Zinc in PDB 8bgo: N,N-Diacetylchitobiose Deacetylase From Pyrococcus Chitonophagus with Substrate N,N-Diacetylchitobiose

Enzymatic activity of N,N-Diacetylchitobiose Deacetylase From Pyrococcus Chitonophagus with Substrate N,N-Diacetylchitobiose

All present enzymatic activity of N,N-Diacetylchitobiose Deacetylase From Pyrococcus Chitonophagus with Substrate N,N-Diacetylchitobiose:
3.5.1.136;

Protein crystallography data

The structure of N,N-Diacetylchitobiose Deacetylase From Pyrococcus Chitonophagus with Substrate N,N-Diacetylchitobiose, PDB code: 8bgo was solved by W.Rypniewski, M.Bejger, K.Biniek-Antosiak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.38 / 3.08
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 79.164, 151.662, 167.092, 90, 93.33, 90
R / Rfree (%) 16.8 / 21.5

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc atom in the N,N-Diacetylchitobiose Deacetylase From Pyrococcus Chitonophagus with Substrate N,N-Diacetylchitobiose (pdb code 8bgo). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the N,N-Diacetylchitobiose Deacetylase From Pyrococcus Chitonophagus with Substrate N,N-Diacetylchitobiose, PDB code: 8bgo:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in 8bgo

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Zinc binding site 1 out of 12 in the N,N-Diacetylchitobiose Deacetylase From Pyrococcus Chitonophagus with Substrate N,N-Diacetylchitobiose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of N,N-Diacetylchitobiose Deacetylase From Pyrococcus Chitonophagus with Substrate N,N-Diacetylchitobiose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:93.3
occ:1.00
 OD2 A:ASP43 2.0 98.2 1.0
O7 O:NAG2 2.1 94.4 1.0
ND1 A:HIS40 2.1 75.3 1.0
NE2 A:HIS151 2.4 86.7 1.0
CG A:ASP43 2.7 100.6 1.0
OD1 A:ASP43 2.7 89.8 1.0
CE1 A:HIS40 3.0 90.6 1.0
CG A:HIS40 3.2 83.1 1.0
CD2 A:HIS151 3.2 79.5 1.0
C7 O:NAG2 3.3 104.9 1.0
CE1 A:HIS151 3.5 102.6 1.0
CB A:HIS40 3.5 78.7 1.0
NE2 C:HIS259 3.7 88.7 1.0
N A:HIS40 4.1 77.5 1.0
N2 O:NAG2 4.1 130.0 1.0
CE1 C:HIS259 4.1 95.6 1.0
CB A:PRO39 4.1 58.5 1.0
CB A:ASP43 4.2 96.9 1.0
C2 O:NAG2 4.2 125.3 1.0
NE2 A:HIS40 4.2 98.9 1.0
O3 O:NAG2 4.3 108.2 1.0
CD2 A:HIS40 4.3 87.6 1.0
C8 O:NAG2 4.4 98.7 1.0
CA A:HIS40 4.4 81.5 1.0
CG A:HIS151 4.4 84.4 1.0
CG A:PRO39 4.5 68.3 1.0
OD1 A:ASP42 4.5 96.0 1.0
ND1 A:HIS151 4.6 86.2 1.0
C3 O:NAG2 4.9 94.9 1.0
C A:PRO39 4.9 64.0 1.0
CD A:PRO39 5.0 67.5 1.0

Zinc binding site 2 out of 12 in 8bgo

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Zinc binding site 2 out of 12 in the N,N-Diacetylchitobiose Deacetylase From Pyrococcus Chitonophagus with Substrate N,N-Diacetylchitobiose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of N,N-Diacetylchitobiose Deacetylase From Pyrococcus Chitonophagus with Substrate N,N-Diacetylchitobiose within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn301

