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Copper in PDB 5mig: The Study of the X-Ray Induced Enzymatic Reduction of Molecular Oxygen to Water For Laccase From Steccherinum Murashkinskyi.the 16-Th Structure of the Series with Total Exposition Time 453 Min. the Crystal Was Quick Refreezing Before This Data Collection.

Enzymatic activity of The Study of the X-Ray Induced Enzymatic Reduction of Molecular Oxygen to Water For Laccase From Steccherinum Murashkinskyi.the 16-Th Structure of the Series with Total Exposition Time 453 Min. the Crystal Was Quick Refreezing Before This Data Collection.

All present enzymatic activity of The Study of the X-Ray Induced Enzymatic Reduction of Molecular Oxygen to Water For Laccase From Steccherinum Murashkinskyi.the 16-Th Structure of the Series with Total Exposition Time 453 Min. the Crystal Was Quick Refreezing Before This Data Collection.:
1.10.3.2;

Protein crystallography data

The structure of The Study of the X-Ray Induced Enzymatic Reduction of Molecular Oxygen to Water For Laccase From Steccherinum Murashkinskyi.the 16-Th Structure of the Series with Total Exposition Time 453 Min. the Crystal Was Quick Refreezing Before This Data Collection., PDB code: 5mig was solved by K.M.Polyakov, S.Gavryushov, T.V.Fedorova, O.A.Glazunova, A.N.Popov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 67.50 / 1.35
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 56.268, 84.415, 112.384, 90.00, 90.00, 90.00
R / Rfree (%) 14.1 / 16.2

Other elements in 5mig:

The structure of The Study of the X-Ray Induced Enzymatic Reduction of Molecular Oxygen to Water For Laccase From Steccherinum Murashkinskyi.the 16-Th Structure of the Series with Total Exposition Time 453 Min. the Crystal Was Quick Refreezing Before This Data Collection. also contains other interesting chemical elements:

Sodium (Na) 1 atom

Copper Binding Sites:

The binding sites of Copper atom in the The Study of the X-Ray Induced Enzymatic Reduction of Molecular Oxygen to Water For Laccase From Steccherinum Murashkinskyi.the 16-Th Structure of the Series with Total Exposition Time 453 Min. the Crystal Was Quick Refreezing Before This Data Collection. (pdb code 5mig). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 4 binding sites of Copper where determined in the The Study of the X-Ray Induced Enzymatic Reduction of Molecular Oxygen to Water For Laccase From Steccherinum Murashkinskyi.the 16-Th Structure of the Series with Total Exposition Time 453 Min. the Crystal Was Quick Refreezing Before This Data Collection., PDB code: 5mig:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in 5mig

Go back to Copper Binding Sites List in 5mig
Copper binding site 1 out of 4 in the The Study of the X-Ray Induced Enzymatic Reduction of Molecular Oxygen to Water For Laccase From Steccherinum Murashkinskyi.the 16-Th Structure of the Series with Total Exposition Time 453 Min. the Crystal Was Quick Refreezing Before This Data Collection.


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of The Study of the X-Ray Induced Enzymatic Reduction of Molecular Oxygen to Water For Laccase From Steccherinum Murashkinskyi.the 16-Th Structure of the Series with Total Exposition Time 453 Min. the Crystal Was Quick Refreezing Before This Data Collection. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu601

b:7.9
occ:0.90
 NE2 A:HIS402 2.0 7.5 1.0
NE2 A:HIS452 2.0 8.8 1.0
NE2 A:HIS112 2.0 7.4 1.0
O A:HOH1106 2.3 10.7 0.5
CE1 A:HIS402 2.9 7.9 1.0
CD2 A:HIS452 2.9 8.2 1.0
CE1 A:HIS112 3.0 7.8 1.0
CE1 A:HIS452 3.0 8.9 1.0
HE1 A:HIS402 3.0 7.6 1.0
CD2 A:HIS402 3.1 7.0 1.0
CD2 A:HIS112 3.1 7.5 1.0
HD2 A:HIS452 3.1 8.1 1.0
HE1 A:HIS112 3.1 7.7 1.0
HE1 A:HIS452 3.2 8.5 1.0
HD2 A:HIS400 3.2 6.5 1.0
HD2 A:HIS112 3.3 7.5 1.0
HD2 A:HIS402 3.3 7.1 1.0
HD2 A:PHE450 3.4 8.8 1.0
HB3 A:PHE450 3.7 7.6 1.0
CD2 A:PHE450 4.0 9.0 1.0
ND1 A:HIS402 4.0 7.0 1.0
ND1 A:HIS452 4.1 7.5 1.0
CG A:HIS452 4.1 7.4 1.0
O A:HOH1206 4.1 23.9 1.0
CD2 A:HIS400 4.1 6.6 1.0
ND1 A:HIS112 4.1 7.7 1.0
HB3 A:PRO80 4.1 6.8 1.0
CG A:HIS402 4.1 6.8 1.0
CG A:HIS112 4.2 7.6 1.0
HE1 A:HIS110 4.2 7.4 1.0
HD2 A:HIS65 4.3 7.1 1.0
CU A:CU603 4.3 6.5 0.8
CD2 A:HIS65 4.5 7.2 1.0
CB A:PHE450 4.5 7.5 1.0
NE2 A:HIS65 4.5 7.3 1.0
HD21 A:LEU459 4.5 9.2 1.0
CG A:PHE450 4.6 8.0 1.0
HB2 A:PHE450 4.7 7.6 1.0
NE2 A:HIS400 4.7 6.8 1.0
HD1 A:HIS402 4.8 7.1 1.0
HE2 A:PHE450 4.8 9.2 1.0
CE2 A:PHE450 4.9 9.2 1.0
HD1 A:HIS452 4.9 7.8 1.0
HD2 A:HIS454 4.9 7.3 1.0
HD1 A:HIS112 4.9 7.7 1.0

Copper binding site 2 out of 4 in 5mig

Go back to Copper Binding Sites List in 5mig
Copper binding site 2 out of 4 in the The Study of the X-Ray Induced Enzymatic Reduction of Molecular Oxygen to Water For Laccase From Steccherinum Murashkinskyi.the 16-Th Structure of the Series with Total Exposition Time 453 Min. the Crystal Was Quick Refreezing Before This Data Collection.


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of The Study of the X-Ray Induced Enzymatic Reduction of Molecular Oxygen to Water For Laccase From Steccherinum Murashkinskyi.the 16-Th Structure of the Series with Total Exposition Time 453 Min. the Crystal Was Quick Refreezing Before This Data Collection. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu602

b:6.9
occ:0.90
 ND1 A:HIS67 1.9 7.3 1.0
NE2 A:HIS110 2.0 7.5 1.0
NE2 A:HIS454 2.1 7.4 1.0
HB2 A:HIS67 2.8 6.2 1.0
O A:HOH1106 2.9 10.7 0.5
CE1 A:HIS67 2.9 6.7 1.0
CE1 A:HIS110 3.0 7.6 1.0
HD2 A:HIS65 3.0 7.1 1.0
CG A:HIS67 3.0 6.2 1.0
CD2 A:HIS110 3.0 6.8 1.0
CE1 A:HIS454 3.0 8.2 1.0
HE1 A:HIS67 3.1 6.8 1.0
HE1 A:HIS454 3.1 7.8 1.0
CD2 A:HIS454 3.2 7.3 1.0
HD2 A:HIS110 3.2 7.0 1.0
HE1 A:HIS110 3.2 7.4 1.0
CB A:HIS67 3.4 6.2 1.0
HD2 A:HIS454 3.4 7.3 1.0
HZ2 A:TRP108 3.5 7.1 1.0
HB2 A:ALA244 3.6 6.3 1.0
CZ2 A:TRP108 3.8 6.9 1.0
CD2 A:HIS65 3.8 7.2 1.0
HB3 A:HIS67 4.0 6.2 1.0
HE1 A:TRP108 4.0 6.6 1.0
CE2 A:TRP108 4.0 7.0 1.0
NE2 A:HIS67 4.0 6.8 1.0
CU A:CU603 4.1 6.5 0.8
CD2 A:HIS67 4.1 7.2 1.0
ND1 A:HIS110 4.1 6.8 1.0
NE1 A:TRP108 4.1 6.4 1.0
CG A:HIS110 4.1 7.0 1.0
ND1 A:HIS454 4.2 7.6 1.0
HD2 A:HIS400 4.2 6.5 1.0
CG A:HIS454 4.3 7.2 1.0
HA A:HIS67 4.3 6.2 1.0
NE2 A:HIS65 4.3 7.3 1.0
HB1 A:ALA244 4.3 6.3 1.0
CB A:ALA244 4.4 6.5 1.0
CD2 A:HIS400 4.4 6.6 1.0
NE2 A:HIS400 4.4 6.8 1.0
CH2 A:TRP108 4.5 7.7 1.0
CA A:HIS67 4.5 6.2 1.0
HH2 A:TRP108 4.7 7.4 1.0
O A:HOH1206 4.8 23.9 1.0
HB3 A:ALA244 4.8 6.3 1.0
HE2 A:HIS67 4.8 6.9 1.0
HD2 A:HIS112 4.9 7.5 1.0
HD1 A:HIS110 4.9 7.0 1.0
CD2 A:TRP108 4.9 6.3 1.0
HD1 A:HIS454 4.9 7.6 1.0
HD2 A:HIS67 5.0 6.9 1.0
HE1 A:HIS452 5.0 8.5 1.0

