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Calcium in PDB 6k8b: The Open State of RGLG1 Vwa Domain

Enzymatic activity of The Open State of RGLG1 Vwa Domain

All present enzymatic activity of The Open State of RGLG1 Vwa Domain:
2.3.2.27;

Protein crystallography data

The structure of The Open State of RGLG1 Vwa Domain, PDB code: 6k8b was solved by Q.Wang, Y.Wu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.96 / 2.21
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 136.180, 136.180, 56.860, 90.00, 90.00, 90.00
R / Rfree (%) 16.7 / 19

Other elements in 6k8b:

The structure of The Open State of RGLG1 Vwa Domain also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the The Open State of RGLG1 Vwa Domain (pdb code 6k8b). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the The Open State of RGLG1 Vwa Domain, PDB code: 6k8b:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 6k8b

Go back to Calcium Binding Sites List in 6k8b
Calcium binding site 1 out of 6 in the The Open State of RGLG1 Vwa Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Open State of RGLG1 Vwa Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:33.1
occ:1.00
 OD1 A:ASP338 2.3 29.5 1.0
O A:PHE349 2.4 30.2 1.0
O A:ASP338 2.4 35.5 1.0
OE2 A:GLU378 2.5 36.5 1.0
OD2 A:ASP347 2.5 35.5 1.0
OD1 A:ASP347 2.5 32.4 1.0
O A:HOH652 2.6 33.9 1.0
OE1 A:GLU378 2.7 33.7 1.0
CG A:ASP347 2.8 35.8 1.0
CD A:GLU378 2.9 36.5 1.0
C A:ASP338 3.4 35.4 1.0
C A:PHE349 3.5 30.1 1.0
CG A:ASP338 3.5 33.0 1.0
CA A:CA502 3.7 34.6 1.0
CA A:ASP338 3.8 34.8 1.0
CB A:ASP338 4.3 34.7 1.0
CB A:ASP347 4.3 36.7 1.0
N A:GLN350 4.3 29.7 1.0
CA A:GLN350 4.3 28.8 1.0
N A:PHE349 4.4 30.7 1.0
CG A:GLU378 4.4 36.3 1.0
OD2 A:ASP338 4.5 39.4 1.0
NH2 A:ARG344 4.5 34.5 1.0
CA A:PHE349 4.5 32.0 1.0
O A:ILE133 4.5 41.0 1.0
N A:ASP339 4.5 35.3 1.0
OD1 A:ASP339 4.5 41.0 1.0
OE1 A:GLN350 4.6 33.1 1.0
CA A:ASP339 4.9 38.4 1.0
CB A:PHE349 4.9 25.5 1.0
NE2 A:GLN382 5.0 29.7 1.0
N A:ILE133 5.0 38.5 1.0
CB A:ILE133 5.0 36.2 1.0
O A:HOH620 5.0 31.0 1.0

Calcium binding site 2 out of 6 in 6k8b

Go back to Calcium Binding Sites List in 6k8b
Calcium binding site 2 out of 6 in the The Open State of RGLG1 Vwa Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Open State of RGLG1 Vwa Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:34.6
occ:1.00
 OE2 A:GLU378 2.3 36.5 1.0
OE1 A:GLN350 2.3 33.1 1.0
O A:HOH617 2.4 35.6 1.0
O A:HOH694 2.5 35.1 1.0
OD1 A:ASP338 2.5 29.5 1.0
O A:HOH620 2.5 31.0 1.0
OD2 A:ASP338 2.6 39.4 1.0
O A:HOH652 2.7 33.9 1.0
CG A:ASP338 2.9 33.0 1.0
CD A:GLN350 3.4 36.3 1.0
CD A:GLU378 3.5 36.5 1.0
CA A:CA501 3.7 33.1 1.0
NE2 A:GLN350 4.0 32.2 1.0
OD1 A:ASP339 4.1 41.0 1.0
O A:ILE133 4.1 41.0 1.0
OD1 A:ASP135 4.2 40.0 1.0
CG A:GLU378 4.2 36.3 1.0
O A:HOH676 4.4 51.3 1.0
CB A:ASP338 4.4 34.7 1.0
OE1 A:GLU378 4.5 33.7 1.0
CA A:GLN350 4.6 28.8 1.0
CG A:GLN350 4.7 29.2 1.0
N A:PHE351 4.7 31.1 1.0
CB A:GLN350 4.7 30.4 1.0
O A:PHE349 4.8 30.2 1.0
O A:ASP338 4.9 35.5 1.0

Calcium binding site 3 out of 6 in 6k8b

Go back to Calcium Binding Sites List in 6k8b
Calcium binding site 3 out of 6 in the The Open State of RGLG1 Vwa Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The Open State of RGLG1 Vwa Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:39.4
occ:1.00
 O A:LEU209 2.3 42.0 1.0
OD2 A:ASP205 2.4 37.0 1.0
O A:HOH701 2.5 46.7 1.0
O A:HOH645 2.5 35.1 1.0
OD1 A:ASP207 2.5 44.5 1.0
OD1 A:ASP205 2.5 39.4 1.0
OD1 A:ASN156 2.6 38.2 1.0
CG A:ASP205 2.8 38.7 1.0
C A:LEU209 3.4 43.6 1.0
CG A:ASP207 3.5 46.0 1.0
CG A:ASN156 3.6 38.7 1.0
OD2 A:ASP207 3.8 50.4 1.0
N A:LEU209 3.9 41.6 1.0
CB A:ASN156 4.0 33.5 1.0
CA A:LEU209 4.0 45.0 1.0
CB A:LEU209 4.2 46.7 1.0
CB A:ASP205 4.3 35.0 1.0
O A:HOH688 4.5 43.9 1.0
N A:ILE210 4.5 38.0 1.0
N A:LEU157 4.6 32.4 1.0
CA A:ASN156 4.6 32.6 1.0
O A:LEU157 4.6 35.9 1.0
CD A:PRO211 4.7 41.4 1.0
N A:ASP207 4.7 39.4 1.0
CA A:ILE210 4.7 41.1 1.0
N A:ASN208 4.8 41.6 1.0
ND2 A:ASN156 4.8 37.6 1.0
CB A:ASP207 4.9 36.9 1.0
CA A:ASP205 4.9 38.3 1.0
N A:GLU206 4.9 36.7 1.0
C A:ASN208 5.0 45.1 1.0

Calcium binding site 4 out of 6 in 6k8b

Go back to Calcium Binding Sites List in 6k8b
Calcium binding site 4 out of 6 in the The Open State of RGLG1 Vwa Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of The Open State of RGLG1 Vwa Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca501

b:34.8
occ:1.00
 OE2 B:GLU378 2.3 34.5 1.0
O B:HOH642 2.4 37.2 1.0
OE1 B:GLN350 2.4 32.5 1.0
O B:HOH608 2.5 35.6 1.0
O B:HOH670 2.5 32.0 1.0
OD1 B:ASP338 2.5 35.5 1.0
OD2 B:ASP338 2.6 36.5 1.0
CG B:ASP338 2.9 33.7 1.0
O B:HOH630 3.0 35.8 1.0
CD B:GLN350 3.5 34.8 1.0
CD B:GLU378 3.5 34.2 1.0
CA B:CA502 3.7 33.3 1.0
OD1 B:ASP339 4.0 44.8 1.0
O B:ILE133 4.1 43.8 1.0
NE2 B:GLN350 4.1 30.5 1.0
OD1 B:ASP135 4.2 43.3 1.0
CG B:GLU378 4.2 33.0 1.0
CB B:ASP338 4.4 34.4 1.0
OE1 B:GLU378 4.5 34.8 1.0
O B:HOH728 4.5 55.2 1.0
CA B:GLN350 4.6 31.1 1.0
N B:PHE351 4.7 34.0 1.0
CG B:GLN350 4.7 24.8 1.0
O B:PHE349 4.8 32.0 1.0
CB B:GLN350 4.8 29.6 1.0
O B:ASP338 4.8 36.8 1.0
O B:HOH722 4.9 54.6 1.0

Calcium binding site 5 out of 6 in 6k8b

Go back to Calcium Binding Sites List in 6k8b
Calcium binding site 5 out of 6 in the The Open State of RGLG1 Vwa Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of The Open State of RGLG1 Vwa Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca502

b:33.3
occ:1.00
 OD1 B:ASP338 2.4 35.5 1.0
O B:ASP338 2.4 36.8 1.0
O B:PHE349 2.4 32.0 1.0
OE2 B:GLU378 2.4 34.5 1.0
OD2 B:ASP347 2.4 38.4 1.0
OD1 B:ASP347 2.5 33.3 1.0
O B:HOH630 2.6 35.8 1.0
OE1 B:GLU378 2.6 34.8 1.0
CG B:ASP347 2.8 39.1 1.0
CD B:GLU378 2.9 34.2 1.0
C B:ASP338 3.4 38.1 1.0
CG B:ASP338 3.6 33.7 1.0
C B:PHE349 3.6 32.5 1.0
CA B:CA501 3.7 34.8 1.0
CA B:ASP338 3.9 36.2 1.0
CB B:ASP347 4.3 33.8 1.0
CB B:ASP338 4.3 34.4 1.0
CG B:GLU378 4.4 33.0 1.0
N B:PHE349 4.4 32.9 1.0
O B:ILE133 4.4 43.8 1.0
NH2 B:ARG344 4.4 34.3 1.0
CA B:GLN350 4.4 31.1 1.0
N B:GLN350 4.4 29.9 1.0
OD2 B:ASP338 4.5 36.5 1.0
CA B:PHE349 4.5 31.3 1.0
N B:ASP339 4.5 34.7 1.0
OD1 B:ASP339 4.6 44.8 1.0
OE1 B:GLN350 4.7 32.5 1.0
N B:ILE133 4.9 43.5 1.0
CA B:ASP339 4.9 41.5 1.0
CB B:ILE133 4.9 40.0 1.0
CB B:PHE349 5.0 29.5 1.0

Calcium binding site 6 out of 6 in 6k8b

Go back to Calcium Binding Sites List in 6k8b
Calcium binding site 6 out of 6 in the The Open State of RGLG1 Vwa Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of The Open State of RGLG1 Vwa Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca503

b:35.9
occ:1.00
 O B:LEU209 2.4 38.4 1.0
OD1 B:ASN156 2.4 36.2 1.0
O B:HOH674 2.4 31.6 1.0
O B:HOH639 2.4 37.5 1.0
OD2 B:ASP205 2.5 34.5 1.0
OD1 B:ASP207 2.5 42.7 1.0
OD1 B:ASP205 2.6 36.9 1.0
CG B:ASP205 2.8 36.1 1.0
CG B:ASN156 3.3 36.4 1.0
CG B:ASP207 3.4 44.5 1.0
C B:LEU209 3.5 39.9 1.0
OD2 B:ASP207 3.7 48.1 1.0
CB B:ASN156 3.8 32.6 1.0
N B:LEU209 4.0 37.5 1.0
CA B:LEU209 4.2 35.6 1.0
CB B:ASP205 4.3 31.0 1.0
CB B:LEU209 4.4 41.3 1.0
CA B:ASN156 4.5 30.8 1.0
ND2 B:ASN156 4.5 37.6 1.0
N B:LEU157 4.5 32.8 1.0
O B:HOH651 4.6 40.1 1.0
N B:ILE210 4.6 36.0 1.0
N B:ASP207 4.6 34.5 1.0
O B:LEU157 4.7 32.3 1.0
CD B:PRO211 4.8 36.1 1.0
CA B:ILE210 4.8 36.6 1.0
CB B:ASP207 4.8 35.1 1.0
N B:ASN208 4.8 41.7 1.0
O B:HOH611 4.8 49.5 1.0
CA B:ASP205 4.9 38.7 1.0
N B:GLU206 4.9 39.5 1.0
C B:ASP205 5.0 40.5 1.0

Reference:

Q.Wang, Y.Wu. The Open State of RGLG1 Vwa Domain To Be Published.
Page generated: Tue Jul 16 10:17:37 2024

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