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Sodium in PDB 3fm1: Crystal Structure Analysis of Fungal Versatile Peroxidase From Pleurotus Eryngii

Enzymatic activity of Crystal Structure Analysis of Fungal Versatile Peroxidase From Pleurotus Eryngii

All present enzymatic activity of Crystal Structure Analysis of Fungal Versatile Peroxidase From Pleurotus Eryngii:
1.11.1.16;

Protein crystallography data

The structure of Crystal Structure Analysis of Fungal Versatile Peroxidase From Pleurotus Eryngii, PDB code: 3fm1 was solved by K.Piontek, A.T.Martinez, T.Choinowski, D.A.Plattner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.71 / 1.78
Space group P 43
Cell size a, b, c (Å), α, β, γ (°) 63.645, 63.645, 99.598, 90.00, 90.00, 90.00
R / Rfree (%) 12.4 / 17.2

Other elements in 3fm1:

The structure of Crystal Structure Analysis of Fungal Versatile Peroxidase From Pleurotus Eryngii also contains other interesting chemical elements:

Manganese (Mn) 1 atom
Zinc (Zn) 3 atoms
Iron (Fe) 4 atoms
Calcium (Ca) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure Analysis of Fungal Versatile Peroxidase From Pleurotus Eryngii (pdb code 3fm1). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Crystal Structure Analysis of Fungal Versatile Peroxidase From Pleurotus Eryngii, PDB code: 3fm1:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 3fm1

Go back to Sodium Binding Sites List in 3fm1
Sodium binding site 1 out of 5 in the Crystal Structure Analysis of Fungal Versatile Peroxidase From Pleurotus Eryngii


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure Analysis of Fungal Versatile Peroxidase From Pleurotus Eryngii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na338

b:10.4
occ:1.00
O A:HOH532 2.2 15.2 0.6
O A:HOH530 2.2 21.3 0.6
OD1 A:ASP146 2.3 14.9 1.0
O A:HOH1174 2.4 10.9 0.6
O A:HOH528 2.4 20.4 0.6
ZN A:ZN333 2.4 19.4 0.4
O A:HOH529 2.7 14.5 0.6
O A:HOH864 3.1 17.2 0.4
O A:HOH534 3.1 13.5 0.4
CG A:ASP146 3.2 17.2 1.0
OD2 A:ASP146 3.5 17.9 1.0
OE1 A:GLN239 3.9 24.9 1.0
O A:HOH774 4.1 11.9 1.0
O A:HOH865 4.2 27.1 1.0
OD2 A:ASP237 4.3 12.7 1.0
OD1 A:ASP237 4.3 16.9 1.0
O A:HOH535 4.5 46.2 1.0
CB A:ASP146 4.6 12.1 1.0
CG A:ASP237 4.7 13.8 1.0
N A:ASP146 4.8 9.9 1.0
CA A:ASP146 4.9 11.8 1.0
O A:HOH539 5.0 53.1 1.0

Sodium binding site 2 out of 5 in 3fm1

Go back to Sodium Binding Sites List in 3fm1
Sodium binding site 2 out of 5 in the Crystal Structure Analysis of Fungal Versatile Peroxidase From Pleurotus Eryngii


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure Analysis of Fungal Versatile Peroxidase From Pleurotus Eryngii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na339

b:14.3
occ:1.00
O A:HOH942 2.1 20.6 0.6
O A:HOH941 2.2 27.2 1.0
O A:HOH940 2.2 24.3 1.0
O A:HOH943 2.3 30.8 1.0
O A:HOH945 2.5 51.9 1.0
O A:HOH944 2.6 24.2 0.5
O A:HOH948 3.9 31.6 1.0
O A:HOH946 4.0 47.3 1.0
OE2 A:GLU26 4.1 25.6 1.0
O A:GLY31 4.1 13.1 1.0
O A:HOH411 4.2 31.1 0.5
OE1 A:GLU26 4.3 16.5 1.0
C A:GLY31 4.6 10.9 1.0
O A:HOH947 4.6 43.8 1.0
CD A:GLU26 4.7 23.1 1.0
CA A:GLY31 4.7 9.4 1.0
CB A:ALA32 4.8 12.0 1.0
O A:HOH949 5.0 32.3 1.0

Sodium binding site 3 out of 5 in 3fm1

Go back to Sodium Binding Sites List in 3fm1
Sodium binding site 3 out of 5 in the Crystal Structure Analysis of Fungal Versatile Peroxidase From Pleurotus Eryngii


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure Analysis of Fungal Versatile Peroxidase From Pleurotus Eryngii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na340

b:17.7
occ:1.00
O A:HOH1171 2.1 30.1 1.0
O A:HOH508 2.2 30.8 1.0
OD2 A:ASP128 2.3 16.1 1.0
O A:HOH506 2.3 36.0 1.0
FE A:FE337 2.5 21.5 0.3
O A:HOH513 2.6 21.5 1.0
CG A:ASP128 3.2 14.9 1.0
OD1 A:ASP128 3.4 13.5 1.0
O A:HOH740 4.0 21.4 1.0
O A:HOH512 4.2 32.0 1.0
O A:HOH1175 4.3 55.1 1.0
CB A:ASP128 4.6 9.7 1.0
O A:HOH502 4.6 38.0 1.0
O A:HOH703 4.7 17.6 1.0
O A:HOH739 5.0 36.9 1.0

Sodium binding site 4 out of 5 in 3fm1

Go back to Sodium Binding Sites List in 3fm1
Sodium binding site 4 out of 5 in the Crystal Structure Analysis of Fungal Versatile Peroxidase From Pleurotus Eryngii


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure Analysis of Fungal Versatile Peroxidase From Pleurotus Eryngii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na341

b:16.6
occ:1.00
O A:HOH1170 2.1 36.9 1.0
O A:HOH524 2.2 22.0 1.0
O A:HOH522 2.2 15.6 1.0
O A:PHE142 2.3 11.4 1.0
O A:HOH525 2.4 14.6 0.5
O A:HOH523 2.5 22.7 1.0
C A:PHE142 3.5 15.3 1.0
CA A:PHE142 4.1 12.0 1.0
O A:HOH414 4.1 11.4 0.5
CB A:PHE142 4.3 9.8 1.0
O A:HOH644 4.3 11.9 1.0
N A:ASP143 4.5 10.5 1.0
C A:ASP143 4.5 9.6 1.0
O A:HOH526 4.5 54.0 1.0
CA A:ASP143 4.7 9.7 1.0
N A:SER144 4.7 8.6 1.0
O A:ASP143 4.8 10.7 1.0

Sodium binding site 5 out of 5 in 3fm1

Go back to Sodium Binding Sites List in 3fm1
Sodium binding site 5 out of 5 in the Crystal Structure Analysis of Fungal Versatile Peroxidase From Pleurotus Eryngii


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure Analysis of Fungal Versatile Peroxidase From Pleurotus Eryngii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na342

b:30.6
occ:1.00
O A:HOH1184 2.2 35.1 1.0
O A:HOH1185 2.3 35.8 1.0
O A:HOH1183 2.3 36.8 1.0
O A:HOH1177 2.3 22.4 1.0
O A:HOH1178 2.4 24.0 1.0
O A:HOH1181 2.6 23.0 0.5
O A:HOH1179 3.6 38.6 1.0
OE1 A:GLU140 3.9 28.0 1.0
O A:HOH1182 4.1 33.5 0.5
OD2 A:ASP143 4.1 13.0 1.0
O A:HOH974 4.1 30.4 0.5
OD1 A:ASP143 4.3 15.3 1.0
O A:HOH367 4.3 21.4 1.0
O A:HOH444 4.3 19.1 1.0
O A:HOH454 4.4 26.0 0.5
O A:HOH533 4.5 35.8 1.0
ND1 A:HIS136 4.5 30.4 1.0
O A:HIS136 4.5 13.5 1.0
CG A:ASP143 4.6 13.1 1.0
CB A:HIS136 4.7 20.2 1.0
CA A:HIS136 4.7 14.5 1.0
O A:VAL138 4.8 9.9 1.0
CD A:GLU140 4.9 21.6 1.0
CG A:GLU140 4.9 15.5 1.0
O A:HOH446 4.9 22.3 1.0
C A:HIS136 4.9 14.0 1.0

Reference:

K.Piontek, T.Choinowski, M.Perez-Boada, F.J.Ruiz-Duenas, M.J.Martinez, D.A.Plattner, A.T.Martinez. Structural and Site-Directed Mutagenesis Study of Versatile Peroxidase Oxidizing Both Mn(II) and Aromatic Substrates To Be Published.
Page generated: Tue Dec 15 06:10:53 2020

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