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Zinc in PDB 2xyb: Crystal Structure of A Fully Functional Laccase From the Ligninolytic Fungus Pycnoporus Cinnabarinus

Enzymatic activity of Crystal Structure of A Fully Functional Laccase From the Ligninolytic Fungus Pycnoporus Cinnabarinus

All present enzymatic activity of Crystal Structure of A Fully Functional Laccase From the Ligninolytic Fungus Pycnoporus Cinnabarinus:
1.10.3.2;

Protein crystallography data

The structure of Crystal Structure of A Fully Functional Laccase From the Ligninolytic Fungus Pycnoporus Cinnabarinus, PDB code: 2xyb was solved by K.Piontek, T.Choinowski, M.Antorini, I.Herpoel-Gimbert, D.A.Plattner, J.C.Sigoillot, M.Asther, K.Winterhalter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 72.55 / 1.75
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 145.296, 62.902, 91.416, 90.00, 126.70, 90.00
R / Rfree (%) 16.4 / 20.8

Other elements in 2xyb:

The structure of Crystal Structure of A Fully Functional Laccase From the Ligninolytic Fungus Pycnoporus Cinnabarinus also contains other interesting chemical elements:

Sodium (Na) 1 atom
Copper (Cu) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of A Fully Functional Laccase From the Ligninolytic Fungus Pycnoporus Cinnabarinus (pdb code 2xyb). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of A Fully Functional Laccase From the Ligninolytic Fungus Pycnoporus Cinnabarinus, PDB code: 2xyb:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 2xyb

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Zinc binding site 1 out of 8 in the Crystal Structure of A Fully Functional Laccase From the Ligninolytic Fungus Pycnoporus Cinnabarinus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of A Fully Functional Laccase From the Ligninolytic Fungus Pycnoporus Cinnabarinus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn526

b:33.2
occ:1.00
OXT A:ACT519 2.0 27.2 1.0
O A:ACT519 2.1 33.9 1.0
OD1 A:ASN442 2.1 33.7 1.0
O A:HOH706 2.1 29.9 1.0
O A:HOH740 2.1 36.7 1.0
ND1 A:HIS402 2.2 31.6 1.0
C A:ACT519 2.5 34.9 1.0
CG A:ASN442 3.0 35.8 1.0
CE1 A:HIS402 3.0 26.2 1.0
ND2 A:ASN442 3.2 41.9 1.0
CG A:HIS402 3.2 29.0 1.0
CB A:HIS402 3.6 26.5 1.0
O A:GLU440 3.9 34.0 1.0
CA A:HIS402 3.9 25.6 1.0
O A:GLY401 3.9 27.3 1.0
CH3 A:ACT519 4.0 35.8 1.0
NE2 A:HIS402 4.2 27.6 1.0
O A:HOH656 4.2 52.7 1.0
O A:HOH1058 4.3 39.8 1.0
CD2 A:HIS402 4.3 28.8 1.0
O A:HOH856 4.4 32.1 1.0
CB A:ASN442 4.5 31.7 1.0
N A:ASN442 4.7 28.8 1.0
CB A:ASN443 4.7 29.7 1.0
N A:ALA403 4.7 25.2 1.0
C A:GLY401 4.8 25.8 1.0
N A:HIS402 4.8 26.8 1.0
C A:HIS402 4.9 25.9 1.0
CA A:ASN442 5.0 25.4 1.0
O A:ALA403 5.0 29.8 1.0

Zinc binding site 2 out of 8 in 2xyb

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Zinc binding site 2 out of 8 in the Crystal Structure of A Fully Functional Laccase From the Ligninolytic Fungus Pycnoporus Cinnabarinus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of A Fully Functional Laccase From the Ligninolytic Fungus Pycnoporus Cinnabarinus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn527

b:38.2
occ:1.00
O A:HOH639 2.0 34.8 1.0
OE2 A:GLU23 2.1 37.3 1.0
O A:HOH633 2.3 28.4 1.0
CD A:GLU23 3.1 31.8 1.0
OE1 A:GLU23 3.4 31.0 1.0
O A:HOH946 4.3 30.2 1.0
O7 A:NAG506 4.4 37.9 1.0
CG A:GLU23 4.4 33.0 1.0
CG A:GLN14 4.5 37.4 1.0
O A:HOH1250 4.6 63.3 1.0
N A:GLN14 4.7 25.3 1.0
CB A:GLN14 4.8 32.7 1.0

Zinc binding site 3 out of 8 in 2xyb

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Zinc binding site 3 out of 8 in the Crystal Structure of A Fully Functional Laccase From the Ligninolytic Fungus Pycnoporus Cinnabarinus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of A Fully Functional Laccase From the Ligninolytic Fungus Pycnoporus Cinnabarinus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn528

b:42.3
occ:1.00
O3 A:SO4521 1.9 63.4 1.0
OD2 A:ASP471 2.0 36.2 1.0
OD2 A:ASP468 2.0 36.9 1.0
O A:HOH1062 2.2 53.3 1.0
S A:SO4521 2.9 70.2 1.0
CG A:ASP468 2.9 38.6 1.0
CG A:ASP471 2.9 36.2 1.0
OD1 A:ASP468 3.1 38.0 1.0
O1 A:SO4521 3.2 72.3 1.0
CB A:ASP471 3.2 29.6 1.0
O4 A:SO4521 3.3 73.5 1.0
O A:HOH670 4.0 51.4 1.0
OD1 A:ASP471 4.1 35.5 1.0
O2 A:SO4521 4.2 70.1 1.0
CB A:SER376 4.2 41.0 1.0
CB A:ASP468 4.3 35.8 1.0
OG A:SER376 4.3 44.1 1.0
O A:HOH1084 4.4 53.7 1.0
CG A:PRO444 4.6 30.6 1.0
CA A:ASP471 4.7 32.0 1.0

Zinc binding site 4 out of 8 in 2xyb

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Zinc binding site 4 out of 8 in the Crystal Structure of A Fully Functional Laccase From the Ligninolytic Fungus Pycnoporus Cinnabarinus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of A Fully Functional Laccase From the Ligninolytic Fungus Pycnoporus Cinnabarinus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn529

b:61.5
occ:1.00
OE1 A:GLU368 2.1 58.6 1.0
O A:HOH1036 2.1 58.1 1.0
O A:HOH624 2.2 48.2 1.0
NE2 A:HIS342 2.2 41.9 1.0
O A:HOH1071 2.7 63.3 1.0
CD A:GLU368 2.9 57.6 1.0
CD2 A:HIS342 3.0 38.0 1.0
OE2 A:GLU368 3.1 62.8 1.0
CE1 A:HIS342 3.2 40.7 1.0
CG A:HIS342 4.2 37.5 1.0
O A:GLU368 4.3 40.0 1.0
ND1 A:HIS342 4.3 39.2 1.0
CG A:GLU368 4.4 52.0 1.0
C A:GLU368 4.7 37.1 1.0
CA A:GLY369 4.8 34.8 1.0
CB A:GLU368 5.0 46.5 1.0

Zinc binding site 5 out of 8 in 2xyb

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Zinc binding site 5 out of 8 in the Crystal Structure of A Fully Functional Laccase From the Ligninolytic Fungus Pycnoporus Cinnabarinus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of A Fully Functional Laccase From the Ligninolytic Fungus Pycnoporus Cinnabarinus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn530

b:53.4
occ:1.00
O A:HOH817 2.1 49.3 1.0
NE2 A:HIS306 2.2 36.0 1.0
O A:HOH1077 2.3 57.1 1.0
O A:HOH1086 2.4 56.1 1.0
O A:HOH1156 2.7 69.6 1.0
O A:HOH664 2.9 41.9 1.0
CD2 A:HIS306 3.0 34.8 1.0
CE1 A:HIS306 3.2 33.8 1.0
CG A:HIS306 4.2 35.1 1.0
O A:VAL303 4.2 31.4 1.0
ND1 A:HIS306 4.3 36.7 1.0
O A:ASP304 4.4 28.3 1.0
CA A:ASP304 4.4 27.1 1.0
C A:ASP304 4.7 29.4 1.0
O A:HOH1239 4.9 57.9 1.0
OD1 A:ASP304 5.0 37.4 1.0

Zinc binding site 6 out of 8 in 2xyb

Go back to Zinc Binding Sites List in 2xyb
Zinc binding site 6 out of 8 in the Crystal Structure of A Fully Functional Laccase From the Ligninolytic Fungus Pycnoporus Cinnabarinus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of A Fully Functional Laccase From the Ligninolytic Fungus Pycnoporus Cinnabarinus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn531

b:54.5
occ:1.00
O A:HOH1064 2.1 40.9 1.0
NE2 A:HIS91 2.2 42.6 1.0
O A:HOH987 2.2 47.5 1.0
O A:HOH1016 2.2 53.5 1.0
O A:HOH1041 2.3 49.7 1.0
O A:HOH1272 2.7 55.3 1.0
CE1 A:HIS91 3.1 37.2 1.0
CD2 A:HIS91 3.1 40.0 1.0
O A:HOH1035 4.1 54.2 1.0
O A:HOH846 4.2 42.4 1.0
ND1 A:HIS91 4.2 39.7 1.0
CG A:HIS91 4.3 36.3 1.0
O A:SER89 4.5 32.2 1.0
O A:HOH826 4.8 38.2 1.0
CG2 A:ILE488 4.8 29.1 1.0

Zinc binding site 7 out of 8 in 2xyb

Go back to Zinc Binding Sites List in 2xyb
Zinc binding site 7 out of 8 in the Crystal Structure of A Fully Functional Laccase From the Ligninolytic Fungus Pycnoporus Cinnabarinus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of A Fully Functional Laccase From the Ligninolytic Fungus Pycnoporus Cinnabarinus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn532

b:63.7
occ:1.00
NE2 A:HIS55 2.2 43.4 1.0
O A:HOH1054 2.3 52.9 1.0
O A:HOH1125 2.4 63.5 1.0
O A:HOH1255 2.6 71.2 1.0
O A:HOH849 2.7 48.9 1.0
CE1 A:HIS55 3.1 36.2 1.0
CD2 A:HIS55 3.2 36.2 1.0
O A:HOH1117 4.0 63.0 1.0
O A:PRO494 4.1 48.2 1.0
ND1 A:HIS55 4.2 33.6 1.0
CG A:HIS55 4.3 33.6 1.0
O A:HOH753 4.5 49.3 1.0
C A:PRO494 4.9 49.0 1.0
O A:HOH1261 5.0 61.0 1.0

Zinc binding site 8 out of 8 in 2xyb

Go back to Zinc Binding Sites List in 2xyb
Zinc binding site 8 out of 8 in the Crystal Structure of A Fully Functional Laccase From the Ligninolytic Fungus Pycnoporus Cinnabarinus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of A Fully Functional Laccase From the Ligninolytic Fungus Pycnoporus Cinnabarinus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn533

b:84.9
occ:1.00
O A:HOH1060 2.1 69.8 1.0
OD2 A:ASP418 2.1 60.6 1.0
O A:HOH995 2.7 55.6 1.0
CG A:ASP418 2.9 47.5 1.0
O A:HOH1094 3.0 73.9 1.0
OD1 A:ASP418 3.0 47.3 1.0
O A:HOH1099 4.2 47.4 1.0
CB A:ASP418 4.3 41.7 1.0

Reference:

K.Piontek, T.Choinowski, M.Antorini, I.Herpoel-Gimbert, M.Asther, D.A.Plattner. Substrate Binding and Copper Geometry in Laccases To Be Published.
Page generated: Wed Dec 16 04:00:56 2020

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