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Zinc in PDB 6ndh: Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Zinc

Protein crystallography data

The structure of Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Zinc, PDB code: 6ndh 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) 47.00 / 2.90
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 131.399, 131.399, 251.358, 90.00, 90.00, 90.00
R / Rfree (%) 22.8 / 28.5

Other elements in 6ndh:

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

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

Zinc Binding Sites:

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

Zinc binding site 1 out of 6 in 6ndh

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:73.5
occ:1.00
 OG C:SER184 2.0 47.2 1.0
OD1 C:ASP283 2.2 45.0 1.0
OG C:SER182 2.7 39.1 1.0
CG C:ASP283 3.0 45.0 1.0
OD2 C:ASP283 3.2 43.7 1.0
O3 B:SO4201 3.2 64.8 1.0
CB C:SER184 3.3 43.0 1.0
NA C:NA402 3.4 40.1 1.0
O4 B:SO4201 3.6 0.5 1.0
OD2 C:ASP180 3.7 52.1 1.0
OG1 C:THR250 3.8 41.1 1.0
S B:SO4201 3.9 0.1 1.0
O C:ASP283 3.9 39.6 1.0
CB C:SER182 3.9 38.6 1.0
O1 B:SO4201 4.1 77.0 1.0
C C:ASP283 4.1 41.3 1.0
CA C:GLY284 4.3 40.8 1.0
CA C:SER184 4.4 47.0 1.0
CB C:ASP283 4.4 42.3 1.0
N C:GLY284 4.4 40.5 1.0
N C:SER184 4.5 49.9 1.0
CG C:ASP180 4.5 45.8 1.0
OD1 C:ASP180 4.6 44.9 1.0
CA C:ASP283 4.8 40.1 1.0

Zinc binding site 2 out of 6 in 6ndh

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn401

b:58.1
occ:1.00
 OG F:SER184 2.4 42.4 1.0
O4 E:SO4203 2.4 89.8 1.0
OG F:SER182 2.5 32.1 1.0
OD1 F:ASP283 2.6 47.8 1.0
NA F:NA402 3.4 30.2 1.0
O3 E:SO4203 3.4 59.9 1.0
S E:SO4203 3.5 87.2 1.0
OD2 F:ASP180 3.6 42.2 1.0
CB F:SER184 3.7 35.9 1.0
CG F:ASP283 3.7 47.7 1.0
CB F:SER182 3.7 35.7 1.0
OG1 F:THR250 3.8 42.7 1.0
O F:ASP283 4.1 42.2 1.0
C F:ASP283 4.1 39.4 1.0
O2 E:SO4203 4.1 53.0 1.0
OD2 F:ASP283 4.2 61.9 1.0
CA F:GLY284 4.3 41.1 1.0
N F:GLY284 4.3 38.5 1.0
CG F:ASP180 4.4 43.1 1.0
OD1 F:ASP180 4.5 50.8 1.0
O1 E:SO4203 4.6 63.9 1.0
N F:SER184 4.8 43.2 1.0
CB F:ASP283 4.8 46.6 1.0
CA F:SER184 4.8 38.0 1.0
CA F:ASP283 4.8 42.0 1.0
CA F:SER182 4.9 31.7 1.0
N F:ASP283 5.0 41.6 1.0

Zinc binding site 3 out of 6 in 6ndh

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn401

b:55.2
occ:1.00
 OG I:SER184 2.4 47.3 1.0
O4 H:SO4202 2.5 95.4 1.0
OG I:SER182 2.5 30.8 1.0
OD1 I:ASP283 2.6 54.0 1.0
NA I:NA402 3.3 33.8 1.0
O3 H:SO4202 3.4 69.0 1.0
S H:SO4202 3.5 95.1 1.0
OD2 I:ASP180 3.6 38.0 1.0
CB I:SER184 3.6 37.1 1.0
CG I:ASP283 3.7 48.2 1.0
CB I:SER182 3.7 33.8 1.0
OG1 I:THR250 3.9 47.7 1.0
O I:ASP283 4.0 38.9 1.0
C I:ASP283 4.1 38.4 1.0
O2 H:SO4202 4.1 57.4 1.0
N I:GLY284 4.2 37.3 1.0
CA I:GLY284 4.3 41.2 1.0
OD2 I:ASP283 4.3 59.8 1.0
CG I:ASP180 4.5 37.5 1.0
OD1 I:ASP180 4.5 45.1 1.0
O1 H:SO4202 4.7 62.5 1.0
N I:SER184 4.8 42.2 1.0
CA I:SER184 4.8 38.1 1.0
CA I:ASP283 4.8 42.8 1.0
CB I:ASP283 4.8 45.7 1.0
CA I:SER182 4.9 31.4 1.0
N I:ASP283 5.0 42.2 1.0

Zinc binding site 4 out of 6 in 6ndh

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn401

b:73.0
occ:1.00
 OG L:SER184 2.0 42.6 1.0
OD1 L:ASP283 2.2 46.0 1.0
OG L:SER182 2.7 42.6 1.0
CG L:ASP283 3.1 46.5 1.0
NA L:NA402 3.1 36.6 1.0
CB L:SER184 3.2 38.9 1.0
OD2 L:ASP283 3.3 47.7 1.0
O3 K:SO4202 3.4 72.3 1.0
O L:ASP283 3.7 41.6 1.0
O4 K:SO4202 3.8 92.5 1.0
OD2 L:ASP180 3.8 54.3 1.0
CB L:SER182 3.9 41.8 1.0
OG1 L:THR250 3.9 41.2 1.0
S K:SO4202 4.0 99.3 1.0
O1 K:SO4202 4.0 81.7 1.0
C L:ASP283 4.1 44.3 1.0
CA L:GLY284 4.3 43.9 1.0
CA L:SER184 4.4 43.8 1.0
N L:SER184 4.4 48.3 1.0
CB L:ASP283 4.5 46.7 1.0
N L:GLY284 4.5 41.4 1.0
CG L:ASP180 4.6 46.5 1.0
OD1 L:ASP180 4.6 45.3 1.0
CA L:ASP283 4.8 43.8 1.0

Zinc binding site 5 out of 6 in 6ndh

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Zn401

b:94.3
occ:1.00
 OG O:SER184 2.1 47.4 1.0
OD1 O:ASP283 2.4 42.5 1.0
OG O:SER182 2.8 49.2 1.0
O4 N:SO4201 3.1 0.7 1.0
CB O:SER184 3.3 56.6 1.0
CG O:ASP283 3.4 48.8 1.0
NA O:NA402 3.6 49.0 1.0
OG1 O:THR250 3.6 43.6 1.0
OD2 O:ASP180 3.7 56.5 1.0
OD2 O:ASP283 3.8 64.9 1.0
CB O:SER182 4.0 49.4 1.0
S N:SO4201 4.1 0.8 1.0
O2 N:SO4201 4.2 97.4 1.0
CA O:GLY284 4.3 54.2 1.0
C O:ASP283 4.3 53.4 1.0
OD1 O:ASP180 4.4 51.5 1.0
O O:ASP283 4.4 63.2 1.0
CG O:ASP180 4.4 46.0 1.0
O1 N:SO4201 4.5 94.0 1.0
N O:GLY284 4.5 46.8 1.0
CA O:SER184 4.5 49.4 1.0
N O:SER184 4.6 46.7 1.0
CB O:ASP283 4.7 45.6 1.0
CA O:ASP283 4.9 51.4 1.0
CB O:THR250 4.9 42.1 1.0

Zinc binding site 6 out of 6 in 6ndh

Go back to Zinc Binding Sites List in 6ndh
Zinc binding site 6 out of 6 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Zn401

b:91.9
occ:1.00
 OG R:SER184 2.1 50.2 1.0
OD1 R:ASP283 2.5 41.5 1.0
OG R:SER182 2.8 48.6 1.0
CB R:SER184 3.3 55.5 1.0
O4 Q:SO4202 3.4 0.5 1.0
O3 Q:SO4202 3.5 0.8 1.0
NA R:NA404 3.5 48.8 1.0
CG R:ASP283 3.5 48.6 1.0
OG1 R:THR250 3.6 45.3 1.0
OD2 R:ASP180 3.8 58.4 1.0
OD2 R:ASP283 3.8 63.4 1.0
S Q:SO4202 3.9 0.9 1.0
CB R:SER182 4.0 48.4 1.0
CA R:GLY284 4.3 53.3 1.0
O R:ASP283 4.3 66.0 1.0
C R:ASP283 4.3 55.0 1.0
O1 Q:SO4202 4.3 97.0 1.0
OD1 R:ASP180 4.4 47.9 1.0
N R:GLY284 4.5 48.4 1.0
CA R:SER184 4.5 47.7 1.0
CG R:ASP180 4.5 46.2 1.0
N R:SER184 4.5 43.5 1.0
CB R:ASP283 4.8 45.4 1.0
CB R:THR250 5.0 43.4 1.0
CA R:ASP283 5.0 51.5 1.0

Reference:

J.Stetefeld, M.D.Mcdougall, P.C.Loewen. Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Zinc Bound To Be Published.
Page generated: Tue Oct 29 03:40:50 2024

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