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Copper in PDB 2qpd: An Unexpected Outcome of Surface-Engineering An Integral Membrane Protein: Improved Crystallization of Cytochrome BA3 Oxidase From Thermus Thermophilus

Enzymatic activity of An Unexpected Outcome of Surface-Engineering An Integral Membrane Protein: Improved Crystallization of Cytochrome BA3 Oxidase From Thermus Thermophilus

All present enzymatic activity of An Unexpected Outcome of Surface-Engineering An Integral Membrane Protein: Improved Crystallization of Cytochrome BA3 Oxidase From Thermus Thermophilus:
1.9.3.1;

Protein crystallography data

The structure of An Unexpected Outcome of Surface-Engineering An Integral Membrane Protein: Improved Crystallization of Cytochrome BA3 Oxidase From Thermus Thermophilus, PDB code: 2qpd was solved by B.Liu, V.M.Luna, Y.Chen, C.D.Stout, J.A.Fee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.98 / 3.25
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 115.190, 115.190, 149.140, 90.00, 90.00, 90.00
R / Rfree (%) 21.5 / 30.7

Other elements in 2qpd:

The structure of An Unexpected Outcome of Surface-Engineering An Integral Membrane Protein: Improved Crystallization of Cytochrome BA3 Oxidase From Thermus Thermophilus also contains other interesting chemical elements:

Iron (Fe) 2 atoms

Copper Binding Sites:

The binding sites of Copper atom in the An Unexpected Outcome of Surface-Engineering An Integral Membrane Protein: Improved Crystallization of Cytochrome BA3 Oxidase From Thermus Thermophilus (pdb code 2qpd). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 3 binding sites of Copper where determined in the An Unexpected Outcome of Surface-Engineering An Integral Membrane Protein: Improved Crystallization of Cytochrome BA3 Oxidase From Thermus Thermophilus, PDB code: 2qpd:
Jump to Copper binding site number: 1; 2; 3;

Copper binding site 1 out of 3 in 2qpd

Go back to Copper Binding Sites List in 2qpd
Copper binding site 1 out of 3 in the An Unexpected Outcome of Surface-Engineering An Integral Membrane Protein: Improved Crystallization of Cytochrome BA3 Oxidase From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of An Unexpected Outcome of Surface-Engineering An Integral Membrane Protein: Improved Crystallization of Cytochrome BA3 Oxidase From Thermus Thermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu803

b:83.6
occ:1.00
 ND1 A:HIS233 1.9 43.4 1.0
NE2 A:HIS283 2.1 25.4 1.0
CE1 A:HIS233 2.3 46.5 1.0
NE2 A:HIS282 2.3 18.5 1.0
CE1 A:HIS283 3.0 37.2 1.0
CE1 A:HIS282 3.0 25.3 1.0
CG A:HIS233 3.0 50.8 1.0
CD2 A:HIS283 3.1 36.9 1.0
NE2 A:HIS233 3.4 27.4 1.0
CD2 A:HIS282 3.5 26.0 1.0
CD2 A:HIS233 3.8 43.6 1.0
ND A:HAS801 3.8 69.0 1.0
CB A:HIS233 3.8 49.5 1.0
C1D A:HAS801 3.9 65.8 1.0
C4D A:HAS801 4.0 56.5 1.0
ND1 A:HIS283 4.1 35.3 1.0
CA A:HIS233 4.2 50.8 1.0
CG A:HIS283 4.2 33.5 1.0
ND1 A:HIS282 4.2 22.9 1.0
C2D A:HAS801 4.2 57.7 1.0
C3D A:HAS801 4.3 66.4 1.0
FE A:HAS801 4.4 56.6 1.0
CHB A:HAS801 4.4 63.6 1.0
CG A:HIS282 4.5 33.1 1.0
NA A:HAS801 4.6 50.9 1.0
C1B A:HAS801 4.6 68.4 1.0
CHA A:HAS801 4.6 61.2 1.0
C1A A:HAS801 4.7 55.2 1.0
NB A:HAS801 4.7 68.6 1.0
OMD A:HAS801 4.7 48.7 1.0
O A:HIS233 4.8 52.8 1.0
C A:HIS233 4.8 48.8 1.0
CE2 A:TYR237 4.8 34.4 1.0
CG2 A:VAL236 4.9 37.4 1.0

Copper binding site 2 out of 3 in 2qpd

Go back to Copper Binding Sites List in 2qpd
Copper binding site 2 out of 3 in the An Unexpected Outcome of Surface-Engineering An Integral Membrane Protein: Improved Crystallization of Cytochrome BA3 Oxidase From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of An Unexpected Outcome of Surface-Engineering An Integral Membrane Protein: Improved Crystallization of Cytochrome BA3 Oxidase From Thermus Thermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu802

b:52.5
occ:1.00
 CU1 B:CUA802 0.0 52.5 1.0
SG B:CYS153 2.3 8.6 1.0
SG B:CYS149 2.4 6.0 1.0
O B:GLN151 2.5 28.8 1.0
CU2 B:CUA802 2.6 50.0 1.0
ND1 B:HIS157 2.7 33.5 1.0
N B:CYS153 2.8 27.0 1.0
CE1 B:HIS157 3.0 19.2 1.0
CG B:HIS157 3.0 14.8 1.0
C B:GLN151 3.2 22.3 1.0
CB B:CYS153 3.2 17.6 1.0
NE2 B:HIS157 3.4 32.2 1.0
CD2 B:HIS157 3.5 31.0 1.0
CA B:CYS153 3.6 20.3 1.0
CB B:HIS157 3.7 14.7 1.0
O B:CYS149 3.7 21.2 1.0
CA B:HIS157 3.7 20.9 1.0
C B:TYR152 3.8 32.5 1.0
N B:TYR152 3.8 22.8 1.0
CA B:TYR152 3.8 27.0 1.0
CB B:CYS149 4.0 11.0 1.0
O B:HIS157 4.0 26.8 1.0
N B:GLN151 4.0 23.2 1.0
CA B:GLN151 4.2 20.6 1.0
C B:HIS157 4.2 25.5 1.0
CG B:MET160 4.2 26.6 1.0
CB B:MET160 4.4 34.9 1.0
C B:CYS149 4.4 16.3 1.0
SD B:MET160 4.5 37.4 1.0
ND1 B:HIS114 4.7 45.4 1.0
C B:CYS153 4.7 22.2 1.0
CA B:CYS149 4.9 7.2 1.0
O B:TYR152 5.0 38.8 1.0
N B:GLY154 5.0 25.7 1.0

Copper binding site 3 out of 3 in 2qpd

Go back to Copper Binding Sites List in 2qpd
Copper binding site 3 out of 3 in the An Unexpected Outcome of Surface-Engineering An Integral Membrane Protein: Improved Crystallization of Cytochrome BA3 Oxidase From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of An Unexpected Outcome of Surface-Engineering An Integral Membrane Protein: Improved Crystallization of Cytochrome BA3 Oxidase From Thermus Thermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu802

b:50.0
occ:1.00
 CU2 B:CUA802 0.0 50.0 1.0
ND1 B:HIS114 2.2 45.4 1.0
SG B:CYS153 2.4 8.6 1.0
SG B:CYS149 2.4 6.0 1.0
CB B:CYS153 2.5 17.6 1.0
CU1 B:CUA802 2.6 52.5 1.0
SD B:MET160 2.6 37.4 1.0
CG B:HIS114 3.0 43.8 1.0
CE B:MET160 3.2 34.0 1.0
CB B:HIS114 3.2 29.1 1.0
CG B:MET160 3.2 26.6 1.0
CE1 B:HIS114 3.3 44.6 1.0
O B:GLN151 3.5 28.8 1.0
CB B:CYS149 3.6 11.0 1.0
CA B:CYS153 3.7 20.3 1.0
CA B:HIS114 3.7 32.7 1.0
N B:CYS153 3.8 27.0 1.0
CB B:MET160 4.0 34.9 1.0
CD2 B:HIS114 4.2 48.8 1.0
NE2 B:HIS114 4.3 58.4 1.0
N B:GLY115 4.5 23.0 1.0
C B:GLN151 4.6 22.3 1.0
C B:HIS114 4.7 27.9 1.0
CD2 B:PHE88 4.7 29.6 1.0
N B:HIS114 4.8 39.0 1.0
CE2 B:PHE88 4.9 21.1 1.0
O B:ILE113 4.9 46.9 1.0
C B:CYS153 4.9 22.2 1.0
CA B:CYS149 5.0 7.2 1.0

Reference:

B.Liu, V.M.Luna, Y.Chen, C.D.Stout, J.A.Fee. An Unexpected Outcome of Surface Engineering An Integral Membrane Protein: Improved Crystallization of Cytochrome Ba(3) From Thermus Thermophilus. Acta Crystallogr.,Sect.F V. 63 1029 2007.
ISSN: ESSN 1744-3091
PubMed: 18084085
DOI: 10.1107/S1744309107054176
Page generated: Tue Jul 30 23:58:40 2024

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