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Zinc in PDB 2zum: Functional Analysis of Hyperthermophilic Endocellulase From the Archaeon Pyrococcus Horikoshii

Enzymatic activity of Functional Analysis of Hyperthermophilic Endocellulase From the Archaeon Pyrococcus Horikoshii

All present enzymatic activity of Functional Analysis of Hyperthermophilic Endocellulase From the Archaeon Pyrococcus Horikoshii:
3.2.1.4;

Protein crystallography data

The structure of Functional Analysis of Hyperthermophilic Endocellulase From the Archaeon Pyrococcus Horikoshii, PDB code: 2zum was solved by H.-W.Kim, K.Ishikawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.58 / 1.95
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 77.150, 77.150, 161.105, 90.00, 90.00, 90.00
R / Rfree (%) 17.2 / 22.1

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Zinc atom in the Functional Analysis of Hyperthermophilic Endocellulase From the Archaeon Pyrococcus Horikoshii (pdb code 2zum). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 18 binding sites of Zinc where determined in the Functional Analysis of Hyperthermophilic Endocellulase From the Archaeon Pyrococcus Horikoshii, PDB code: 2zum:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 18 in 2zum

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Zinc binding site 1 out of 18 in the Functional Analysis of Hyperthermophilic Endocellulase From the Archaeon Pyrococcus Horikoshii


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Functional Analysis of Hyperthermophilic Endocellulase From the Archaeon Pyrococcus Horikoshii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn460

b:37.8
occ:0.50
ZN A:ZN460 0.0 37.8 0.5
O A:HOH533 1.9 27.4 1.0
OE1 A:GLU342 2.3 24.0 1.0
OE1 A:GLU201 2.4 30.4 1.0
O A:HOH795 2.6 40.2 1.0
CD A:GLU201 3.1 28.8 1.0
CD A:GLU342 3.1 24.7 1.0
OE2 A:GLU201 3.2 30.9 1.0
OE2 A:GLU342 3.3 23.3 1.0
ZN A:ZN460 3.5 88.5 0.5
OH A:TYR299 3.8 27.8 1.0
CE2 A:TYR299 4.1 31.0 1.0
ND1 A:HIS297 4.2 23.7 1.0
O A:HOH556 4.2 35.1 1.0
CZ A:TYR299 4.3 31.6 1.0
CG A:GLU201 4.4 25.4 1.0
O A:HOH495 4.4 30.7 1.0
CG A:GLU342 4.5 23.2 1.0
CE1 A:HIS297 4.7 24.1 1.0
OD1 A:ASN200 4.7 27.7 1.0
O3 A:GOL472 4.7 52.3 1.0
CD1 A:ILE162 4.8 26.9 1.0
CB A:GLU342 4.8 23.9 1.0
C3 A:GOL472 4.9 51.5 1.0
ND2 A:ASN200 4.9 16.4 1.0

Zinc binding site 2 out of 18 in 2zum

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Zinc binding site 2 out of 18 in the Functional Analysis of Hyperthermophilic Endocellulase From the Archaeon Pyrococcus Horikoshii


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Functional Analysis of Hyperthermophilic Endocellulase From the Archaeon Pyrococcus Horikoshii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn460

b:88.5
occ:0.50
ZN A:ZN460 0.0 88.5 0.5
O A:HOH830 2.4 54.8 1.0
ZN A:ZN460 3.5 37.8 0.5
OH A:TYR299 3.8 27.8 1.0
NE1 A:TRP377 3.8 24.8 1.0
CD1 A:TRP377 4.1 25.1 1.0
O A:HOH795 4.1 40.2 1.0
CE2 A:TRP377 4.1 26.7 1.0
CZ A:TYR299 4.2 31.6 1.0
OE1 A:GLU342 4.3 24.0 1.0
OG A:SER383 4.6 39.9 1.0
O A:HOH712 4.6 52.0 1.0
OD2 A:ASP385 4.6 50.7 1.0
CG A:TRP377 4.6 26.1 1.0
CZ2 A:TRP377 4.6 26.8 1.0
CD2 A:TRP377 4.6 25.1 1.0
CE2 A:TYR299 4.7 31.0 1.0
CE1 A:TYR299 4.7 34.9 1.0
O3 A:GOL472 4.8 52.3 1.0
CG2 A:THR386 4.8 35.6 1.0
O A:HOH556 4.8 35.1 1.0
O A:HOH533 4.8 27.4 1.0

Zinc binding site 3 out of 18 in 2zum

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Zinc binding site 3 out of 18 in the Functional Analysis of Hyperthermophilic Endocellulase From the Archaeon Pyrococcus Horikoshii


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Functional Analysis of Hyperthermophilic Endocellulase From the Archaeon Pyrococcus Horikoshii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn461

b:20.6
occ:0.70
ZN A:ZN461 0.0 20.6 0.7
O A:HOH562 1.6 42.1 1.0
O A:HOH840 1.9 32.4 1.0
NE2 A:HIS76 2.0 22.0 1.0
O A:HOH839 2.1 30.0 1.0
OE2 A:GLU108 2.4 29.0 1.0
ZN A:ZN463 2.4 49.1 0.4
O A:HOH833 2.8 40.6 1.0
CE1 A:HIS76 3.0 17.8 1.0
CD2 A:HIS76 3.0 18.5 1.0
ZN A:ZN463 3.1 23.3 0.6
CD A:GLU108 3.4 36.3 1.0
OE1 A:GLU108 3.7 36.6 1.0
ZN A:ZN461 3.8 54.1 0.3
O A:PRO74 4.0 20.5 1.0
ND1 A:HIS76 4.1 20.3 1.0
CG A:HIS76 4.1 15.6 1.0
O A:HOH553 4.2 26.6 1.0
CA A:PRO74 4.4 20.7 1.0
C A:PRO74 4.6 20.6 1.0
CB A:PRO74 4.7 20.1 1.0
CG A:GLU108 4.8 32.9 1.0
O A:HOH848 4.8 41.5 1.0
CB A:GLU108 4.9 25.3 1.0
CG2 A:THR114 4.9 25.8 1.0

Zinc binding site 4 out of 18 in 2zum

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Zinc binding site 4 out of 18 in the Functional Analysis of Hyperthermophilic Endocellulase From the Archaeon Pyrococcus Horikoshii


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Functional Analysis of Hyperthermophilic Endocellulase From the Archaeon Pyrococcus Horikoshii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn461

b:54.1
occ:0.30
ZN A:ZN461 0.0 54.1 0.3
ZN A:ZN463 1.8 49.1 0.4
O A:HOH562 2.7 42.1 1.0
O A:HOH586 2.8 36.3 1.0
OE1 A:GLU108 3.0 36.6 1.0
ZN A:ZN463 3.2 23.3 0.6
CD A:GLU108 3.7 36.3 1.0
ZN A:ZN461 3.8 20.6 0.7
OE2 A:GLU108 3.9 29.0 1.0
O A:HOH553 4.1 26.6 1.0
CG2 A:THR114 4.5 25.8 1.0
O A:HOH833 4.6 40.6 1.0
O A:HOH834 4.7 54.7 1.0
NE2 A:HIS76 4.8 22.0 1.0
O A:HOH789 4.8 52.5 1.0
O A:HOH839 4.8 30.0 1.0
CG A:GLU108 4.8 32.9 1.0
OG1 A:THR114 5.0 26.1 1.0

Zinc binding site 5 out of 18 in 2zum

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Zinc binding site 5 out of 18 in the Functional Analysis of Hyperthermophilic Endocellulase From the Archaeon Pyrococcus Horikoshii


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Functional Analysis of Hyperthermophilic Endocellulase From the Archaeon Pyrococcus Horikoshii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn462

b:43.1
occ:0.70
ZN A:ZN462 0.0 43.1 0.7
ZN A:ZN462 1.7 37.2 0.3
OD1 A:ASP321 2.0 41.1 1.0
NE2 A:HIS325 2.2 44.2 1.0
O A:HOH838 2.4 54.9 1.0
CG A:ASP321 2.7 40.0 1.0
OD2 A:ASP321 2.8 42.7 1.0
O A:HOH835 2.8 59.9 1.0
CD2 A:HIS325 2.9 42.5 1.0
O A:HOH832 3.1 47.7 1.0
CE1 A:HIS325 3.3 47.3 1.0
O A:HOH704 4.0 50.7 1.0
CG A:HIS325 4.2 42.0 1.0
CB A:ASP321 4.2 40.7 1.0
ND1 A:HIS325 4.3 44.9 1.0
O A:ASP321 4.6 39.5 1.0
CA A:ASP321 4.9 40.7 1.0
CD2 A:TYR324 4.9 38.3 1.0

Zinc binding site 6 out of 18 in 2zum

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Zinc binding site 6 out of 18 in the Functional Analysis of Hyperthermophilic Endocellulase From the Archaeon Pyrococcus Horikoshii


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Functional Analysis of Hyperthermophilic Endocellulase From the Archaeon Pyrococcus Horikoshii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn462

b:37.2
occ:0.30
ZN A:ZN462 0.0 37.2 0.3
ZN A:ZN462 1.7 43.1 0.7
O A:HOH832 2.1 47.7 1.0
OD1 A:ASP321 2.4 41.1 1.0
O A:HOH838 3.1 54.9 1.0
NE2 A:HIS325 3.2 44.2 1.0
CG A:ASP321 3.5 40.0 1.0
O A:HOH835 3.7 59.9 1.0
CD2 A:HIS325 3.9 42.5 1.0
OD2 A:ASP321 4.0 42.7 1.0
CE1 A:HIS325 4.1 47.3 1.0
CD2 A:TYR324 4.2 38.3 1.0
O A:HOH610 4.4 49.4 1.0
O A:HOH704 4.5 50.7 1.0
CE2 A:TYR324 4.5 40.6 1.0
CB A:ASP321 4.8 40.7 1.0
CG A:TYR324 4.9 34.6 1.0

