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Magnesium in PDB 2vsc: Structure of the Immunoglobulin-Superfamily Ectodomain of Human CD47

Protein crystallography data

The structure of Structure of the Immunoglobulin-Superfamily Ectodomain of Human CD47, PDB code: 2vsc was solved by D.Hatherley, S.C.Graham, J.Turner, K.Harlos, D.I.Stuart, A.N.Barclay, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.19 / 1.90
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 201.137, 47.502, 56.811, 90.00, 99.31, 90.00
R / Rfree (%) 21.6 / 26.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of the Immunoglobulin-Superfamily Ectodomain of Human CD47 (pdb code 2vsc). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of the Immunoglobulin-Superfamily Ectodomain of Human CD47, PDB code: 2vsc:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 2vsc

Go back to Magnesium Binding Sites List in 2vsc
Magnesium binding site 1 out of 2 in the Structure of the Immunoglobulin-Superfamily Ectodomain of Human CD47


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the Immunoglobulin-Superfamily Ectodomain of Human CD47 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1120

b:26.3
occ:1.00
O A:HOH2078 2.2 21.9 1.0
O A:HOH2077 2.2 26.2 1.0
O A:HOH2082 2.2 22.1 1.0
O A:HOH2079 2.2 22.2 1.0
O A:HOH2081 2.2 24.1 1.0
O A:HOH2080 2.2 25.2 1.0
O B:LEU101 3.6 17.6 1.0
O A:LEU101 3.7 21.3 1.0
O A:HOH2076 4.2 25.5 1.0
OE2 A:GLU100 4.3 21.9 1.0
CB A:GLU100 4.3 21.1 1.0
OE2 B:GLU100 4.3 22.9 1.0
CD A:ARG103 4.3 24.4 1.0
OE2 B:GLU29 4.4 27.7 1.0
CB B:GLU100 4.4 21.2 1.0
OE1 A:GLU29 4.4 27.4 1.0
O A:GLU100 4.4 22.2 1.0
O B:GLU100 4.4 21.3 1.0
C A:LEU101 4.7 24.1 1.0
C B:LEU101 4.7 20.3 1.0
CG A:ARG103 4.7 25.5 1.0
C B:GLU100 4.7 21.7 1.0
C A:GLU100 4.7 22.5 1.0
NE B:ARG103 4.9 20.9 1.0
CG B:ARG103 4.9 17.9 1.0
OE1 A:GLU35 5.0 32.7 1.0
CD A:GLU100 5.0 21.1 1.0

Magnesium binding site 2 out of 2 in 2vsc

Go back to Magnesium Binding Sites List in 2vsc
Magnesium binding site 2 out of 2 in the Structure of the Immunoglobulin-Superfamily Ectodomain of Human CD47


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the Immunoglobulin-Superfamily Ectodomain of Human CD47 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1120

b:25.2
occ:1.00
O C:HOH2119 2.2 25.6 1.0
O C:HOH2122 2.2 22.7 1.0
O C:HOH2120 2.2 24.0 1.0
O C:HOH2123 2.2 22.2 1.0
O C:HOH2121 2.2 24.9 1.0
O C:HOH2124 2.2 23.1 1.0
O C:LEU101 3.7 20.7 1.0
O D:LEU101 3.7 26.2 1.0
O C:HOH2118 4.0 24.3 1.0
O C:HOH2117 4.2 28.1 1.0
CB D:GLU100 4.3 24.5 1.0
OE2 C:GLU29 4.3 36.6 1.0
OE2 C:GLU100 4.3 26.9 1.0
OE2 D:GLU29 4.3 27.4 1.0
CB C:GLU100 4.3 25.1 1.0
OE2 D:GLU100 4.3 20.1 1.0
O D:GLU100 4.5 26.1 1.0
O C:GLU100 4.5 25.8 1.0
C C:LEU101 4.7 23.7 1.0
C D:GLU100 4.7 26.6 1.0
C D:LEU101 4.8 29.2 1.0
C C:GLU100 4.8 24.9 1.0

Reference:

D.Hatherley, S.C.Graham, J.Turner, K.Harlos, D.I.Stuart, A.N.Barclay. Paired Receptor Specificity Explained By Structures of Signal Regulatory Proteins Alone and Complexed with CD47. Mol.Cell V. 31 266 2008.
ISSN: ISSN 1097-2765
PubMed: 18657508
DOI: 10.1016/J.MOLCEL.2008.05.026
Page generated: Wed Aug 14 05:18:58 2024

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