Atomistry » Calcium » PDB 5i77-5ik8 » 5ihd
Atomistry »
  Calcium »
    PDB 5i77-5ik8 »
      5ihd »

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: Sun Jul 14 20:32:06 2024

Last articles

Ca in 3CZT
Ca in 3CVG
Ca in 3CV1
Ca in 3CU2
Ca in 3CU9
Ca in 3CTN
Ca in 3CTZ
Ca in 3CSI
Ca in 3CQO
Ca in 3CSU
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy