Atomistry » Copper » PDB 2xv2-2z7w » 2yxw
Atomistry »
  Copper »
    PDB 2xv2-2z7w »
      2yxw »

Copper in PDB 2yxw: The Deletion Mutant of Multicopper Oxidase Cueo

Protein crystallography data

The structure of The Deletion Mutant of Multicopper Oxidase Cueo, PDB code: 2yxw was solved by Y.Higuchi, H.Komori, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.90 / 1.50
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 50.326, 51.573, 86.698, 83.77, 90.38, 67.14
R / Rfree (%) 17.7 / 20.7

Copper Binding Sites:

The binding sites of Copper atom in the The Deletion Mutant of Multicopper Oxidase Cueo (pdb code 2yxw). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 10 binding sites of Copper where determined in the The Deletion Mutant of Multicopper Oxidase Cueo, PDB code: 2yxw:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Copper binding site 1 out of 10 in 2yxw

Go back to Copper Binding Sites List in 2yxw
Copper binding site 1 out of 10 in the The Deletion Mutant of Multicopper Oxidase Cueo


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of The Deletion Mutant of Multicopper Oxidase Cueo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu701

b:22.4
occ:1.00
ND1 A:HIS505 2.0 23.5 1.0
ND1 A:HIS443 2.1 20.2 1.0
SG A:CYS500 2.2 21.8 1.0
CE1 A:HIS443 3.0 22.1 1.0
CG A:HIS505 3.0 20.7 1.0
CE1 A:HIS505 3.0 22.9 1.0
CG A:HIS443 3.1 21.2 1.0
CB A:CYS500 3.2 21.1 1.0
SD A:MET510 3.3 23.1 1.0
CB A:HIS505 3.3 22.3 1.0
CB A:HIS443 3.5 21.7 1.0
CA A:HIS443 3.7 21.3 1.0
O A:LEU442 3.7 23.6 1.0
CB A:LEU502 4.0 21.0 1.0
NE2 A:HIS443 4.1 22.2 1.0
CE A:MET510 4.1 22.1 1.0
NE2 A:HIS505 4.1 22.4 1.0
CD2 A:HIS505 4.1 22.7 1.0
CD2 A:HIS443 4.2 21.7 1.0
C A:LEU442 4.4 22.3 1.0
N A:HIS443 4.4 21.1 1.0
CD1 A:LEU502 4.6 23.2 1.0
CA A:CYS500 4.6 21.1 1.0
CG A:MET510 4.8 21.5 1.0
CG A:LEU502 4.8 22.4 1.0
CA A:HIS505 4.9 21.9 1.0
O A:LEU502 4.9 21.0 1.0
C A:HIS443 4.9 21.7 1.0
N A:LEU502 5.0 21.5 1.0

Copper binding site 2 out of 10 in 2yxw

Go back to Copper Binding Sites List in 2yxw
Copper binding site 2 out of 10 in the The Deletion Mutant of Multicopper Oxidase Cueo


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of The Deletion Mutant of Multicopper Oxidase Cueo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu703

b:33.4
occ:1.00
NE2 A:HIS446 1.9 24.9 1.0
NE2 A:HIS101 2.0 24.6 1.0
O A:HOH755 2.7 14.6 1.0
O1 A:C2O702 2.7 36.7 1.0
CE1 A:HIS101 2.9 26.9 1.0
CE1 A:HIS446 2.9 23.5 1.0
CD2 A:HIS446 2.9 22.9 1.0
CD2 A:HIS101 3.0 24.5 1.0
CD2 A:HIS448 3.1 25.4 1.0
NE2 A:HIS448 3.2 24.0 1.0
CA A:HIS103 3.5 21.9 1.0
CG A:HIS103 3.5 22.5 1.0
ND1 A:HIS103 3.5 22.5 1.0
CU2 A:C2O702 3.6 29.2 1.0
CG A:HIS448 3.7 23.2 1.0
CB A:HIS103 3.7 21.6 1.0
CE1 A:HIS448 3.8 25.6 1.0
CU3 A:C2O702 3.9 25.4 1.0
ND1 A:HIS446 4.0 25.0 1.0
ND1 A:HIS101 4.0 25.9 1.0
CG A:HIS446 4.0 22.0 1.0
ND1 A:HIS448 4.0 24.8 1.0
CD2 A:HIS103 4.1 24.3 1.0
CG A:HIS101 4.1 24.3 1.0
CE1 A:HIS103 4.2 21.9 1.0
N A:GLY104 4.2 23.0 1.0
C A:HIS103 4.4 23.1 1.0
N A:HIS103 4.4 23.2 1.0
NE2 A:HIS103 4.5 22.5 1.0
CA A:HIS448 4.5 22.8 1.0
CB A:HIS448 4.6 24.1 1.0
O A:HOH740 4.6 14.3 1.0
O A:HOH720 4.7 11.4 1.0
O A:TRP102 4.8 23.5 1.0
C A:TRP102 4.9 23.4 1.0
N A:HIS448 4.9 22.3 1.0

Copper binding site 3 out of 10 in 2yxw

Go back to Copper Binding Sites List in 2yxw
Copper binding site 3 out of 10 in the The Deletion Mutant of Multicopper Oxidase Cueo


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of The Deletion Mutant of Multicopper Oxidase Cueo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu704

b:21.3
occ:1.00
NE2 A:HIS494 2.0 26.1 1.0
OE1 A:GLU110 2.3 31.2 1.0
O A:HOH1035 2.4 31.7 1.0
CD2 A:HIS494 2.9 26.6 1.0
CE1 A:HIS494 3.0 26.6 1.0
CD A:GLU110 3.3 30.9 1.0
OE2 A:GLU110 3.8 39.1 1.0
CG A:HIS494 4.1 24.6 1.0
ND1 A:HIS494 4.1 26.6 1.0
OE1 A:GLU493 4.3 30.6 1.0
CG A:GLU110 4.4 27.9 1.0

Copper binding site 4 out of 10 in 2yxw

Go back to Copper Binding Sites List in 2yxw
Copper binding site 4 out of 10 in the The Deletion Mutant of Multicopper Oxidase Cueo


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of The Deletion Mutant of Multicopper Oxidase Cueo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu702

b:29.2
occ:1.00
CU2 A:C2O702 0.0 29.2 1.0
O1 A:C2O702 2.0 36.7 1.0
NE2 A:HIS143 2.0 27.6 1.0
NE2 A:HIS448 2.0 24.0 1.0
NE2 A:HIS499 2.1 23.1 1.0
CE1 A:HIS448 2.9 25.6 1.0
CE1 A:HIS143 3.0 25.6 1.0
CE1 A:HIS499 3.0 26.2 1.0
CD2 A:HIS143 3.0 28.3 1.0
CD2 A:HIS448 3.1 25.4 1.0
CD2 A:HIS499 3.1 24.3 1.0
O A:HOH816 3.3 28.3 1.0
CD2 A:HIS446 3.5 22.9 1.0
CU A:CU703 3.6 33.4 1.0
CU3 A:C2O702 3.9 25.4 1.0
NE2 A:HIS101 3.9 24.6 1.0
CD2 A:HIS101 3.9 24.5 1.0
NE2 A:HIS446 4.0 24.9 1.0
ND1 A:HIS448 4.1 24.8 1.0
ND1 A:HIS143 4.1 29.7 1.0
ND1 A:HIS499 4.1 24.6 1.0
CG A:HIS143 4.2 27.9 1.0
CG A:HIS448 4.2 23.2 1.0
CG A:HIS499 4.2 21.8 1.0
CE1 A:HIS141 4.5 24.7 1.0
CE1 A:HIS101 4.6 26.9 1.0
CD2 A:HIS501 4.6 24.1 1.0
CG A:HIS101 4.7 24.3 1.0
NE2 A:HIS501 4.7 22.2 1.0
NE2 A:HIS141 4.7 20.5 1.0
CG A:HIS446 4.7 22.0 1.0
OE1 A:GLU506 4.8 35.5 1.0
CB A:MET497 4.9 23.3 1.0

Copper binding site 5 out of 10 in 2yxw

Go back to Copper Binding Sites List in 2yxw
Copper binding site 5 out of 10 in the The Deletion Mutant of Multicopper Oxidase Cueo


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of The Deletion Mutant of Multicopper Oxidase Cueo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu702

b:25.4
occ:1.00
CU3 A:C2O702 0.0 25.4 1.0
O1 A:C2O702 2.0 36.7 1.0
ND1 A:HIS103 2.0 22.5 1.0
NE2 A:HIS141 2.0 20.5 1.0
NE2 A:HIS501 2.1 22.2 1.0
CE1 A:HIS141 2.9 24.7 1.0
CE1 A:HIS103 2.9 21.9 1.0
CD2 A:HIS501 3.0 24.1 1.0
CE1 A:HIS501 3.1 24.1 1.0
CG A:HIS103 3.1 22.5 1.0
CD2 A:HIS141 3.1 23.4 1.0
CB A:HIS103 3.5 21.6 1.0
CU2 A:C2O702 3.9 29.2 1.0
CU A:CU703 3.9 33.4 1.0
CD2 A:HIS101 4.1 24.5 1.0
NE2 A:HIS103 4.1 22.5 1.0
ND1 A:HIS141 4.1 24.4 1.0
CZ2 A:TRP139 4.1 21.9 1.0
O A:HOH816 4.1 28.3 1.0
CD2 A:HIS446 4.1 22.9 1.0
CD2 A:HIS103 4.2 24.3 1.0
NE2 A:HIS446 4.2 24.9 1.0
ND1 A:HIS501 4.2 22.8 1.0
CG A:HIS501 4.2 23.3 1.0
CG A:HIS141 4.2 22.8 1.0
NE2 A:HIS101 4.4 24.6 1.0
CE2 A:TRP139 4.4 21.3 1.0
NE1 A:TRP139 4.5 21.6 1.0
CA A:HIS103 4.7 21.9 1.0
CE1 A:HIS499 4.8 26.2 1.0
CH2 A:TRP139 4.8 22.9 1.0
NE2 A:HIS143 4.9 27.6 1.0
NE2 A:HIS499 4.9 23.1 1.0
CG A:HIS446 4.9 22.0 1.0
CE1 A:HIS446 5.0 23.5 1.0

Copper binding site 6 out of 10 in 2yxw

Go back to Copper Binding Sites List in 2yxw
Copper binding site 6 out of 10 in the The Deletion Mutant of Multicopper Oxidase Cueo


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of The Deletion Mutant of Multicopper Oxidase Cueo within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu701

b:18.6
occ:1.00
ND1 B:HIS443 2.0 13.4 1.0
ND1 B:HIS505 2.0 17.4 1.0
SG B:CYS500 2.3 18.9 1.0
CE1 B:HIS443 2.9 17.4 1.0
CE1 B:HIS505 3.0 14.8 1.0
CG B:HIS443 3.0 18.6 1.0
CG B:HIS505 3.0 16.5 1.0
CB B:CYS500 3.1 18.7 1.0
SD B:MET510 3.3 20.2 1.0
CB B:HIS505 3.4 17.3 1.0
CB B:HIS443 3.4 18.9 1.0
CA B:HIS443 3.7 19.6 1.0
O B:LEU442 3.9 21.3 1.0
CB B:LEU502 4.1 16.6 1.0
NE2 B:HIS443 4.1 18.5 1.0
NE2 B:HIS505 4.1 16.3 1.0
CD2 B:HIS443 4.1 18.3 1.0
CD2 B:HIS505 4.1 17.2 1.0
CE B:MET510 4.1 21.5 1.0
N B:HIS443 4.5 19.5 1.0
C B:LEU442 4.5 20.9 1.0
CA B:CYS500 4.6 18.4 1.0
CD1 B:LEU502 4.7 16.6 1.0
CG B:MET510 4.8 20.0 1.0
CG B:LEU502 4.9 16.6 1.0
CA B:HIS505 4.9 17.6 1.0
O B:LEU502 4.9 16.2 1.0
C B:HIS443 4.9 19.3 1.0

Copper binding site 7 out of 10 in 2yxw

Go back to Copper Binding Sites List in 2yxw
Copper binding site 7 out of 10 in the The Deletion Mutant of Multicopper Oxidase Cueo


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of The Deletion Mutant of Multicopper Oxidase Cueo within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu703

b:29.7
occ:1.00
NE2 B:HIS446 2.0 19.6 1.0
NE2 B:HIS101 2.0 20.2 1.0
O B:HOH803 2.6 19.4 1.0
CE1 B:HIS101 2.8 21.1 1.0
O1 B:C2O702 2.9 24.9 1.0
CD2 B:HIS446 2.9 20.4 1.0
CE1 B:HIS446 3.0 21.1 1.0
NE2 B:HIS448 3.0 21.6 1.0
CD2 B:HIS448 3.1 22.8 1.0
CD2 B:HIS101 3.1 21.7 1.0
CU2 B:C2O702 3.5 24.3 1.0
CA B:HIS103 3.6 18.5 1.0
CE1 B:HIS448 3.6 20.9 1.0
CG B:HIS103 3.6 18.1 1.0
ND1 B:HIS103 3.6 18.3 1.0
CG B:HIS448 3.6 20.4 1.0
CB B:HIS103 3.8 19.1 1.0
ND1 B:HIS448 3.9 21.7 1.0
ND1 B:HIS101 4.0 20.8 1.0
CU3 B:C2O702 4.0 20.4 1.0
CG B:HIS446 4.0 19.0 1.0
ND1 B:HIS446 4.1 20.0 1.0
CG B:HIS101 4.1 19.8 1.0
CD2 B:HIS103 4.2 19.1 1.0
CE1 B:HIS103 4.2 19.4 1.0
N B:GLY104 4.3 18.6 1.0
C B:HIS103 4.5 19.0 1.0
O B:HOH715 4.5 18.0 1.0
CA B:HIS448 4.5 20.4 1.0
NE2 B:HIS103 4.5 18.3 1.0
N B:HIS103 4.5 18.3 1.0
CB B:HIS448 4.5 20.1 1.0
O B:HOH719 4.7 15.9 1.0
O B:TRP102 4.8 18.9 1.0
N B:HIS448 5.0 19.7 1.0
C B:TRP102 5.0 18.8 1.0
NE2 B:HIS499 5.0 19.4 1.0

Copper binding site 8 out of 10 in 2yxw

Go back to Copper Binding Sites List in 2yxw
Copper binding site 8 out of 10 in the The Deletion Mutant of Multicopper Oxidase Cueo


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of The Deletion Mutant of Multicopper Oxidase Cueo within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu705

b:30.2
occ:1.00
NE2 B:HIS518 2.0 24.1 1.0
NE2 B:HIS520 2.0 26.5 1.0
O B:HOH955 2.7 38.6 1.0
CD2 B:HIS518 3.0 22.7 1.0
CD2 B:HIS520 3.0 26.5 1.0
CE1 B:HIS520 3.0 26.2 1.0
CE1 B:HIS518 3.0 23.6 1.0
ND1 B:HIS520 4.1 27.4 1.0
CG B:HIS520 4.1 26.2 1.0
ND1 B:HIS518 4.1 22.0 1.0
CG B:HIS518 4.1 22.5 1.0
O B:HOH1003 4.6 32.3 1.0

Copper binding site 9 out of 10 in 2yxw

Go back to Copper Binding Sites List in 2yxw
Copper binding site 9 out of 10 in the The Deletion Mutant of Multicopper Oxidase Cueo


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 9 of The Deletion Mutant of Multicopper Oxidase Cueo within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu702

b:24.3
occ:1.00
CU2 B:C2O702 0.0 24.3 1.0
O1 B:C2O702 2.0 24.9 1.0
NE2 B:HIS143 2.0 20.6 1.0
NE2 B:HIS448 2.1 21.6 1.0
NE2 B:HIS499 2.1 19.4 1.0
CE1 B:HIS448 2.9 20.9 1.0
CE1 B:HIS499 3.0 20.2 1.0
CD2 B:HIS143 3.0 23.7 1.0
CE1 B:HIS143 3.0 21.4 1.0
CD2 B:HIS499 3.1 19.8 1.0
CD2 B:HIS448 3.2 22.8 1.0
O B:HOH982 3.5 35.9 1.0
CD2 B:HIS446 3.5 20.4 1.0
CU B:CU703 3.5 29.7 1.0
NE2 B:HIS101 3.8 20.2 1.0
CD2 B:HIS101 3.8 21.7 1.0
CU3 B:C2O702 3.8 20.4 1.0
NE2 B:HIS446 4.0 19.6 1.0
ND1 B:HIS448 4.1 21.7 1.0
ND1 B:HIS499 4.1 19.9 1.0
ND1 B:HIS143 4.1 22.6 1.0
CG B:HIS143 4.2 21.0 1.0
CG B:HIS499 4.2 18.6 1.0
CG B:HIS448 4.2 20.4 1.0
CE1 B:HIS141 4.5 21.2 1.0
NE2 B:HIS501 4.5 16.7 1.0
CD2 B:HIS501 4.6 18.5 1.0
CE1 B:HIS101 4.6 21.1 1.0
NE2 B:HIS141 4.7 15.8 1.0
CG B:HIS101 4.7 19.8 1.0
CG B:HIS446 4.7 19.0 1.0
OE1 B:GLU506 4.9 26.6 1.0
CB B:MET497 5.0 19.9 1.0
ND1 B:HIS103 5.0 18.3 1.0

Copper binding site 10 out of 10 in 2yxw

Go back to Copper Binding Sites List in 2yxw
Copper binding site 10 out of 10 in the The Deletion Mutant of Multicopper Oxidase Cueo


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 10 of The Deletion Mutant of Multicopper Oxidase Cueo within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu702

b:20.4
occ:1.00
CU3 B:C2O702 0.0 20.4 1.0
O1 B:C2O702 1.9 24.9 1.0
NE2 B:HIS141 2.0 15.8 1.0
ND1 B:HIS103 2.0 18.3 1.0
NE2 B:HIS501 2.0 16.7 1.0
CE1 B:HIS103 2.9 19.4 1.0
CE1 B:HIS141 2.9 21.2 1.0
CE1 B:HIS501 3.0 17.5 1.0
CD2 B:HIS501 3.1 18.5 1.0
CD2 B:HIS141 3.1 21.0 1.0
CG B:HIS103 3.1 18.1 1.0
CB B:HIS103 3.6 19.1 1.0
CU2 B:C2O702 3.8 24.3 1.0
CU B:CU703 4.0 29.7 1.0
O B:HOH982 4.0 35.9 1.0
CD2 B:HIS101 4.0 21.7 1.0
NE2 B:HIS103 4.0 18.3 1.0
ND1 B:HIS141 4.1 18.6 1.0
CZ2 B:TRP139 4.1 19.5 1.0
ND1 B:HIS501 4.1 17.8 1.0
CG B:HIS141 4.2 18.1 1.0
CG B:HIS501 4.2 18.8 1.0
CD2 B:HIS446 4.2 20.4 1.0
CD2 B:HIS103 4.2 19.1 1.0
NE2 B:HIS446 4.2 19.6 1.0
NE2 B:HIS101 4.3 20.2 1.0
CE2 B:TRP139 4.5 18.7 1.0
NE1 B:TRP139 4.5 18.7 1.0
CA B:HIS103 4.7 18.5 1.0
CH2 B:TRP139 4.8 17.7 1.0
CE1 B:HIS499 4.8 20.2 1.0
NE2 B:HIS143 4.9 20.6 1.0
NE2 B:HIS499 4.9 19.4 1.0
CG B:HIS446 5.0 19.0 1.0

Reference:

K.Kataoka, H.Komori, Y.Ueki, Y.Konno, Y.Kamitaka, S.Kurose, S.Tsujimura, Y.Higuchi, K.Kano, D.Seo, T.Sakurai. Structure and Function of the Engineered Multicopper Oxidase Cueo From Escherichia Coli--Deletion of the Methionine-Rich Helical Region Covering the Substrate-Binding Site J.Mol.Biol. V. 373 141 2007.
ISSN: ISSN 0022-2836
PubMed: 17804014
DOI: 10.1016/J.JMB.2007.07.041
Page generated: Wed Jul 31 00:26:14 2024

Last articles

Ca in 2OS8
Ca in 2OO4
Ca in 2OR4
Ca in 2OQU
Ca in 2OOT
Ca in 2OKX
Ca in 2OMY
Ca in 2OMV
Ca in 2OMX
Ca in 2OMU
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy