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Copper in PDB 6rho: Single Crystal Serial Study of the X-Ray Induced Enzymatic Reduction of Molecular Oxygen to Water For Laccase From Steccherinum Murashkinskyi at Sub-Atomic Resolution. Twentieth Structure of the Series with 4065 Kgy Dose.

Enzymatic activity of Single Crystal Serial Study of the X-Ray Induced Enzymatic Reduction of Molecular Oxygen to Water For Laccase From Steccherinum Murashkinskyi at Sub-Atomic Resolution. Twentieth Structure of the Series with 4065 Kgy Dose.

All present enzymatic activity of Single Crystal Serial Study of the X-Ray Induced Enzymatic Reduction of Molecular Oxygen to Water For Laccase From Steccherinum Murashkinskyi at Sub-Atomic Resolution. Twentieth Structure of the Series with 4065 Kgy Dose.:
1.10.3.2;

Protein crystallography data

The structure of Single Crystal Serial Study of the X-Ray Induced Enzymatic Reduction of Molecular Oxygen to Water For Laccase From Steccherinum Murashkinskyi at Sub-Atomic Resolution. Twentieth Structure of the Series with 4065 Kgy Dose., PDB code: 6rho 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 / 1.07
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 56.430, 84.300, 112.670, 90.00, 90.00, 90.00
R / Rfree (%) 12.6 / 14.3

Copper Binding Sites:

The binding sites of Copper atom in the Single Crystal Serial Study of the X-Ray Induced Enzymatic Reduction of Molecular Oxygen to Water For Laccase From Steccherinum Murashkinskyi at Sub-Atomic Resolution. Twentieth Structure of the Series with 4065 Kgy Dose. (pdb code 6rho). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 4 binding sites of Copper where determined in the Single Crystal Serial Study of the X-Ray Induced Enzymatic Reduction of Molecular Oxygen to Water For Laccase From Steccherinum Murashkinskyi at Sub-Atomic Resolution. Twentieth Structure of the Series with 4065 Kgy Dose., PDB code: 6rho:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in 6rho

Go back to Copper Binding Sites List in 6rho
Copper binding site 1 out of 4 in the Single Crystal Serial Study of the X-Ray Induced Enzymatic Reduction of Molecular Oxygen to Water For Laccase From Steccherinum Murashkinskyi at Sub-Atomic Resolution. Twentieth Structure of the Series with 4065 Kgy Dose.


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Single Crystal Serial Study of the X-Ray Induced Enzymatic Reduction of Molecular Oxygen to Water For Laccase From Steccherinum Murashkinskyi at Sub-Atomic Resolution. Twentieth Structure of the Series with 4065 Kgy Dose. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu501

b:9.5
occ:0.95
NE2 A:HIS452 2.0 10.3 1.0
NE2 A:HIS402 2.0 8.5 1.0
NE2 A:HIS112 2.0 9.6 1.0
O A:HOH601 2.3 9.4 0.2
O1 A:OXY509 2.4 9.3 0.1
O2 A:OXY509 2.5 9.3 0.1
CE1 A:HIS402 2.9 9.0 1.0
CD2 A:HIS452 3.0 10.0 1.0
HE1 A:HIS402 3.0 6.8 1.0
CE1 A:HIS452 3.0 9.9 1.0
CE1 A:HIS112 3.0 10.3 1.0
CD2 A:HIS402 3.1 8.2 1.0
CD2 A:HIS112 3.1 8.4 1.0
HD2 A:HIS452 3.1 10.4 1.0
HE1 A:HIS112 3.2 6.6 1.0
HE1 A:HIS452 3.2 10.3 1.0
HD2 A:PHE450 3.2 6.6 1.0
HD2 A:HIS400 3.3 9.7 1.0
HD2 A:HIS112 3.3 6.6 1.0
HD2 A:HIS402 3.3 6.8 1.0
HB3 A:PHE450 3.6 6.8 1.0
O A:HOH605 3.9 16.2 0.8
CD2 A:PHE450 3.9 10.8 1.0
ND1 A:HIS402 4.0 8.3 1.0
HB3 A:PRO80 4.1 5.5 1.0
ND1 A:HIS452 4.1 9.5 1.0
CG A:HIS452 4.1 9.2 1.0
CD2 A:HIS400 4.1 8.2 1.0
CG A:HIS402 4.2 8.0 1.0
ND1 A:HIS112 4.2 10.3 1.0
CG A:HIS112 4.2 9.0 1.0
HE1 A:HIS110 4.3 10.3 1.0
HD2 A:HIS65 4.3 9.7 1.0
CB A:PHE450 4.4 9.6 1.0
CU A:CU503 4.4 8.3 0.8
CD2 A:HIS65 4.5 8.1 1.0
NE2 A:HIS65 4.5 8.3 1.0
HD21 A:LEU459 4.5 7.7 1.0
HB2 A:PHE450 4.6 6.8 1.0
CG A:PHE450 4.6 9.0 1.0
HE2 A:PHE450 4.7 6.6 1.0
NE2 A:HIS400 4.7 8.3 1.0
CE2 A:PHE450 4.7 13.0 1.0
HD1 A:HIS402 4.8 6.8 1.0
HD1 A:HIS452 4.9 10.4 1.0
HD2 A:HIS454 4.9 5.6 1.0
HD1 A:HIS112 5.0 6.6 1.0
HD22 A:LEU459 5.0 7.7 1.0
CB A:PRO80 5.0 9.2 1.0

Copper binding site 2 out of 4 in 6rho

Go back to Copper Binding Sites List in 6rho
Copper binding site 2 out of 4 in the Single Crystal Serial Study of the X-Ray Induced Enzymatic Reduction of Molecular Oxygen to Water For Laccase From Steccherinum Murashkinskyi at Sub-Atomic Resolution. Twentieth Structure of the Series with 4065 Kgy Dose.


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Single Crystal Serial Study of the X-Ray Induced Enzymatic Reduction of Molecular Oxygen to Water For Laccase From Steccherinum Murashkinskyi at Sub-Atomic Resolution. Twentieth Structure of the Series with 4065 Kgy Dose. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu502

b:8.6
occ:0.95
ND1 A:HIS67 1.9 8.3 1.0
NE2 A:HIS110 1.9 8.3 1.0
NE2 A:HIS454 2.1 8.5 1.0
O2 A:OXY509 2.7 9.3 0.1
HB2 A:HIS67 2.8 5.5 1.0
CE1 A:HIS67 2.9 8.1 1.0
CD2 A:HIS110 2.9 8.0 1.0
O A:HOH601 3.0 9.4 0.2
CE1 A:HIS110 3.0 8.5 1.0
CE1 A:HIS454 3.0 8.9 1.0
HD2 A:HIS65 3.0 9.7 1.0
CG A:HIS67 3.0 8.2 1.0
HE1 A:HIS454 3.1 5.6 1.0
HE1 A:HIS67 3.1 5.6 1.0
HD2 A:HIS110 3.1 10.3 1.0
HE1 A:HIS110 3.2 10.3 1.0
CD2 A:HIS454 3.2 8.6 1.0
O1 A:OXY509 3.3 9.3 0.1
CB A:HIS67 3.4 7.7 1.0
HZ2 A:TRP108 3.4 6.1 1.0
HD2 A:HIS454 3.5 5.6 1.0
HB2 A:ALA244 3.6 6.1 1.0
CZ2 A:TRP108 3.7 8.4 1.0
CD2 A:HIS65 3.8 8.1 1.0
HE1 A:TRP108 4.0 6.1 1.0
CE2 A:TRP108 4.0 8.2 1.0
HB3 A:HIS67 4.0 5.5 1.0
NE2 A:HIS67 4.0 9.1 1.0
ND1 A:HIS110 4.1 8.4 1.0
NE1 A:TRP108 4.1 8.5 1.0
CG A:HIS110 4.1 8.1 1.0
CD2 A:HIS67 4.1 8.3 1.0
CU A:CU503 4.1 8.3 0.8
ND1 A:HIS454 4.2 8.6 1.0
HD2 A:HIS400 4.3 9.7 1.0
CG A:HIS454 4.3 8.2 1.0
HA A:HIS67 4.3 4.8 1.0
NE2 A:HIS65 4.3 8.3 1.0
HB1 A:ALA244 4.3 6.1 1.0
CB A:ALA244 4.4 8.5 1.0
CD2 A:HIS400 4.4 8.2 1.0
NE2 A:HIS400 4.4 8.3 1.0
CH2 A:TRP108 4.5 8.8 1.0
O A:HOH605 4.5 16.2 0.8
CA A:HIS67 4.5 7.7 1.0
HH2 A:TRP108 4.6 6.1 1.0
HE2 A:HIS67 4.8 5.6 1.0
HB3 A:ALA244 4.8 6.1 1.0
CD2 A:TRP108 4.9 8.2 1.0
HD1 A:HIS110 4.9 10.3 1.0
HD1 A:HIS454 4.9 5.6 1.0
HD2 A:HIS112 4.9 6.6 1.0
HD2 A:HIS67 5.0 5.6 1.0

Copper binding site 3 out of 4 in 6rho

Go back to Copper Binding Sites List in 6rho
Copper binding site 3 out of 4 in the Single Crystal Serial Study of the X-Ray Induced Enzymatic Reduction of Molecular Oxygen to Water For Laccase From Steccherinum Murashkinskyi at Sub-Atomic Resolution. Twentieth Structure of the Series with 4065 Kgy Dose.


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Single Crystal Serial Study of the X-Ray Induced Enzymatic Reduction of Molecular Oxygen to Water For Laccase From Steccherinum Murashkinskyi at Sub-Atomic Resolution. Twentieth Structure of the Series with 4065 Kgy Dose. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu503

b:8.3
occ:0.83
NE2 A:HIS65 1.8 8.3 1.0
NE2 A:HIS400 1.8 8.3 1.0
O A:HOH1029 2.6 8.0 1.0
CE1 A:HIS65 2.8 8.9 1.0
CD2 A:HIS400 2.9 8.2 1.0
CE1 A:HIS400 2.9 8.0 1.0
CD2 A:HIS65 2.9 8.1 1.0
HE1 A:HIS65 3.0 9.7 1.0
HA A:HIS67 3.0 4.8 1.0
HD2 A:HIS400 3.1 9.7 1.0
HE1 A:HIS400 3.1 9.7 1.0
HD2 A:HIS65 3.2 9.7 1.0
H A:GLY68 3.2 4.8 1.0
O2 A:OXY509 3.3 9.3 0.1
CD2 A:HIS402 3.4 8.2 1.0
NE2 A:HIS402 3.4 8.5 1.0
ND1 A:HIS67 3.6 8.3 1.0
HD2 A:HIS402 3.6 6.8 1.0
HA A:HIS402 3.7 5.5 1.0
CG A:HIS402 3.7 8.0 1.0
CE1 A:HIS402 3.8 9.0 1.0
O A:HOH601 3.8 9.4 0.2
CG A:HIS67 3.8 8.2 1.0
CA A:HIS67 3.9 7.7 1.0
ND1 A:HIS402 3.9 8.3 1.0
ND1 A:HIS65 4.0 8.6 1.0
CE1 A:HIS67 4.0 8.1 1.0
ND1 A:HIS400 4.0 8.2 1.0
N A:GLY68 4.0 8.3 1.0
CG A:HIS65 4.0 8.0 1.0
CG A:HIS400 4.0 8.2 1.0
CU A:CU502 4.1 8.6 0.9
HE1 A:HIS402 4.2 6.8 1.0
HB2 A:HIS67 4.2 5.5 1.0
CB A:HIS67 4.2 7.7 1.0
HE1 A:HIS67 4.3 5.6 1.0
CD2 A:HIS67 4.4 8.3 1.0
NE2 A:HIS67 4.4 9.1 1.0
CA A:HIS402 4.4 8.0 1.0
CU A:CU501 4.4 9.5 0.9
HD1 A:HIS402 4.4 6.8 1.0
O1 A:OXY509 4.5 9.3 0.1
C A:HIS67 4.5 8.5 1.0
CB A:HIS402 4.5 8.3 1.0
O A:HOH815 4.6 11.6 1.0
O A:HOH730 4.7 12.8 1.0
HD1 A:HIS65 4.7 9.7 1.0
HB3 A:HIS402 4.7 6.8 1.0
HD1 A:HIS400 4.8 9.7 1.0
HA2 A:GLY68 4.8 5.7 1.0
N A:HIS402 4.8 7.8 1.0
HD2 A:HIS67 4.9 5.6 1.0
HE2 A:HIS67 4.9 5.6 1.0
O A:LEU401 4.9 8.9 1.0
N A:HIS67 5.0 7.9 1.0
HD2 A:HIS112 5.0 6.6 1.0
O A:TRP66 5.0 8.4 1.0

Copper binding site 4 out of 4 in 6rho

Go back to Copper Binding Sites List in 6rho
Copper binding site 4 out of 4 in the Single Crystal Serial Study of the X-Ray Induced Enzymatic Reduction of Molecular Oxygen to Water For Laccase From Steccherinum Murashkinskyi at Sub-Atomic Resolution. Twentieth Structure of the Series with 4065 Kgy Dose.


