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Calcium in PDB 5ihd: Calcium(II) and Copper(II) Bound to the Z-Dna Form of D(Cgcgcg), Complexed By L-Lactate and Succinate

Protein crystallography data

The structure of Calcium(II) and Copper(II) Bound to the Z-Dna Form of D(Cgcgcg), Complexed By L-Lactate and Succinate, PDB code: 5ihd was solved by M.Rohner, A.Medina-Molner, B.Spingler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.22 / 1.57
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 27.487, 35.576, 31.044, 90.00, 107.50, 90.00
R / Rfree (%) 16.1 / 19

Other elements in 5ihd:

The structure of Calcium(II) and Copper(II) Bound to the Z-Dna Form of D(Cgcgcg), Complexed By L-Lactate and Succinate also contains other interesting chemical elements:

Copper (Cu) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Calcium(II) and Copper(II) Bound to the Z-Dna Form of D(Cgcgcg), Complexed By L-Lactate and Succinate (pdb code 5ihd). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Calcium(II) and Copper(II) Bound to the Z-Dna Form of D(Cgcgcg), Complexed By L-Lactate and Succinate, PDB code: 5ihd:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 5ihd

Go back to Calcium Binding Sites List in 5ihd
Calcium binding site 1 out of 2 in the Calcium(II) and Copper(II) Bound to the Z-Dna Form of D(Cgcgcg), Complexed By L-Lactate and Succinate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Calcium(II) and Copper(II) Bound to the Z-Dna Form of D(Cgcgcg), Complexed By L-Lactate and Succinate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca102

b:14.5
occ:1.00
OP1 A:DG2 2.3 18.1 1.0
O A:HOH222 2.4 16.6 1.0
P A:DG2 3.6 16.2 1.0
C3' A:DC1 4.1 13.9 1.0
O A:HOH214 4.2 28.1 1.0
O3' A:DC1 4.2 16.7 1.0
OP2 A:DG2 4.4 18.4 1.0
O5' A:DC1 4.7 27.0 1.0
O5' A:DG2 4.8 17.0 1.0
C2' A:DC1 5.0 14.3 1.0

Calcium binding site 2 out of 2 in 5ihd

Go back to Calcium Binding Sites List in 5ihd
Calcium binding site 2 out of 2 in the Calcium(II) and Copper(II) Bound to the Z-Dna Form of D(Cgcgcg), Complexed By L-Lactate and Succinate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Calcium(II) and Copper(II) Bound to the Z-Dna Form of D(Cgcgcg), Complexed By L-Lactate and Succinate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca102

b:19.1
occ:1.00
OP1 C:DG2 2.3 12.3 1.0
O C:HOH218 2.5 24.7 1.0
O C:HOH220 2.5 24.1 1.0
P C:DG2 3.7 11.5 1.0
O5' C:DC1 4.3 12.9 0.5
O C:HOH207 4.3 17.9 1.0
O5' C:DG2 4.5 11.9 1.0
C3' C:DC1 4.5 12.0 1.0
O C:HOH223 4.6 32.2 1.0
O3' C:DC1 4.6 10.4 1.0
OP2 C:DG2 4.6 12.3 1.0
O C:HOH210 4.7 21.4 1.0

Reference:

M.Rohner, A.Medina-Molner, B.Spingler. N,N,O and N,O,N Meridional Cis Coordination of Two Guanines to Copper(II) By D(Cgcgcg)2. Inorg.Chem. V. 55 6130 2016.
ISSN: ISSN 0020-1669
PubMed: 27266259
DOI: 10.1021/ACS.INORGCHEM.6B00672
Page generated: Sat Dec 12 05:30:25 2020

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