Atomistry » Copper » PDB 6ri4-6vow » 6rik
Atomistry »
  Copper »
    PDB 6ri4-6vow »
      6rik »

Copper in PDB 6rik: Single Crystal Serial Study of the Inhibition of Laccases From Steccherinum Murashkinskyi By Fluoride Anions at Sub-Atomic Resolution. Thirteenth Structure of the Series with 5200 Kgy Dose.

Enzymatic activity of Single Crystal Serial Study of the Inhibition of Laccases From Steccherinum Murashkinskyi By Fluoride Anions at Sub-Atomic Resolution. Thirteenth Structure of the Series with 5200 Kgy Dose.

All present enzymatic activity of Single Crystal Serial Study of the Inhibition of Laccases From Steccherinum Murashkinskyi By Fluoride Anions at Sub-Atomic Resolution. Thirteenth Structure of the Series with 5200 Kgy Dose.:
1.10.3.2;

Protein crystallography data

The structure of Single Crystal Serial Study of the Inhibition of Laccases From Steccherinum Murashkinskyi By Fluoride Anions at Sub-Atomic Resolution. Thirteenth Structure of the Series with 5200 Kgy Dose., PDB code: 6rik 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) 67.46 / 1.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 56.300, 84.370, 112.320, 90.00, 90.00, 90.00
R / Rfree (%) 12.3 / 15.2

Other elements in 6rik:

The structure of Single Crystal Serial Study of the Inhibition of Laccases From Steccherinum Murashkinskyi By Fluoride Anions at Sub-Atomic Resolution. Thirteenth Structure of the Series with 5200 Kgy Dose. also contains other interesting chemical elements:

Fluorine (F) 1 atom

Copper Binding Sites:

The binding sites of Copper atom in the Single Crystal Serial Study of the Inhibition of Laccases From Steccherinum Murashkinskyi By Fluoride Anions at Sub-Atomic Resolution. Thirteenth Structure of the Series with 5200 Kgy Dose. (pdb code 6rik). 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 Inhibition of Laccases From Steccherinum Murashkinskyi By Fluoride Anions at Sub-Atomic Resolution. Thirteenth Structure of the Series with 5200 Kgy Dose., PDB code: 6rik:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in 6rik

Go back to Copper Binding Sites List in 6rik
Copper binding site 1 out of 4 in the Single Crystal Serial Study of the Inhibition of Laccases From Steccherinum Murashkinskyi By Fluoride Anions at Sub-Atomic Resolution. Thirteenth Structure of the Series with 5200 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 Inhibition of Laccases From Steccherinum Murashkinskyi By Fluoride Anions at Sub-Atomic Resolution. Thirteenth Structure of the Series with 5200 Kgy Dose. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu501

b:11.9
occ:0.95
NE2 A:HIS112 2.0 11.9 1.0
NE2 A:HIS402 2.0 9.6 1.0
NE2 A:HIS452 2.0 12.5 1.0
O A:HOH978 2.3 10.2 0.2
CE1 A:HIS402 2.9 11.5 1.0
CD2 A:HIS452 2.9 12.3 1.0
CE1 A:HIS112 3.0 13.2 1.0
CE1 A:HIS452 3.0 12.6 1.0
HE1 A:HIS402 3.0 12.6 1.0
CD2 A:HIS112 3.0 9.7 1.0
CD2 A:HIS402 3.1 11.1 1.0
HD2 A:HIS452 3.1 12.4 1.0
HE1 A:HIS112 3.1 12.9 1.0
HE1 A:HIS452 3.2 12.4 1.0
HD2 A:HIS400 3.2 16.8 1.0
HD2 A:HIS112 3.2 12.9 1.0
HD2 A:PHE450 3.2 12.9 1.0
HD2 A:HIS402 3.3 12.6 1.0
HB3 A:PHE450 3.6 12.6 1.0
O A:HOH1061 3.8 26.5 1.0
CD2 A:PHE450 3.9 13.3 1.0
HB3 A:PRO80 4.1 12.1 1.0
ND1 A:HIS402 4.1 10.3 1.0
CG A:HIS452 4.1 11.5 1.0
CD2 A:HIS400 4.1 10.7 1.0
ND1 A:HIS452 4.1 11.6 1.0
ND1 A:HIS112 4.1 13.5 1.0
CG A:HIS402 4.2 10.6 1.0
CG A:HIS112 4.2 11.6 1.0
HE1 A:HIS110 4.2 15.6 1.0
HD2 A:HIS65 4.3 17.1 1.0
CU A:CU503 4.3 10.5 0.8
CD2 A:HIS65 4.4 9.7 1.0
CB A:PHE450 4.4 11.9 1.0
NE2 A:HIS65 4.5 9.8 1.0
HD21 A:LEU459 4.5 13.8 1.0
HB2 A:PHE450 4.6 12.6 1.0
CG A:PHE450 4.6 11.0 1.0
HE2 A:PHE450 4.6 12.9 1.0
NE2 A:HIS400 4.7 9.9 1.0
CE2 A:PHE450 4.7 16.9 1.0
HD1 A:HIS402 4.8 12.6 1.0
HD1 A:HIS452 4.9 12.4 1.0
HD1 A:HIS112 4.9 12.9 1.0
HD2 A:HIS454 4.9 10.8 1.0
HD22 A:LEU459 5.0 13.8 1.0
CB A:PRO80 5.0 11.6 1.0

Copper binding site 2 out of 4 in 6rik

Go back to Copper Binding Sites List in 6rik
Copper binding site 2 out of 4 in the Single Crystal Serial Study of the Inhibition of Laccases From Steccherinum Murashkinskyi By Fluoride Anions at Sub-Atomic Resolution. Thirteenth Structure of the Series with 5200 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 Inhibition of Laccases From Steccherinum Murashkinskyi By Fluoride Anions at Sub-Atomic Resolution. Thirteenth Structure of the Series with 5200 Kgy Dose. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu502

b:10.4
occ:0.95
NE2 A:HIS110 1.9 9.5 1.0
ND1 A:HIS67 1.9 10.3 1.0
NE2 A:HIS454 2.1 10.1 1.0
HB2 A:HIS67 2.8 10.8 1.0
CE1 A:HIS110 2.9 10.3 1.0
O A:HOH978 2.9 10.2 0.2
CE1 A:HIS67 2.9 9.6 1.0
CD2 A:HIS110 2.9 8.7 1.0
HD2 A:HIS65 3.0 17.1 1.0
CE1 A:HIS454 3.0 11.7 1.0
CG A:HIS67 3.0 10.3 1.0
HE1 A:HIS454 3.1 10.8 1.0
HE1 A:HIS67 3.1 10.8 1.0
HD2 A:HIS110 3.1 15.6 1.0
HE1 A:HIS110 3.1 15.6 1.0
CD2 A:HIS454 3.2 10.3 1.0
CB A:HIS67 3.4 10.3 1.0
HD2 A:HIS454 3.4 10.8 1.0
HZ2 A:TRP108 3.4 12.8 1.0
HB2 A:ALA244 3.7 12.9 1.0
CZ2 A:TRP108 3.7 10.4 1.0
CD2 A:HIS65 3.8 9.7 1.0
CE2 A:TRP108 4.0 9.7 1.0
HE1 A:TRP108 4.0 12.8 1.0
HB3 A:HIS67 4.0 10.8 1.0
CU A:CU503 4.0 10.5 0.8
NE2 A:HIS67 4.0 11.0 1.0
ND1 A:HIS110 4.1 10.4 1.0
CG A:HIS110 4.1 9.7 1.0
CD2 A:HIS67 4.1 10.4 1.0
NE1 A:TRP108 4.1 10.8 1.0
ND1 A:HIS454 4.2 10.1 1.0
HD2 A:HIS400 4.2 16.8 1.0
NE2 A:HIS65 4.3 9.8 1.0
HA A:HIS67 4.3 10.6 1.0
CG A:HIS454 4.3 10.0 1.0
HB1 A:ALA244 4.4 12.9 1.0
CD2 A:HIS400 4.4 10.7 1.0
NE2 A:HIS400 4.4 9.9 1.0
CB A:ALA244 4.4 10.9 1.0
CH2 A:TRP108 4.5 11.1 1.0
CA A:HIS67 4.5 9.5 1.0
O A:HOH1061 4.5 26.5 1.0
HH2 A:TRP108 4.7 12.8 1.0
HE2 A:HIS67 4.8 10.8 1.0
HB3 A:ALA244 4.9 12.9 1.0
HD2 A:HIS112 4.9 12.9 1.0
HD1 A:HIS110 4.9 15.6 1.0
CD2 A:TRP108 4.9 9.8 1.0
HD1 A:HIS454 4.9 10.8 1.0
CG A:HIS65 5.0 10.1 1.0
HE1 A:HIS452 5.0 12.4 1.0

Copper binding site 3 out of 4 in 6rik

Go back to Copper Binding Sites List in 6rik
Copper binding site 3 out of 4 in the Single Crystal Serial Study of the Inhibition of Laccases From Steccherinum Murashkinskyi By Fluoride Anions at Sub-Atomic Resolution. Thirteenth Structure of the Series with 5200 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 Inhibition of Laccases From Steccherinum Murashkinskyi By Fluoride Anions at Sub-Atomic Resolution. Thirteenth Structure of the Series with 5200 Kgy Dose. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu503

b:10.5
occ:0.83
NE2 A:HIS65 1.8 9.8 1.0
NE2 A:HIS400 1.9 9.9 1.0
F A:F509 2.6 16.1 0.8
O A:HOH679 2.7 16.0 0.2
CE1 A:HIS65 2.8 10.9 1.0
CD2 A:HIS400 2.8 10.7 1.0
CE1 A:HIS400 2.9 10.0 1.0
CD2 A:HIS65 2.9 9.7 1.0
HE1 A:HIS65 3.0 17.1 1.0
HA A:HIS67 3.0 10.6 1.0
HD2 A:HIS400 3.0 16.8 1.0
HE1 A:HIS400 3.1 16.8 1.0
HD2 A:HIS65 3.2 17.1 1.0
H A:GLY68 3.2 10.6 1.0
CD2 A:HIS402 3.3 11.1 1.0
NE2 A:HIS402 3.4 9.6 1.0
ND1 A:HIS67 3.5 10.3 1.0
HD2 A:HIS402 3.6 12.6 1.0
O A:HOH978 3.7 10.2 0.2
HA A:HIS402 3.7 14.4 1.0
CG A:HIS402 3.7 10.6 1.0
CE1 A:HIS402 3.7 11.5 1.0
CG A:HIS67 3.8 10.3 1.0
CA A:HIS67 3.9 9.5 1.0
CE1 A:HIS67 3.9 9.6 1.0
ND1 A:HIS402 3.9 10.3 1.0
ND1 A:HIS65 4.0 10.1 1.0
ND1 A:HIS400 4.0 10.1 1.0
N A:GLY68 4.0 9.8 1.0
CG A:HIS65 4.0 10.1 1.0
CG A:HIS400 4.0 10.2 1.0
CU A:CU502 4.0 10.4 0.9
HB2 A:HIS67 4.1 10.8 1.0
CB A:HIS67 4.2 10.3 1.0
HE1 A:HIS402 4.2 12.6 1.0
HE1 A:HIS67 4.2 10.8 1.0
CU A:CU501 4.3 11.9 0.9
CD2 A:HIS67 4.4 10.4 1.0
NE2 A:HIS67 4.4 11.0 1.0
CA A:HIS402 4.4 10.4 1.0
HD1 A:HIS402 4.5 12.6 1.0
C A:HIS67 4.5 9.8 1.0
CB A:HIS402 4.6 10.3 1.0
O A:HOH707 4.6 13.8 1.0
O A:HOH742 4.7 13.5 1.0
HD1 A:HIS65 4.7 17.1 1.0
HB3 A:HIS402 4.8 12.6 1.0
HD1 A:HIS400 4.8 16.8 1.0
N A:HIS402 4.9 10.5 1.0
HD2 A:HIS112 4.9 12.9 1.0
HA2 A:GLY68 4.9 11.6 1.0
HD2 A:HIS454 4.9 10.8 1.0
HD2 A:HIS67 4.9 10.8 1.0
N A:HIS67 4.9 9.8 1.0
HE2 A:HIS67 5.0 10.8 1.0
O A:LEU401 5.0 10.9 1.0
O A:TRP66 5.0 10.5 1.0

Copper binding site 4 out of 4 in 6rik

Go back to Copper Binding Sites List in 6rik
Copper binding site 4 out of 4 in the Single Crystal Serial Study of the Inhibition of Laccases From Steccherinum Murashkinskyi By Fluoride Anions at Sub-Atomic Resolution. Thirteenth Structure of the Series with 5200 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 Inhibition of Laccases From Steccherinum Murashkinskyi By Fluoride Anions at Sub-Atomic Resolution. Thirteenth Structure of the Series with 5200 Kgy Dose. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu504

b:10.6
occ:0.85
ND1 A:HIS397 2.0 11.6 1.0
ND1 A:HIS458 2.0 11.6 1.0
SG A:CYS453 2.2 12.1 1.0
HD11 A:ILE455 2.7 12.4 1.0
CE1 A:HIS397 2.9 12.1 1.0
CE1 A:HIS458 3.0 12.2 1.0
HB A:ILE455 3.0 12.4 1.0
HD2 A:PHE463 3.0 15.5 1.0
HB3 A:HIS397 3.1 15.1 1.0
CG A:HIS458 3.1 11.3 1.0
CG A:HIS397 3.1 10.7 1.0
HE1 A:HIS397 3.1 12.3 1.0
HB2 A:HIS458 3.1 12.4 1.0
HE1 A:HIS458 3.1 12.3 1.0
HB3 A:HIS458 3.3 12.4 1.0
CB A:CYS453 3.3 11.7 1.0
CB A:HIS458 3.4 11.6 1.0
HA A:HIS397 3.4 12.4 1.0
HB2 A:CYS453 3.4 11.4 1.0
HB3 A:CYS453 3.5 11.4 1.0
CB A:HIS397 3.5 12.1 1.0
HE2 A:PHE463 3.5 15.5 1.0
CD1 A:ILE455 3.6 12.6 1.0
HD2 A:PRO398 3.8 12.4 1.0
CD2 A:PHE463 3.8 11.9 1.0
CB A:ILE455 3.9 11.1 1.0
H A:ILE455 3.9 12.4 1.0
HD12 A:ILE455 4.0 12.4 1.0
CA A:HIS397 4.0 12.1 1.0
CE2 A:PHE463 4.0 11.7 1.0
CG1 A:ILE455 4.1 12.1 1.0
NE2 A:HIS397 4.1 12.6 1.0
HG13 A:ILE455 4.1 12.4 1.0
NE2 A:HIS458 4.1 13.0 1.0
CD2 A:HIS397 4.2 12.7 1.0
CD2 A:HIS458 4.2 12.4 1.0
HD13 A:ILE455 4.2 12.4 1.0
HB2 A:HIS397 4.4 15.1 1.0
HG21 A:ILE455 4.5 12.4 1.0
HG22 A:ILE455 4.6 12.4 1.0
CG2 A:ILE455 4.6 11.6 1.0
HZ A:PHE341 4.6 14.8 1.0
CD A:PRO398 4.6 12.6 1.0
CA A:CYS453 4.7 11.2 1.0
O A:GLY394 4.7 16.7 1.0
N A:ILE455 4.8 10.9 1.0
CZ A:PHE341 4.8 14.7 1.0
HE1 A:PHE399 4.8 15.1 1.0
HA A:CYS453 4.8 10.9 1.0
HE2 A:HIS397 4.8 12.3 1.0
HA2 A:GLY395 4.9 15.0 1.0
HD3 A:PRO398 4.9 12.4 1.0
HE2 A:PHE341 4.9 14.8 1.0
HE2 A:HIS458 4.9 12.3 1.0
CA A:HIS458 4.9 11.8 1.0
CA A:ILE455 4.9 11.2 1.0
CE2 A:PHE341 4.9 13.4 1.0
C A:HIS397 5.0 11.4 1.0
HB3 A:PHE463 5.0 12.5 1.0
N A:HIS397 5.0 12.5 1.0
O A:ILE455 5.0 12.0 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: Sun Dec 13 11:25:40 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy