Atomistry » Zinc » PDB 6n7p-6ngh » 6ndh
Atomistry »
  Zinc »
    PDB 6n7p-6ngh »
      6ndh »

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

Go back to Zinc Binding Sites List in 6ndh
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

Go back to Zinc Binding Sites List in 6ndh
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

Go back to Zinc Binding Sites List in 6ndh
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

Go back to Zinc Binding Sites List in 6ndh
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

Go back to Zinc Binding Sites List in 6ndh
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy