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Calcium in PDB 6k8a: RGLG1 Vwa Domain with Midas Is Occupied By Water

Enzymatic activity of RGLG1 Vwa Domain with Midas Is Occupied By Water

All present enzymatic activity of RGLG1 Vwa Domain with Midas Is Occupied By Water:
2.3.2.27;

Protein crystallography data

The structure of RGLG1 Vwa Domain with Midas Is Occupied By Water, PDB code: 6k8a 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) 48.01 / 2.40
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 136.280, 136.280, 55.370, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 21.1

Calcium Binding Sites:

The binding sites of Calcium atom in the RGLG1 Vwa Domain with Midas Is Occupied By Water (pdb code 6k8a). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the RGLG1 Vwa Domain with Midas Is Occupied By Water, PDB code: 6k8a:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 6k8a

Go back to Calcium Binding Sites List in 6k8a
Calcium binding site 1 out of 6 in the RGLG1 Vwa Domain with Midas Is Occupied By Water


Mono view


Stereo pair view

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

b:41.7
occ:1.00
 O A:PHE349 2.3 40.2 1.0
OD1 A:ASP347 2.4 42.0 1.0
O A:ASP338 2.4 47.6 1.0
OD1 A:ASP338 2.4 44.1 1.0
OE2 A:GLU378 2.4 44.7 1.0
O A:HOH630 2.5 41.1 1.0
OD2 A:ASP347 2.5 48.9 1.0
OE1 A:GLU378 2.5 44.8 1.0
CG A:ASP347 2.8 45.8 1.0
CD A:GLU378 2.8 43.4 1.0
C A:ASP338 3.4 46.7 1.0
C A:PHE349 3.5 43.3 1.0
CG A:ASP338 3.6 45.7 1.0
CA A:ASP338 3.8 45.9 1.0
CA A:CA502 3.9 46.3 1.0
CB A:ASP347 4.3 41.8 1.0
CB A:ASP338 4.3 47.4 1.0
CG A:GLU378 4.3 47.5 1.0
N A:PHE349 4.4 44.5 1.0
N A:GLN350 4.4 44.6 1.0
CA A:GLN350 4.4 42.2 1.0
O A:ILE133 4.4 49.8 1.0
CA A:PHE349 4.4 43.0 1.0
NH2 A:ARG344 4.5 40.9 1.0
N A:ASP339 4.5 48.2 1.0
OD2 A:ASP338 4.6 50.5 1.0
OE1 A:GLN350 4.6 43.2 1.0
OD1 A:ASP339 4.6 50.8 1.0
O A:HOH620 4.9 46.3 1.0
CB A:PHE349 4.9 41.9 1.0
CA A:ASP339 4.9 50.9 1.0
CB A:ILE133 4.9 44.6 1.0
C A:ASP347 5.0 43.2 1.0
O A:ASP347 5.0 38.7 1.0
N A:ILE133 5.0 47.7 1.0

Calcium binding site 2 out of 6 in 6k8a

Go back to Calcium Binding Sites List in 6k8a
Calcium binding site 2 out of 6 in the RGLG1 Vwa Domain with Midas Is Occupied By Water


Mono view


Stereo pair view

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

b:46.3
occ:1.00
 O A:HOH622 2.3 44.2 1.0
OE1 A:GLN350 2.3 43.2 1.0
OE2 A:GLU378 2.4 44.7 1.0
O A:HOH647 2.4 42.9 1.0
O A:HOH620 2.5 46.3 1.0
OD1 A:ASP338 2.6 44.1 1.0
OD2 A:ASP338 2.6 50.5 1.0
CG A:ASP338 2.9 45.7 1.0
O A:HOH630 3.0 41.1 1.0
CD A:GLN350 3.4 44.7 1.0
CD A:GLU378 3.6 43.4 1.0
CA A:CA501 3.9 41.7 1.0
NE2 A:GLN350 3.9 40.7 1.0
OD1 A:ASP339 4.0 50.8 1.0
OD1 A:ASP135 4.1 53.3 1.0
O A:ILE133 4.2 49.8 1.0
CG A:GLU378 4.2 47.5 1.0
CB A:ASP338 4.5 47.4 1.0
O A:HOH608 4.5 49.9 1.0
OE1 A:GLU378 4.6 44.8 1.0
CG A:GLN350 4.7 42.8 1.0
CA A:GLN350 4.7 42.2 1.0
N A:PHE351 4.8 42.1 1.0
O A:PHE349 4.9 40.2 1.0
CB A:GLN350 4.9 40.6 1.0

Calcium binding site 3 out of 6 in 6k8a

Go back to Calcium Binding Sites List in 6k8a
Calcium binding site 3 out of 6 in the RGLG1 Vwa Domain with Midas Is Occupied By Water


Mono view


Stereo pair view

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

b:47.4
occ:1.00
 O A:LEU209 2.3 51.9 1.0
OD1 A:ASP205 2.4 49.7 1.0
O A:HOH652 2.4 44.0 1.0
OD1 A:ASN156 2.5 46.5 1.0
O A:HOH659 2.5 46.2 1.0
OD1 A:ASP207 2.5 55.5 1.0
OD2 A:ASP205 2.6 52.5 1.0
CG A:ASP205 2.8 48.4 1.0
C A:LEU209 3.4 53.0 1.0
CG A:ASN156 3.5 48.5 1.0
CG A:ASP207 3.5 53.0 1.0
CB A:ASN156 3.8 43.6 1.0
OD2 A:ASP207 3.8 54.5 1.0
N A:LEU209 3.9 55.0 1.0
CA A:LEU209 4.1 54.2 1.0
CB A:ASP205 4.3 45.8 1.0
O A:HOH663 4.4 47.5 1.0
CB A:LEU209 4.4 56.6 1.0
CA A:ASN156 4.4 43.8 1.0
N A:ILE210 4.5 51.5 1.0
N A:LEU157 4.5 45.0 1.0
CA A:ILE210 4.6 51.7 1.0
O A:LEU157 4.6 50.2 1.0
CD A:PRO211 4.6 55.3 1.0
ND2 A:ASN156 4.7 50.9 1.0
N A:ASP207 4.7 51.8 1.0
N A:ASN208 4.8 50.8 1.0
CB A:ASP207 4.8 54.1 1.0
CA A:ASP205 4.9 47.6 1.0
C A:ASN156 5.0 44.0 1.0
C A:ASP205 5.0 50.2 1.0
C A:ASN208 5.0 57.2 1.0

Calcium binding site 4 out of 6 in 6k8a

Go back to Calcium Binding Sites List in 6k8a
Calcium binding site 4 out of 6 in the RGLG1 Vwa Domain with Midas Is Occupied By Water


Mono view


Stereo pair view

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

b:48.1
occ:1.00
 O B:LEU209 2.3 50.1 1.0
OD2 B:ASP205 2.4 48.9 1.0
OD1 B:ASP207 2.4 56.0 1.0
O B:HOH629 2.4 44.6 1.0
OD1 B:ASN156 2.4 49.3 1.0
O B:HOH655 2.5 49.3 1.0
OD1 B:ASP205 2.8 50.9 1.0
CG B:ASP205 2.9 49.1 1.0
CG B:ASN156 3.4 50.0 1.0
CG B:ASP207 3.4 54.1 1.0
C B:LEU209 3.5 50.3 1.0
OD2 B:ASP207 3.7 56.4 1.0
CB B:ASN156 3.8 44.7 1.0
N B:LEU209 4.0 53.8 1.0
CA B:LEU209 4.2 52.8 1.0
CB B:LEU209 4.4 60.3 1.0
CB B:ASP205 4.4 42.2 1.0
N B:ILE210 4.5 52.2 1.0
CA B:ASN156 4.5 43.7 1.0
ND2 B:ASN156 4.5 46.9 1.0
O B:HOH659 4.6 42.9 1.0
N B:ASP207 4.6 46.8 1.0
N B:LEU157 4.6 47.7 1.0
O B:LEU157 4.7 43.3 1.0
CD B:PRO211 4.7 48.9 1.0
CA B:ILE210 4.7 51.4 1.0
N B:ASN208 4.8 53.1 1.0
CB B:ASP207 4.8 48.9 1.0
CA B:ASP205 5.0 50.5 1.0

Calcium binding site 5 out of 6 in 6k8a

Go back to Calcium Binding Sites List in 6k8a
Calcium binding site 5 out of 6 in the RGLG1 Vwa Domain with Midas Is Occupied By Water


Mono view


Stereo pair view

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

b:48.0
occ:1.00
 OE2 B:GLU378 2.4 48.2 1.0
O B:HOH609 2.4 56.2 1.0
O B:HOH603 2.5 51.3 1.0
OE1 B:GLN350 2.5 44.9 1.0
O B:HOH650 2.5 47.0 1.0
OD1 B:ASP338 2.6 47.7 1.0
OD2 B:ASP338 2.6 50.9 1.0
CG B:ASP338 3.0 46.0 1.0
O B:HOH615 3.0 45.5 1.0
CD B:GLU378 3.6 48.6 1.0
CA B:CA503 3.6 46.6 1.0
CD B:GLN350 3.6 44.3 1.0
OD1 B:ASP339 3.9 57.1 1.0
O B:ILE133 4.0 59.4 1.0
O B:HOH604 4.1 52.4 1.0
NE2 B:GLN350 4.2 36.4 1.0
OD1 B:ASP135 4.2 61.4 1.0
CG B:GLU378 4.2 46.7 1.0
CB B:ASP338 4.5 42.8 1.0
OE1 B:GLU378 4.5 49.5 1.0
O B:HOH664 4.8 64.2 1.0
CA B:GLN350 4.8 39.1 1.0
O B:PHE349 4.8 42.2 1.0
CG B:GLN350 4.8 41.8 1.0
N B:PHE351 4.8 43.6 1.0
O B:HOH619 4.9 54.0 1.0
O B:ASP338 4.9 47.7 1.0
CG B:ASP339 4.9 57.3 1.0
CB B:GLN350 4.9 37.3 1.0

Calcium binding site 6 out of 6 in 6k8a

Go back to Calcium Binding Sites List in 6k8a
Calcium binding site 6 out of 6 in the RGLG1 Vwa Domain with Midas Is Occupied By Water


Mono view


Stereo pair view

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

b:46.6
occ:1.00
 OE2 B:GLU378 2.3 48.2 1.0
OD1 B:ASP338 2.4 47.7 1.0
O B:PHE349 2.4 42.2 1.0
O B:ASP338 2.4 47.7 1.0
OD1 B:ASP347 2.5 51.0 1.0
O B:HOH615 2.5 45.5 1.0
OD2 B:ASP347 2.6 46.5 1.0
OE1 B:GLU378 2.6 49.5 1.0
CD B:GLU378 2.8 48.6 1.0
CG B:ASP347 2.9 49.2 1.0
C B:ASP338 3.3 50.1 1.0
CG B:ASP338 3.5 46.0 1.0
CA B:CA502 3.6 48.0 1.0
C B:PHE349 3.6 40.7 1.0
CA B:ASP338 3.8 47.7 1.0
CB B:ASP338 4.2 42.8 1.0
CG B:GLU378 4.4 46.7 1.0
CB B:ASP347 4.4 51.9 1.0
OD2 B:ASP338 4.4 50.9 1.0
CA B:GLN350 4.4 39.1 1.0
O B:ILE133 4.4 59.4 1.0
OD1 B:ASP339 4.4 57.1 1.0
N B:GLN350 4.4 38.4 1.0
N B:PHE349 4.5 42.6 1.0
N B:ASP339 4.5 48.8 1.0
CA B:PHE349 4.5 41.4 1.0
OE1 B:GLN350 4.5 44.9 1.0
NH2 B:ARG344 4.6 44.0 1.0
CA B:ASP339 4.9 54.1 1.0
CB B:PHE349 5.0 40.9 1.0

Reference:

Q.Wang, Y.Wu. RGLG1 Vwa Domain with Midas Is Occupied By Water To Be Published.
Page generated: Wed Jul 9 15:26:12 2025

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