Magnesium in PDB 5thp: Rhodocetin in Complex with the Integrin ALPHA2-A Domain

Protein crystallography data

The structure of Rhodocetin in Complex with the Integrin ALPHA2-A Domain, PDB code: 5thp was solved by M.Mcdougall, G.L.Orriss, J.Stetefeld, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.87 / 3.01
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 130.763, 130.763, 251.351, 90.00, 90.00, 90.00
R / Rfree (%) 22.1 / 27

Other elements in 5thp:

The structure of Rhodocetin in Complex with the Integrin ALPHA2-A Domain also contains other interesting chemical elements:

Chlorine (Cl) 35 atoms
Sodium (Na) 31 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain (pdb code 5thp). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain, PDB code: 5thp:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 5thp

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Magnesium binding site 1 out of 6 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Rhodocetin in Complex with the Integrin ALPHA2-A Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg404

b:84.3
occ:1.00
OG C:SER182 1.9 83.1 1.0
OD1 C:ASP283 1.9 91.3 1.0
O C:HOH503 2.0 22.0 1.0
OG1 C:THR250 2.4 90.2 1.0
OG C:SER184 2.4 74.9 1.0
CG C:ASP283 2.6 74.0 1.0
OD1 C:ASP180 2.6 0.7 1.0
OD2 C:ASP180 2.6 0.7 1.0
OD2 C:ASP283 2.6 70.1 1.0
CG C:ASP180 2.8 0.8 1.0
CB C:SER182 3.0 80.8 1.0
CB C:THR250 3.7 89.9 1.0
CB C:SER184 3.8 87.4 1.0
CB C:ASP283 4.0 71.5 1.0
CG2 C:THR250 4.1 81.6 1.0
CA C:SER182 4.2 86.4 1.0
CB C:ASP180 4.3 79.8 1.0
N C:SER182 4.4 87.1 1.0
N C:GLY284 4.4 76.9 1.0
N C:ASP283 4.5 91.7 1.0
CA C:ASP283 4.6 79.5 1.0
C C:ASP283 4.6 78.9 1.0
C C:SER182 4.6 90.9 1.0
CA C:THR250 4.7 0.0 1.0
N C:SER184 4.7 0.7 1.0
CA C:SER184 4.7 99.7 1.0
O1 C:SO4409 4.7 0.3 1.0
O C:SER182 4.8 94.3 1.0

Magnesium binding site 2 out of 6 in 5thp

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Magnesium binding site 2 out of 6 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Rhodocetin in Complex with the Integrin ALPHA2-A Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg404

b:0.0
occ:1.00
OG F:SER184 2.0 97.3 1.0
OD1 F:ASP283 2.3 0.3 1.0
OD2 F:ASP283 2.3 91.2 1.0
O1 F:SO4401 2.4 0.7 1.0
OG F:SER182 2.4 76.2 1.0
CG F:ASP283 2.6 92.7 1.0
CB F:SER182 3.0 74.9 1.0
CB F:SER184 3.4 95.2 1.0
S F:SO4401 3.7 97.5 1.0
OG1 F:THR250 3.9 78.1 1.0
CB F:ASP283 4.1 73.4 1.0
O4 F:SO4401 4.1 91.2 1.0
O2 F:SO4401 4.2 91.8 1.0
N F:SER184 4.2 86.8 1.0
CA F:SER182 4.4 71.9 1.0
CA F:SER184 4.4 89.3 1.0
N F:GLY284 4.4 69.0 1.0
C F:ASP283 4.6 78.6 1.0
OD2 F:ASP180 4.6 67.8 1.0
C F:SER182 4.6 66.1 1.0
CA F:GLY284 4.7 68.8 1.0
OD1 F:ASP180 4.8 76.8 1.0
O3 F:SO4401 4.8 93.5 1.0
CA F:ASP283 4.8 81.6 1.0
O F:SER182 4.9 65.2 1.0
O F:ASP283 5.0 81.7 1.0
N F:ASN183 5.0 66.5 1.0

