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Zinc in PDB 3eqn: Crystal Structure of Beta-1,3-Glucanase From Phanerochaete Chrysosporium (LAM55A)

Enzymatic activity of Crystal Structure of Beta-1,3-Glucanase From Phanerochaete Chrysosporium (LAM55A)

All present enzymatic activity of Crystal Structure of Beta-1,3-Glucanase From Phanerochaete Chrysosporium (LAM55A):
3.2.1.58;

Protein crystallography data

The structure of Crystal Structure of Beta-1,3-Glucanase From Phanerochaete Chrysosporium (LAM55A), PDB code: 3eqn was solved by T.Ishida, S.Fushinobu, R.Kawai, M.Kitaoka, K.Igarashi, M.Samejima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.21 / 1.70
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 66.281, 67.148, 105.183, 81.04, 76.34, 61.45
R / Rfree (%) 14.9 / 18.4

Other elements in 3eqn:

The structure of Crystal Structure of Beta-1,3-Glucanase From Phanerochaete Chrysosporium (LAM55A) also contains other interesting chemical elements:

Sodium (Na) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Beta-1,3-Glucanase From Phanerochaete Chrysosporium (LAM55A) (pdb code 3eqn). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of Beta-1,3-Glucanase From Phanerochaete Chrysosporium (LAM55A), PDB code: 3eqn:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 3eqn

Go back to Zinc Binding Sites List in 3eqn
Zinc binding site 1 out of 6 in the Crystal Structure of Beta-1,3-Glucanase From Phanerochaete Chrysosporium (LAM55A)


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 Beta-1,3-Glucanase From Phanerochaete Chrysosporium (LAM55A) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn756

b:37.2
occ:1.00
 O A:HOH1343 2.0 26.3 1.0
NE2 A:HIS508 2.1 14.8 1.0
O A:GLY600 2.2 13.4 1.0
O A:HOH1262 2.9 34.4 1.0
CE1 A:HIS508 3.0 16.4 1.0
CD2 A:HIS508 3.1 15.1 1.0
C A:GLY600 3.3 13.4 1.0
CD A:PRO601 3.6 13.6 1.0
O A:HOH1421 3.8 18.1 1.0
N A:PRO601 3.9 13.1 1.0
O A:HOH1341 3.9 27.5 1.0
O A:HOH1342 4.0 34.1 1.0
ND1 A:HIS508 4.2 16.4 1.0
CG A:HIS508 4.3 15.6 1.0
O A:GLN599 4.4 13.2 1.0
CA A:GLY600 4.5 13.8 1.0
N A:GLY600 4.6 13.7 1.0
C A:GLN599 4.6 13.8 1.0
O A:SER562 5.0 12.6 1.0

Zinc binding site 2 out of 6 in 3eqn

Go back to Zinc Binding Sites List in 3eqn
Zinc binding site 2 out of 6 in the Crystal Structure of Beta-1,3-Glucanase From Phanerochaete Chrysosporium (LAM55A)


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 Beta-1,3-Glucanase From Phanerochaete Chrysosporium (LAM55A) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn757

b:20.2
occ:1.00
 O A:HOH1364 1.9 20.9 1.0
O A:HOH1375 2.0 14.2 1.0
O A:ACT768 2.1 21.1 1.0
NE2 A:HIS383 2.2 11.5 1.0
OXT A:ACT768 2.6 21.1 1.0
C A:ACT768 2.7 21.2 1.0
CD2 A:HIS383 3.1 12.9 1.0
CE1 A:HIS383 3.2 11.8 1.0
OD2 A:ASP488 3.6 18.5 1.0
OG1 A:THR487 3.7 12.6 1.0
O A:PRO384 3.8 14.0 1.0
CB A:THR487 3.9 11.0 1.0
O A:HOH1109 4.0 29.5 1.0
NH1 A:ARG154 4.1 14.3 1.0
CH3 A:ACT768 4.2 20.6 1.0
CG A:HIS383 4.3 12.3 1.0
ND1 A:HIS383 4.3 10.7 1.0
CG1 A:VAL449 4.3 14.4 1.0
CG2 A:THR487 4.5 9.4 1.0
CG A:GLN385 4.6 14.9 1.0
CG A:ASP488 4.7 16.1 1.0
CA A:GLN385 4.8 13.4 1.0
C A:PRO384 4.8 13.4 1.0

Zinc binding site 3 out of 6 in 3eqn

Go back to Zinc Binding Sites List in 3eqn
Zinc binding site 3 out of 6 in the Crystal Structure of Beta-1,3-Glucanase From Phanerochaete Chrysosporium (LAM55A)


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 Beta-1,3-Glucanase From Phanerochaete Chrysosporium (LAM55A) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn758

b:13.8
occ:1.00
 OD2 A:ASP575 2.0 11.9 1.0
ND1 A:HIS576 2.1 11.9 1.0
O A:HOH1441 2.2 11.9 1.0
O A:HOH1438 2.3 13.4 1.0
O A:HOH1440 2.3 10.7 1.0
O A:HOH1439 2.3 14.8 1.0
CG A:ASP575 3.0 12.0 1.0
CE1 A:HIS576 3.0 12.7 1.0
CG A:HIS576 3.2 12.1 1.0
OD1 A:ASP575 3.4 13.5 1.0
CB A:HIS576 3.7 11.3 1.0
O2 A:GOL766 3.9 25.1 1.0
OD1 A:ASN147 4.1 13.2 1.0
NE2 A:HIS576 4.2 13.2 1.0
O A:HOH881 4.2 16.3 1.0
CD2 A:HIS576 4.3 12.8 1.0
CB A:ASP575 4.3 11.0 1.0
O A:HOH1442 4.3 16.0 1.0
O1 A:GOL764 4.4 12.1 1.0
N A:HIS576 4.4 10.5 1.0
OH A:TYR636 4.5 11.9 1.0
CE2 A:TYR636 4.5 13.1 1.0
C A:ASP575 4.7 10.9 1.0
CA A:HIS576 4.7 11.0 1.0
NE2 A:GLN585 4.7 21.5 1.0
O A:HOH1271 4.8 31.6 1.0
CG A:ASN147 4.9 11.1 1.0
C3 A:GOL764 4.9 14.1 1.0
ND2 A:ASN147 5.0 12.4 1.0

Zinc binding site 4 out of 6 in 3eqn

Go back to Zinc Binding Sites List in 3eqn
Zinc binding site 4 out of 6 in the Crystal Structure of Beta-1,3-Glucanase From Phanerochaete Chrysosporium (LAM55A)


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 Beta-1,3-Glucanase From Phanerochaete Chrysosporium (LAM55A) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn756

b:17.8
occ:1.00
 OXT B:ACT765 2.0 17.1 1.0
O B:HOH1334 2.0 14.9 1.0
O B:HOH1326 2.1 12.8 1.0
NE2 B:HIS383 2.1 10.9 1.0
O B:ACT765 2.6 17.1 1.0
C B:ACT765 2.7 17.4 1.0
CD2 B:HIS383 3.1 10.0 1.0
CE1 B:HIS383 3.2 11.0 1.0
OD2 B:ASP488 3.5 17.5 1.0
O B:PRO384 3.7 12.0 1.0
OG1 B:THR487 3.8 11.8 1.0
CB B:THR487 3.9 10.1 1.0
O B:HOH1412 3.9 30.8 1.0
NH1 B:ARG154 4.1 12.6 1.0
CH3 B:ACT765 4.1 17.3 1.0
ND1 B:HIS383 4.2 9.2 1.0
CG B:HIS383 4.2 10.2 1.0
CG2 B:THR487 4.4 10.4 1.0
CG1 B:VAL449 4.5 12.8 1.0
CG B:GLN385 4.6 13.5 1.0
CG B:ASP488 4.6 13.7 1.0
CA B:GLN385 4.7 12.2 1.0
C B:PRO384 4.7 11.3 1.0

Zinc binding site 5 out of 6 in 3eqn

Go back to Zinc Binding Sites List in 3eqn
Zinc binding site 5 out of 6 in the Crystal Structure of Beta-1,3-Glucanase From Phanerochaete Chrysosporium (LAM55A)


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 Beta-1,3-Glucanase From Phanerochaete Chrysosporium (LAM55A) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn757

b:21.1
occ:1.00
 O B:HOH1336 2.0 18.7 1.0
O B:GLY600 2.1 10.2 1.0
NE2 B:HIS508 2.1 12.9 1.0
O B:HOH1463 2.4 37.5 1.0
CD2 B:HIS508 3.0 10.6 1.0
CE1 B:HIS508 3.1 11.7 1.0
C B:GLY600 3.2 10.4 1.0
CD B:PRO601 3.5 10.2 1.0
O B:HOH1403 3.6 27.3 1.0
O B:HOH959 3.7 16.0 1.0
N B:PRO601 3.8 10.1 1.0
ND1 B:HIS508 4.2 13.2 1.0
CG B:HIS508 4.2 12.6 1.0
O B:HOH1421 4.2 38.4 1.0
CA B:GLY600 4.4 10.7 1.0
O B:GLN599 4.5 12.1 1.0
N B:GLY600 4.5 11.8 1.0
O B:HOH1345 4.6 41.5 1.0
O B:HOH1320 4.6 36.1 1.0
C B:GLN599 4.6 12.0 1.0
O B:SER562 4.9 10.6 1.0
CG B:PRO601 4.9 9.7 1.0

Zinc binding site 6 out of 6 in 3eqn

Go back to Zinc Binding Sites List in 3eqn
Zinc binding site 6 out of 6 in the Crystal Structure of Beta-1,3-Glucanase From Phanerochaete Chrysosporium (LAM55A)


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 Beta-1,3-Glucanase From Phanerochaete Chrysosporium (LAM55A) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn758

b:14.4
occ:1.00
 OD2 B:ASP575 2.0 11.5 1.0
O B:HOH1448 2.1 12.5 1.0
ND1 B:HIS576 2.1 12.8 1.0
O B:HOH1447 2.2 11.2 1.0
O B:HOH1449 2.2 13.2 1.0
O B:HOH1446 2.4 15.2 1.0
CE1 B:HIS576 3.0 12.2 1.0
CG B:ASP575 3.0 12.0 1.0
CG B:HIS576 3.2 11.1 1.0
OD1 B:ASP575 3.3 13.6 1.0
CB B:HIS576 3.7 12.0 1.0
NE2 B:HIS576 4.1 12.6 1.0
OD1 B:ASN147 4.2 13.6 1.0
CD2 B:HIS576 4.3 13.3 1.0
C3 B:GOL763 4.3 27.6 1.0
O B:HOH1362 4.3 15.5 1.0
O B:HOH828 4.3 16.4 1.0
CB B:ASP575 4.3 10.9 1.0
O3 B:GOL762 4.4 16.0 1.0
N B:HIS576 4.4 11.0 1.0
OH B:TYR636 4.5 12.1 1.0
O2 B:GOL763 4.6 29.5 1.0
CE2 B:TYR636 4.6 12.4 1.0
C B:ASP575 4.6 11.2 1.0
CA B:HIS576 4.7 11.2 1.0
NE2 B:GLN585 4.7 22.8 1.0
O B:HOH862 4.8 26.5 1.0
C1 B:GOL762 4.8 16.3 1.0
CG B:ASN147 4.9 12.4 1.0
O B:ASP575 4.9 11.6 1.0

Reference:

T.Ishida, S.Fushinobu, R.Kawai, M.Kitaoka, K.Igarashi, M.Samejima. Crystal Structure of Glycoside Hydrolase Family 55 Beta -1,3-Glucanase From the Basidiomycete Phanerochaete Chrysosporium J.Biol.Chem. V. 284 10100 2009.
ISSN: ISSN 0021-9258
PubMed: 19193645
DOI: 10.1074/JBC.M808122200
Page generated: Thu Oct 24 12:54:09 2024

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