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Manganese in PDB 6ndd: Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Manganese Bound

Protein crystallography data

The structure of Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Manganese Bound, PDB code: 6ndd 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) 48.01 / 3.05
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 130.712, 130.712, 251.800, 90.00, 90.00, 90.00
R / Rfree (%) 21.7 / 27.4

Other elements in 6ndd:

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

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

Manganese Binding Sites:

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

Manganese binding site 1 out of 6 in 6ndd

Go back to Manganese Binding Sites List in 6ndd
Manganese binding site 1 out of 6 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Manganese Bound


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Manganese Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn401

b:47.4
occ:1.00
OG C:SER184 1.8 41.3 1.0
OD1 C:ASP283 2.1 36.1 1.0
OG C:SER182 2.5 40.8 1.0
O4 C:SO4402 2.9 1.0 1.0
CG C:ASP283 3.0 43.4 1.0
CB C:SER184 3.0 41.3 1.0
NA C:NA403 3.0 32.6 1.0
OD2 C:ASP283 3.2 45.1 1.0
O2 C:SO4402 3.2 87.2 1.0
S C:SO4402 3.6 0.1 1.0
OD2 C:ASP180 3.6 56.6 1.0
CB C:SER182 3.6 43.9 1.0
O C:ASP283 3.7 51.9 1.0
OG1 C:THR250 3.8 59.0 1.0
O1 C:SO4402 4.1 68.6 1.0
C C:ASP283 4.1 47.2 1.0
CA C:SER184 4.2 43.3 1.0
N C:SER184 4.3 53.3 1.0
CB C:ASP283 4.4 44.0 1.0
CA C:GLY284 4.4 41.1 1.0
N C:GLY284 4.5 41.3 1.0
CG C:ASP180 4.5 55.7 1.0
OD1 C:ASP180 4.7 64.9 1.0
CA C:ASP283 4.8 42.9 1.0
O3 C:SO4402 4.9 73.4 1.0
CA C:SER182 4.9 40.3 1.0
N C:ILE185 5.0 44.5 1.0

Manganese binding site 2 out of 6 in 6ndd

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Manganese Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn401

b:41.5
occ:1.00
OG F:SER184 2.1 50.3 1.0
OG F:SER182 2.4 26.4 1.0
OD1 F:ASP283 2.4 58.1 1.0
O4 F:SO4402 2.5 76.1 1.0
NA F:NA403 3.1 26.4 1.0
OD2 F:ASP180 3.3 38.2 1.0
CB F:SER184 3.3 44.1 1.0
CB F:SER182 3.5 29.8 1.0
CG F:ASP283 3.5 63.7 1.0
S F:SO4402 3.5 0.0 1.0
O2 F:SO4402 3.6 85.5 1.0
O F:ASP283 3.8 43.0 1.0
OG1 F:THR250 3.9 48.6 1.0
O3 F:SO4402 3.9 57.3 1.0
C F:ASP283 4.0 43.8 1.0
OD2 F:ASP283 4.1 77.6 1.0
CG F:ASP180 4.2 37.2 1.0
N F:GLY284 4.4 42.7 1.0
CA F:GLY284 4.4 48.8 1.0
OD1 F:ASP180 4.4 39.7 1.0
CA F:SER184 4.5 42.7 1.0
N F:SER184 4.6 47.2 1.0
CB F:ASP283 4.6 58.1 1.0
CA F:ASP283 4.7 47.4 1.0
CA F:SER182 4.8 29.6 1.0
O1 F:SO4402 4.8 54.9 1.0
N F:ASP283 4.9 47.8 1.0

Manganese binding site 3 out of 6 in 6ndd

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Manganese Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mn401

b:41.2
occ:1.00
OG I:SER184 2.0 53.2 1.0
OG I:SER182 2.3 29.8 1.0
OD1 I:ASP283 2.4 59.1 1.0
O1 I:SO4402 2.5 77.5 1.0
NA I:NA403 3.1 30.1 1.0
CB I:SER184 3.2 45.6 1.0
OD2 I:ASP180 3.3 31.4 1.0
S I:SO4402 3.4 0.8 1.0
CB I:SER182 3.4 34.0 1.0
O3 I:SO4402 3.5 92.5 1.0
CG I:ASP283 3.6 62.7 1.0
O2 I:SO4402 3.8 66.6 1.0
OG1 I:THR250 3.8 53.4 1.0
O I:ASP283 3.9 44.4 1.0
C I:ASP283 4.0 46.9 1.0
CG I:ASP180 4.2 33.6 1.0
N I:GLY284 4.2 44.9 1.0
OD2 I:ASP283 4.2 66.5 1.0
CA I:GLY284 4.3 49.6 1.0
OD1 I:ASP180 4.4 35.0 1.0
CA I:SER184 4.4 43.2 1.0
N I:SER184 4.5 48.7 1.0
CB I:ASP283 4.6 61.0 1.0
CA I:ASP283 4.7 49.1 1.0
O4 I:SO4402 4.7 61.7 1.0
CA I:SER182 4.8 33.0 1.0
N I:ASP283 4.9 47.8 1.0