Zinc binding site 7 out of 18 in 2zum

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Zinc binding site 7 out of 18 in the Functional Analysis of Hyperthermophilic Endocellulase From the Archaeon Pyrococcus Horikoshii


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Functional Analysis of Hyperthermophilic Endocellulase From the Archaeon Pyrococcus Horikoshii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn463

b:49.1
occ:0.40
ZN A:ZN463 0.0 49.1 0.4
ZN A:ZN463 1.7 23.3 0.6
ZN A:ZN461 1.8 54.1 0.3
O A:HOH562 2.0 42.1 1.0
ZN A:ZN461 2.4 20.6 0.7
OE1 A:GLU108 2.4 36.6 1.0
O A:HOH833 2.8 40.6 1.0
OE2 A:GLU108 2.8 29.0 1.0
CD A:GLU108 3.0 36.3 1.0
O A:HOH840 3.7 32.4 1.0
O A:HOH839 3.7 30.0 1.0
NE2 A:HIS76 4.0 22.0 1.0
O A:HOH586 4.2 36.3 1.0
O A:HOH553 4.4 26.6 1.0
CG A:GLU108 4.5 32.9 1.0
CD2 A:HIS76 4.8 18.5 1.0
O A:HOH834 4.9 54.7 1.0
CE1 A:HIS76 4.9 17.8 1.0

Zinc binding site 8 out of 18 in 2zum

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Zinc binding site 8 out of 18 in the Functional Analysis of Hyperthermophilic Endocellulase From the Archaeon Pyrococcus Horikoshii


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Functional Analysis of Hyperthermophilic Endocellulase From the Archaeon Pyrococcus Horikoshii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn463

b:23.3
occ:0.60
ZN A:ZN463 0.0 23.3 0.6
ZN A:ZN463 1.7 49.1 0.4
O A:HOH833 1.9 40.6 1.0
OE1 A:GLU108 2.0 36.6 1.0
CD A:GLU108 2.7 36.3 1.0
OE2 A:GLU108 2.7 29.0 1.0
ZN A:ZN461 3.1 20.6 0.7
ZN A:ZN461 3.2 54.1 0.3
O A:HOH562 3.5 42.1 1.0
O A:HOH840 3.5 32.4 1.0
CG A:GLU108 4.1 32.9 1.0
O A:HOH834 4.2 54.7 1.0
O A:HOH848 4.4 41.5 1.0
O A:HOH839 4.8 30.0 1.0
NE2 A:HIS76 4.8 22.0 1.0

Zinc binding site 9 out of 18 in 2zum

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Zinc binding site 9 out of 18 in the Functional Analysis of Hyperthermophilic Endocellulase From the Archaeon Pyrococcus Horikoshii


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Functional Analysis of Hyperthermophilic Endocellulase From the Archaeon Pyrococcus Horikoshii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn464

b:18.7
occ:0.40
ZN A:ZN464 0.0 18.7 0.4
ZN A:ZN464 1.2 23.8 0.3
ZN A:ZN464 1.5 42.4 0.3
NE2 A:HIS62 1.9 31.7 1.0
CE1 A:HIS62 2.8 32.2 1.0
CD2 A:HIS62 3.0 31.3 1.0
OD1 A:ASP410 3.2 60.5 1.0
O A:HOH837 3.4 54.9 1.0
ND1 A:HIS62 4.0 29.8 1.0
CG A:HIS62 4.1 31.5 1.0
CG A:ASP410 4.4 57.0 1.0
O A:HOH816 4.6 46.7 1.0
CZ A:PHE64 4.8 29.6 1.0

Zinc binding site 10 out of 18 in 2zum

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Zinc binding site 10 out of 18 in the Functional Analysis of Hyperthermophilic Endocellulase From the Archaeon Pyrococcus Horikoshii


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Functional Analysis of Hyperthermophilic Endocellulase From the Archaeon Pyrococcus Horikoshii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn464

b:23.8
occ:0.30
ZN A:ZN464 0.0 23.8 0.3
ZN A:ZN464 1.2 18.7 0.4
ZN A:ZN464 2.2 42.4 0.3
O A:HOH837 2.4 54.9 1.0
NE2 A:HIS62 2.4 31.7 1.0
CD2 A:HIS62 3.0 31.3 1.0
OD1 A:ASP410 3.3 60.5 1.0
CE1 A:HIS62 3.6 32.2 1.0
CG A:HIS62 4.3 31.5 1.0
CG A:ASP410 4.5 57.0 1.0
ND1 A:HIS62 4.6 29.8 1.0
CZ A:PHE64 4.6 29.6 1.0
O A:HOH805 4.8 44.3 1.0

Reference:

H.-W.Kim, K.Ishikawa. Structure of Hyperthermophilic Endocellulase From Pyrococcus Horikoshii Proteins V. 78 496 2009.
ISSN: ISSN 0887-3585
PubMed: 19847920
DOI: 10.1002/PROT.22602
Page generated: Wed Dec 16 04:05:44 2020

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