Magnesium binding site 3 out of 6 in 5thp

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Magnesium binding site 3 out of 6 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Rhodocetin in Complex with the Integrin ALPHA2-A Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg403

b:51.7
occ:1.00
OG I:SER182 1.9 71.7 1.0
OD1 I:ASP283 2.3 88.3 1.0
O1 I:SO4407 2.5 0.4 1.0
OG1 I:THR250 2.6 95.9 1.0
OD2 I:ASP180 2.6 53.5 1.0
OG I:SER184 2.6 53.5 1.0
CB I:SER182 2.9 75.5 1.0
OD1 I:ASP180 3.0 52.5 1.0
CG I:ASP180 3.1 53.2 1.0
CG I:ASP283 3.4 76.4 1.0
OD2 I:ASP283 3.7 83.1 1.0
S I:SO4407 3.9 0.2 1.0
CB I:THR250 3.9 72.7 1.0
CB I:SER184 3.9 59.3 1.0
CA I:SER182 4.2 62.0 1.0
CG2 I:THR250 4.4 64.9 1.0
O2 I:SO4407 4.4 0.9 1.0
O4 I:SO4407 4.4 0.5 1.0
N I:GLY284 4.5 74.2 1.0
CB I:ASP180 4.5 55.2 1.0
N I:SER182 4.5 63.9 1.0
CB I:ASP283 4.7 60.3 1.0
C I:SER182 4.8 65.0 1.0
CA I:GLY284 4.9 65.2 1.0
C I:ASP283 4.9 81.1 1.0
O3 I:SO4407 4.9 0.7 1.0
N I:SER184 4.9 74.4 1.0
N I:ASP283 4.9 65.8 1.0
CA I:THR250 4.9 65.8 1.0
O I:SER182 5.0 76.1 1.0
CA I:SER184 5.0 55.8 1.0

Magnesium binding site 4 out of 6 in 5thp

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Magnesium binding site 4 out of 6 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Rhodocetin in Complex with the Integrin ALPHA2-A Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg403

b:0.1
occ:1.00
OG L:SER184 2.9 66.8 1.0
CA L:GLY284 3.3 72.3 1.0
N L:GLY284 3.3 74.0 1.0
C L:ASP283 3.4 84.9 1.0
O L:ASP283 3.4 0.3 1.0
O L:HOH502 3.5 41.0 1.0
O3 L:SO4406 3.7 0.1 1.0
CB L:SER184 3.8 68.0 1.0
O4 L:SO4406 4.0 0.6 1.0
CB L:ASP283 4.0 65.1 1.0
OG1 L:THR250 4.1 0.7 1.0
OG L:SER182 4.1 94.5 1.0
O1 L:SO4406 4.1 0.9 1.0
S L:SO4406 4.2 0.4 1.0
CG L:ASP283 4.3 72.7 1.0
OD2 L:ASP283 4.3 72.3 1.0
CA L:ASP283 4.3 82.3 1.0
CB L:SER182 4.4 83.8 1.0
C L:GLY284 4.5 73.0 1.0
OD2 L:ASP180 4.5 54.5 1.0
CD2 L:TYR314 4.6 82.6 1.0
CG L:TYR314 4.8 81.5 1.0
N L:ASP283 4.9 89.4 1.0
CB L:TYR314 5.0 70.1 1.0
OD1 L:ASP283 5.0 90.2 1.0

