Calcium in PDB 6lna: Ydiu Complex with Ampnpp and MN2+

The structure of Ydiu Complex with Ampnpp and MN2+, PDB code: 6lna was solved by B.Li, Y.Yang, Y.Ma, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.44 / 1.70
Space group	I 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	112.43, 73.541, 122.649, 90, 102.49, 90
R / Rfree (%)	14 / 18.6

The structure of Ydiu Complex with Ampnpp and MN2+ also contains other interesting chemical elements:

Manganese

(Mn)

4 atoms

The binding sites of Calcium atom in the Ydiu Complex with Ampnpp and MN2+ (pdb code 6lna). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Ydiu Complex with Ampnpp and MN2+, PDB code: 6lna:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Ydiu Complex with Ampnpp and MN2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Ydiu Complex with Ampnpp and MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:15.0 occ:1.00 OD2 A:ASP265 2.3 8.6 1.0 O A:HOH1162 2.4 19.3 1.0 O A:HOH857 2.5 16.7 1.0 O A:HOH1084 2.5 19.3 1.0 CG A:ASP265 3.3 8.6 1.0 OD1 A:ASP265 3.7 7.5 1.0 O A:HOH1086 4.3 20.3 1.0 O A:HOH743 4.3 19.5 1.0 O A:HOH773 4.3 14.4 1.0 O A:HOH683 4.4 26.9 1.0 O A:HOH1155 4.5 20.3 1.0 O A:HOH1292 4.6 30.0 1.0 CB A:ASP265 4.6 6.1 1.0 CB A:ARG357 4.6 10.7 1.0 O A:HOH1103 4.8 11.8 1.0 CG A:ARG357 4.8 18.7 1.0 OD1 A:ASP467 4.9 16.6 1.0 NH2 A:ARG464 4.9 9.3 1.0

Calcium binding site 2 out of 2 in the Ydiu Complex with Ampnpp and MN2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Ydiu Complex with Ampnpp and MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca504 b:15.0 occ:1.00 OD2 B:ASP265 2.4 11.3 1.0 O B:HOH1197 2.4 28.0 1.0 O B:HOH1016 2.4 13.6 1.0 O B:HOH728 2.5 18.2 1.0 CG B:ASP265 3.4 12.9 1.0 OD1 B:ASP265 3.8 9.4 1.0 O B:HOH889 4.2 17.3 1.0 CB B:ARG357 4.5 11.0 1.0 O B:HOH1368 4.5 21.2 1.0 O B:HOH1409 4.6 36.8 1.0 CB B:ASP265 4.7 10.9 1.0 O B:ARG357 4.7 8.9 1.0 NH2 B:ARG464 4.9 10.3 1.0

B.Li, B.Li, Y.Yang, Y.Ma. N/A N/A.