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Single Crystal Serial Study of the X-Ray Induced Enzymatic Reduction of Molecular Oxygen to Water For Laccase From Steccherinum Murashkinskyi at Sub-Atomic Resolution. Twentieth Structure of the Series with 4065 Kgy Dose. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu504

b:8.5
occ:0.78
ND1 A:HIS458 2.0 9.8 1.0
ND1 A:HIS397 2.0 9.9 1.0
SG A:CYS453 2.2 10.6 1.0
HD11 A:ILE455 2.7 6.6 1.0
CE1 A:HIS397 3.0 9.9 1.0
CE1 A:HIS458 3.0 10.8 1.0
HB A:ILE455 3.0 6.6 1.0
CG A:HIS458 3.1 9.6 1.0
CG A:HIS397 3.1 9.7 1.0
HD2 A:PHE463 3.1 9.3 1.0
HB3 A:HIS397 3.1 9.2 1.0
HE1 A:HIS397 3.1 7.0 1.0
HB2 A:HIS458 3.1 6.6 1.0
HE1 A:HIS458 3.2 9.7 1.0
HB3 A:HIS458 3.3 6.6 1.0
CB A:CYS453 3.3 9.7 1.0
HB2 A:CYS453 3.4 6.3 1.0
CB A:HIS458 3.4 9.1 1.0
HA A:HIS397 3.4 6.6 1.0
HB3 A:CYS453 3.4 6.3 1.0
CB A:HIS397 3.5 9.6 1.0
CD1 A:ILE455 3.6 9.8 1.0
HE2 A:PHE463 3.6 9.3 1.0
HD2 A:PRO398 3.8 6.6 1.0
CB A:ILE455 3.9 9.2 1.0
CD2 A:PHE463 3.9 9.8 1.0
H A:ILE455 3.9 6.6 1.0
HD12 A:ILE455 4.0 6.6 1.0
CA A:HIS397 4.0 9.4 1.0
CG1 A:ILE455 4.1 9.7 1.0
HG13 A:ILE455 4.1 6.6 1.0
CE2 A:PHE463 4.1 9.6 1.0
NE2 A:HIS397 4.1 10.4 1.0
NE2 A:HIS458 4.1 11.0 1.0
HD13 A:ILE455 4.2 6.6 1.0
CD2 A:HIS397 4.2 10.8 1.0
CD2 A:HIS458 4.2 10.5 1.0
HB2 A:HIS397 4.4 9.2 1.0
HG21 A:ILE455 4.6 6.6 1.0
CD A:PRO398 4.6 9.3 1.0
HZ A:PHE341 4.6 17.6 1.0
HG22 A:ILE455 4.6 6.6 1.0
CG2 A:ILE455 4.7 9.6 1.0
CA A:CYS453 4.7 8.3 1.0
O A:GLY394 4.7 14.4 1.0
CZ A:PHE341 4.8 12.4 1.0
N A:ILE455 4.8 8.9 1.0
HA A:CYS453 4.9 5.6 1.0
HD3 A:PRO398 4.9 6.6 1.0
HE1 A:PHE399 4.9 9.0 1.0
HE2 A:HIS397 4.9 7.0 1.0
CA A:ILE455 4.9 9.0 1.0
HE2 A:PHE341 4.9 17.6 1.0
HE2 A:HIS458 4.9 9.7 1.0
CA A:HIS458 4.9 10.1 1.0
HA2 A:GLY395 4.9 9.2 1.0
CE2 A:PHE341 5.0 11.6 1.0
C A:HIS397 5.0 9.0 1.0
HG12 A:ILE455 5.0 6.6 1.0
HB3 A:PHE463 5.0 7.1 1.0

Reference:

K.M.Polyakov, S.Gavryushov, T.V.Fedorova, O.A.Glazunova, A.N.Popov. The Subatomic Resolution Study of Laccase Inhibition By Chloride and Fluoride Anions Using Single-Crystal Serial Crystallography: Insights Into the Enzymatic Reaction Mechanism. Acta Crystallogr D Struct V. 75 804 2019BIOL.
ISSN: ISSN 2059-7983
PubMed: 31478903
DOI: 10.1107/S2059798319010684
Page generated: Wed Jul 31 07:00:33 2024

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