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Copper in PDB 5g3b: Preserving Metallic Sites Affected By Radiation Damage: the CUT2 Case in Thermus Thermophilus Multicopper Oxidase

Enzymatic activity of Preserving Metallic Sites Affected By Radiation Damage: the CUT2 Case in Thermus Thermophilus Multicopper Oxidase

All present enzymatic activity of Preserving Metallic Sites Affected By Radiation Damage: the CUT2 Case in Thermus Thermophilus Multicopper Oxidase:
1.10.3.2;

Protein crystallography data

The structure of Preserving Metallic Sites Affected By Radiation Damage: the CUT2 Case in Thermus Thermophilus Multicopper Oxidase, PDB code: 5g3b was solved by R.R.Ruiz-Arellano, A.Diaz, E.Rosas, E.Rudino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.69 / 1.69
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 93.744, 110.332, 96.484, 90.00, 90.00, 90.00
R / Rfree (%) 13.9 / 17.9

Other elements in 5g3b:

The structure of Preserving Metallic Sites Affected By Radiation Damage: the CUT2 Case in Thermus Thermophilus Multicopper Oxidase also contains other interesting chemical elements:

Sodium (Na) 1 atom

Copper Binding Sites:

The binding sites of Copper atom in the Preserving Metallic Sites Affected By Radiation Damage: the CUT2 Case in Thermus Thermophilus Multicopper Oxidase (pdb code 5g3b). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 3 binding sites of Copper where determined in the Preserving Metallic Sites Affected By Radiation Damage: the CUT2 Case in Thermus Thermophilus Multicopper Oxidase, PDB code: 5g3b:
Jump to Copper binding site number: 1; 2; 3;

Copper binding site 1 out of 3 in 5g3b

Go back to Copper Binding Sites List in 5g3b
Copper binding site 1 out of 3 in the Preserving Metallic Sites Affected By Radiation Damage: the CUT2 Case in Thermus Thermophilus Multicopper Oxidase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Preserving Metallic Sites Affected By Radiation Damage: the CUT2 Case in Thermus Thermophilus Multicopper Oxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1470

b:14.3
occ:0.26
NE2 A:HIS398 1.7 7.7 1.0
NE2 A:HIS444 1.8 10.1 1.0
CE1 A:HIS398 2.6 6.6 1.0
CD2 A:HIS444 2.7 7.9 1.0
CE1 A:HIS137 2.8 16.7 1.0
ND1 A:HIS137 2.8 16.2 1.0
CD2 A:HIS398 2.8 7.5 1.0
CE1 A:HIS444 2.9 8.2 1.0
CD2 A:HIS95 3.5 10.7 1.0
CD2 A:HIS396 3.6 7.9 1.0
NE2 A:HIS95 3.7 10.5 1.0
ND1 A:HIS398 3.8 7.1 1.0
O A:HOH2251 3.8 16.6 1.0
NE2 A:HIS137 3.8 22.5 1.0
CG A:HIS398 3.9 5.9 1.0
CG A:HIS137 3.9 13.2 1.0
CG A:HIS444 3.9 8.6 1.0
ND1 A:HIS444 3.9 7.2 1.0
NE2 A:HIS396 4.1 7.5 1.0
CG A:HIS95 4.2 8.8 1.0
CD2 A:HIS137 4.4 17.0 1.0
CE1 A:HIS95 4.4 10.8 1.0
CG2 A:VAL442 4.4 8.2 1.0
ND1 A:HIS95 4.7 8.9 1.0
OE1 A:GLU451 4.7 6.8 0.4
CB A:HIS137 4.8 10.3 1.0
CG A:HIS396 4.9 5.9 1.0
CD A:GLU451 4.9 7.1 0.4
OE2 A:GLU451 4.9 15.4 0.4
CB A:HIS95 5.0 11.2 1.0

Copper binding site 2 out of 3 in 5g3b

Go back to Copper Binding Sites List in 5g3b
Copper binding site 2 out of 3 in the Preserving Metallic Sites Affected By Radiation Damage: the CUT2 Case in Thermus Thermophilus Multicopper Oxidase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Preserving Metallic Sites Affected By Radiation Damage: the CUT2 Case in Thermus Thermophilus Multicopper Oxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1471

b:9.8
occ:0.84
ND1 A:HIS393 2.1 7.8 1.0
ND1 A:HIS450 2.1 8.2 1.0
SG A:CYS445 2.1 8.7 1.0
CE1 A:HIS393 2.9 14.1 1.0
CE1 A:HIS450 3.1 11.3 1.0
CG A:HIS450 3.1 7.6 1.0
CG A:HIS393 3.2 8.5 1.0
CB A:CYS445 3.2 4.2 1.0
CB A:HIS450 3.4 5.2 1.0
SD A:MET455 3.4 4.5 0.4
CB A:HIS393 3.7 10.6 1.0
SD A:MET455 3.8 13.4 0.6
CB A:ILE447 3.9 3.3 1.0
CD1 A:ILE447 4.0 8.3 1.0
CE A:MET455 4.0 15.1 0.4
CA A:HIS393 4.0 8.1 1.0
NE2 A:HIS393 4.1 10.1 1.0
NE2 A:HIS450 4.2 6.4 1.0
CD2 A:HIS450 4.2 8.2 1.0
CD2 A:HIS393 4.3 7.1 1.0
CG1 A:ILE447 4.4 6.6 1.0
O A:ASP392 4.5 7.0 1.0
CE A:MET455 4.5 5.5 0.6
CD A:PRO394 4.5 3.5 1.0
CA A:CYS445 4.6 4.0 1.0
N A:ILE447 4.7 6.3 1.0
O A:ILE447 4.7 5.8 1.0
CG2 A:ILE447 4.8 6.0 1.0
CA A:ILE447 4.9 6.3 1.0
CA A:HIS450 4.9 6.7 1.0
C A:HIS393 5.0 6.8 1.0
CG A:MET455 5.0 9.9 0.4

Copper binding site 3 out of 3 in 5g3b

Go back to Copper Binding Sites List in 5g3b
Copper binding site 3 out of 3 in the Preserving Metallic Sites Affected By Radiation Damage: the CUT2 Case in Thermus Thermophilus Multicopper Oxidase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Preserving Metallic Sites Affected By Radiation Damage: the CUT2 Case in Thermus Thermophilus Multicopper Oxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1472

b:8.8
occ:0.99
ND1 A:HIS97 2.0 6.9 1.0
NE2 A:HIS135 2.0 7.4 1.0
NE2 A:HIS446 2.1 5.5 1.0
CE1 A:HIS97 2.9 5.8 1.0
CE1 A:HIS446 2.9 5.8 1.0
CD2 A:HIS135 2.9 7.0 1.0
CE1 A:HIS135 3.0 8.0 1.0
CG A:HIS97 3.0 6.5 1.0
CD2 A:HIS446 3.2 7.7 1.0
CB A:HIS97 3.4 4.8 1.0
CZ2 A:TRP133 3.5 6.4 1.0
CD2 A:HIS95 3.7 10.7 1.0
CE2 A:TRP133 3.8 5.4 1.0
NE1 A:TRP133 4.0 4.4 1.0
NE2 A:HIS97 4.0 5.8 1.0
ND1 A:HIS135 4.1 6.7 1.0
CG A:HIS135 4.1 6.3 1.0
ND1 A:HIS446 4.1 5.4 1.0
CD2 A:HIS97 4.1 7.3 1.0
NE2 A:HIS95 4.2 10.5 1.0
CG A:HIS446 4.2 4.7 1.0
CH2 A:TRP133 4.3 4.4 1.0
NE2 A:HIS396 4.3 7.5 1.0
CD2 A:HIS396 4.4 7.9 1.0
CA A:HIS97 4.7 7.5 1.0
CD2 A:TRP133 4.8 4.6 1.0
CG A:HIS95 4.8 8.8 1.0
CD1 A:TRP133 5.0 3.7 1.0

Reference:

R.Ruiz-Arellano, A.Diaz, E.Rosas, V.Stojanoff, E.Rudino. Preserving Metallic Sites Affected By Radiation Damage the CUT2 Case in Thermus Thermophilus Multicopper Oxidase To Be Published.
Page generated: Sun Dec 13 11:17:38 2020

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