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Magnesium in PDB 8frb: Mouse Acidic Mammalian Chitinase, Catalytic Domain in Complex with N, N'-Diacetylchitobiose at pH 5.25

Enzymatic activity of Mouse Acidic Mammalian Chitinase, Catalytic Domain in Complex with N, N'-Diacetylchitobiose at pH 5.25

All present enzymatic activity of Mouse Acidic Mammalian Chitinase, Catalytic Domain in Complex with N, N'-Diacetylchitobiose at pH 5.25:
3.2.1.14;

Protein crystallography data

The structure of Mouse Acidic Mammalian Chitinase, Catalytic Domain in Complex with N, N'-Diacetylchitobiose at pH 5.25, PDB code: 8frb was solved by R.E.Diaz, J.S.Fraser, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 57.29 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 91.926, 106.963, 146.492, 90, 90, 90
R / Rfree (%) 14.2 / 17.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Mouse Acidic Mammalian Chitinase, Catalytic Domain in Complex with N, N'-Diacetylchitobiose at pH 5.25 (pdb code 8frb). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Mouse Acidic Mammalian Chitinase, Catalytic Domain in Complex with N, N'-Diacetylchitobiose at pH 5.25, PDB code: 8frb:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 8frb

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Magnesium binding site 1 out of 5 in the Mouse Acidic Mammalian Chitinase, Catalytic Domain in Complex with N, N'-Diacetylchitobiose at pH 5.25


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Mouse Acidic Mammalian Chitinase, Catalytic Domain in Complex with N, N'-Diacetylchitobiose at pH 5.25 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:18.4
occ:0.58
 O C:HOH710 1.9 28.4 1.0
O C:HOH547 1.9 30.5 1.0
O A:HOH655 2.2 41.0 1.0
O A:SER277 2.2 27.8 1.0
O A:HOH511 2.3 29.1 1.0
HD21 C:ASN275 3.4 72.0 1.0
C A:SER277 3.5 20.3 1.0
HD22 C:ASN275 3.6 72.0 1.0
HA A:ASP278 3.6 19.9 1.0
ND2 C:ASN275 3.8 60.0 1.0
HB2 A:SER277 3.9 27.3 1.0
H A:ASN279 4.0 22.6 1.0
O C:HOH861 4.1 41.8 1.0
OD1 C:ASP278 4.1 32.3 1.0
OD2 C:ASP278 4.3 35.9 1.0
N A:ASP278 4.3 19.4 1.0
HA A:SER277 4.3 31.9 1.0
OD1 A:ASN279 4.3 20.7 1.0
CA A:ASP278 4.4 16.6 1.0
CA A:SER277 4.4 26.6 1.0
HD22 A:ASN279 4.5 31.2 1.0
CB A:SER277 4.6 22.7 1.0
CG C:ASP278 4.6 38.4 1.0
N A:ASN279 4.7 18.8 1.0
O A:HOH818 4.7 27.5 1.0
CG A:ASN279 4.8 24.9 1.0
ND2 A:ASN279 4.8 26.0 1.0

Magnesium binding site 2 out of 5 in 8frb

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Magnesium binding site 2 out of 5 in the Mouse Acidic Mammalian Chitinase, Catalytic Domain in Complex with N, N'-Diacetylchitobiose at pH 5.25


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Mouse Acidic Mammalian Chitinase, Catalytic Domain in Complex with N, N'-Diacetylchitobiose at pH 5.25 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg401

b:17.6
occ:0.61
 O B:HOH826 1.9 33.0 1.0
O B:HOH526 2.0 26.4 1.0
HD3 B:PRO284 3.9 18.5 1.0
OD2 B:ASP278 4.0 22.6 1.0
O B:HOH583 4.3 24.0 1.0
OD1 B:ASP278 4.5 18.6 1.0
HA B:ALA283 4.5 13.5 1.0
CG B:ASP278 4.7 15.1 1.0
CD B:PRO284 4.7 15.5 1.0
HD2 B:PRO284 4.9 18.5 1.0
O B:GLY282 4.9 15.6 1.0
HG3 B:PRO284 4.9 29.3 1.0

Magnesium binding site 3 out of 5 in 8frb

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Magnesium binding site 3 out of 5 in the Mouse Acidic Mammalian Chitinase, Catalytic Domain in Complex with N, N'-Diacetylchitobiose at pH 5.25


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Mouse Acidic Mammalian Chitinase, Catalytic Domain in Complex with N, N'-Diacetylchitobiose at pH 5.25 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg401

b:20.6
occ:0.68
 O A:HOH592 2.0 29.3 1.0
O A:HOH792 2.0 27.8 1.0
O C:SER277 2.2 23.5 1.0
O C:HOH541 2.3 34.0 1.0
O C:HOH786 2.3 31.3 1.0
HD21 A:ASN275 3.2 72.6 1.0
HA C:ASP278 3.4 24.7 1.0
C C:SER277 3.4 20.3 1.0
HG A:SER277 3.8 39.7 1.0
HD22 A:ASN275 3.9 72.6 1.0
ND2 A:ASN275 3.9 60.5 1.0
H C:ASN279 3.9 21.8 1.0
HB3 C:SER277 4.0 38.5 1.0
CA C:ASP278 4.2 20.6 1.0
N C:ASP278 4.2 23.7 1.0
O C:HOH809 4.3 41.1 1.0
OD1 C:ASP278 4.3 32.3 1.0
OG A:SER277 4.3 33.1 1.0
OD1 C:ASN279 4.3 19.7 1.0
HD22 C:ASN279 4.4 22.0 1.0
O C:HOH694 4.4 47.4 1.0
HA C:SER277 4.4 35.7 1.0
CA C:SER277 4.4 29.8 1.0
N C:ASN279 4.6 18.1 1.0
CB C:SER277 4.7 32.1 1.0
O C:HOH834 4.7 28.4 1.0
ND2 C:ASN279 4.7 18.3 1.0
CG C:ASN279 4.7 22.0 1.0
C C:ASP278 5.0 26.7 1.0

Magnesium binding site 4 out of 5 in 8frb

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Magnesium binding site 4 out of 5 in the Mouse Acidic Mammalian Chitinase, Catalytic Domain in Complex with N, N'-Diacetylchitobiose at pH 5.25


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Mouse Acidic Mammalian Chitinase, Catalytic Domain in Complex with N, N'-Diacetylchitobiose at pH 5.25 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg401

b:21.6
occ:0.72
 O B:HOH881 2.0 24.1 1.0
O B:HOH796 2.1 29.8 1.0
O D:HOH635 2.1 23.7 1.0
O B:HOH934 2.1 29.8 1.0
O D:HOH741 2.1 33.6 1.0
O D:HOH605 2.2 23.5 1.0
O B:HOH733 3.7 35.3 1.0
HD22 D:ASN85 3.8 32.4 1.0
O D:HOH808 4.1 23.8 1.0
O B:HOH800 4.1 28.4 1.0
OD1 D:ASP82 4.1 24.7 1.0
HA D:ASP82 4.2 17.1 1.0
O D:HOH745 4.2 26.8 1.0
O B:HOH711 4.3 30.9 1.0
O B:HOH679 4.3 29.2 1.0
O D:HOH634 4.3 33.3 1.0
HB3 D:ASN81 4.3 14.3 1.0
O D:ASN81 4.3 14.8 1.0
O B:HOH885 4.4 42.8 1.0
ND2 D:ASN85 4.5 27.0 1.0
OD1 B:ASP288 4.5 36.8 1.0
C D:ASN81 4.7 12.5 1.0
HE3 D:LYS84 4.8 19.7 1.0
HD21 D:ASN85 4.9 32.4 1.0
HA B:TRP218 4.9 19.1 1.0
HB2 D:ASN81 4.9 14.3 1.0
HB3 B:TRP218 5.0 11.2 1.0
N D:ASP82 5.0 16.0 1.0

Magnesium binding site 5 out of 5 in 8frb

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Magnesium binding site 5 out of 5 in the Mouse Acidic Mammalian Chitinase, Catalytic Domain in Complex with N, N'-Diacetylchitobiose at pH 5.25


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Mouse Acidic Mammalian Chitinase, Catalytic Domain in Complex with N, N'-Diacetylchitobiose at pH 5.25 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg402

b:19.7
occ:0.65
 O D:HOH848 2.0 27.6 1.0
O D:HOH841 2.0 35.1 1.0
O D:HOH875 2.1 26.8 1.0
O D:HOH626 4.0 32.4 1.0
O D:HOH696 4.2 28.6 1.0
O D:HOH665 4.2 27.5 1.0
O D:HOH778 4.4 30.2 1.0
HA D:TRP218 4.5 13.4 1.0
O D:HOH804 4.6 35.6 1.0
HB3 D:TRP218 4.7 15.1 1.0
OD1 D:ASP288 5.0 32.6 1.0

Reference:

R.E.Diaz, J.S.Fraser. Structural Characterization of Ligand Binding and pH-Specific Enzymatic Activity of Mouse Acidic Mammalian Chitinase To Be Published.
Page generated: Fri Oct 4 02:50:09 2024

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