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Copper in PDB 5nq9: Crystal Structure of Laccases From Pycnoporus Sanguineus, Izoform II, Monoclinic

Enzymatic activity of Crystal Structure of Laccases From Pycnoporus Sanguineus, Izoform II, Monoclinic

All present enzymatic activity of Crystal Structure of Laccases From Pycnoporus Sanguineus, Izoform II, Monoclinic:
1.10.3.2;

Protein crystallography data

The structure of Crystal Structure of Laccases From Pycnoporus Sanguineus, Izoform II, Monoclinic, PDB code: 5nq9 was solved by M.Orlikowska, M.De J.Rostro-Alanis, A.Bujacz, C.Hernandez-Luna, R.Rubio, R.Parra, G.Bujacz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.65 / 2.72
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 90.459, 61.962, 103.307, 90.00, 109.82, 90.00
R / Rfree (%) 17 / 24.6

Copper Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Copper atom in the Crystal Structure of Laccases From Pycnoporus Sanguineus, Izoform II, Monoclinic (pdb code 5nq9). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 12 binding sites of Copper where determined in the Crystal Structure of Laccases From Pycnoporus Sanguineus, Izoform II, Monoclinic, PDB code: 5nq9:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Copper binding site 1 out of 12 in 5nq9

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Copper binding site 1 out of 12 in the Crystal Structure of Laccases From Pycnoporus Sanguineus, Izoform II, Monoclinic


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Crystal Structure of Laccases From Pycnoporus Sanguineus, Izoform II, Monoclinic within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu601

b:52.4
occ:1.00
 ND1 A:HIS477 2.0 58.6 1.0
ND1 A:HIS416 2.0 52.1 1.0
SG A:CYS472 2.2 54.5 1.0
CE1 A:HIS477 2.9 58.7 1.0
CG A:HIS477 3.0 55.3 1.0
CE1 A:HIS416 3.0 49.3 1.0
CG A:HIS416 3.0 49.6 1.0
CB A:HIS477 3.3 51.3 1.0
CB A:HIS416 3.4 49.0 1.0
CD1 A:ILE474 3.4 46.2 1.0
CB A:CYS472 3.5 49.5 1.0
CB A:ILE474 3.8 44.6 1.0
CD2 A:PHE482 3.8 49.0 1.0
CA A:HIS416 3.8 49.5 1.0
CE2 A:PHE482 3.9 48.7 1.0
NE2 A:HIS477 4.0 58.9 1.0
CD2 A:HIS477 4.1 57.3 1.0
NE2 A:HIS416 4.1 50.2 1.0
CG1 A:ILE474 4.1 44.7 1.0
CD2 A:HIS416 4.1 49.4 1.0
CG2 A:ILE474 4.5 44.9 1.0
CD A:PRO417 4.6 45.8 1.0
CA A:CYS472 4.8 49.8 1.0
CA A:HIS477 4.8 48.4 1.0
C A:HIS416 4.9 47.3 1.0
CA A:ILE474 4.9 44.8 1.0
N A:ILE474 4.9 44.1 1.0
N A:HIS416 4.9 50.9 1.0
O A:ILE474 4.9 47.5 1.0

Copper binding site 2 out of 12 in 5nq9

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Copper binding site 2 out of 12 in the Crystal Structure of Laccases From Pycnoporus Sanguineus, Izoform II, Monoclinic


