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Magnesium in PDB 5mra: Human Scbd (Sorcin Calcium Binding Domain) in Complex with Doxorubicin

Protein crystallography data

The structure of Human Scbd (Sorcin Calcium Binding Domain) in Complex with Doxorubicin, PDB code: 5mra was solved by A.Ilari, A.Fiorillo, G.Colotti, I.Genovese, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 76.94 / 3.74
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 92.229, 104.831, 113.273, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / 28.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Human Scbd (Sorcin Calcium Binding Domain) in Complex with Doxorubicin (pdb code 5mra). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the Human Scbd (Sorcin Calcium Binding Domain) in Complex with Doxorubicin, PDB code: 5mra:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 5mra

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Magnesium binding site 1 out of 10 in the Human Scbd (Sorcin Calcium Binding Domain) in Complex with Doxorubicin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Scbd (Sorcin Calcium Binding Domain) in Complex with Doxorubicin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg201

b:0.6
occ:1.00
 OD2 A:ASP115 2.7 0.8 1.0
O A:PHE112 3.3 0.1 1.0
OE1 A:GLU124 3.4 0.8 1.0
OE2 A:GLU124 3.7 0.5 1.0
O A:THR119 3.7 0.8 1.0
OD1 A:ASP113 3.8 0.4 1.0
CG A:ASP115 3.9 0.4 1.0
CD A:GLU124 4.0 0.7 1.0
OD1 A:ASP121 4.2 0.5 1.0
C A:PHE112 4.5 0.5 1.0
CA A:VAL120 4.6 0.6 1.0
OG A:SER117 4.6 0.0 1.0
CA A:ASP113 4.7 0.8 1.0
OD1 A:ASP115 4.7 0.0 1.0
C A:THR119 4.7 0.8 1.0
CB A:ASP115 4.9 0.1 1.0
CG2 A:VAL120 4.9 0.6 1.0
CG A:ASP113 4.9 0.2 1.0

Magnesium binding site 2 out of 10 in 5mra

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Magnesium binding site 2 out of 10 in the Human Scbd (Sorcin Calcium Binding Domain) in Complex with Doxorubicin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Scbd (Sorcin Calcium Binding Domain) in Complex with Doxorubicin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:0.1
occ:1.00
 OD1 A:ASP83 2.7 0.4 1.0
O A:THR89 2.9 0.9 1.0
OD2 A:ASP85 2.9 0.5 1.0
OD1 A:ASP85 3.3 0.1 1.0
OE1 A:GLU94 3.4 0.6 1.0
CG A:ASP85 3.4 0.5 1.0
OG A:SER87 3.6 0.5 1.0
OE1 A:GLN48 3.6 0.2 1.0
CG A:ASP83 3.8 0.5 1.0
OG1 A:THR89 3.9 0.6 1.0
C A:THR89 3.9 0.9 1.0
CA A:ASP83 4.0 0.6 1.0
CB A:ASP83 4.2 0.2 1.0
O A:LEU82 4.3 0.4 1.0
CA A:MET90 4.3 0.1 1.0
CD A:GLU94 4.4 0.0 1.0
N A:MET90 4.6 0.7 1.0
OE2 A:GLU94 4.7 0.1 1.0
C A:ASP83 4.8 0.2 1.0
CB A:SER87 4.8 0.7 1.0
N A:ARG84 4.8 0.9 1.0
CD A:GLN48 4.8 0.4 1.0
CB A:ASP85 4.9 0.4 1.0
N A:ASP85 4.9 0.9 1.0
CA A:THR89 4.9 0.4 1.0
OD2 A:ASP83 4.9 0.3 1.0
CB A:THR89 5.0 0.3 1.0

Magnesium binding site 3 out of 10 in 5mra

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Magnesium binding site 3 out of 10 in the Human Scbd (Sorcin Calcium Binding Domain) in Complex with Doxorubicin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Human Scbd (Sorcin Calcium Binding Domain) in Complex with Doxorubicin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg203

b:0.7
occ:1.00
 OD1 A:ASP50 3.2 0.0 1.0
OE1 A:GLU53 3.3 0.4 1.0
OD2 A:ASP52 3.5 0.9 1.0
OD2 A:ASP50 3.8 0.1 1.0
CG A:ASP50 3.9 0.1 1.0
CD A:GLU53 4.0 0.6 1.0
NE2 A:GLN45 4.3 0.4 1.0
CG A:ASP52 4.4 0.2 1.0
CB A:ASP52 4.4 0.8 1.0
CG A:GLU53 4.5 0.4 1.0
OE2 A:GLU53 4.9 0.7 1.0

