Calcium in PDB 7kii: Muscovy Duck Circovirus Rep Domain Complexed with A Single-Stranded Dna 10-Mer Comprising the Cleavage Site and MN2+

The structure of Muscovy Duck Circovirus Rep Domain Complexed with A Single-Stranded Dna 10-Mer Comprising the Cleavage Site and MN2+, PDB code: 7kii was solved by K.J.Tompkins, W.R.Gordon, K.Shi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.56 / 1.30
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	55.417, 66.343, 71.259, 90, 90, 90
R / Rfree (%)	14.9 / 18.4

The structure of Muscovy Duck Circovirus Rep Domain Complexed with A Single-Stranded Dna 10-Mer Comprising the Cleavage Site and MN2+ also contains other interesting chemical elements:

Manganese

(Mn)

1 atom

The binding sites of Calcium atom in the Muscovy Duck Circovirus Rep Domain Complexed with A Single-Stranded Dna 10-Mer Comprising the Cleavage Site and MN2+ (pdb code 7kii). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Muscovy Duck Circovirus Rep Domain Complexed with A Single-Stranded Dna 10-Mer Comprising the Cleavage Site and MN2+, PDB code: 7kii:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Muscovy Duck Circovirus Rep Domain Complexed with A Single-Stranded Dna 10-Mer Comprising the Cleavage Site and MN2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Muscovy Duck Circovirus Rep Domain Complexed with A Single-Stranded Dna 10-Mer Comprising the Cleavage Site and MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:25.5 occ:1.00 N A:LYS10 3.1 16.9 1.0 O A:HOH425 3.2 27.1 1.0 O A:HOH369 3.3 24.8 1.0 N A:ARG11 3.3 15.9 1.0 O A:HOH355 3.7 21.3 1.0 CA A:LYS10 3.8 16.4 1.0 CB A:TYR9 3.9 17.9 1.0 CB A:LYS10 3.9 17.9 1.0 CA A:TYR9 4.0 17.5 1.0 CG A:ARG11 4.0 18.2 1.0 CB A:ARG11 4.0 17.2 1.0 C A:TYR9 4.0 17.2 1.0 CD1 A:TYR9 4.0 20.1 1.0 C A:LYS10 4.1 16.6 1.0 CA A:ARG11 4.2 15.7 1.0 CG A:TYR9 4.5 18.1 1.0 CD A:ARG11 4.5 19.2 1.0 O A:ARG11 4.7 16.2 1.0 O A:HOH357 4.7 22.1 1.0 CG A:LYS10 4.7 18.8 1.0 C A:ARG11 5.0 16.1 1.0

Calcium binding site 2 out of 2 in the Muscovy Duck Circovirus Rep Domain Complexed with A Single-Stranded Dna 10-Mer Comprising the Cleavage Site and MN2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Muscovy Duck Circovirus Rep Domain Complexed with A Single-Stranded Dna 10-Mer Comprising the Cleavage Site and MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca203 b:43.8 occ:0.50 O A:HOH343 3.0 26.9 1.0 N A:GLU22 3.4 20.5 1.0 N A:PHE21 3.6 19.3 1.0 CB A:PHE21 3.6 22.8 1.0 CB A:THR20 3.8 19.7 1.0 CB A:GLU22 4.0 27.3 1.0 OG1 A:THR20 4.0 19.7 1.0 CA A:PHE21 4.0 20.4 1.0 C A:PHE21 4.1 19.9 1.0 CA A:GLU22 4.3 22.2 1.0 C A:THR20 4.4 18.1 1.0 CA A:THR20 4.6 18.3 1.0 O A:HOH330 4.7 32.6 1.0 CG A:PHE21 4.7 26.1 1.0 CG2 A:THR20 4.8 20.4 1.0 CD1 A:PHE21 4.8 27.7 1.0 OE1 A:GLU22 5.0 37.5 1.0

K.Tompkins, K.J.Tompkins, W.R.Gordon, K.Shi. N/A N/A.