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Crystal Structure of Laccases From Pycnoporus Sanguineus, Izoform II, Monoclinic within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu602

b:56.0
occ:1.00
 NE2 A:HIS419 1.9 45.8 1.0
NE2 A:HIS85 2.0 48.0 1.0
CD2 A:HIS419 2.9 42.6 1.0
O A:HOH729 2.9 48.4 1.0
CE1 A:HIS85 2.9 46.6 1.0
CE1 A:HIS419 3.0 42.8 1.0
CD2 A:HIS85 3.0 43.8 1.0
CE1 A:HIS421 3.2 54.5 1.0
NE2 A:HIS421 3.2 55.3 1.0
O2 A:PER605 3.3 69.9 1.0
ND1 A:HIS87 3.3 45.1 1.0
O1 A:PER605 3.5 76.8 1.0
ND1 A:HIS421 3.5 54.2 1.0
CD2 A:HIS421 3.6 52.5 1.0
CE1 A:HIS87 3.6 45.4 1.0
CG A:HIS421 3.8 53.1 1.0
CG A:HIS87 3.8 43.1 1.0
CG A:HIS419 4.0 41.9 1.0
ND1 A:HIS419 4.0 42.0 1.0
ND1 A:HIS85 4.0 46.4 1.0
CU A:CU603 4.0 46.9 1.0
CA A:HIS87 4.1 44.9 1.0
CG A:HIS85 4.1 43.3 1.0
N A:GLY88 4.1 47.2 1.0
NE2 A:HIS87 4.2 43.3 1.0
CU A:CU604 4.2 49.1 1.0
CD2 A:HIS87 4.4 43.0 1.0
CB A:HIS87 4.4 42.3 1.0
CA A:HIS421 4.6 48.8 1.0
C A:HIS87 4.6 45.6 1.0
CB A:HIS421 4.7 51.5 1.0
O A:HOH718 4.8 39.4 1.0
NE2 A:HIS132 4.9 40.3 1.0

Copper binding site 3 out of 12 in 5nq9

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Copper binding site 3 out of 12 in the Crystal Structure of Laccases From Pycnoporus Sanguineus, Izoform II, Monoclinic


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Crystal Structure of Laccases From Pycnoporus Sanguineus, Izoform II, Monoclinic within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu603

b:46.9
occ:1.00
 O1 A:PER605 2.0 76.8 1.0
ND1 A:HIS87 2.0 45.1 1.0
NE2 A:HIS130 2.1 36.5 1.0
NE2 A:HIS473 2.1 44.0 1.0
CE1 A:HIS87 2.7 45.4 1.0
CE1 A:HIS473 3.0 43.3 1.0
CD2 A:HIS130 3.0 35.1 1.0
CE1 A:HIS130 3.1 35.0 1.0
CG A:HIS87 3.1 43.1 1.0
CD2 A:HIS473 3.2 40.1 1.0
O2 A:PER605 3.4 69.9 1.0
CZ2 A:TRP128 3.4 40.8 1.0
CB A:HIS87 3.7 42.3 1.0
CE2 A:TRP128 3.8 40.9 1.0
NE2 A:HIS87 3.9 43.3 1.0
CD2 A:HIS85 4.0 43.8 1.0
CU A:CU602 4.0 56.0 1.0
CH2 A:TRP128 4.1 42.7 1.0
NE1 A:TRP128 4.1 40.1 1.0
CD2 A:HIS87 4.1 43.0 1.0
ND1 A:HIS473 4.1 42.4 1.0
CG A:HIS130 4.2 35.1 1.0
ND1 A:HIS130 4.2 35.2 1.0
CG A:HIS473 4.3 42.1 1.0
NE2 A:HIS85 4.4 48.0 1.0
CB A:ALA262 4.4 40.4 1.0
CD2 A:HIS419 4.5 42.6 1.0
NE2 A:HIS419 4.6 45.8 1.0
CA A:HIS87 4.7 44.9 1.0
CD2 A:TRP128 4.8 41.5 1.0
CZ3 A:TRP128 5.0 43.0 1.0

Copper binding site 4 out of 12 in 5nq9

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Copper binding site 4 out of 12 in the Crystal Structure of Laccases From Pycnoporus Sanguineus, Izoform II, Monoclinic


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Crystal Structure of Laccases From Pycnoporus Sanguineus, Izoform II, Monoclinic within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu604

b:49.1
occ:1.00
 O2 A:PER605 1.8 69.9 1.0
NE2 A:HIS421 2.0 55.3 1.0
NE2 A:HIS471 2.0 51.1 1.0
NE2 A:HIS132 2.0 40.3 1.0
CE1 A:HIS132 2.5 38.2 1.0
CE1 A:HIS421 2.8 54.5 1.0
CD2 A:HIS471 2.9 52.7 1.0
CE1 A:HIS471 3.0 49.5 1.0
CD2 A:HIS421 3.0 52.5 1.0
CD2 A:HIS132 3.2 37.6 1.0
O1 A:PER605 3.3 76.8 1.0
CD2 A:HIS419 3.8 42.6 1.0
ND1 A:HIS132 3.8 36.0 1.0
ND1 A:HIS421 4.0 54.2 1.0
CG A:HIS471 4.0 52.8 1.0
ND1 A:HIS471 4.1 50.0 1.0
CG A:HIS421 4.1 53.1 1.0
CG A:HIS132 4.1 37.8 1.0
CD2 A:PHE469 4.2 52.6 1.0
CU A:CU602 4.2 56.0 1.0
CB A:PHE469 4.2 52.8 1.0
NE2 A:HIS419 4.5 45.8 1.0
CG A:PRO100 4.6 48.6 1.0
CG A:PHE469 4.6 53.9 1.0
CD2 A:HIS85 4.6 43.8 1.0
NE2 A:HIS85 4.7 48.0 1.0
CG A:HIS419 4.9 41.9 1.0

Copper binding site 5 out of 12 in 5nq9

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Copper binding site 5 out of 12 in the Crystal Structure of Laccases From Pycnoporus Sanguineus, Izoform II, Monoclinic


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Crystal Structure of Laccases From Pycnoporus Sanguineus, Izoform II, Monoclinic within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu627

b:0.2
occ:1.00
 OE1 A:GLU44 2.0 77.5 1.0
CD A:GLU44 2.9 62.3 1.0
OE2 A:GLU44 3.2 61.5 1.0
O A:HOH722 3.3 36.9 1.0
O7 A:NAG613 4.0 47.2 1.0
CG A:GLU44 4.2 57.5 1.0

Copper binding site 6 out of 12 in 5nq9

Go back to Copper Binding Sites List in 5nq9
Copper binding site 6 out of 12 in the Crystal Structure of Laccases From Pycnoporus Sanguineus, Izoform II, Monoclinic


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Crystal Structure of Laccases From Pycnoporus Sanguineus, Izoform II, Monoclinic within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu628

b:0.7
occ:1.00
 OD2 A:ASP205 2.0 79.3 1.0
CG A:ASP205 3.1 62.6 1.0
CB A:ASP205 3.6 57.5 1.0
CD2 A:LEU195 4.1 46.4 1.0
OD1 A:ASP205 4.2 58.7 1.0

Copper binding site 7 out of 12 in 5nq9

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Copper binding site 7 out of 12 in the Crystal Structure of Laccases From Pycnoporus Sanguineus, Izoform II, Monoclinic


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of Crystal Structure of Laccases From Pycnoporus Sanguineus, Izoform II, Monoclinic within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu602

b:46.5
occ:1.00
 ND1 C:HIS416 2.0 49.7 1.0
ND1 C:HIS477 2.0 45.8 1.0
SG C:CYS472 2.3 49.5 1.0
CE1 C:HIS416 2.9 47.3 1.0
CE1 C:HIS477 3.0 44.8 1.0
CG C:HIS416 3.1 46.9 1.0
CG C:HIS477 3.1 43.8 1.0
CB C:CYS472 3.4 45.8 1.0
CB C:HIS477 3.4 46.0 1.0
CB C:HIS416 3.4 46.1 1.0
CD1 C:ILE474 3.5 44.4 1.0
CB C:ILE474 3.7 45.5 1.0
CD2 C:PHE482 3.8 50.1 1.0
CE2 C:PHE482 3.9 49.9 1.0
CA C:HIS416 3.9 45.7 1.0
CG1 C:ILE474 4.0 44.7 1.0
NE2 C:HIS416 4.1 46.5 1.0
NE2 C:HIS477 4.1 42.4 1.0
CD2 C:HIS416 4.2 46.8 1.0
CD2 C:HIS477 4.2 42.5 1.0
CG2 C:ILE474 4.4 46.0 1.0
CD C:PRO417 4.6 47.4 1.0
CA C:CYS472 4.7 45.5 1.0
N C:ILE474 4.8 44.7 1.0
CA C:ILE474 4.8 46.3 1.0
C C:HIS416 4.9 45.6 1.0
CA C:HIS477 4.9 46.9 1.0
O C:GLY413 4.9 44.0 1.0
N C:HIS416 5.0 45.5 1.0
O C:ILE474 5.0 49.2 1.0

Copper binding site 8 out of 12 in 5nq9

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Copper binding site 8 out of 12 in the Crystal Structure of Laccases From Pycnoporus Sanguineus, Izoform II, Monoclinic


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of Crystal Structure of Laccases From Pycnoporus Sanguineus, Izoform II, Monoclinic within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu603

b:58.8
occ:1.00
 NE2 C:HIS85 2.0 61.8 1.0
NE2 C:HIS419 2.0 51.9 1.0
CD2 C:HIS85 2.9 59.3 1.0
CE1 C:HIS419 2.9 48.5 1.0
CE1 C:HIS85 3.0 58.6 1.0
CD2 C:HIS419 3.0 48.7 1.0
O1 C:PER601 3.1 63.0 1.0
NE2 C:HIS421 3.2 58.0 1.0
CD2 C:HIS421 3.4 56.7 1.0
ND1 C:HIS87 3.4 51.5 1.0
O2 C:PER601 3.4 71.2 1.0
CE1 C:HIS421 3.5 58.1 1.0
CG C:HIS87 3.7 51.4 1.0
CG C:HIS421 3.7 56.9 1.0
CE1 C:HIS87 3.8 54.5 1.0
ND1 C:HIS421 3.8 59.3 1.0
CA C:HIS87 3.9 49.8 1.0
ND1 C:HIS419 4.0 45.5 1.0
ND1 C:HIS85 4.1 57.8 1.0
CG C:HIS85 4.1 59.2 1.0
CG C:HIS419 4.1 47.8 1.0
N C:GLY88 4.2 49.3 1.0
CU C:CU605 4.2 47.7 1.0
CB C:HIS87 4.2 50.3 1.0
NE2 C:HIS87 4.2 49.7 1.0
CD2 C:HIS87 4.2 52.8 1.0
CU C:CU604 4.4 52.7 1.0
CA C:HIS421 4.5 56.2 1.0
C C:HIS87 4.5 48.7 1.0
CB C:HIS421 4.7 58.3 1.0
O C:LEU420 4.9 57.6 1.0
O C:TRP86 5.0 46.7 1.0
N C:HIS87 5.0 49.8 1.0

Copper binding site 9 out of 12 in 5nq9

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Copper binding site 9 out of 12 in the Crystal Structure of Laccases From Pycnoporus Sanguineus, Izoform II, Monoclinic


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 9 of Crystal Structure of Laccases From Pycnoporus Sanguineus, Izoform II, Monoclinic within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu604

b:52.7
occ:1.00
 O2 C:PER601 1.9 71.2 1.0
NE2 C:HIS421 2.0 58.0 1.0
NE2 C:HIS471 2.0 48.4 1.0
NE2 C:HIS132 2.1 52.9 1.0
CE1 C:HIS421 2.8 58.1 1.0
CD2 C:HIS471 2.9 44.5 1.0
CE1 C:HIS132 3.0 53.9 1.0
CD2 C:HIS421 3.0 56.7 1.0
CD2 C:HIS132 3.1 51.4 1.0
CE1 C:HIS471 3.1 45.3 1.0
O1 C:PER601 3.4 63.0 1.0
CD2 C:HIS419 3.9 48.7 1.0
ND1 C:HIS421 3.9 59.3 1.0
CG C:HIS471 4.0 44.8 1.0
CG C:HIS421 4.1 56.9 1.0
ND1 C:HIS471 4.1 45.6 1.0
ND1 C:HIS132 4.1 52.4 1.0
CG C:HIS132 4.2 50.5 1.0
CD2 C:PHE469 4.4 60.2 1.0
CU C:CU603 4.4 58.8 1.0
CB C:PHE469 4.4 58.6 1.0
NE2 C:HIS419 4.5 51.9 1.0
CG C:PRO100 4.6 54.1 1.0
CD2 C:HIS85 4.7 59.3 1.0
NE2 C:HIS85 4.7 61.8 1.0
CG C:PHE469 4.8 59.1 1.0
CD2 C:HIS473 4.9 40.9 1.0
NE2 C:HIS473 4.9 43.2 1.0

Copper binding site 10 out of 12 in 5nq9

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Copper binding site 10 out of 12 in the Crystal Structure of Laccases From Pycnoporus Sanguineus, Izoform II, Monoclinic


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 10 of Crystal Structure of Laccases From Pycnoporus Sanguineus, Izoform II, Monoclinic within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu605

b:47.7
occ:1.00
 O1 C:PER601 1.9 63.0 1.0
ND1 C:HIS87 2.0 51.5 1.0
NE2 C:HIS130 2.1 45.2 1.0
NE2 C:HIS473 2.1 43.2 1.0
CE1 C:HIS87 2.9 54.5 1.0
CD2 C:HIS130 2.9 42.3 1.0
CE1 C:HIS473 3.0 42.0 1.0
CG C:HIS87 3.2 51.4 1.0
CE1 C:HIS130 3.2 42.0 1.0
CD2 C:HIS473 3.2 40.9 1.0
CZ2 C:TRP128 3.2 48.9 1.0
O2 C:PER601 3.3 71.2 1.0
CB C:HIS87 3.6 50.3 1.0
CE2 C:TRP128 3.6 52.9 1.0
NE1 C:TRP128 3.8 51.3 1.0
CD2 C:HIS85 4.0 59.3 1.0
CH2 C:TRP128 4.0 47.5 1.0
NE2 C:HIS87 4.1 49.7 1.0
CG C:HIS130 4.1 41.7 1.0
ND1 C:HIS473 4.1 41.9 1.0
CU C:CU603 4.2 58.8 1.0
ND1 C:HIS130 4.2 41.0 1.0
CD2 C:HIS87 4.2 52.8 1.0
CB C:ALA262 4.2 45.4 1.0
CG C:HIS473 4.3 43.5 1.0
NE2 C:HIS85 4.6 61.8 1.0
CD2 C:HIS419 4.7 48.7 1.0
NE2 C:HIS419 4.7 51.9 1.0
CD2 C:TRP128 4.7 49.3 1.0
CA C:HIS87 4.8 49.8 1.0
CD1 C:TRP128 4.9 49.1 1.0
CZ3 C:TRP128 5.0 47.2 1.0

Reference:

M.Orlikowska, M.De J Rostro-Alanis, A.Bujacz, C.Hernandez-Luna, R.Rubio, R.Parra, G.Bujacz. Structural Studies of Two Thermostable Laccases From the White-Rot Fungus Pycnoporus Sanguineus. Int. J. Biol. Macromol. V. 107 1629 2018.
ISSN: ISSN 1879-0003
PubMed: 29055703
DOI: 10.1016/J.IJBIOMAC.2017.10.024
Page generated: Sun Dec 13 11:19:07 2020

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