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Copper in PDB 3uad: Multicopper Oxidase Cueo Mutant C500SE506Q (DATA5)

Protein crystallography data

The structure of Multicopper Oxidase Cueo Mutant C500SE506Q (DATA5), PDB code: 3uad was solved by H.Komori, K.Kataoka, T.Sakurai, Y.Higuchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.477, 91.186, 53.314, 90.00, 102.91, 90.00
R / Rfree (%) 13 / n/a

Copper Binding Sites:

The binding sites of Copper atom in the Multicopper Oxidase Cueo Mutant C500SE506Q (DATA5) (pdb code 3uad). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 5 binding sites of Copper where determined in the Multicopper Oxidase Cueo Mutant C500SE506Q (DATA5), PDB code: 3uad:
Jump to Copper binding site number: 1; 2; 3; 4; 5;

Copper binding site 1 out of 5 in 3uad

Go back to Copper Binding Sites List in 3uad
Copper binding site 1 out of 5 in the Multicopper Oxidase Cueo Mutant C500SE506Q (DATA5)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Multicopper Oxidase Cueo Mutant C500SE506Q (DATA5) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1002

b:14.2
occ:0.42
CU A:CU1002 0.0 14.2 0.4
CU A:CU1002 1.0 5.9 0.5
O A:O1005 2.1 21.3 0.4
O A:O1005 2.1 21.5 0.5
NE2 A:HIS501 2.1 9.3 1.0
ND1 A:HIS103 2.1 8.3 1.0
O A:O1006 2.2 14.5 0.5
NE2 A:HIS141 2.3 9.4 1.0
CD2 A:HIS501 2.9 8.9 1.0
CE1 A:HIS103 3.0 8.5 1.0
CE1 A:HIS141 3.0 10.2 1.0
CG A:HIS103 3.2 7.4 1.0
CE1 A:HIS501 3.3 9.2 1.0
CU A:CU1003 3.4 11.9 0.5
CD2 A:HIS141 3.5 9.3 1.0
CB A:HIS103 3.6 8.0 1.0
CU A:CU1004 3.8 10.4 0.8
O A:HOH2001 3.8 23.3 1.0
CD2 A:HIS446 3.9 9.3 1.0
NE2 A:HIS446 4.0 9.9 1.0
CD2 A:HIS101 4.0 10.3 1.0
NE2 A:HIS103 4.1 8.0 1.0
CU A:CU1003 4.2 8.8 0.4
CG A:HIS501 4.2 7.8 1.0
CD2 A:HIS103 4.2 8.0 1.0
ND1 A:HIS501 4.3 9.4 1.0
ND1 A:HIS141 4.3 8.9 1.0
NE2 A:HIS101 4.3 10.4 1.0
CZ2 A:TRP139 4.4 8.1 1.0
CE1 A:HIS499 4.5 13.3 1.0
CG A:HIS141 4.6 8.7 1.0
NE2 A:HIS499 4.6 10.4 1.0
CG A:HIS446 4.7 8.9 1.0
CA A:HIS103 4.7 7.5 1.0
CE2 A:TRP139 4.8 7.8 1.0
NE1 A:TRP139 4.8 7.6 1.0
NE2 A:HIS143 4.9 11.1 1.0
CE1 A:HIS446 4.9 9.5 1.0

Copper binding site 2 out of 5 in 3uad

Go back to Copper Binding Sites List in 3uad
Copper binding site 2 out of 5 in the Multicopper Oxidase Cueo Mutant C500SE506Q (DATA5)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Multicopper Oxidase Cueo Mutant C500SE506Q (DATA5) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1002

b:5.9
occ:0.48
CU A:CU1002 0.0 5.9 0.5
CU A:CU1002 1.0 14.2 0.4
ND1 A:HIS103 1.9 8.3 1.0
NE2 A:HIS141 1.9 9.4 1.0
NE2 A:HIS501 2.1 9.3 1.0
CD2 A:HIS141 2.9 9.3 1.0
CE1 A:HIS103 2.9 8.5 1.0
CG A:HIS103 3.0 7.4 1.0
CE1 A:HIS501 3.0 9.2 1.0
CE1 A:HIS141 3.0 10.2 1.0
O A:O1005 3.0 21.5 0.5
O A:O1005 3.0 21.3 0.4
O A:O1006 3.1 14.5 0.5
CD2 A:HIS501 3.2 8.9 1.0
CB A:HIS103 3.3 8.0 1.0
CZ2 A:TRP139 3.4 8.1 1.0
CE2 A:TRP139 3.8 7.8 1.0
NE1 A:TRP139 3.9 7.6 1.0
NE2 A:HIS103 4.0 8.0 1.0
CD2 A:HIS103 4.0 8.0 1.0
CG A:HIS141 4.0 8.7 1.0
ND1 A:HIS141 4.1 8.9 1.0
ND1 A:HIS501 4.1 9.4 1.0
CH2 A:TRP139 4.2 8.5 1.0
CG A:HIS501 4.3 7.8 1.0
O A:HOH2001 4.3 23.3 1.0
CU A:CU1003 4.4 11.9 0.5
CD2 A:HIS101 4.4 10.3 1.0
CU A:CU1004 4.5 10.4 0.8
NE2 A:HIS446 4.7 9.9 1.0
CD2 A:HIS446 4.7 9.3 1.0
CA A:HIS103 4.7 7.5 1.0
CD2 A:TRP139 4.8 7.4 1.0
NE2 A:HIS101 4.9 10.4 1.0
CD1 A:TRP139 4.9 7.3 1.0

Copper binding site 3 out of 5 in 3uad

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Copper binding site 3 out of 5 in the Multicopper Oxidase Cueo Mutant C500SE506Q (DATA5)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Multicopper Oxidase Cueo Mutant C500SE506Q (DATA5) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1003

b:11.9
occ:0.46
CU A:CU1003 0.0 11.9 0.5
CU A:CU1003 0.8 8.8 0.4
O A:O1005 1.5 21.3 0.4
O A:O1005 1.7 21.5 0.5
O A:O1006 2.1 14.5 0.5
NE2 A:HIS448 2.1 10.3 1.0
NE2 A:HIS143 2.2 11.1 1.0
NE2 A:HIS499 2.2 10.4 1.0
CE1 A:HIS499 3.0 13.3 1.0
CD2 A:HIS143 3.1 10.3 1.0
CE1 A:HIS448 3.1 10.9 1.0
CD2 A:HIS448 3.2 10.1 1.0
CE1 A:HIS143 3.2 11.5 1.0
CD2 A:HIS499 3.3 11.6 1.0
CU A:CU1002 3.4 14.2 0.4
O A:HOH2001 3.4 23.3 1.0
CD2 A:HIS446 3.6 9.3 1.0
CU A:CU1004 3.6 10.4 0.8
CD2 A:HIS101 3.8 10.3 1.0
NE2 A:HIS101 3.8 10.4 1.0
NE2 A:HIS446 3.9 9.9 1.0
ND1 A:HIS448 4.2 11.1 1.0
ND1 A:HIS499 4.2 14.3 1.0
CG A:HIS143 4.3 9.4 1.0
CG A:HIS448 4.3 10.4 1.0
ND1 A:HIS143 4.3 10.9 1.0
CU A:CU1002 4.4 5.9 0.5
CE1 A:HIS141 4.4 10.2 1.0
CG A:HIS499 4.4 9.8 1.0
CG A:HIS101 4.6 9.5 1.0
NE2 A:HIS501 4.6 9.3 1.0
CE1 A:HIS101 4.7 10.3 1.0
NE2 A:HIS141 4.7 9.4 1.0
CD2 A:HIS501 4.7 8.9 1.0
CG A:HIS446 4.8 8.9 1.0
OE1 A:GLN506 4.9 18.4 1.0
CB A:MET497 5.0 11.1 1.0

Copper binding site 4 out of 5 in 3uad

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Copper binding site 4 out of 5 in the Multicopper Oxidase Cueo Mutant C500SE506Q (DATA5)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Multicopper Oxidase Cueo Mutant C500SE506Q (DATA5) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1003

b:8.8
occ:0.44
CU A:CU1003 0.0 8.8 0.4
CU A:CU1003 0.8 11.9 0.5
NE2 A:HIS448 1.8 10.3 1.0
NE2 A:HIS499 1.9 10.4 1.0
NE2 A:HIS143 2.0 11.1 1.0
O A:O1005 2.2 21.3 0.4
O A:O1005 2.4 21.5 0.5
CD2 A:HIS499 2.7 11.6 1.0
CE1 A:HIS448 2.8 10.9 1.0
O A:O1006 2.9 14.5 0.5
CE1 A:HIS143 2.9 11.5 1.0
CD2 A:HIS448 2.9 10.1 1.0
CE1 A:HIS499 2.9 13.3 1.0
CD2 A:HIS143 3.1 10.3 1.0
O A:HOH2001 3.7 23.3 1.0
CD2 A:HIS446 3.8 9.3 1.0
CG A:HIS499 3.9 9.8 1.0
ND1 A:HIS448 3.9 11.1 1.0
ND1 A:HIS499 4.0 14.3 1.0
CG A:HIS448 4.0 10.4 1.0
ND1 A:HIS143 4.1 10.9 1.0
CU A:CU1004 4.1 10.4 0.8
CU A:CU1002 4.2 14.2 0.4
CB A:MET497 4.2 11.1 1.0
CG A:HIS143 4.2 9.4 1.0
NE2 A:HIS101 4.3 10.4 1.0
CD2 A:HIS101 4.3 10.3 1.0
NE2 A:HIS446 4.3 9.9 1.0
CG A:MET497 4.7 11.5 1.0
OE1 A:GLN506 4.8 18.4 1.0
CE1 A:HIS101 5.0 10.3 1.0
CG A:HIS101 5.0 9.5 1.0

Copper binding site 5 out of 5 in 3uad

Go back to Copper Binding Sites List in 3uad
Copper binding site 5 out of 5 in the Multicopper Oxidase Cueo Mutant C500SE506Q (DATA5)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Multicopper Oxidase Cueo Mutant C500SE506Q (DATA5) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1004

b:10.4
occ:0.80
NE2 A:HIS446 1.9 9.9 1.0
NE2 A:HIS101 2.0 10.4 1.0
O A:O1006 2.0 14.5 0.5
OXT A:ACT1007 2.2 14.8 0.5
O A:HOH2002 2.3 13.9 0.5
CE1 A:HIS101 2.9 10.3 1.0
CE1 A:HIS446 2.9 9.5 1.0
CD2 A:HIS446 3.0 9.3 1.0
CD2 A:HIS101 3.0 10.3 1.0
CD2 A:HIS448 3.2 10.1 1.0
C A:ACT1007 3.2 13.3 0.5
NE2 A:HIS448 3.3 10.3 1.0
O A:ACT1007 3.5 11.9 0.5
CA A:HIS103 3.6 7.5 1.0
CG A:HIS103 3.6 7.4 1.0
CU A:CU1003 3.6 11.9 0.5
CG A:HIS448 3.7 10.4 1.0
O A:O1005 3.8 21.3 0.4
ND1 A:HIS103 3.8 8.3 1.0
CB A:HIS103 3.8 8.0 1.0
CU A:CU1002 3.8 14.2 0.4
CE1 A:HIS448 3.9 10.9 1.0
ND1 A:HIS446 4.0 9.4 1.0
ND1 A:HIS101 4.0 10.5 1.0
CU A:CU1003 4.1 8.8 0.4
CG A:HIS446 4.1 8.9 1.0
CD2 A:HIS103 4.1 8.0 1.0
ND1 A:HIS448 4.1 11.1 1.0
CG A:HIS101 4.1 9.5 1.0
O A:O1005 4.2 21.5 0.5
N A:GLY104 4.2 8.8 1.0
CE1 A:HIS103 4.3 8.5 1.0
CA A:HIS448 4.5 11.3 1.0
C A:HIS103 4.5 7.8 1.0
N A:HIS103 4.5 7.9 1.0
CU A:CU1002 4.5 5.9 0.5
NE2 A:HIS103 4.5 8.0 1.0
O A:HOH2004 4.5 20.2 0.5
CH3 A:ACT1007 4.6 18.7 0.5
CB A:HIS448 4.6 11.6 1.0
O A:TRP102 4.8 10.5 1.0
N A:HIS448 4.9 10.8 1.0
C A:TRP102 5.0 8.1 1.0

Reference:

H.Komori, R.Sugiyama, K.Kataoka, Y.Higuchi, T.Sakurai. An O-Centered Structure of the Trinuclear Copper Center in the CYS500SER/GLU506GLN Mutant of Cueo and Structural Changes in Low to High X-Ray Dose Conditions. Angew.Chem.Int.Ed.Engl. V. 51 1861 2012.
ISSN: ISSN 1433-7851
PubMed: 22250058
DOI: 10.1002/ANIE.201107739
Page generated: Fri Sep 4 08:36:54 2020
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