b:92.4
occ:1.00
 OD2 H:ASP43 2.0 88.6 1.0
O7 V:NAG2 2.1 98.4 1.0
ND1 H:HIS40 2.1 75.1 1.0
NE2 H:HIS151 2.3 75.8 1.0
CG H:ASP43 2.7 94.9 1.0
OD1 H:ASP43 2.8 70.2 1.0
CE1 H:HIS40 3.0 90.2 1.0
CG H:HIS40 3.1 84.6 1.0
CD2 H:HIS151 3.2 72.5 1.0
C7 V:NAG2 3.2 117.3 1.0
CE1 H:HIS151 3.4 97.3 1.0
CB H:HIS40 3.5 76.9 1.0
NE2 G:HIS259 3.8 88.3 1.0
CE1 G:HIS259 4.0 97.5 1.0
N H:HIS40 4.1 83.6 1.0
CB H:PRO39 4.1 62.8 1.0
N2 V:NAG2 4.1 145.3 1.0
NE2 H:HIS40 4.2 90.7 1.0
CB H:ASP43 4.2 103.5 1.0
C8 V:NAG2 4.2 100.5 1.0
C2 V:NAG2 4.2 137.3 1.0
CD2 H:HIS40 4.3 86.7 1.0
CG H:HIS151 4.4 83.5 1.0
CA H:HIS40 4.4 84.5 1.0
ND1 H:HIS151 4.5 88.8 1.0
O3 V:NAG2 4.5 108.5 1.0
CG H:PRO39 4.5 66.6 1.0
OD1 H:ASP42 4.6 104.3 1.0
C H:PRO39 4.9 77.3 1.0
C3 V:NAG2 4.9 116.4 1.0
CD H:PRO39 5.0 68.9 1.0

Zinc binding site 3 out of 12 in 8bgo

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Zinc binding site 3 out of 12 in the N,N-Diacetylchitobiose Deacetylase From Pyrococcus Chitonophagus with Substrate N,N-Diacetylchitobiose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of N,N-Diacetylchitobiose Deacetylase From Pyrococcus Chitonophagus with Substrate N,N-Diacetylchitobiose within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Zn301

b:88.0
occ:1.00
 OD2 K:ASP43 1.9 101.3 1.0
O7 Y:NAG2 2.1 97.0 1.0
ND1 K:HIS40 2.3 65.1 1.0
NE2 K:HIS151 2.3 71.1 1.0
OD1 K:ASP43 2.4 98.4 1.0
CG K:ASP43 2.5 96.3 1.0
CD2 K:HIS151 3.2 77.5 1.0
CE1 K:HIS40 3.2 84.7 1.0
CG K:HIS40 3.3 83.2 1.0
CE1 K:HIS151 3.3 83.7 1.0
C7 Y:NAG2 3.4 93.0 1.0
CB K:HIS40 3.6 84.5 1.0
NE2 L:HIS259 3.7 95.2 1.0
CB K:ASP43 4.0 86.5 1.0
CE1 L:HIS259 4.0 98.8 1.0
N K:HIS40 4.1 76.4 1.0
CB K:PRO39 4.1 77.5 1.0
C8 Y:NAG2 4.3 95.8 1.0
N2 Y:NAG2 4.3 125.7 1.0
CG K:HIS151 4.4 76.8 1.0
NE2 K:HIS40 4.4 79.6 1.0
C2 Y:NAG2 4.4 137.8 1.0
O3 Y:NAG2 4.4 131.0 1.0
CG K:PRO39 4.4 79.9 1.0
CD2 K:HIS40 4.5 83.4 1.0
ND1 K:HIS151 4.5 65.1 1.0
CA K:HIS40 4.5 83.0 1.0
OD1 K:ASP42 4.5 107.0 1.0
CD K:PRO39 4.8 75.1 1.0
CA K:ASP43 4.9 89.8 1.0
C K:PRO39 4.9 75.8 1.0

Zinc binding site 4 out of 12 in 8bgo

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Zinc binding site 4 out of 12 in the N,N-Diacetylchitobiose Deacetylase From Pyrococcus Chitonophagus with Substrate N,N-Diacetylchitobiose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of N,N-Diacetylchitobiose Deacetylase From Pyrococcus Chitonophagus with Substrate N,N-Diacetylchitobiose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:86.5
occ:1.00
 O7 P:NAG2 2.1 94.6 1.0
OD2 B:ASP43 2.1 77.5 1.0
ND1 B:HIS40 2.1 79.2 1.0
NE2 B:HIS151 2.4 70.9 1.0
CG B:ASP43 2.8 98.6 1.0
OD1 B:ASP43 2.8 90.7 1.0
CE1 B:HIS40 3.0 83.0 1.0
CG B:HIS40 3.2 84.2 1.0
CD2 B:HIS151 3.2 82.4 1.0
C7 P:NAG2 3.2 108.3 1.0
CE1 B:HIS151 3.5 85.2 1.0
CB B:HIS40 3.5 82.1 1.0
NE2 A:HIS259 3.7 91.5 1.0
O3 P:NAG2 3.8 103.1 1.0
CE1 A:HIS259 4.0 98.8 1.0
C2 P:NAG2 4.1 129.3 1.0
N2 P:NAG2 4.1 117.9 1.0
N B:HIS40 4.2 79.3 1.0
NE2 B:HIS40 4.2 70.4 1.0
CB B:PRO39 4.2 81.2 1.0
CD2 B:HIS40 4.2 83.6 1.0
C8 P:NAG2 4.3 98.1 1.0
CB B:ASP43 4.3 103.7 1.0
CG B:HIS151 4.5 79.9 1.0
CA B:HIS40 4.5 84.4 1.0
C3 P:NAG2 4.5 111.7 1.0
ND1 B:HIS151 4.6 88.1 1.0
OD1 B:ASP42 4.6 99.7 1.0
CG B:PRO39 4.6 78.5 1.0
C B:PRO39 5.0 76.9 1.0

Zinc binding site 5 out of 12 in 8bgo

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Zinc binding site 5 out of 12 in the N,N-Diacetylchitobiose Deacetylase From Pyrococcus Chitonophagus with Substrate N,N-Diacetylchitobiose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of N,N-Diacetylchitobiose Deacetylase From Pyrococcus Chitonophagus with Substrate N,N-Diacetylchitobiose within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn301

b:92.8
occ:1.00
 OD2 E:ASP43 1.9 111.9 1.0
O7 S:NAG2 2.1 101.2 1.0
NE2 E:HIS151 2.3 75.0 1.0
OD1 E:ASP43 2.3 102.7 1.0
ND1 E:HIS40 2.4 65.2 1.0
CG E:ASP43 2.4 102.7 1.0
CD2 E:HIS151 3.3 72.7 1.0
CE1 E:HIS151 3.3 88.2 1.0
C7 S:NAG2 3.3 109.0 1.0
CE1 E:HIS40 3.3 82.6 1.0
CG E:HIS40 3.4 79.5 1.0
CB E:HIS40 3.7 86.2 1.0
NE2 F:HIS259 3.7 99.9 1.0
CB E:ASP43 3.9 89.9 1.0
CE1 F:HIS259 4.1 107.2 1.0
N E:HIS40 4.2 86.6 1.0
N2 S:NAG2 4.2 133.3 1.0
CB E:PRO39 4.2 64.4 1.0
C8 S:NAG2 4.2 105.9 1.0
O3 S:NAG2 4.3 125.6 1.0
C2 S:NAG2 4.3 149.5 1.0
CG E:HIS151 4.4 77.4 1.0
ND1 E:HIS151 4.5 76.8 1.0
OD1 E:ASP42 4.5 108.9 1.0
NE2 E:HIS40 4.5 83.5 1.0
CA E:HIS40 4.5 87.5 1.0
CG E:PRO39 4.6 66.8 1.0
CD2 E:HIS40 4.6 80.4 1.0
CA E:ASP43 4.9 87.7 1.0
C3 S:NAG2 4.9 126.2 1.0
CD E:PRO39 4.9 68.8 1.0
CD2 F:HIS259 5.0 100.0 1.0

Zinc binding site 6 out of 12 in 8bgo

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Zinc binding site 6 out of 12 in the N,N-Diacetylchitobiose Deacetylase From Pyrococcus Chitonophagus with Substrate N,N-Diacetylchitobiose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of N,N-Diacetylchitobiose Deacetylase From Pyrococcus Chitonophagus with Substrate N,N-Diacetylchitobiose within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn301

b:101.4
occ:1.00
 OD2 L:ASP43 2.1 100.0 1.0
O7 Z:NAG2 2.1 94.3 1.0
ND1 L:HIS40 2.2 85.6 1.0
NE2 L:HIS151 2.4 92.0 1.0
OD1 L:ASP43 2.7 86.9 1.0
CG L:ASP43 2.7 95.5 1.0
CE1 L:HIS40 3.1 90.5 1.0
CG L:HIS40 3.2 93.0 1.0
CD2 L:HIS151 3.3 88.0 1.0
C7 Z:NAG2 3.3 110.3 1.0
CE1 L:HIS151 3.5 102.6 1.0
CB L:HIS40 3.6 86.1 1.0
NE2 J:HIS259 3.7 85.7 1.0
CE1 J:HIS259 4.1 100.2 1.0
O3 Z:NAG2 4.1 90.7 1.0
C2 Z:NAG2 4.2 139.8 1.0
N2 Z:NAG2 4.2 140.2 1.0
CB L:ASP43 4.2 101.8 1.0
N L:HIS40 4.2 87.6 1.0
CB L:PRO39 4.3 67.3 1.0
NE2 L:HIS40 4.3 85.9 1.0
CD2 L:HIS40 4.4 90.1 1.0
C8 Z:NAG2 4.4 102.7 1.0
CG L:HIS151 4.5 93.2 1.0
CA L:HIS40 4.5 89.5 1.0
OD1 L:ASP42 4.5 134.3 1.0
ND1 L:HIS151 4.5 95.2 1.0
CG L:PRO39 4.7 68.2 1.0
C3 Z:NAG2 4.7 109.4 1.0

Zinc binding site 7 out of 12 in 8bgo

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Zinc binding site 7 out of 12 in the N,N-Diacetylchitobiose Deacetylase From Pyrococcus Chitonophagus with Substrate N,N-Diacetylchitobiose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of N,N-Diacetylchitobiose Deacetylase From Pyrococcus Chitonophagus with Substrate N,N-Diacetylchitobiose within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn301

b:99.9
occ:1.00
 OD2 G:ASP43 2.1 80.3 1.0
O7 U:NAG2 2.1 100.9 1.0
ND1 G:HIS40 2.1 85.4 1.0
NE2 G:HIS151 2.4 95.2 1.0
CG G:ASP43 2.7 85.2 1.0
OD1 G:ASP43 2.8 84.7 1.0
CE1 G:HIS40 3.0 94.2 1.0
CG G:HIS40 3.2 87.9 1.0
C7 U:NAG2 3.2 105.7 1.0
CD2 G:HIS151 3.3 92.6 1.0
CE1 G:HIS151 3.5 113.7 1.0
CB G:HIS40 3.5 98.5 1.0
NE2 I:HIS259 3.7 103.3 1.0
O3 U:NAG2 4.0 137.1 1.0
CE1 I:HIS259 4.0 109.6 1.0
C2 U:NAG2 4.0 132.6 1.0
N2 U:NAG2 4.0 125.4 1.0
N G:HIS40 4.1 91.7 1.0
CB G:PRO39 4.2 72.8 1.0
NE2 G:HIS40 4.2 87.3 1.0
CB G:ASP43 4.2 92.2 1.0
C8 U:NAG2 4.3 93.8 1.0
CD2 G:HIS40 4.3 86.8 1.0
CA G:HIS40 4.5 99.2 1.0
CG G:HIS151 4.5 91.6 1.0
OD1 G:ASP42 4.5 96.8 1.0
ND1 G:HIS151 4.6 103.5 1.0
C3 U:NAG2 4.6 121.0 1.0
CG G:PRO39 4.6 76.4 1.0
CD2 I:HIS259 4.9 99.0 1.0
C G:PRO39 5.0 83.5 1.0

Zinc binding site 8 out of 12 in 8bgo

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Zinc binding site 8 out of 12 in the N,N-Diacetylchitobiose Deacetylase From Pyrococcus Chitonophagus with Substrate N,N-Diacetylchitobiose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of N,N-Diacetylchitobiose Deacetylase From Pyrococcus Chitonophagus with Substrate N,N-Diacetylchitobiose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:98.0
occ:1.00
 ND1 C:HIS40 2.0 69.2 1.0
OD2 C:ASP43 2.0 88.8 1.0
O7 Q:NAG2 2.1 95.8 1.0
NE2 C:HIS151 2.3 99.0 1.0
CG C:ASP43 2.8 90.9 1.0
OD1 C:ASP43 2.8 70.2 1.0
CE1 C:HIS40 2.9 82.5 1.0
CG C:HIS40 3.1 78.8 1.0
CD2 C:HIS151 3.1 84.2 1.0
C7 Q:NAG2 3.2 115.3 1.0
CE1 C:HIS151 3.5 105.1 1.0
CB C:HIS40 3.5 87.2 1.0
NE2 B:HIS259 3.9 81.0 1.0
CB C:PRO39 4.1 82.7 1.0
N C:HIS40 4.1 86.2 1.0
NE2 C:HIS40 4.1 78.7 1.0
N2 Q:NAG2 4.1 133.8 1.0
CE1 B:HIS259 4.1 96.5 1.0
CD2 C:HIS40 4.2 81.5 1.0
C8 Q:NAG2 4.2 111.4 1.0
C2 Q:NAG2 4.2 132.3 1.0
CB C:ASP43 4.2 84.3 1.0
O3 Q:NAG2 4.3 119.6 1.0
CG C:HIS151 4.4 85.7 1.0
CA C:HIS40 4.4 90.5 1.0
CG C:PRO39 4.5 86.0 1.0
ND1 C:HIS151 4.5 86.7 1.0
OD1 C:ASP42 4.6 105.0 1.0
C3 Q:NAG2 4.8 110.4 1.0
C C:PRO39 4.9 91.5 1.0
CD C:PRO39 5.0 79.2 1.0

Zinc binding site 9 out of 12 in 8bgo

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Zinc binding site 9 out of 12 in the N,N-Diacetylchitobiose Deacetylase From Pyrococcus Chitonophagus with Substrate N,N-Diacetylchitobiose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of N,N-Diacetylchitobiose Deacetylase From Pyrococcus Chitonophagus with Substrate N,N-Diacetylchitobiose within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn301

b:102.4
occ:1.00
 OD2 I:ASP43 2.0 87.4 1.0
O7 W:NAG2 2.1 93.3 1.0
ND1 I:HIS40 2.1 85.3 1.0
NE2 I:HIS151 2.3 79.1 1.0
CG I:ASP43 2.7 99.8 1.0
OD1 I:ASP43 2.8 87.8 1.0
CE1 I:HIS40 3.0 89.5 1.0
C7 W:NAG2 3.1 100.0 1.0
CD2 I:HIS151 3.2 81.4 1.0
CG I:HIS40 3.2 87.1 1.0
CE1 I:HIS151 3.4 104.1 1.0
CB I:HIS40 3.5 89.5 1.0
O3 W:NAG2 3.7 100.5 1.0
NE2 H:HIS259 3.8 90.5 1.0
N2 W:NAG2 4.0 122.5 1.0
C8 W:NAG2 4.0 87.4 1.0
C2 W:NAG2 4.1 127.7 1.0
CB I:PRO39 4.1 77.3 1.0
N I:HIS40 4.1 83.9 1.0
CE1 H:HIS259 4.1 96.3 1.0
CB I:ASP43 4.2 107.2 1.0
NE2 I:HIS40 4.2 79.8 1.0
CD2 I:HIS40 4.3 82.0 1.0
CG I:HIS151 4.4 88.6 1.0
CA I:HIS40 4.4 84.6 1.0
ND1 I:HIS151 4.5 92.6 1.0
C3 W:NAG2 4.5 118.3 1.0
CG I:PRO39 4.5 77.2 1.0
OD1 I:ASP42 4.6 96.8 1.0
C I:PRO39 4.9 84.2 1.0
CD I:PRO39 5.0 73.2 1.0

Zinc binding site 10 out of 12 in 8bgo

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Zinc binding site 10 out of 12 in the N,N-Diacetylchitobiose Deacetylase From Pyrococcus Chitonophagus with Substrate N,N-Diacetylchitobiose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of N,N-Diacetylchitobiose Deacetylase From Pyrococcus Chitonophagus with Substrate N,N-Diacetylchitobiose within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn301

b:107.9
occ:1.00
 OD2 J:ASP43 2.0 97.3 1.0
O7 X:NAG2 2.1 112.9 1.0
ND1 J:HIS40 2.2 88.7 1.0
NE2 J:HIS151 2.4 93.8 1.0
CG J:ASP43 2.7 99.1 1.0
OD1 J:ASP43 2.7 88.1 1.0
CE1 J:HIS40 3.1 105.2 1.0
CG J:HIS40 3.2 94.7 1.0
C7 X:NAG2 3.3 124.6 1.0
CD2 J:HIS151 3.3 97.0 1.0
CE1 J:HIS151 3.5 115.2 1.0
CB J:HIS40 3.6 88.8 1.0
NE2 K:HIS259 3.7 98.7 1.0
CE1 K:HIS259 4.0 100.8 1.0
O3 X:NAG2 4.1 111.8 1.0
N2 X:NAG2 4.1 145.9 1.0
C2 X:NAG2 4.2 146.3 1.0
CB J:ASP43 4.2 108.6 1.0
N J:HIS40 4.2 92.8 1.0
CB J:PRO39 4.3 80.3 1.0
NE2 J:HIS40 4.3 101.5 1.0
C8 X:NAG2 4.3 117.8 1.0
CD2 J:HIS40 4.3 101.6 1.0
CA J:HIS40 4.5 92.6 1.0
CG J:HIS151 4.5 98.3 1.0
OD1 J:ASP42 4.5 118.8 1.0
ND1 J:HIS151 4.6 110.8 1.0
C3 X:NAG2 4.6 120.6 1.0
CG J:PRO39 4.7 83.3 1.0

Reference:

K.Biniek-Antosiak, M.Bejger, J.Sliwiak, D.Baranowski, A.S.A.Mohammed, D.I.Svergun, W.Rypniewski. Structural, Thermodynamic and Enzymatic Characterization of N , N -Diacetylchitobiose Deacetylase From Pyrococcus Chitonophagus. Int J Mol Sci V. 23 2022.
ISSN: ESSN 1422-0067
PubMed: 36555375
DOI: 10.3390/IJMS232415736
Page generated: Wed Oct 30 18:18:51 2024

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