Magnesium binding site 4 out of 10 in 5mra

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Magnesium binding site 4 out of 10 in the Human Scbd (Sorcin Calcium Binding Domain) in Complex with Doxorubicin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Human Scbd (Sorcin Calcium Binding Domain) in Complex with Doxorubicin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg201

b:0.2
occ:1.00
 O B:THR89 2.8 0.7 1.0
OG B:SER87 2.9 1.0 1.0
OE2 B:GLU94 3.2 0.7 1.0
OD1 B:ASP85 3.2 0.6 1.0
O B:ASP83 3.2 0.1 1.0
OD2 B:ASP85 3.4 0.9 1.0
CA B:ASP83 3.5 0.1 1.0
CB B:ASP83 3.6 0.2 1.0
CG B:ASP85 3.6 0.2 1.0
C B:ASP83 3.8 0.9 1.0
C B:THR89 3.8 0.6 1.0
OE1 B:GLU94 3.8 0.7 1.0
CD B:GLU94 3.9 0.7 1.0
CB B:SER87 3.9 0.6 1.0
CA B:MET90 4.1 0.9 1.0
OG1 B:THR89 4.3 0.5 1.0
OE1 B:GLN48 4.4 0.1 1.0
N B:MET90 4.4 0.4 1.0
NE2 B:GLN48 4.4 1.0 1.0
CB B:MET90 4.8 0.5 1.0
CD B:GLN48 4.8 0.1 1.0
N B:ASP83 4.8 0.6 1.0
O B:LEU82 4.8 0.6 1.0
CG B:ASP83 4.9 1.0 1.0
CA B:THR89 4.9 0.2 1.0
N B:GLY91 5.0 0.5 1.0

Magnesium binding site 5 out of 10 in 5mra

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Magnesium binding site 5 out of 10 in the Human Scbd (Sorcin Calcium Binding Domain) in Complex with Doxorubicin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Human Scbd (Sorcin Calcium Binding Domain) in Complex with Doxorubicin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg202

b:0.1
occ:1.00
 OD1 B:ASP113 2.7 0.1 1.0
OE1 B:GLU124 3.0 0.5 1.0
O B:THR119 3.8 0.4 1.0
CA B:VAL120 3.9 0.1 1.0
CG B:ASP113 3.9 0.6 1.0
OD1 B:ASP115 4.0 0.3 1.0
CG2 B:THR119 4.1 0.6 1.0
OD2 B:ASP115 4.1 0.8 1.0
C B:THR119 4.1 0.7 1.0
CD B:GLU124 4.2 0.7 1.0
N B:VAL120 4.2 0.4 1.0
OG B:SER117 4.2 0.1 1.0
N B:ASP121 4.4 0.5 1.0
CG B:ASP115 4.5 0.4 1.0
O B:PHE112 4.5 0.5 1.0
CB B:ASP113 4.6 1.0 1.0
C B:VAL120 4.6 0.1 1.0
OE2 B:GLU124 4.7 0.2 1.0
CB B:VAL120 4.9 0.2 1.0
OD2 B:ASP113 4.9 0.9 1.0

Magnesium binding site 6 out of 10 in 5mra

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Magnesium binding site 6 out of 10 in the Human Scbd (Sorcin Calcium Binding Domain) in Complex with Doxorubicin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Human Scbd (Sorcin Calcium Binding Domain) in Complex with Doxorubicin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg201

