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Copper in PDB 1jes: Crystal Structure of A Copper-Mediated Base Pair in Dna

Protein crystallography data

The structure of Crystal Structure of A Copper-Mediated Base Pair in Dna, PDB code: 1jes was solved by S.Atwell, E.Meggers, G.Spraggon, P.G.Schultz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 25.343, 34.359, 31.093, 90.00, 101.13, 90.00
R / Rfree (%) 16.9 / 20.2

Copper Binding Sites:

The binding sites of Copper atom in the Crystal Structure of A Copper-Mediated Base Pair in Dna (pdb code 1jes). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 2 binding sites of Copper where determined in the Crystal Structure of A Copper-Mediated Base Pair in Dna, PDB code: 1jes:
Jump to Copper binding site number: 1; 2;

Copper binding site 1 out of 2 in 1jes

Go back to Copper Binding Sites List in 1jes
Copper binding site 1 out of 2 in the Crystal Structure of A Copper-Mediated Base Pair in Dna


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Crystal Structure of A Copper-Mediated Base Pair in Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu25

b:12.6
occ:1.00
N3 B:DRP20 1.9 11.1 1.0
N3 A:DPY5 1.9 7.5 1.0
O72 A:DPY5 2.3 19.0 1.0
O82 A:DPY5 2.3 13.2 1.0
C4 B:DRP20 2.7 12.4 1.0
C4 A:DPY5 2.7 9.4 1.0
C2 A:DPY5 2.8 8.9 1.0
C2 B:DRP20 2.9 16.2 1.0
C8 A:DPY5 3.0 11.7 1.0
C7 A:DPY5 3.0 16.0 1.0
O4' B:DT19 3.0 19.8 1.0
O6 A:DG4 3.1 12.6 1.0
C6 A:DG4 3.4 9.1 1.0
N1 A:DG4 3.7 9.3 1.0
N1 B:DT19 3.8 12.2 1.0
C1' B:DT19 3.8 14.3 1.0
C6 B:DT19 3.9 13.7 1.0
C5 A:DPY5 4.1 9.8 1.0
C5 B:DRP20 4.1 14.7 1.0
C4' B:DT19 4.1 19.9 1.0
C5 A:DG4 4.1 8.6 1.0
C1 A:DPY5 4.1 7.6 1.0
O71 A:DPY5 4.2 20.0 1.0
C1 B:DRP20 4.2 15.8 1.0
O81 A:DPY5 4.2 14.8 1.0
N4 B:DC21 4.3 9.5 1.0
C2 B:DT19 4.4 10.8 1.0
O B:HOH82 4.4 32.8 1.0
N3 B:DC21 4.4 9.0 1.0
C5 B:DT19 4.5 13.0 1.0
C5' B:DT19 4.6 23.1 1.0
C6 A:DPY5 4.6 10.6 1.0
C6 B:DRP20 4.6 16.5 1.0
C4 B:DC21 4.7 7.5 1.0
N7 A:DG4 4.7 9.3 1.0
C2 A:DG4 4.7 8.0 1.0
O A:HOH98 4.9 30.7 1.0
O2 B:DT19 4.9 13.3 1.0
N3 B:DT19 5.0 11.5 1.0
O A:HOH29 5.0 31.1 1.0
C4 A:DG4 5.0 10.3 1.0

Copper binding site 2 out of 2 in 1jes

Go back to Copper Binding Sites List in 1jes
Copper binding site 2 out of 2 in the Crystal Structure of A Copper-Mediated Base Pair in Dna


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Crystal Structure of A Copper-Mediated Base Pair in Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu26

b:13.2
occ:1.00
N3 A:DRP8 1.9 10.9 1.0
N3 B:DPY17 1.9 9.8 1.0
O72 B:DPY17 2.2 20.7 1.0
O82 B:DPY17 2.3 12.9 1.0
C4 A:DRP8 2.7 18.4 1.0
C4 B:DPY17 2.8 9.2 1.0
C2 B:DPY17 2.8 9.7 1.0
C2 A:DRP8 2.8 15.8 1.0
C8 B:DPY17 2.9 13.6 1.0
C7 B:DPY17 2.9 15.3 1.0
O4' A:DT7 3.2 16.0 1.0
O6 B:DG16 3.2 14.7 1.0
C6 B:DG16 3.4 10.4 1.0
N1 A:DT7 3.8 13.3 1.0
C6 A:DT7 3.8 10.0 1.0
N1 B:DG16 3.9 11.3 1.0
C1' A:DT7 3.9 11.4 1.0
C5 B:DG16 4.0 10.9 1.0
C5 A:DRP8 4.1 20.7 1.0
C5 B:DPY17 4.1 11.3 1.0
O71 B:DPY17 4.1 18.9 1.0
C1 B:DPY17 4.1 8.7 1.0
C1 A:DRP8 4.1 17.4 1.0
O81 B:DPY17 4.1 13.9 1.0
O B:HOH62 4.3 29.0 1.0
C4' A:DT7 4.3 16.4 1.0
C2 A:DT7 4.3 11.4 1.0
C5 A:DT7 4.4 9.1 1.0
N7 B:DG16 4.5 13.2 1.0
N4 A:DC9 4.6 14.5 1.0
C6 A:DRP8 4.6 16.9 1.0
C6 B:DPY17 4.6 11.8 1.0
C5' A:DT7 4.7 16.5 1.0
O B:HOH76 4.7 31.4 1.0
N3 A:DC9 4.7 11.1 1.0
C2 B:DG16 4.8 10.2 1.0
N3 A:DT7 4.8 10.2 1.0
C4 B:DG16 4.9 10.2 1.0
O2 A:DT7 4.9 14.7 1.0
C4 A:DT7 4.9 9.9 1.0

Reference:

S.Atwell, E.Meggers, G.Spraggon, P.G.Schultz. Structure of A Copper-Mediated Base Pair in Dna J.Am.Chem.Soc. V. 123 12364 2001.
ISSN: ISSN 0002-7863
PubMed: 11734038
DOI: 10.1021/JA011822E
Page generated: Wed Oct 28 14:15:05 2020
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