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Calcium in PDB 7dh6: Crystal Structure of PLRG1

Protein crystallography data

The structure of Crystal Structure of PLRG1, PDB code: 7dh6 was solved by X.Wang, C.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.16 / 2.58
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 68.005, 82.124, 99.388, 90.00, 99.44, 90.00
R / Rfree (%) 22.6 / 27.6

Other elements in 7dh6:

The structure of Crystal Structure of PLRG1 also contains other interesting chemical elements:

Nickel (Ni) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of PLRG1 (pdb code 7dh6). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of PLRG1, PDB code: 7dh6:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 7dh6

Go back to Calcium Binding Sites List in 7dh6
Calcium binding site 1 out of 3 in the Crystal Structure of PLRG1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of PLRG1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca601

b:58.3
occ:1.00
O B:ASP460 2.4 52.1 1.0
O B:ASP432 2.5 41.2 1.0
O B:SER463 2.5 41.8 1.0
O B:HOH724 2.6 48.0 1.0
C B:ASP460 3.6 52.2 1.0
C B:ASP432 3.6 40.6 1.0
C B:SER463 3.7 40.0 1.0
CA B:GLY464 4.3 34.8 1.0
CA B:ASN433 4.4 41.9 1.0
CA B:ASP460 4.4 52.5 1.0
N B:ASN433 4.4 41.5 1.0
N B:GLY464 4.4 37.0 1.0
OD1 B:ASP432 4.5 46.6 1.0
CB B:ASP460 4.5 51.6 1.0
OG B:SER463 4.5 46.8 1.0
CG B:ASP432 4.5 45.3 1.0
N B:SER461 4.6 52.3 1.0
CA B:ASP432 4.6 38.9 1.0
CA B:SER461 4.6 48.7 1.0
CB B:ASP432 4.7 40.9 1.0
N B:SER463 4.7 44.7 1.0
CA B:SER463 4.8 43.7 1.0
OD2 B:ASP432 4.9 48.0 1.0

Calcium binding site 2 out of 3 in 7dh6

Go back to Calcium Binding Sites List in 7dh6
Calcium binding site 2 out of 3 in the Crystal Structure of PLRG1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of PLRG1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca602

b:51.3
occ:1.00
O C:SER463 2.6 43.5 1.0
O C:ASP432 2.7 41.5 1.0
O C:SER461 3.2 64.5 1.0
C C:SER463 3.7 43.1 1.0
C C:ASP432 3.8 39.6 1.0
OD1 C:ASP432 3.9 50.7 1.0
N C:SER463 4.2 54.1 1.0
C C:SER461 4.3 64.6 1.0
CG C:ASP432 4.4 48.4 1.0
CA C:ASN433 4.4 37.3 1.0
N C:ASN433 4.6 37.8 1.0
CA C:GLY464 4.6 38.2 1.0
N C:GLY464 4.6 39.8 1.0
CA C:SER463 4.6 48.2 1.0
CA C:ASP432 4.8 39.5 1.0
OD2 C:ASP432 4.9 49.9 1.0
CB C:ASP432 4.9 43.5 1.0
OG C:SER463 5.0 47.6 1.0

Calcium binding site 3 out of 3 in 7dh6

Go back to Calcium Binding Sites List in 7dh6
Calcium binding site 3 out of 3 in the Crystal Structure of PLRG1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of PLRG1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca601

b:50.5
occ:1.00
O D:SER463 2.3 46.7 1.0
O D:HOH705 2.5 28.7 1.0
O D:ASP432 2.7 31.6 1.0
O D:SER461 3.0 56.5 1.0
C D:SER463 3.5 42.9 1.0
OD2 D:ASP432 3.6 45.4 1.0
N D:SER463 3.8 53.1 1.0
C D:ASP432 3.9 33.4 1.0
CG D:ASP432 4.2 41.0 1.0
C D:SER461 4.2 56.8 1.0
CA D:SER463 4.3 49.0 1.0
N D:GLY464 4.5 37.6 1.0
OG D:SER463 4.5 51.6 1.0
CA D:GLY464 4.5 36.6 1.0
CA D:ASN433 4.6 34.4 1.0
N D:ASN433 4.7 34.1 1.0
OD1 D:ASP432 4.8 40.1 1.0
C D:GLU462 4.8 55.5 1.0
CA D:GLU462 4.8 54.5 1.0
CA D:ASP432 4.8 34.6 1.0
CB D:ASP432 4.9 36.9 1.0
CB D:SER463 5.0 52.1 1.0

Reference:

X.Wang, C.Xu. Crystal Structure of PLRG1 To Be Published.
Page generated: Wed Jul 9 21:36:38 2025

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