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Praseodymium in PDB 6nde: Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Prasedymium

Protein crystallography data

The structure of Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Prasedymium, PDB code: 6nde was solved by J.Stetefeld, M.D.Mcdougall, P.C.Loewen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.57 / 3.50
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 132.351, 132.351, 254.244, 90.00, 90.00, 90.00
R / Rfree (%) 29 / 36.9

Other elements in 6nde:

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

Chlorine (Cl) 9 atoms
Sodium (Na) 6 atoms

Praseodymium Binding Sites:

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

Praseodymium binding site 1 out of 6 in 6nde

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


Mono view


Stereo pair view

A full contact list of Praseodymium with other atoms in the Pr binding site number 1 of Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Prasedymium within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Pr401

b:0.3
occ:1.00
OG C:SER184 2.2 92.7 1.0
OD1 C:ASP283 2.7 0.8 1.0
OG C:SER182 2.8 0.2 1.0
CB C:SER184 3.4 97.0 1.0
CG C:ASP283 3.5 0.2 1.0
O3 B:SO4201 3.5 0.1 1.0
O4 B:SO4201 3.6 0.9 1.0
OG1 C:THR250 3.8 76.1 1.0
OD2 C:ASP283 3.8 0.7 1.0
CB C:SER182 3.9 96.0 1.0
NA C:NA402 4.0 66.7 1.0
S B:SO4201 4.0 0.4 1.0
CA C:GLY284 4.1 82.2 1.0
C C:ASP283 4.1 93.4 1.0
OD1 C:ASP180 4.1 84.3 1.0
N C:GLY284 4.2 77.4 1.0
O C:ASP283 4.2 70.8 1.0
O1 B:SO4201 4.2 0.4 1.0
OD2 C:ASP180 4.3 92.3 1.0
CA C:SER184 4.6 96.3 1.0
CG C:ASP180 4.6 100.0 1.0
N C:SER184 4.6 97.3 1.0
CB C:ASP283 4.7 0.2 1.0
CA C:ASP283 4.8 0.9 1.0

Praseodymium binding site 2 out of 6 in 6nde

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


Mono view


Stereo pair view

A full contact list of Praseodymium with other atoms in the Pr binding site number 2 of Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Prasedymium within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Pr401

b:0.8
occ:1.00
OG F:SER182 2.5 97.3 1.0
OD1 F:ASP283 2.7 0.0 1.0
OG F:SER184 2.7 0.3 1.0
CB F:SER182 3.5 0.7 1.0
CB F:SER184 3.6 0.8 1.0
O3 E:SO4203 3.6 0.4 1.0
OD2 F:ASP180 3.6 88.5 1.0
O4 E:SO4203 3.7 0.4 1.0
CG F:ASP283 3.9 0.8 1.0
O F:ASP283 4.0 82.3 1.0
NA F:NA402 4.1 75.7 1.0
S E:SO4203 4.1 0.3 1.0
C F:ASP283 4.2 1.0 1.0
OG1 F:THR250 4.3 82.2 1.0
O2 E:SO4203 4.4 0.6 1.0
CG F:ASP180 4.4 76.6 1.0
N F:GLY284 4.5 0.2 1.0
OD1 F:ASP180 4.5 57.7 1.0
CA F:GLY284 4.5 0.9 1.0
N F:SER184 4.5 0.9 1.0
CA F:SER184 4.6 0.4 1.0
OD2 F:ASP283 4.7 0.6 1.0
CA F:SER182 4.8 89.2 1.0
CB F:ASP283 4.9 0.7 1.0
CA F:ASP283 4.9 94.8 1.0

Praseodymium binding site 3 out of 6 in 6nde

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


Mono view


Stereo pair view

A full contact list of Praseodymium with other atoms in the Pr binding site number 3 of Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Prasedymium within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Pr401

b:0.2
occ:1.00
OG I:SER182 2.4 97.8 1.0
OG I:SER184 2.7 0.1 1.0
OD1 I:ASP283 2.7 0.8 1.0
CB I:SER184 3.5 0.7 1.0
CB I:SER182 3.5 91.8 1.0
OD2 I:ASP180 3.7 80.4 1.0
O4 H:SO4202 3.7 97.9 1.0
O3 H:SO4202 3.8 0.4 1.0
CG I:ASP283 4.0 0.4 1.0
S H:SO4202 4.1 0.2 1.0
O I:ASP283 4.2 87.8 1.0
NA I:NA402 4.2 75.8 1.0
O2 H:SO4202 4.3 0.4 1.0
C I:ASP283 4.4 0.2 1.0
N I:SER184 4.4 0.7 1.0
CG I:ASP180 4.4 74.8 1.0
CA I:SER184 4.4 98.2 1.0
OD1 I:ASP180 4.5 50.4 1.0
OG1 I:THR250 4.5 84.6 1.0
N I:GLY284 4.6 0.3 1.0
CA I:GLY284 4.7 0.8 1.0
OD2 I:ASP283 4.7 0.4 1.0
CA I:SER182 4.7 81.3 1.0
C I:SER184 4.9 95.6 1.0
C I:SER182 5.0 74.8 1.0
CB I:ASP283 5.0 0.7 1.0

Praseodymium binding site 4 out of 6 in 6nde

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


Mono view


Stereo pair view

A full contact list of Praseodymium with other atoms in the Pr binding site number 4 of Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Prasedymium within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Pr401

b:0.8
occ:1.00
OG L:SER184 2.3 92.3 1.0
OD1 L:ASP283 2.7 0.8 1.0
OG L:SER182 2.9 0.3 1.0
CB L:SER184 3.5 92.6 1.0
CG L:ASP283 3.5 0.6 1.0
O3 K:SO4202 3.7 0.1 1.0
OG1 L:THR250 3.8 83.6 1.0
OD2 L:ASP283 3.9 0.8 1.0
NA L:NA402 4.0 55.8 1.0
O L:ASP283 4.0 67.1 1.0
C L:ASP283 4.0 94.0 1.0
CB L:SER182 4.0 0.4 1.0
CA L:GLY284 4.0 96.9 1.0
OD1 L:ASP180 4.1 88.3 1.0
O4 K:SO4202 4.1 0.7 1.0
N L:GLY284 4.1 84.2 1.0
S K:SO4202 4.3 0.5 1.0
O1 K:SO4202 4.4 0.1 1.0
OD2 L:ASP180 4.4 93.2 1.0
CG L:ASP180 4.6 99.9 1.0
CB L:ASP283 4.7 0.8 1.0
CA L:SER184 4.7 97.6 1.0
N L:SER184 4.7 90.8 1.0
CA L:ASP283 4.7 0.4 1.0
N L:ASP283 5.0 91.1 1.0

Praseodymium binding site 5 out of 6 in 6nde

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


Mono view


Stereo pair view

A full contact list of Praseodymium with other atoms in the Pr binding site number 5 of Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Prasedymium within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Pr401

b:0.6
occ:1.00
OG O:SER184 2.1 0.1 1.0
OD1 O:ASP283 2.7 72.2 1.0
OG O:SER182 3.0 0.2 1.0
CB O:SER184 3.3 0.6 1.0
CG O:ASP283 3.5 86.9 1.0
OD2 O:ASP283 3.8 0.1 1.0
OD2 O:ASP180 4.0 94.8 1.0
O4 N:SO4201 4.1 0.2 1.0
OG1 O:THR250 4.1 64.9 1.0
NA O:NA402 4.1 73.5 1.0
CB O:SER182 4.1 0.1 1.0
C O:ASP283 4.2 94.1 1.0
O O:ASP283 4.3 75.1 1.0
CA O:GLY284 4.3 0.1 1.0
N O:GLY284 4.4 0.1 1.0
CA O:SER184 4.5 0.9 1.0
OD1 O:ASP180 4.5 81.3 1.0
N O:SER184 4.6 98.8 1.0
CG O:ASP180 4.6 92.7 1.0
O2 N:SO4201 4.7 0.5 1.0
CB O:ASP283 4.7 85.4 1.0
S N:SO4201 4.8 0.6 1.0
CA O:ASP283 4.9 91.3 1.0
O1 N:SO4201 5.0 0.0 1.0
C O:SER184 5.0 0.8 1.0

Praseodymium binding site 6 out of 6 in 6nde

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


Mono view


Stereo pair view

A full contact list of Praseodymium with other atoms in the Pr binding site number 6 of Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Prasedymium within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Pr401

b:0.5
occ:1.00
OG R:SER184 2.0 0.2 1.0
OD1 R:ASP283 2.8 80.2 1.0
OG R:SER182 3.0 0.3 1.0
CB R:SER184 3.3 0.9 1.0
CG R:ASP283 3.6 94.0 1.0
OD2 R:ASP283 3.9 93.7 1.0
OD2 R:ASP180 3.9 0.9 1.0
O R:ASP283 3.9 72.1 1.0
CB R:SER182 4.0 0.5 1.0
OG1 R:THR250 4.1 61.5 1.0
NA R:NA404 4.1 67.8 1.0
O3 Q:SO4202 4.1 0.1 1.0
C R:ASP283 4.2 93.9 1.0
CA R:GLY284 4.3 0.4 1.0
CA R:SER184 4.4 0.5 1.0
O4 Q:SO4202 4.4 0.7 1.0
N R:GLY284 4.4 0.9 1.0
N R:SER184 4.4 83.4 1.0
OD1 R:ASP180 4.5 86.5 1.0
CG R:ASP180 4.5 97.4 1.0
CB R:ASP283 4.7 89.0 1.0
S Q:SO4202 4.8 0.8 1.0
CA R:ASP283 4.9 93.5 1.0
C R:SER184 4.9 0.2 1.0

Reference:

J.Stetefeld, M.D.Mcdougall, P.C.Loewen. Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Prasedymium Bound To Be Published.
Page generated: Wed Dec 16 02:03:14 2020

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