b:0.4
occ:1.00
 OD1 C:ASP46 2.6 0.5 1.0
O C:ALA43 2.7 0.4 1.0
O C:GLN48 2.8 0.2 1.0
O C:HOH301 3.0 0.4 1.0
OE2 C:GLU53 3.5 0.4 1.0
CG C:ASP46 3.5 0.2 1.0
OE1 C:GLU53 3.5 0.5 1.0
OD2 C:ASP46 3.6 0.8 1.0
C C:ALA43 3.8 0.9 1.0
CD C:GLU53 3.9 0.8 1.0
C C:GLN48 3.9 0.9 1.0
CA C:ALA43 4.4 1.0 1.0
O C:VAL42 4.5 0.7 1.0
CA C:ILE49 4.7 0.8 1.0
O C:ASP46 4.7 0.7 1.0
N C:ILE49 4.7 0.5 1.0
CA C:GLN48 4.8 0.6 1.0
CB C:GLN48 4.8 0.4 1.0
N C:GLY44 4.8 0.4 1.0
CB C:ASP46 5.0 0.7 1.0
N C:GLN48 5.0 0.9 1.0

Magnesium binding site 7 out of 10 in 5mra

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Magnesium binding site 7 out of 10 in the Human Scbd (Sorcin Calcium Binding Domain) in Complex with Doxorubicin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Human Scbd (Sorcin Calcium Binding Domain) in Complex with Doxorubicin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg202

b:0.4
occ:1.00
 OD1 C:ASP83 2.4 0.5 1.0
O C:ARG84 2.6 0.6 1.0
OG1 C:THR89 2.7 0.2 1.0
OD2 C:ASP85 3.0 0.3 1.0
OG C:SER87 3.1 0.1 1.0
CG C:ASP83 3.4 0.4 1.0
C C:ARG84 3.8 0.5 1.0
N C:SER87 3.9 0.7 1.0
CG C:ASP85 3.9 0.9 1.0
N C:THR89 3.9 0.6 1.0
O C:THR89 4.0 0.1 1.0
CB C:SER87 4.0 0.1 1.0
CB C:THR89 4.0 0.4 1.0
OD2 C:ASP83 4.1 0.4 1.0
N C:ARG84 4.1 0.5 1.0
CA C:ASP83 4.1 0.6 1.0
C C:ASP83 4.2 0.2 1.0
C C:THR89 4.2 0.7 1.0
CB C:ASP83 4.2 0.8 1.0
CA C:THR89 4.3 0.3 1.0
CA C:SER87 4.3 0.3 1.0
N C:GLY88 4.4 0.6 1.0
C C:SER87 4.5 0.3 1.0
N C:MET86 4.5 0.5 1.0
CA C:ARG84 4.6 0.6 1.0
OD1 C:ASP85 4.6 0.2 1.0
C C:ASP85 4.7 0.3 1.0
N C:ASP85 4.7 0.3 1.0
CB C:ASP85 4.8 0.5 1.0
CA C:ASP85 4.9 0.9 1.0
NE2 C:GLN48 4.9 0.1 1.0
CG2 C:THR89 4.9 0.8 1.0
O C:ASP83 4.9 0.7 1.0
N C:MET90 5.0 0.5 1.0

Magnesium binding site 8 out of 10 in 5mra

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Magnesium binding site 8 out of 10 in the Human Scbd (Sorcin Calcium Binding Domain) in Complex with Doxorubicin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Human Scbd (Sorcin Calcium Binding Domain) in Complex with Doxorubicin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg203

b:0.9
occ:1.00
 OE2 C:GLU124 3.0 0.7 1.0
OE1 C:GLU124 3.1 0.7 1.0
OG1 C:THR114 3.3 0.9 1.0
CD C:GLU124 3.4 0.9 1.0
OD1 C:ASP113 3.6 0.2 1.0
O C:THR119 3.7 0.6 1.0
N C:THR114 4.2 0.8 1.0
OD2 C:ASP121 4.2 0.9 1.0
CB C:THR114 4.6 0.6 1.0
CA C:VAL120 4.7 0.2 1.0
CG C:ASP121 4.7 0.5 1.0
CA C:ASP113 4.7 0.7 1.0
CG C:ASP113 4.8 0.0 1.0
C C:THR119 4.8 0.3 1.0
CG2 C:THR114 4.9 0.2 1.0
CG C:GLU124 4.9 0.1 1.0
C C:ASP113 5.0 0.3 1.0
OD1 C:ASP121 5.0 0.0 1.0