Copper binding site 3 out of 4 in 5mig

Go back to Copper Binding Sites List in 5mig
Copper binding site 3 out of 4 in the The Study of the X-Ray Induced Enzymatic Reduction of Molecular Oxygen to Water For Laccase From Steccherinum Murashkinskyi.the 16-Th Structure of the Series with Total Exposition Time 453 Min. the Crystal Was Quick Refreezing Before This Data Collection.


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of The Study of the X-Ray Induced Enzymatic Reduction of Molecular Oxygen to Water For Laccase From Steccherinum Murashkinskyi.the 16-Th Structure of the Series with Total Exposition Time 453 Min. the Crystal Was Quick Refreezing Before This Data Collection. 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 7.3 1.0
O A:HOH1036 2.6 8.1 1.0
CE1 A:HIS65 2.8 6.7 1.0
CD2 A:HIS400 2.8 6.6 1.0
CE1 A:HIS400 2.9 6.6 1.0
CD2 A:HIS65 2.9 7.2 1.0
HE1 A:HIS65 3.0 6.8 1.0
HD2 A:HIS400 3.0 6.5 1.0
HA A:HIS67 3.1 6.2 1.0
HD2 A:HIS65 3.1 7.1 1.0
HE1 A:HIS400 3.1 6.5 1.0
H A:GLY68 3.3 6.1 1.0
CD2 A:HIS402 3.4 7.0 1.0
NE2 A:HIS402 3.4 7.5 1.0
ND1 A:HIS67 3.6 7.3 1.0
HD2 A:HIS402 3.6 7.1 1.0
HA A:HIS402 3.7 6.5 1.0
CG A:HIS402 3.7 6.8 1.0
O A:HOH1106 3.7 10.7 0.5
CE1 A:HIS402 3.8 7.9 1.0
CG A:HIS67 3.8 6.2 1.0
ND1 A:HIS402 3.9 7.0 1.0
CE1 A:HIS67 3.9 6.7 1.0
CA A:HIS67 3.9 6.2 1.0
ND1 A:HIS65 4.0 6.7 1.0
CG A:HIS400 4.0 6.2 1.0
ND1 A:HIS400 4.0 6.1 1.0
CG A:HIS65 4.0 6.9 1.0
N A:GLY68 4.0 5.9 1.0
CU A:CU602 4.1 6.9 0.9
HB2 A:HIS67 4.2 6.2 1.0
CB A:HIS67 4.2 6.2 1.0
HE1 A:HIS402 4.2 7.6 1.0
HE1 A:HIS67 4.3 6.8 1.0
CU A:CU601 4.3 7.9 0.9
CD2 A:HIS67 4.3 7.2 1.0
NE2 A:HIS67 4.4 6.8 1.0
CA A:HIS402 4.4 6.5 1.0
HD1 A:HIS402 4.5 7.1 1.0
C A:HIS67 4.5 6.4 1.0
CB A:HIS402 4.6 6.7 1.0
O A:HOH867 4.6 8.9 1.0
O A:HOH825 4.7 7.8 1.0
HD1 A:HIS65 4.7 6.7 1.0
HB3 A:HIS402 4.8 6.7 1.0
HA2 A:GLY68 4.8 6.4 1.0
HD1 A:HIS400 4.8 6.2 1.0
N A:HIS402 4.8 6.3 1.0
HD2 A:HIS67 4.9 6.9 1.0
HD2 A:HIS454 4.9 7.3 1.0
O A:LEU401 4.9 7.0 1.0
HE2 A:HIS67 4.9 6.9 1.0
HD2 A:HIS112 5.0 7.5 1.0
N A:HIS67 5.0 6.1 1.0

Copper binding site 4 out of 4 in 5mig

Go back to Copper Binding Sites List in 5mig
Copper binding site 4 out of 4 in the The Study of the X-Ray Induced Enzymatic Reduction of Molecular Oxygen to Water For Laccase From Steccherinum Murashkinskyi.the 16-Th Structure of the Series with Total Exposition Time 453 Min. the Crystal Was Quick Refreezing Before This Data Collection.


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of The Study of the X-Ray Induced Enzymatic Reduction of Molecular Oxygen to Water For Laccase From Steccherinum Murashkinskyi.the 16-Th Structure of the Series with Total Exposition Time 453 Min. the Crystal Was Quick Refreezing Before This Data Collection. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu604

b:7.1
occ:0.90
 ND1 A:HIS458 2.0 7.6 1.0
ND1 A:HIS397 2.0 7.4 1.0
SG A:CYS453 2.2 7.8 1.0
HD11 A:ILE455 2.6 6.9 1.0
CE1 A:HIS397 2.9 7.9 1.0
CE1 A:HIS458 3.0 8.2 1.0
HB A:ILE455 3.0 7.3 1.0
CG A:HIS458 3.0 8.1 1.0
HD2 A:PHE463 3.1 7.3 1.0
HE1 A:HIS397 3.1 7.9 1.0
HB3 A:HIS397 3.1 7.8 1.0
HB2 A:HIS458 3.1 8.1 1.0
CG A:HIS397 3.1 7.5 1.0
HE1 A:HIS458 3.2 8.1 1.0
HB3 A:HIS458 3.3 8.1 1.0
CB A:CYS453 3.3 7.3 1.0
HB2 A:CYS453 3.3 7.3 1.0
CB A:HIS458 3.4 8.0 1.0
HA A:HIS397 3.4 7.8 1.0
HB3 A:CYS453 3.4 7.3 1.0
CB A:HIS397 3.5 7.9 1.0
HE2 A:PHE463 3.6 7.8 1.0
CD1 A:ILE455 3.6 6.7 1.0
HD2 A:PRO398 3.8 7.2 1.0
CD2 A:PHE463 3.8 7.0 1.0
CB A:ILE455 3.9 7.0 1.0
H A:ILE455 3.9 7.7 1.0
HD12 A:ILE455 3.9 6.9 1.0
CA A:HIS397 4.0 7.9 1.0
CG1 A:ILE455 4.1 7.3 1.0
NE2 A:HIS397 4.1 8.4 1.0
CE2 A:PHE463 4.1 8.0 1.0
HG13 A:ILE455 4.1 7.1 1.0
NE2 A:HIS458 4.1 8.5 1.0
HD13 A:ILE455 4.2 6.9 1.0
CD2 A:HIS458 4.2 7.8 1.0
CD2 A:HIS397 4.2 8.8 1.0
HB2 A:HIS397 4.4 7.8 1.0
HG21 A:ILE455 4.5 7.4 1.0
HZ A:PHE341 4.6 8.7 1.0
HG22 A:ILE455 4.6 7.4 1.0
O A:GLY394 4.6 11.1 1.0
CG2 A:ILE455 4.6 7.6 1.0
CA A:CYS453 4.7 6.9 1.0
CD A:PRO398 4.7 7.2 1.0
CZ A:PHE341 4.7 8.7 1.0
N A:ILE455 4.8 7.4 1.0
HD3 A:PRO398 4.8 7.2 1.0
HA A:CYS453 4.8 7.0 1.0
HE2 A:HIS397 4.8 8.3 1.0
HE2 A:PHE341 4.8 8.5 1.0
HE1 A:PHE399 4.9 8.1 1.0
CE2 A:PHE341 4.9 8.4 1.0
CA A:HIS458 4.9 8.3 1.0
CA A:ILE455 4.9 7.9 1.0
HE2 A:HIS458 4.9 8.2 1.0
HA2 A:GLY395 4.9 10.0 1.0
N A:HIS397 5.0 7.8 1.0
C A:HIS397 5.0 7.5 1.0
O A:ILE455 5.0 7.5 1.0
HB3 A:PHE463 5.0 7.6 1.0

Reference:

K.M.Polyakov, S.Gavryushov, S.Ivanova, T.V.Fedorova, O.A.Glazunova, A.N.Popov, O.V.Koroleva. Structural Study of the X-Ray-Induced Enzymatic Reduction of Molecular Oxygen to Water By Steccherinum Murashkinskyi Laccase: Insights Into the Reaction Mechanism. Acta Crystallogr D Struct V. 73 388 2017BIOL.
ISSN: ISSN 2059-7983
PubMed: 28471364
DOI: 10.1107/S2059798317003667
Page generated: Wed Jul 31 04:37:23 2024

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