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Copper in PDB 5e9n: Steccherinum Murashkinskyi Laccase at 0.95 Resolution

Enzymatic activity of Steccherinum Murashkinskyi Laccase at 0.95 Resolution

All present enzymatic activity of Steccherinum Murashkinskyi Laccase at 0.95 Resolution:
1.10.3.2;

Protein crystallography data

The structure of Steccherinum Murashkinskyi Laccase at 0.95 Resolution, PDB code: 5e9n was solved by K.M.Polyakov, O.A.Glazunova, T.V.Fedorova, O.V.Koroleva, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 0.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 55.510, 83.270, 111.040, 90.00, 90.00, 90.00
R / Rfree (%) 12.1 / 13.9

Other elements in 5e9n:

The structure of Steccherinum Murashkinskyi Laccase at 0.95 Resolution also contains other interesting chemical elements:

Sodium (Na) 1 atom

Copper Binding Sites:

The binding sites of Copper atom in the Steccherinum Murashkinskyi Laccase at 0.95 Resolution (pdb code 5e9n). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the Steccherinum Murashkinskyi Laccase at 0.95 Resolution, PDB code: 5e9n:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 5e9n

Go back to Copper Binding Sites List in 5e9n
Copper binding site 1 out of 6 in the Steccherinum Murashkinskyi Laccase at 0.95 Resolution


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Steccherinum Murashkinskyi Laccase at 0.95 Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu601

b:6.9
occ:0.70
CU A:CU601 0.0 6.9 0.7
CU A:CU601 0.8 6.6 0.2
NE2 A:HIS452 1.9 9.6 1.0
NE2 A:HIS402 1.9 7.0 1.0
NE2 A:HIS112 2.0 7.6 1.0
O A:HOH1125 2.5 15.8 0.7
CD2 A:HIS452 2.8 8.7 1.0
CE1 A:HIS402 2.9 7.3 1.0
CE1 A:HIS112 2.9 8.5 1.0
CE1 A:HIS452 2.9 8.8 1.0
HD2 A:HIS452 3.0 8.8 1.0
HE1 A:HIS402 3.0 9.2 1.0
CD2 A:HIS402 3.0 7.0 1.0
HE1 A:HIS112 3.0 8.3 1.0
CD2 A:HIS112 3.1 7.2 1.0
HD2 A:PHE450 3.1 8.3 1.0
HE1 A:HIS452 3.2 8.2 1.0
HD2 A:HIS402 3.3 7.1 1.0
HD2 A:HIS400 3.3 7.0 1.0
HD2 A:HIS112 3.3 7.4 1.0
HB3 A:PHE450 3.5 9.1 1.0
O A:HOH1238 3.8 8.4 0.5
CD2 A:PHE450 3.8 8.5 1.0
CG A:HIS452 4.0 7.8 1.0
HB3 A:PRO80 4.0 7.7 1.0
ND1 A:HIS402 4.0 6.7 1.0
ND1 A:HIS452 4.0 7.8 1.0
ND1 A:HIS112 4.1 8.1 1.0
CG A:HIS402 4.1 6.3 1.0
CD2 A:HIS400 4.1 6.7 1.0
CG A:HIS112 4.2 7.0 1.0
HE1 A:HIS110 4.3 7.4 1.0
CB A:PHE450 4.3 7.3 1.0
HD2 A:HIS65 4.4 7.1 1.0
HB2 A:PHE450 4.4 9.1 1.0
CU A:CU603 4.4 6.5 0.8
CG A:PHE450 4.4 7.1 1.0
HD21 A:LEU459 4.5 9.3 1.0
CD2 A:HIS65 4.5 7.0 1.0
NE2 A:HIS65 4.6 6.9 1.0
HE2 A:PHE450 4.6 8.3 1.0
CE2 A:PHE450 4.6 10.0 1.0
CU A:CU602 4.7 9.2 0.2
NE2 A:HIS400 4.7 6.8 1.0
HD1 A:HIS402 4.8 9.2 1.0
HD1 A:HIS452 4.8 8.2 1.0
HD1 A:HIS112 4.8 8.3 1.0
HD22 A:LEU459 4.8 9.3 1.0
CB A:PRO80 4.9 7.5 1.0
HG3 A:PRO80 5.0 7.3 1.0
HD2 A:HIS454 5.0 8.0 1.0

Copper binding site 2 out of 6 in 5e9n

Go back to Copper Binding Sites List in 5e9n
Copper binding site 2 out of 6 in the Steccherinum Murashkinskyi Laccase at 0.95 Resolution