Magnesium binding site 5 out of 6 in 5thp

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Magnesium binding site 5 out of 6 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Rhodocetin in Complex with the Integrin ALPHA2-A Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Mg405

b:0.7
occ:1.00
OG O:SER182 2.1 88.1 1.0
CB O:SER184 2.3 0.8 1.0
OG O:SER184 3.1 0.8 1.0
OD2 O:ASP180 3.3 0.6 1.0
CA O:SER184 3.5 0.5 1.0
CB O:SER182 3.5 82.5 1.0
N O:SER184 3.6 0.1 1.0
O1 O:SO4402 3.7 1.0 1.0
OG1 O:THR250 3.7 99.8 1.0
O2 O:SO4402 3.8 0.8 1.0
CB O:ASP283 3.8 0.5 1.0
OD2 O:ASP283 3.9 0.7 1.0
C O:SER184 4.2 0.3 1.0
S O:SO4402 4.2 0.5 1.0
CG O:ASP283 4.2 0.5 1.0
CG O:ASP180 4.2 80.4 1.0
OD1 O:ASP180 4.3 74.6 1.0
C O:SER182 4.4 88.9 1.0
O O:SER182 4.5 89.1 1.0
O4 O:SO4402 4.5 0.8 1.0
N O:GLY284 4.5 96.6 1.0
CA O:SER182 4.5 80.8 1.0
C O:ASP283 4.5 98.7 1.0
CA O:ASP283 4.6 97.0 1.0
N O:ILE185 4.7 0.8 1.0
O O:SER184 4.8 0.3 1.0
C O:ASN183 4.9 93.3 1.0
N O:ASN183 4.9 87.8 1.0
N O:ASP283 4.9 94.3 1.0
CB O:THR250 5.0 77.1 1.0
CA O:GLY284 5.0 0.0 1.0
CG1 O:ILE185 5.0 0.0 1.0

Magnesium binding site 6 out of 6 in 5thp

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Magnesium binding site 6 out of 6 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Rhodocetin in Complex with the Integrin ALPHA2-A Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Mg402

b:47.2
occ:1.00
OG R:SER184 2.0 56.5 1.0
O4 R:SO4404 2.3 0.3 1.0
CB R:SER184 2.9 58.0 1.0
OG R:SER182 3.0 97.1 1.0
OG1 R:THR250 3.2 0.8 1.0
CB R:ASP283 3.5 71.0 1.0
OD2 R:ASP180 3.5 82.6 1.0
N R:GLY284 3.6 65.3 1.0
C R:ASP283 3.7 76.0 1.0
S R:SO4404 3.7 0.5 1.0
OD2 R:ASP283 3.8 0.4 1.0
CA R:GLY284 4.0 74.4 1.0
CG R:ASP283 4.0 0.6 1.0
CA R:ASP283 4.1 68.5 1.0
O R:ASP283 4.1 90.8 1.0
CG R:ASP180 4.2 74.6 1.0
OD1 R:ASP180 4.2 86.8 1.0
O1 R:SO4404 4.2 0.8 1.0
CB R:SER182 4.3 74.3 1.0
CA R:SER184 4.3 59.3 1.0
CB R:THR250 4.3 80.0 1.0
O R:HOH506 4.4 58.0 1.0
O2 R:SO4404 4.4 0.1 1.0
N R:ASP283 4.4 62.5 1.0
N R:SER184 4.6 80.0 1.0
O3 R:SO4404 4.6 95.5 1.0
CG2 R:THR250 4.7 75.4 1.0
C R:SER184 4.9 60.5 1.0
C R:GLY284 5.0 79.6 1.0
OD1 R:ASP283 5.0 0.4 1.0

Reference:

J.A.Eble, M.Mcdougall, G.L.Orriss, S.Niland, B.Johanningmeier, G.Pohlentz, M.Meier, S.Karrasch, M.I.Estevao-Costa, A.Martins Lima, J.Stetefeld. Dramatic and Concerted Conformational Changes Enable Rhodocetin to Block Alpha 2 Beta 1 Integrin Selectively. Plos Biol. V. 15 01492 2017.
ISSN: ESSN 1545-7885
PubMed: 28704364
DOI: 10.1371/JOURNAL.PBIO.2001492
Page generated: Mon Dec 14 21:12:05 2020

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