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Copper in PDB 6k3d: Structure of Multicopper Oxidase Mutant

Protein crystallography data

The structure of Structure of Multicopper Oxidase Mutant, PDB code: 6k3d was solved by H.Sakuraba, T.Ohshida, T.Satomura, K.Yoneda, T.Ohshima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.93 / 1.92
Space group I 41
Cell size a, b, c (Å), α, β, γ (°) 102.948, 102.948, 118.700, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 21

Copper Binding Sites:

The binding sites of Copper atom in the Structure of Multicopper Oxidase Mutant (pdb code 6k3d). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 4 binding sites of Copper where determined in the Structure of Multicopper Oxidase Mutant, PDB code: 6k3d:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in 6k3d

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Copper binding site 1 out of 4 in the Structure of Multicopper Oxidase Mutant


Mono view


Stereo pair view

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

b:25.6
occ:1.00
ND1 A:HIS465 2.0 23.3 1.0
ND1 A:HIS391 2.1 22.0 1.0
SG A:CYS460 2.2 25.1 1.0
CE1 A:HIS465 2.9 24.9 1.0
CE1 A:HIS391 3.0 25.8 1.0
CG A:HIS465 3.1 22.9 1.0
CB A:CYS460 3.1 27.4 1.0
CG A:HIS391 3.2 23.0 1.0
SD A:MET470 3.4 25.7 1.0
CB A:HIS465 3.5 23.8 1.0
CB A:HIS391 3.5 23.1 1.0
CB A:ASN462 3.9 21.4 1.0
CA A:HIS391 3.9 23.1 1.0
CE A:MET470 4.1 23.5 1.0
NE2 A:HIS465 4.1 23.0 1.0
CD2 A:HIS465 4.2 24.8 1.0
NE2 A:HIS391 4.2 24.5 1.0
CD2 A:HIS391 4.3 26.0 1.0
CD A:PRO392 4.5 23.7 1.0
O A:PRO390 4.5 28.6 1.0
CA A:CYS460 4.5 24.0 1.0
CG A:ASN462 4.6 27.0 1.0
ND2 A:ASN462 4.8 23.9 1.0
C A:HIS391 4.8 24.2 1.0
N A:ASN462 4.9 23.0 1.0
N A:HIS391 4.9 23.9 1.0
CG A:MET470 4.9 24.5 1.0
N A:PRO392 5.0 23.4 1.0
CA A:HIS465 5.0 25.8 1.0
CA A:ASN462 5.0 24.3 1.0

Copper binding site 2 out of 4 in 6k3d

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Copper binding site 2 out of 4 in the Structure of Multicopper Oxidase Mutant


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Structure of Multicopper Oxidase Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu702

b:38.1
occ:1.00
NE2 A:HIS394 1.9 25.9 1.0
NE2 A:HIS92 2.0 28.6 1.0
CD2 A:HIS394 2.8 26.1 1.0
O A:HOH934 2.8 27.1 1.0
CD2 A:HIS92 2.9 29.1 1.0
O1 A:C2O703 2.9 27.9 1.0
CE1 A:HIS92 3.0 26.4 1.0
CE1 A:HIS394 3.0 26.9 1.0
CD2 A:HIS396 3.2 24.4 1.0
NE2 A:HIS396 3.2 27.8 1.0
ND1 A:HIS94 3.5 30.3 1.0
CU2 A:C2O703 3.6 36.3 1.0
CG A:HIS396 3.7 27.7 1.0
CE1 A:HIS396 3.7 25.5 1.0
CG A:HIS94 3.8 27.2 1.0
CA A:HIS94 3.9 25.0 1.0
CU3 A:C2O703 4.0 32.8 1.0
CE1 A:HIS94 4.0 25.3 1.0
CG A:HIS394 4.0 25.9 1.0
N A:GLY95 4.0 24.3 1.0
ND1 A:HIS396 4.0 27.5 1.0
ND1 A:HIS92 4.0 27.8 1.0
CG A:HIS92 4.0 27.5 1.0
ND1 A:HIS394 4.1 26.6 1.0
CB A:HIS94 4.1 26.4 1.0
C A:HIS94 4.5 27.8 1.0
CD2 A:HIS94 4.5 26.5 1.0
CA A:HIS396 4.5 26.3 1.0
NE2 A:HIS94 4.6 26.2 1.0
CB A:HIS396 4.6 26.3 1.0
O A:HOH904 4.7 35.2 1.0
N A:HIS396 4.9 23.6 1.0
NE2 A:HIS459 4.9 27.9 1.0
N A:HIS94 4.9 25.8 1.0

