Calcium in PDB 7ozq: Crystal Structure of Archaeal L7AE Bound to Eukaryotic Kink-Loop

The structure of Crystal Structure of Archaeal L7AE Bound to Eukaryotic Kink-Loop, PDB code: 7ozq was solved by S.Hoefler, P.Lukat, T.Carlomagno, W.Blankenfeldt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	54.50 / 1.91
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	109.391, 61.598, 138.611, 90, 108.36, 90
R / Rfree (%)	17.3 / 21.9

The structure of Crystal Structure of Archaeal L7AE Bound to Eukaryotic Kink-Loop also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Sodium	(Na)	6 atoms

The binding sites of Calcium atom in the Crystal Structure of Archaeal L7AE Bound to Eukaryotic Kink-Loop (pdb code 7ozq). 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 Archaeal L7AE Bound to Eukaryotic Kink-Loop, PDB code: 7ozq:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of Archaeal L7AE Bound to Eukaryotic Kink-Loop


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 Archaeal L7AE Bound to Eukaryotic Kink-Loop within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca102 b:41.8 occ:0.50 O E:HOH233 2.4 27.8 1.0 O E:HOH250 2.4 25.9 1.0 N7 E:A16 2.6 30.4 1.0 H62 E:A16 3.1 34.4 1.0 C8 E:A16 3.5 29.4 1.0 H8 E:A16 3.6 35.2 1.0 C5 E:A16 3.6 32.3 1.0 N6 E:A16 3.8 28.7 1.0 HO2' E:G15 4.1 36.1 1.0 C6 E:A16 4.1 29.8 1.0 O E:HOH281 4.2 39.7 1.0 H62 E:A17 4.4 32.2 1.0 O E:HOH262 4.4 43.7 1.0 O E:HOH284 4.5 43.3 1.0 H61 E:A16 4.5 34.4 1.0 OP1 E:A16 4.5 24.6 1.0 N6 E:A17 4.5 26.8 1.0 N9 E:A16 4.7 26.3 1.0 O2' E:G15 4.7 30.1 1.0 O3' E:G15 4.7 28.3 1.0 H61 E:A17 4.7 32.2 1.0 C4 E:A16 4.7 26.9 1.0 C6 E:A17 5.0 29.1 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of Archaeal L7AE Bound to Eukaryotic Kink-Loop


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 Archaeal L7AE Bound to Eukaryotic Kink-Loop within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca103 b:77.4 occ:1.00 O E:HOH225 2.1 40.3 1.0 O E:HOH204 2.3 38.4 1.0 O E:HOH252 2.5 49.8 1.0 OP2 E:G15 2.6 27.8 1.0 O E:ACT101 3.0 47.5 1.0 OXT E:ACT101 3.0 44.7 1.0 C E:ACT101 3.3 41.6 1.0 O E:HOH229 3.7 37.5 1.0 P E:G15 3.9 30.1 1.0 H8 E:G15 3.9 32.1 1.0 O5' E:G15 4.1 25.8 1.0 H3' E:C14 4.2 37.7 1.0 O E:HOH215 4.3 48.1 1.0 N7 E:G15 4.4 29.6 1.0 C8 E:G15 4.4 26.8 1.0 OP2 E:C14 4.6 29.4 1.0 OP2 E:A16 4.7 26.4 1.0 H3' E:G15 4.7 29.4 1.0 CH3 E:ACT101 4.7 36.9 1.0 OP1 E:G15 4.8 29.8 1.0 H3 E:ACT101 4.9 44.2 1.0 O5' E:C14 5.0 31.6 1.0 O3' E:C14 5.0 28.6 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of Archaeal L7AE Bound to Eukaryotic Kink-Loop


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 Archaeal L7AE Bound to Eukaryotic Kink-Loop within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca106 b:45.1 occ:0.50 O F:HOH240 2.5 27.2 1.0 O F:HOH246 2.6 26.6 1.0 N7 F:A16 2.6 25.8 1.0 H62 F:A16 3.1 38.2 1.0 C8 F:A16 3.5 25.2 1.0 C5 F:A16 3.5 28.0 1.0 H8 F:A16 3.6 30.2 1.0 N6 F:A16 3.8 31.8 1.0 C6 F:A16 4.0 30.6 1.0 HO2' F:G15 4.1 34.8 1.0 H61 F:A16 4.5 38.2 1.0 O F:HOH264 4.5 35.6 1.0 H62 F:A17 4.5 36.4 1.0 OP1 F:A16 4.6 28.2 1.0 N9 F:A16 4.6 29.1 1.0 O F:HOH269 4.6 39.6 1.0 N6 F:A17 4.6 30.3 1.0 C4 F:A16 4.6 29.3 1.0 O2' F:G15 4.7 29.0 1.0 O3' F:G15 4.7 28.9 1.0 H61 F:A17 4.8 36.4 1.0

S.Hofler, P.Lukat, W.Blankenfeldt, T.Carlomagno. Eukaryotic Box C/D Methylation Machinery Has Two Non-Symmetric Protein Assembly Sites. Sci Rep V. 11 17561 2021.
ISSN: ESSN 2045-2322
PubMed: 34475498
DOI: 10.1038/S41598-021-97030-Y