Magnesium binding site 9 out of 10 in 5mra

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Magnesium binding site 9 out of 10 in the Human Scbd (Sorcin Calcium Binding Domain) in Complex with Doxorubicin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Human Scbd (Sorcin Calcium Binding Domain) in Complex with Doxorubicin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg201

b:0.1
occ:1.00
 OD1 D:ASP115 2.8 0.2 1.0
OE1 D:GLU124 2.9 0.3 1.0
O D:THR119 3.2 0.9 1.0
OE2 D:GLU124 3.3 0.3 1.0
CG D:ASP115 3.4 0.5 1.0
CD D:GLU124 3.5 0.4 1.0
OD2 D:ASP115 3.5 0.4 1.0
OG1 D:THR114 3.6 0.5 1.0
N D:THR114 4.1 0.9 1.0
OG D:SER117 4.1 0.2 1.0
OD1 D:ASP113 4.1 0.8 1.0
OD2 D:ASP121 4.2 0.0 1.0
CE A:MET32 4.2 0.7 1.0
C D:THR119 4.3 0.7 1.0
N D:ASP115 4.4 0.7 1.0
OG1 D:THR119 4.5 0.6 1.0
CA D:ASP113 4.5 0.3 1.0
CA D:VAL120 4.5 0.1 1.0
O D:PHE112 4.5 0.8 1.0
C D:ASP113 4.6 0.1 1.0
CB D:ASP115 4.6 0.9 1.0
N D:ASP121 4.7 0.9 1.0
CB D:THR114 4.8 0.6 1.0
N D:VAL120 4.9 0.4 1.0
C D:VAL120 4.9 0.9 1.0
CA D:THR114 4.9 0.9 1.0
CG D:ASP121 5.0 0.3 1.0

Magnesium binding site 10 out of 10 in 5mra

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Magnesium binding site 10 out of 10 in the Human Scbd (Sorcin Calcium Binding Domain) in Complex with Doxorubicin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Human Scbd (Sorcin Calcium Binding Domain) in Complex with Doxorubicin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg202

b:0.6
occ:1.00
 O D:THR89 2.2 0.7 1.0
OD1 D:ASP85 2.5 0.8 1.0
OD1 D:ASP83 3.2 0.4 1.0
C D:THR89 3.4 0.4 1.0
CG D:ASP85 3.4 0.5 1.0
OG D:SER87 3.5 0.7 1.0
O D:LEU82 3.5 0.9 1.0
N D:ARG84 3.5 0.4 1.0
OE1 D:GLU94 3.6 0.5 1.0
N D:ASP85 3.7 0.6 1.0
CA D:ASP83 3.7 0.8 1.0
OD2 D:ASP85 3.9 0.8 1.0
O D:ASP85 4.1 0.3 1.0
C D:ASP83 4.1 0.8 1.0
CA D:MET90 4.2 0.2 1.0
N D:MET90 4.2 0.1 1.0
CG D:ASP83 4.3 0.5 1.0
N D:THR89 4.3 0.7 1.0
OE1 D:GLN48 4.3 0.6 1.0
CA D:ARG84 4.4 0.2 1.0
CB D:ARG84 4.4 0.5 1.0
NE2 D:GLN48 4.4 0.2 1.0
C D:LEU82 4.4 0.2 1.0
CA D:THR89 4.5 0.5 1.0
CA D:ASP85 4.5 0.8 1.0
C D:ARG84 4.5 0.6 1.0
CD D:GLU94 4.6 0.3 1.0
CB D:ASP85 4.6 0.5 1.0
N D:ASP83 4.6 0.0 1.0
CD D:GLN48 4.6 0.4 1.0
CB D:ASP83 4.6 0.7 1.0
C D:ASP85 4.7 0.7 1.0
CB D:SER87 4.7 1.0 1.0
CB D:MET90 4.8 0.6 1.0

Reference:

I.Genovese, A.Fiorillo, A.Ilari, S.Masciarelli, F.Fazi, G.Colotti. Binding of Doxorubicin to Sorcin Impairs Cell Death and Increases Drug Resistance in Cancer Cells. Cell Death Dis V. 8 E2950 2017.
ISSN: ISSN 2041-4889
PubMed: 28726784
DOI: 10.1038/CDDIS.2017.342
Page generated: Sun Sep 29 22:06:12 2024

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