Copper binding site 3 out of 4 in 6k3d

Go back to Copper Binding Sites List in 6k3d
Copper binding site 3 out of 4 in the Structure of Multicopper Oxidase Mutant


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Structure of Multicopper Oxidase Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu703

b:36.3
occ:1.00
CU2 A:C2O703 0.0 36.3 1.0
O1 A:C2O703 2.1 27.9 1.0
NE2 A:HIS396 2.2 27.8 1.0
NE2 A:HIS134 2.2 31.5 1.0
NE2 A:HIS459 2.2 27.9 1.0
CE1 A:HIS396 3.0 25.5 1.0
CD2 A:HIS134 3.0 30.3 1.0
CE1 A:HIS459 3.1 29.3 1.0
CD2 A:HIS459 3.3 26.9 1.0
CD2 A:HIS396 3.3 24.4 1.0
CE1 A:HIS134 3.3 35.1 1.0
CU A:CU702 3.6 38.1 1.0
CD2 A:HIS394 3.7 26.1 1.0
CD2 A:HIS92 3.8 29.1 1.0
NE2 A:HIS92 4.0 28.6 1.0
CU3 A:C2O703 4.1 32.8 1.0
ND1 A:HIS396 4.2 27.5 1.0
ND1 A:HIS459 4.2 26.2 1.0
CG A:HIS134 4.2 32.3 1.0
NE2 A:HIS394 4.3 25.9 1.0
CG A:HIS459 4.3 27.5 1.0
CG A:HIS396 4.3 27.7 1.0
ND1 A:HIS134 4.3 34.4 1.0
NE2 A:HIS461 4.6 26.1 1.0
CD2 A:HIS461 4.6 29.1 1.0
OE2 A:GLU466 4.6 41.1 1.0
CG A:HIS92 4.6 27.5 1.0
CE1 A:HIS132 4.7 26.7 1.0
OE1 A:GLU466 4.7 37.3 1.0
CE1 A:HIS92 4.8 26.4 1.0
CD A:GLU466 4.8 36.8 1.0
NE2 A:HIS132 4.9 27.2 1.0
CG A:HIS394 5.0 25.9 1.0

Copper binding site 4 out of 4 in 6k3d

Go back to Copper Binding Sites List in 6k3d
Copper binding site 4 out of 4 in the Structure of Multicopper Oxidase Mutant


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Structure of Multicopper Oxidase Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu703

b:32.8
occ:1.00
CU3 A:C2O703 0.0 32.8 1.0
O1 A:C2O703 2.1 27.9 1.0
NE2 A:HIS132 2.1 27.2 1.0
ND1 A:HIS94 2.2 30.3 1.0
NE2 A:HIS461 2.3 26.1 1.0
CE1 A:HIS132 3.1 26.7 1.0
CE1 A:HIS94 3.1 25.3 1.0
CG A:HIS94 3.1 27.2 1.0
CD2 A:HIS132 3.2 23.6 1.0
CD2 A:HIS461 3.2 29.1 1.0
CE1 A:HIS461 3.3 25.5 1.0
CB A:HIS94 3.5 26.4 1.0
CD2 A:HIS92 3.8 29.1 1.0
CU A:CU702 4.0 38.1 1.0
CU2 A:C2O703 4.1 36.3 1.0
ND1 A:HIS132 4.2 27.9 1.0
NE2 A:HIS94 4.2 26.2 1.0
CD2 A:HIS94 4.3 26.5 1.0
CG A:HIS132 4.3 26.2 1.0
CG A:HIS461 4.4 26.1 1.0
ND1 A:HIS461 4.4 25.0 1.0
NE2 A:HIS92 4.4 28.6 1.0
CD2 A:HIS394 4.4 26.1 1.0
NE2 A:HIS394 4.4 25.9 1.0
CA A:HIS94 4.6 25.0 1.0
CB A:ALA269 4.6 23.2 1.0
CD1 A:LEU130 4.8 29.7 1.0

Reference:

H.Sakuraba, T.Ohdhida, T.Satomura, K.Yoneda, T.Ohshima. Structure of Multicopper Oxidase Mutant To Be Published.
Page generated: Sun Dec 13 11:23:25 2020

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