Manganese binding site 4 out of 6 in 6ndd

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Manganese Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mn401

b:47.0
occ:1.00
OG L:SER184 1.8 36.5 1.0
OD1 L:ASP283 2.1 36.5 1.0
OG L:SER182 2.5 44.1 1.0
NA L:NA402 2.8 32.3 1.0
CG L:ASP283 2.9 41.2 1.0
OD2 L:ASP283 3.0 41.1 1.0
CB L:SER184 3.1 39.4 1.0
O1 K:SO4202 3.2 0.3 1.0
O3 K:SO4202 3.6 93.6 1.0
CB L:SER182 3.6 42.8 1.0
OD2 L:ASP180 3.7 55.7 1.0
OG1 L:THR250 3.8 50.8 1.0
O L:ASP283 3.8 52.1 1.0
S K:SO4202 3.8 0.8 1.0
C L:ASP283 4.1 49.8 1.0
O4 K:SO4202 4.1 89.7 1.0
CA L:SER184 4.3 41.1 1.0
CB L:ASP283 4.3 43.5 1.0
CA L:GLY284 4.3 44.0 1.0
N L:SER184 4.4 48.1 1.0
N L:GLY284 4.5 45.0 1.0
CG L:ASP180 4.5 58.0 1.0
OD1 L:ASP180 4.6 72.1 1.0
CA L:ASP283 4.8 41.1 1.0
CA L:SER182 4.9 38.8 1.0

Manganese binding site 5 out of 6 in 6ndd

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Manganese Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Mn401

b:63.0
occ:1.00
OG O:SER184 2.1 51.2 1.0
OD1 O:ASP283 2.3 38.4 1.0
O1 N:SO4201 2.4 0.9 1.0
OG O:SER182 2.5 58.0 1.0
CG O:ASP283 3.2 42.8 1.0
CB O:SER184 3.2 57.4 1.0
NA O:NA402 3.3 40.3 1.0
OD2 O:ASP283 3.4 54.5 1.0
OG1 O:THR250 3.4 39.5 1.0
S N:SO4201 3.6 0.6 1.0
CB O:SER182 3.6 57.4 1.0
OD2 O:ASP180 3.6 52.6 1.0
O2 N:SO4201 3.9 0.8 1.0
CA O:GLY284 4.1 64.8 1.0
O4 N:SO4201 4.1 94.5 1.0
O O:ASP283 4.2 73.3 1.0
C O:ASP283 4.2 60.0 1.0
OD1 O:ASP180 4.3 48.0 1.0
N O:GLY284 4.4 57.9 1.0
CG O:ASP180 4.4 45.5 1.0
CA O:SER184 4.4 52.6 1.0
N O:SER184 4.5 43.6 1.0
CB O:ASP283 4.6 39.3 1.0
O3 N:SO4201 4.8 99.3 1.0
CB O:THR250 4.8 36.2 1.0
CA O:ASP283 4.9 47.0 1.0
CA O:SER182 4.9 56.8 1.0

Manganese binding site 6 out of 6 in 6ndd

Go back to Manganese Binding Sites List in 6ndd
Manganese binding site 6 out of 6 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Manganese Bound


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Manganese Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Mn401

b:62.6
occ:1.00
OG R:SER184 2.0 39.3 1.0
OD1 R:ASP283 2.3 29.5 1.0
OG R:SER182 2.5 56.9 1.0
O4 Q:SO4202 2.9 0.4 1.0
NA R:NA404 3.1 35.2 1.0
O3 Q:SO4202 3.2 95.1 1.0
CB R:SER184 3.2 44.9 1.0
CG R:ASP283 3.3 36.0 1.0
OG1 R:THR250 3.4 32.3 1.0
S Q:SO4202 3.6 0.3 1.0
CB R:SER182 3.6 52.9 1.0
OD2 R:ASP180 3.6 61.0 1.0
OD2 R:ASP283 3.6 44.1 1.0
CA R:GLY284 4.1 58.7 1.0
O1 Q:SO4202 4.1 92.8 1.0
C R:ASP283 4.3 57.5 1.0
OD1 R:ASP180 4.3 54.9 1.0
N R:GLY284 4.3 55.4 1.0
O R:ASP283 4.3 70.4 1.0
CG R:ASP180 4.4 49.5 1.0
CA R:SER184 4.4 46.1 1.0
N R:SER184 4.4 40.6 1.0
CB R:ASP283 4.7 34.8 1.0
CB R:THR250 4.8 33.5 1.0
O2 Q:SO4202 4.8 85.7 1.0
CA R:SER182 4.9 54.8 1.0
CA R:ASP283 4.9 44.6 1.0

Reference:

J.Stetefeld, M.D.Mcdougall, P.C.Loewen. Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Manganese Bound To Be Published.
Page generated: Tue Dec 15 04:57:54 2020

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