C:ASP707 4.4 29.2 0.5
C C:PRO704 4.8 40.1 0.5
O C:SER671 4.8 36.6 0.5
CG C:GLU674 4.8 35.6 0.5
O C:ASP670 4.9 29.6 0.5
CA C:SER671 4.9 34.8 0.5

Calcium binding site 4 out of 6 in 2ox8

Go back to Calcium Binding Sites List in 2ox8
Calcium binding site 4 out of 6 in the Human Scavenger Receptor C-Type Lectin Carbohydrate- Recognition Domain.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Human Scavenger Receptor C-Type Lectin Carbohydrate- Recognition Domain. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca6

b:33.2
occ:0.50
OE2 D:GLU674 2.1 42.3 0.5
O D:GLU706 2.2 29.5 0.5
OD1 D:ASN697 2.7 34.7 0.5
OD2 D:ASP670 2.7 33.8 0.5
OD1 D:ASP707 2.9 26.6 0.5
OD1 D:ASP670 3.2 33.6 0.5
CG D:ASP670 3.3 33.2 0.5
CD D:GLU674 3.4 42.8 0.5
C D:GLU706 3.5 27.9 0.5
CG D:ASN697 3.6 36.3 0.5
CB D:ASN697 3.8 36.7 0.5
CZ2 D:TRP677 4.0 29.5 0.5
CG D:ASP707 4.0 27.6 0.5
CA D:ASN697 4.1 37.9 0.5
OE1 D:GLU674 4.2 42.6 0.5
CG D:GLU674 4.2 42.1 0.5
CA D:ASP707 4.3 27.5 0.5
N D:ASP707 4.3 27.2 0.5
N D:GLU706 4.4 29.8 0.5
CA D:GLU706 4.4 29.0 0.5
OD2 D:ASP719 4.4 35.0 0.5
CH2 D:TRP677 4.6 28.5 0.5
N D:ASN675 4.6 41.0 0.5
CE2 D:TRP677 4.7 30.7 0.5
CB D:ASP670 4.7 32.2 0.5
CB D:ASP707 4.7 27.4 0.5
CB D:GLU706 4.7 27.6 0.5
ND2 D:ASN697 4.8 36.4 0.5
N D:ASN697 4.9 38.7 0.5
NE1 D:TRP677 5.0 30.9 0.5
OD2 D:ASP707 5.0 28.1 0.5

Calcium binding site 5 out of 6 in 2ox8

Go back to Calcium Binding Sites List in 2ox8
Calcium binding site 5 out of 6 in the Human Scavenger Receptor C-Type Lectin Carbohydrate- Recognition Domain.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Human Scavenger Receptor C-Type Lectin Carbohydrate- Recognition Domain. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca7

b:28.7
occ:0.50
OE1 D:GLU706 2.2 19.8 0.5
OD1 D:ASP696 2.3 39.4 0.5
OD2 D:ASP696 2.5 41.0 0.5
CG D:ASP696 2.7 39.8 0.5
OD1 D:ASP719 2.9 36.4 0.5
OE1 D:GLN694 2.9 31.8 0.5
O D:ASP719 2.9 31.7 0.5
CD D:GLU706 3.1 23.3 0.5
OE2 D:GLU706 3.2 23.9 0.5
CG D:ASP719 3.3 34.8 0.5
OD2 D:ASP719 3.4 35.0 0.5
OD1 D:ASN718 3.4 36.7 0.5
ND2 D:ASN718 3.8 35.8 0.5
CG D:ASN718 4.0 36.6 0.5
N D:ASP696 4.0 37.9 0.5
C D:ASP719 4.0 32.8 0.5
CB D:ASP696 4.1 39.8 0.5
CD D:GLN694 4.2 31.5 0.5
N D:ASN697 4.3 38.7 0.5
N D:ASP719 4.4 34.0 0.5
CB D:TRP698 4.4 38.2 0.5
N D:TRP698 4.4 38.5 0.5
CB D:ASP719 4.4 33.7 0.5
CG D:GLU706 4.5 24.3 0.5
CA D:ASP696 4.5 38.6 0.5
CA D:ASP719 4.5 33.8 0.5
C D:ASP696 4.8 39.1 0.5
CB D:GLU706 4.9 27.6 0.5
NE2 D:GLN694 4.9 29.3 0.5

Calcium binding site 6 out of 6 in 2ox8

Go back to Calcium Binding Sites List in 2ox8
Calcium binding site 6 out of 6 in the Human Scavenger Receptor C-Type Lectin Carbohydrate- Recognition Domain.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Human Scavenger Receptor C-Type Lectin Carbohydrate- Recognition Domain. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca8

b:30.9
occ:0.50
OD2 D:ASP707 2.1 28.1 0.5
OE1 D:GLU674 2.3 42.6 0.5
CG D:ASP707 3.1 27.6 0.5
OD1 D:ASP707 3.5 26.6 0.5
CD D:GLU674 3.5 42.8 0.5
O D:PRO704 3.8 38.2 0.5
OE2 D:GLU674 4.2 42.3 0.5
O D:ASP670 4.4 32.5 0.5
CB D:ASP707 4.4 27.4 0.5
CG D:GLU674 4.6 42.1 0.5
CA D:SER671 4.8 35.1 0.5
CB D:GLU674 4.8 41.4 0.5
C D:PRO704 5.0 37.6 0.5

Reference:

H.Feinberg, M.E.Taylor, W.I.Weis. Scavenger Receptor C-Type Lectin Binds to the Leukocyte Cell Surface Glycan Lewis(X) By A Novel Mechanism. J.Biol.Chem. V. 282 17250 2007.
ISSN: ISSN 0021-9258
PubMed: 17420244
DOI: 10.1074/JBC.M701624200
Page generated: Sat Dec 12 03:49:10 2020

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