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Calcium in PDB 5hch: X-Ray Structure of A Lectin-Bound Dna Duplex Containing An Unnatural Phenanthrenyl Pair

Protein crystallography data

The structure of X-Ray Structure of A Lectin-Bound Dna Duplex Containing An Unnatural Phenanthrenyl Pair, PDB code: 5hch was solved by P.Roethlisberger, A.Istrate, M.J.Marcaida Lopez, R.Visini, A.Stocker, C.J.Leumann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.62 / 2.90
Space group P 62 2 2
Cell size a, b, c (Å), α, β, γ (°) 60.451, 60.451, 204.828, 90.00, 90.00, 120.00
R / Rfree (%) 22.7 / 25.7

Other elements in 5hch:

The structure of X-Ray Structure of A Lectin-Bound Dna Duplex Containing An Unnatural Phenanthrenyl Pair also contains other interesting chemical elements:

Sodium (Na) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the X-Ray Structure of A Lectin-Bound Dna Duplex Containing An Unnatural Phenanthrenyl Pair (pdb code 5hch). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the X-Ray Structure of A Lectin-Bound Dna Duplex Containing An Unnatural Phenanthrenyl Pair, PDB code: 5hch:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 5hch

Go back to Calcium Binding Sites List in 5hch
Calcium binding site 1 out of 2 in the X-Ray Structure of A Lectin-Bound Dna Duplex Containing An Unnatural Phenanthrenyl Pair


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of X-Ray Structure of A Lectin-Bound Dna Duplex Containing An Unnatural Phenanthrenyl Pair within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca201

b:61.0
occ:1.00
OE2 A:GLU95 2.2 52.0 1.0
O03 E:61J101 2.3 78.7 1.0
OD1 A:ASP99 2.5 77.9 1.0
OD1 A:ASP101 2.5 95.8 1.0
OE1 A:GLU95 2.5 90.5 1.0
CD A:GLU95 2.7 78.2 1.0
O04 E:61J101 2.7 80.4 1.0
OD2 A:ASP104 2.8 73.3 1.0
OD1 A:ASP104 2.9 69.9 1.0
C03 E:61J101 3.2 81.8 1.0
CG A:ASP101 3.2 94.2 1.0
CG A:ASP104 3.2 70.2 1.0
OD2 A:ASP101 3.3 0.4 1.0
C04 E:61J101 3.3 81.2 1.0
CG A:ASP99 3.6 78.5 1.0
CA A:CA202 3.8 64.3 1.0
OD2 A:ASP99 4.0 78.4 1.0
N A:ASP101 4.2 74.4 1.0
CG A:GLU95 4.2 64.3 1.0
OD1 A:ASP96 4.3 75.3 1.0
N A:GLY97 4.3 93.7 1.0
N A:TYR102 4.4 72.9 1.0
C02 E:61J101 4.5 83.3 1.0
CB A:ASP101 4.5 82.8 1.0
N A:ASN100 4.6 90.8 1.0
CA A:GLY97 4.6 92.7 1.0
CB A:ASP104 4.7 68.1 1.0
N A:ASP99 4.7 89.0 1.0
OD1 A:ASN103 4.7 77.8 1.0
O02 E:61J101 4.7 81.5 1.0
C05 E:61J101 4.8 85.0 1.0
N A:ASP96 4.8 75.2 1.0
CA A:ASP101 4.8 73.9 1.0
CB A:ASP99 4.9 98.6 1.0
N A:THR98 4.9 90.5 1.0
CA A:GLU95 5.0 54.5 1.0
C A:ASP99 5.0 89.9 1.0

Calcium binding site 2 out of 2 in 5hch

Go back to Calcium Binding Sites List in 5hch
Calcium binding site 2 out of 2 in the X-Ray Structure of A Lectin-Bound Dna Duplex Containing An Unnatural Phenanthrenyl Pair


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of X-Ray Structure of A Lectin-Bound Dna Duplex Containing An Unnatural Phenanthrenyl Pair within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca202

b:64.3
occ:1.00
O02 E:61J101 2.4 81.5 1.0
O A:ASN21 2.4 91.6 1.0
OD1 A:ASP104 2.4 69.9 1.0
O03 E:61J101 2.5 78.7 1.0
OD1 A:ASN103 2.6 77.8 1.0
OD2 A:ASP101 2.9 0.4 1.0
OD1 A:ASP101 3.3 95.8 1.0
C03 E:61J101 3.3 81.8 1.0
CG A:ASP101 3.4 94.2 1.0
C02 E:61J101 3.4 83.3 1.0
O A:HOH304 3.6 63.4 1.0
C A:ASN21 3.6 77.3 1.0
CG A:ASN103 3.6 68.1 1.0
CG A:ASP104 3.7 70.2 1.0
C04 E:61J101 3.7 81.2 1.0
CA A:CA201 3.8 61.0 1.0
ND2 A:ASN103 4.1 64.4 1.0
CB A:ASN21 4.1 72.0 1.0
N A:ASP104 4.2 65.4 1.0
CA A:ASP104 4.3 65.6 1.0
OD2 A:ASP104 4.5 73.3 1.0
O04 E:61J101 4.5 80.4 1.0
CB A:SER22 4.5 62.5 1.0
N A:SER22 4.5 78.1 1.0
CA A:ASN21 4.5 69.8 1.0
CA A:SER22 4.5 72.0 1.0
C01 E:61J101 4.6 87.1 1.0
CB A:ASP104 4.6 68.1 1.0
CB A:ASP101 4.7 82.8 1.0
C A:ASN103 4.7 69.5 1.0
OD2 A:ASP99 4.8 78.4 1.0
O01 E:61J101 4.8 86.4 1.0
C06 E:61J101 4.9 88.7 1.0
C05 E:61J101 4.9 85.0 1.0
CB A:ASN103 4.9 62.9 1.0
N A:ASN103 5.0 65.8 1.0

Reference:

P.Roethlisberger, A.Istrate, M.J.Marcaida Lopez, R.Visini, A.Stocker, J.L.Reymond, C.J.Leumann. X-Ray Structure of A Lectin-Bound Dna Duplex Containing An Unnatural Phenanthrenyl Pair. Chem.Commun.(Camb.) V. 52 4749 2016.
ISSN: ESSN 1364-548X
PubMed: 26898721
DOI: 10.1039/C6CC00374E
Page generated: Sat Dec 12 05:28:15 2020

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