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Copper in PDB 5hr3: Crystal Structure of Thioredoxin N106A Mutant

Protein crystallography data

The structure of Crystal Structure of Thioredoxin N106A Mutant, PDB code: 5hr3 was solved by M.E.Noguera, D.S.Vazquez, E.I.Howard, A.Cousido-Siah, A.Mitschler, A.Podjarny, J.Santos, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 16.23 / 1.10
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 29.238, 33.124, 47.185, 75.75, 88.85, 68.83
R / Rfree (%) 14.2 / 16.3

Copper Binding Sites:

The binding sites of Copper atom in the Crystal Structure of Thioredoxin N106A Mutant (pdb code 5hr3). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 3 binding sites of Copper where determined in the Crystal Structure of Thioredoxin N106A Mutant, PDB code: 5hr3:
Jump to Copper binding site number: 1; 2; 3;

Copper binding site 1 out of 3 in 5hr3

Go back to Copper Binding Sites List in 5hr3
Copper binding site 1 out of 3 in the Crystal Structure of Thioredoxin N106A Mutant


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 Thioredoxin N106A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu201

b:27.2
occ:0.52
O A:HOH324 1.8 30.0 1.0
O A:HOH367 2.7 33.2 1.0
CU A:CU202 2.7 37.0 0.6
N A:ASP2 3.0 38.6 1.0
O A:HOH305 4.0 33.9 1.0
OD1 A:ASP43 4.2 26.0 1.0
CG A:ASP43 4.4 23.1 1.0
CA A:ASP2 4.4 33.7 1.0
HB3 A:ASP43 4.4 23.4 1.0
HB3 A:ASP2 4.6 46.8 1.0
OD2 A:ASP43 4.6 28.5 1.0
HA A:ASP2 4.7 40.4 1.0
H A:LYS3 4.7 27.8 1.0
OD1 A:ASP2 4.7 57.6 1.0
CB A:ASP43 5.0 19.5 1.0

Copper binding site 2 out of 3 in 5hr3

Go back to Copper Binding Sites List in 5hr3
Copper binding site 2 out of 3 in the Crystal Structure of Thioredoxin N106A Mutant


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 Thioredoxin N106A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu202

b:37.0
occ:0.60
OD1 A:ASP2 2.0 57.6 1.0
N A:ASP2 2.1 38.6 1.0
CU A:CU201 2.7 27.2 0.5
HB3 A:ASP2 2.8 46.8 1.0
CG A:ASP2 2.8 42.7 1.0
CB A:ASP2 3.0 39.0 1.0
CA A:ASP2 3.0 33.7 1.0
H A:LYS3 3.4 27.8 1.0
O A:HOH324 3.5 30.0 1.0
HA A:ASP2 3.7 40.4 1.0
O A:HOH367 3.9 33.2 1.0
N A:LYS3 4.0 23.2 1.0
HB2 A:ASP2 4.0 46.8 1.0
C A:ASP2 4.0 28.7 1.0
OD2 A:ASP2 4.0 45.4 1.0
O A:HOH305 4.1 33.9 1.0
HG3 A:LYS3 4.2 39.3 1.0

Copper binding site 3 out of 3 in 5hr3

Go back to Copper Binding Sites List in 5hr3
Copper binding site 3 out of 3 in the Crystal Structure of Thioredoxin N106A Mutant


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Crystal Structure of Thioredoxin N106A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu202

b:25.6
occ:0.50
O B:HOH319 2.0 36.7 1.0
N B:ASP2 2.1 39.1 1.0
OD1 B:ASP2 2.4 77.7 1.0
O B:HOH353 2.5 28.2 1.0
HB3 B:ASP2 3.0 62.2 1.0
CA B:ASP2 3.2 38.2 1.0
CG B:ASP2 3.2 65.3 1.0
CB B:ASP2 3.3 51.8 1.0
H B:LYS3 3.5 38.0 1.0
HA B:ASP2 3.8 45.9 1.0
OD1 B:ASP43 4.0 22.8 1.0
O B:HOH301 4.1 33.3 1.0
CG B:ASP43 4.1 19.9 1.0
N B:LYS3 4.1 31.7 1.0
HB3 B:ASP43 4.2 22.6 1.0
C B:ASP2 4.2 38.5 1.0
HB2 B:ASP2 4.3 62.2 1.0
OD2 B:ASP2 4.4 80.3 1.0
OD2 B:ASP43 4.4 20.9 1.0
CB B:ASP43 4.7 18.9 1.0
HG3 B:LYS3 4.8 44.5 1.0

Reference:

M.E.Noguera, D.S.Vazquez, G.Ferrer-Sueta, W.A.Agudelo, E.Howard, R.M.Rasia, B.Manta, A.Cousido-Siah, A.Mitschler, A.Podjarny, J.Santos. Structural Variability of E. Coli Thioredoxin Captured in the Crystal Structures of Single-Point Mutants. Sci Rep V. 7 42343 2017.
ISSN: ESSN 2045-2322
PubMed: 28181556
DOI: 10.1038/SREP42343
Page generated: Sun Dec 13 11:17:46 2020

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