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Steccherinum Murashkinskyi Laccase at 0.95 Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu601

b:6.6
occ:0.20
CU A:CU601 0.0 6.6 0.2
CU A:CU601 0.8 6.9 0.7
O A:HOH1125 1.7 15.8 0.7
NE2 A:HIS402 2.0 7.0 1.0
NE2 A:HIS112 2.2 7.6 1.0
NE2 A:HIS452 2.2 9.6 1.0
HD2 A:HIS400 2.9 7.0 1.0
CE1 A:HIS402 2.9 7.3 1.0
CD2 A:HIS112 3.0 7.2 1.0
CE1 A:HIS452 3.0 8.8 1.0
HE1 A:HIS402 3.1 9.2 1.0
CD2 A:HIS402 3.1 7.0 1.0
HD2 A:HIS112 3.1 7.4 1.0
HE1 A:HIS452 3.1 8.2 1.0
CE1 A:HIS112 3.3 8.5 1.0
HD2 A:HIS402 3.3 7.1 1.0
CD2 A:HIS452 3.3 8.7 1.0
HE1 A:HIS112 3.6 8.3 1.0
HD2 A:HIS452 3.6 8.8 1.0
O A:HOH1238 3.6 8.4 0.5
CD2 A:HIS400 3.7 6.7 1.0
HD2 A:HIS65 3.7 7.1 1.0
HE1 A:HIS110 3.8 7.4 1.0
CU A:CU603 3.8 6.5 0.8
HD2 A:PHE450 3.9 8.3 1.0
CU A:CU602 3.9 9.2 0.2
CD2 A:HIS65 3.9 7.0 1.0
NE2 A:HIS65 4.0 6.9 1.0
ND1 A:HIS402 4.1 6.7 1.0
HB3 A:PHE450 4.1 9.1 1.0
CG A:HIS402 4.2 6.3 1.0
NE2 A:HIS400 4.2 6.8 1.0
ND1 A:HIS452 4.2 7.8 1.0
CG A:HIS112 4.3 7.0 1.0
ND1 A:HIS112 4.4 8.1 1.0
CG A:HIS452 4.4 7.8 1.0
HB3 A:PRO80 4.4 7.7 1.0
HD2 A:HIS454 4.5 8.0 1.0
NE2 A:HIS454 4.5 7.0 1.0
CE1 A:HIS110 4.6 7.2 1.0
CU A:CU602 4.6 5.9 0.7
CD2 A:PHE450 4.6 8.5 1.0
CD2 A:HIS454 4.6 6.7 1.0
CG A:HIS65 4.7 6.8 1.0
HD21 A:LEU459 4.8 9.3 1.0
CE1 A:HIS65 4.8 6.9 1.0
HD1 A:HIS402 4.8 9.2 1.0
CG A:HIS400 4.9 6.5 1.0
CB A:PHE450 4.9 7.3 1.0
NE2 A:HIS110 4.9 7.1 1.0
HB3 A:HIS400 5.0 6.8 1.0
HD1 A:HIS452 5.0 8.2 1.0
HB2 A:PHE450 5.0 9.1 1.0

Copper binding site 3 out of 6 in 5e9n

Go back to Copper Binding Sites List in 5e9n
Copper binding site 3 out of 6 in the Steccherinum Murashkinskyi Laccase at 0.95 Resolution


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Steccherinum Murashkinskyi Laccase at 0.95 Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu602

b:5.9
occ:0.70
CU A:CU602 0.0 5.9 0.7
CU A:CU602 0.6 9.2 0.2
ND1 A:HIS67 1.9 6.6 1.0
NE2 A:HIS110 2.0 7.1 1.0
NE2 A:HIS454 2.1 7.0 1.0
HB2 A:HIS67 2.7 6.9 1.0
O A:HOH1125 2.9 15.8 0.7
CE1 A:HIS67 2.9 6.3 1.0
CG A:HIS67 2.9 6.1 1.0
CE1 A:HIS454 2.9 6.5 1.0
CD2 A:HIS110 2.9 6.7 1.0
CE1 A:HIS110 3.0 7.2 1.0
HE1 A:HIS454 3.0 6.8 1.0
HD2 A:HIS65 3.1 7.1 1.0
HE1 A:HIS67 3.1 8.0 1.0
HD2 A:HIS110 3.1 6.9 1.0
CD2 A:HIS454 3.2 6.7 1.0
HE1 A:HIS110 3.2 7.4 1.0
CB A:HIS67 3.3 6.6 1.0
HZ2 A:TRP108 3.4 8.1 1.0
HD2 A:HIS454 3.4 8.0 1.0
HB2 A:ALA244 3.5 8.1 1.0
CZ2 A:TRP108 3.6 6.9 1.0
HE1 A:TRP108 3.8 8.1 1.0
CD2 A:HIS65 3.9 7.0 1.0
CE2 A:TRP108 3.9 6.5 1.0
HB3 A:HIS67 3.9 6.9 1.0
NE1 A:TRP108 4.0 6.6 1.0
NE2 A:HIS67 4.0 7.0 1.0
CD2 A:HIS67 4.0 7.2 1.0
ND1 A:HIS110 4.1 7.2 1.0
CG A:HIS110 4.1 6.7 1.0
CU A:CU603 4.1 6.5 0.8
ND1 A:HIS454 4.1 6.7 1.0
HA A:HIS67 4.2 6.8 1.0
HB1 A:ALA244 4.2 8.1 1.0
CG A:HIS454 4.3 6.6 1.0
CB A:ALA244 4.3 6.3 1.0
HD2 A:HIS400 4.3 7.0 1.0
NE2 A:HIS65 4.3 6.9 1.0
CH2 A:TRP108 4.4 7.1 1.0
CA A:HIS67 4.4 6.4 1.0
CD2 A:HIS400 4.4 6.7 1.0
NE2 A:HIS400 4.4 6.8 1.0
O A:HOH1238 4.5 8.4 0.5
CU A:CU601 4.6 6.6 0.2
HH2 A:TRP108 4.6 8.2 1.0
HB3 A:ALA244 4.7 8.1 1.0
HE2 A:HIS67 4.8 8.0 1.0
CD2 A:TRP108 4.8 6.3 1.0
HD1 A:HIS110 4.8 7.4 1.0
HD1 A:HIS454 4.9 6.8 1.0
HD2 A:HIS67 4.9 8.0 1.0
CD1 A:TRP108 4.9 6.6 1.0
HD2 A:HIS112 4.9 7.4 1.0

Copper binding site 4 out of 6 in 5e9n

Go back to Copper Binding Sites List in 5e9n
Copper binding site 4 out of 6 in the Steccherinum Murashkinskyi Laccase at 0.95 Resolution


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Steccherinum Murashkinskyi Laccase at 0.95 Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu602

b:9.2
occ:0.20
CU A:CU602 0.0 9.2 0.2
CU A:CU602 0.6 5.9 0.7
NE2 A:HIS454 1.9 7.0 1.0
NE2 A:HIS110 2.1 7.1 1.0
ND1 A:HIS67 2.1 6.6 1.0
O A:HOH1125 2.2 15.8 0.7
HD2 A:HIS65 2.8 7.1 1.0
CE1 A:HIS110 2.8 7.2 1.0
HE1 A:HIS110 2.9 7.4 1.0
CE1 A:HIS454 2.9 6.5 1.0
CD2 A:HIS454 3.0 6.7 1.0
CE1 A:HIS67 3.0 6.3 1.0
HB2 A:HIS67 3.1 6.9 1.0
HE1 A:HIS454 3.1 6.8 1.0
HE1 A:HIS67 3.2 8.0 1.0
HD2 A:HIS454 3.2 8.0 1.0
CD2 A:HIS110 3.2 6.7 1.0
CG A:HIS67 3.2 6.1 1.0
HD2 A:HIS110 3.5 6.9 1.0
CD2 A:HIS65 3.6 7.0 1.0
CB A:HIS67 3.7 6.6 1.0
CU A:CU603 3.8 6.5 0.8
HD2 A:HIS400 3.8 7.0 1.0
HZ2 A:TRP108 3.9 8.1 1.0
HB2 A:ALA244 3.9 8.1 1.0
CU A:CU601 3.9 6.6 0.2
CD2 A:HIS400 4.0 6.7 1.0
NE2 A:HIS65 4.0 6.9 1.0
ND1 A:HIS110 4.1 7.2 1.0
ND1 A:HIS454 4.1 6.7 1.0
NE2 A:HIS400 4.1 6.8 1.0
O A:HOH1238 4.1 8.4 0.5
CG A:HIS454 4.1 6.6 1.0
CZ2 A:TRP108 4.2 6.9 1.0
NE2 A:HIS67 4.2 7.0 1.0
HA A:HIS67 4.3 6.8 1.0
CG A:HIS110 4.3 6.7 1.0
CD2 A:HIS67 4.3 7.2 1.0
HB3 A:HIS67 4.3 6.9 1.0
HE1 A:TRP108 4.4 8.1 1.0
HD2 A:HIS112 4.5 7.4 1.0
HB1 A:ALA244 4.5 8.1 1.0
CE2 A:TRP108 4.5 6.5 1.0
HE1 A:HIS452 4.5 8.2 1.0
NE1 A:TRP108 4.6 6.6 1.0
CA A:HIS67 4.6 6.4 1.0
CB A:ALA244 4.6 6.3 1.0
CU A:CU601 4.7 6.9 0.7
HD1 A:HIS110 4.8 7.4 1.0
CG A:HIS65 4.8 6.8 1.0
HD1 A:HIS454 4.8 6.8 1.0
CG A:HIS400 4.8 6.5 1.0
CH2 A:TRP108 4.9 7.1 1.0
CE1 A:HIS400 4.9 6.8 1.0
HB3 A:HIS65 4.9 9.8 1.0
HB3 A:ALA244 5.0 8.1 1.0
HE2 A:HIS67 5.0 8.0 1.0

Copper binding site 5 out of 6 in 5e9n

Go back to Copper Binding Sites List in 5e9n
Copper binding site 5 out of 6 in the Steccherinum Murashkinskyi Laccase at 0.95 Resolution


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Steccherinum Murashkinskyi Laccase at 0.95 Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu603

b:6.5
occ:0.80
NE2 A:HIS400 1.9 6.8 1.0
NE2 A:HIS65 1.9 6.9 1.0
O A:HOH996 2.5 9.4 1.0
CE1 A:HIS65 2.8 6.9 1.0
CD2 A:HIS400 2.9 6.7 1.0
CE1 A:HIS400 2.9 6.8 1.0
CD2 A:HIS65 2.9 7.0 1.0
HA A:HIS67 3.0 6.8 1.0
HE1 A:HIS65 3.0 7.2 1.0
HD2 A:HIS400 3.1 7.0 1.0
HE1 A:HIS400 3.1 6.9 1.0
H A:GLY68 3.1 6.8 1.0
HD2 A:HIS65 3.2 7.1 1.0
CD2 A:HIS402 3.3 7.0 1.0
NE2 A:HIS402 3.4 7.0 1.0
ND1 A:HIS67 3.5 6.6 1.0
HD2 A:HIS402 3.5 7.1 1.0
O A:HOH1125 3.6 15.8 0.7
HA A:HIS402 3.6 6.7 1.0
CG A:HIS402 3.7 6.3 1.0
CU A:CU602 3.8 9.2 0.2
CE1 A:HIS402 3.8 7.3 1.0
CG A:HIS67 3.8 6.1 1.0
CU A:CU601 3.8 6.6 0.2
CA A:HIS67 3.9 6.4 1.0
CE1 A:HIS67 3.9 6.3 1.0
ND1 A:HIS402 3.9 6.7 1.0
ND1 A:HIS65 3.9 7.2 1.0
N A:GLY68 3.9 6.7 1.0
ND1 A:HIS400 4.0 6.3 1.0
CG A:HIS400 4.0 6.5 1.0
CG A:HIS65 4.0 6.8 1.0
CU A:CU602 4.1 5.9 0.7
HB2 A:HIS67 4.2 6.9 1.0
CB A:HIS67 4.2 6.6 1.0
HE1 A:HIS67 4.2 8.0 1.0
HE1 A:HIS402 4.2 9.2 1.0
CD2 A:HIS67 4.3 7.2 1.0
NE2 A:HIS67 4.4 7.0 1.0
CA A:HIS402 4.4 6.5 1.0
CU A:CU601 4.4 6.9 0.7
C A:HIS67 4.4 6.5 1.0
HD1 A:HIS402 4.4 9.2 1.0
CB A:HIS402 4.5 6.8 1.0
O A:HOH859 4.5 9.6 1.0
O A:HOH850 4.6 8.2 1.0
HD1 A:HIS65 4.7 7.2 1.0
HB3 A:HIS402 4.7 9.2 1.0
HA2 A:GLY68 4.7 7.1 1.0
HD1 A:HIS400 4.7 6.9 1.0
N A:HIS402 4.8 6.3 1.0
HD2 A:HIS67 4.9 8.0 1.0
N A:HIS67 4.9 6.2 1.0
O A:LEU401 4.9 6.7 1.0
HE2 A:HIS67 4.9 8.0 1.0
HD2 A:HIS454 4.9 8.0 1.0
HD2 A:HIS112 4.9 7.4 1.0
O A:TRP66 4.9 6.9 1.0
CA A:GLY68 5.0 6.5 1.0

Copper binding site 6 out of 6 in 5e9n

Go back to Copper Binding Sites List in 5e9n
Copper binding site 6 out of 6 in the Steccherinum Murashkinskyi Laccase at 0.95 Resolution


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Steccherinum Murashkinskyi Laccase at 0.95 Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu604

b:6.8
occ:0.90
ND1 A:HIS458 2.0 7.5 1.0
ND1 A:HIS397 2.0 7.1 1.0
SG A:CYS453 2.2 7.5 1.0
HD11 A:ILE455 2.6 8.7 1.0
CE1 A:HIS397 2.9 7.6 1.0
HB A:ILE455 2.9 8.7 1.0
CE1 A:HIS458 3.0 8.2 1.0
CG A:HIS458 3.0 7.5 1.0
HB3 A:HIS397 3.0 12.4 1.0
HD2 A:PHE463 3.0 12.9 1.0
CG A:HIS397 3.1 7.2 1.0
HE1 A:HIS397 3.1 8.2 1.0
HB2 A:HIS458 3.1 8.7 1.0
HE1 A:HIS458 3.1 8.5 1.0
HB3 A:HIS458 3.2 8.7 1.0
CB A:CYS453 3.3 7.2 1.0
HA A:HIS397 3.3 8.7 1.0
CB A:HIS458 3.3 7.9 1.0
HB2 A:CYS453 3.4 7.6 1.0
HB3 A:CYS453 3.4 7.6 1.0
CB A:HIS397 3.4 7.1 1.0
HE2 A:PHE463 3.5 12.9 1.0
CD1 A:ILE455 3.5 8.3 1.0
HD2 A:PRO398 3.7 8.7 1.0
CD2 A:PHE463 3.8 7.2 1.0
CB A:ILE455 3.8 7.4 1.0
H A:ILE455 3.9 8.7 1.0
HD12 A:ILE455 3.9 8.7 1.0
CA A:HIS397 3.9 7.0 1.0
CE2 A:PHE463 4.0 8.0 1.0
CG1 A:ILE455 4.0 7.8 1.0
NE2 A:HIS397 4.1 8.2 1.0
HG13 A:ILE455 4.1 8.7 1.0
NE2 A:HIS458 4.1 8.5 1.0
HD13 A:ILE455 4.1 8.7 1.0
CD2 A:HIS458 4.1 8.2 1.0
CD2 A:HIS397 4.1 7.9 1.0
HB2 A:HIS397 4.3 12.4 1.0
HG21 A:ILE455 4.5 8.7 1.0
HZ A:PHE341 4.5 12.5 1.0
CD A:PRO398 4.6 7.1 1.0
HG22 A:ILE455 4.6 8.7 1.0
CA A:CYS453 4.6 6.6 1.0
CG2 A:ILE455 4.6 7.4 1.0
O A:GLY394 4.6 10.6 1.0
CZ A:PHE341 4.7 9.6 1.0
N A:ILE455 4.7 6.9 1.0
HA A:CYS453 4.8 6.7 1.0
HE2 A:PHE341 4.8 12.5 1.0
HE1 A:PHE399 4.8 11.1 1.0
HA2 A:GLY395 4.8 15.2 1.0
HD3 A:PRO398 4.8 8.7 1.0
CE2 A:PHE341 4.8 9.0 1.0
HE2 A:HIS397 4.8 8.2 1.0
CA A:HIS458 4.8 8.0 1.0
CA A:ILE455 4.8 7.0 1.0
HE2 A:HIS458 4.9 8.5 1.0
C A:HIS397 4.9 6.7 1.0
N A:HIS397 4.9 7.2 1.0
O A:ILE455 5.0 7.8 1.0
HG12 A:ILE455 5.0 8.7 1.0
HB3 A:PHE463 5.0 7.6 1.0
HD2 A:HIS458 5.0 8.5 1.0

Reference:

O.A.Glazunova, K.M.Polyakov, K.V.Moiseenko, S.A.Kurzeev, T.V.Fedorova. Structure-Function Study of Two New Middle-Redox Potential Laccases From Basidiomycetes Antrodiella Faginea and Steccherinum Murashkinskyi. Int. J. Biol. Macromol. V. 118 406 2018.
ISSN: ISSN 1879-0003
PubMed: 29890251
DOI: 10.1016/J.IJBIOMAC.2018.06.038
Page generated: Sun Dec 13 11:17:26 2020

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