Calcium in PDB 9mr6: X-Ray Crystal Structure of SAMHD1 From Rhizophagus Irregularis

The structure of X-Ray Crystal Structure of SAMHD1 From Rhizophagus Irregularis, PDB code: 9mr6 was solved by J.C.Lachowicz, C.Zizola, T.G.Grove, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.50 / 2.27
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	84.359, 85.42, 87.035, 104.58, 111.65, 99.51
R / Rfree (%)	22 / 28

The structure of X-Ray Crystal Structure of SAMHD1 From Rhizophagus Irregularis also contains other interesting chemical elements:

Manganese

(Mn)

4 atoms

The binding sites of Calcium atom in the X-Ray Crystal Structure of SAMHD1 From Rhizophagus Irregularis (pdb code 9mr6). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the X-Ray Crystal Structure of SAMHD1 From Rhizophagus Irregularis, PDB code: 9mr6:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the X-Ray Crystal Structure of SAMHD1 From Rhizophagus Irregularis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of X-Ray Crystal Structure of SAMHD1 From Rhizophagus Irregularis within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca605 b:76.9 occ:1.00 O1B A:GTP603 1.8 79.2 1.0 O1G A:GTP603 2.1 79.5 1.0 PB A:GTP603 3.1 70.6 1.0 PG A:GTP603 3.2 71.5 1.0 O3B A:GTP603 3.6 52.5 1.0 O3G A:GTP603 3.7 74.8 1.0 O5' A:GTP603 4.1 71.4 1.0 O2B A:GTP603 4.1 59.2 1.0 O3A A:GTP603 4.2 74.4 1.0 O2A A:GTP603 4.2 70.2 1.0 PA A:GTP603 4.4 55.2 1.0 NZ A:LYS13 4.5 39.3 1.0 O2G A:GTP603 4.5 60.5 1.0

Calcium binding site 2 out of 4 in the X-Ray Crystal Structure of SAMHD1 From Rhizophagus Irregularis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of X-Ray Crystal Structure of SAMHD1 From Rhizophagus Irregularis within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:82.2 occ:1.00 O1B A:GTP601 1.9 87.0 1.0 O3G A:GTP601 2.3 77.7 1.0 O1A A:GTP601 2.7 70.8 1.0 PB A:GTP601 3.2 77.5 1.0 PG A:GTP601 3.5 78.0 1.0 O3B A:GTP601 3.7 76.2 1.0 PA A:GTP601 3.9 54.4 1.0 O3A A:GTP601 3.9 67.2 1.0 NZ B:LYS13 4.3 70.5 1.0 O2B A:GTP601 4.3 82.1 1.0 O2G A:GTP601 4.5 90.1 1.0 O1G A:GTP601 4.5 73.2 1.0 C5' A:GTP601 4.7 56.4 1.0 O5' A:GTP601 4.8 67.3 1.0 CG2 A:VAL255 4.9 33.6 1.0 O2A A:GTP601 4.9 50.8 1.0 CE B:LYS13 5.0 68.7 1.0

Calcium binding site 3 out of 4 in the X-Ray Crystal Structure of SAMHD1 From Rhizophagus Irregularis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of X-Ray Crystal Structure of SAMHD1 From Rhizophagus Irregularis within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:81.2 occ:1.00 O1B D:GTP602 2.0 84.8 1.0 O2G D:GTP602 2.0 80.8 1.0 O2A D:GTP602 3.1 64.0 1.0 PB D:GTP602 3.2 81.7 1.0 PG D:GTP602 3.3 94.7 1.0 O3B D:GTP602 3.5 67.6 1.0 NH2 C:ARG14 3.8 63.7 1.0 PA D:GTP602 4.1 68.0 1.0 O3A D:GTP602 4.1 59.7 1.0 O3G D:GTP602 4.2 94.6 1.0 O1G D:GTP602 4.3 70.3 1.0 O2B D:GTP602 4.3 68.3 1.0 NZ D:LYS324 4.3 72.3 1.0 C5' D:GTP602 4.4 68.6 1.0 NZ C:LYS13 4.4 67.1 1.0 CZ C:ARG14 4.7 91.1 1.0 NH1 C:ARG14 4.8 92.4 1.0 O5' D:GTP602 4.8 77.1 1.0 O3' D:GTP602 5.0 78.6 1.0

Calcium binding site 4 out of 4 in the X-Ray Crystal Structure of SAMHD1 From Rhizophagus Irregularis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of X-Ray Crystal Structure of SAMHD1 From Rhizophagus Irregularis within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca605 b:80.0 occ:1.00 O1B D:GTP601 2.2 74.4 1.0 O1G D:GTP601 2.2 73.5 1.0 O2A D:GTP601 2.5 59.4 1.0 PB D:GTP601 3.3 72.5 1.0 PG D:GTP601 3.4 75.0 1.0 PA D:GTP601 3.4 49.8 1.0 O3B D:GTP601 3.5 66.9 1.0 O5' D:GTP601 3.6 56.4 1.0 O3A D:GTP601 3.8 67.7 1.0 NZ D:LYS13 3.8 53.8 1.0 O3G D:GTP601 4.2 66.8 1.0 O2G D:GTP601 4.5 69.9 1.0 O2B D:GTP601 4.6 81.8 1.0 O3' D:GTP601 4.6 53.4 1.0 O1A D:GTP601 4.8 45.3 1.0 CE D:LYS13 4.9 62.6 1.0 C5' D:GTP601 5.0 46.8 1.0

L.Pan, J.C.Lachowicz, I.Paddy, E.Xu, Q.Yang, C.Zizola, A.Milne, T.G.Grove, M.-E.Pandelia. Activation and Allostery in A Fungal SAMHD1 Hydrolase; An Evolutionary Blueprint For Dntp Catabolism To Be Published.