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: Thu Oct 17 05:35:32 2024

Last articles

Zn in 9FD2
Zn in 9GUW
Zn in 9GUX
Zn in 9F7C
Zn in 9GUR
Zn in 9F7A
Zn in 9DDE
Zn in 9DBY
Zn in 9EBZ
Zn in 9DGG
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy