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

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy