Atomistry » Zinc » PDB 2xxh-2y7d » 2xyb
Atomistry »
  Zinc »
    PDB 2xxh-2y7d »
      2xyb »

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

Go back to Zinc Binding Sites List in 2xyb
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

Go back to Zinc Binding Sites List in 2xyb
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

Go back to Zinc Binding Sites List in 2xyb
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

Go back to Zinc Binding Sites List in 2xyb
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

Go back to Zinc Binding Sites List in 2xyb
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

Last articles

Zn in 7RRP
Zn in 7OKY
Zn in 7OL0
Zn in 7OKX
Zn in 7ONB
Zn in 7RSF
Zn in 7OUF
Zn in 7OUG
Zn in 7OUH
Zn in 7RGN
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy