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Sodium in PDB 1lzs: Structural Changes of the Active Site Cleft and Different Saccharide Binding Modes in Human Lysozyme Co-Crystallized with Hexa-N-Acetyl- Chitohexaose at pH 4.0

Enzymatic activity of Structural Changes of the Active Site Cleft and Different Saccharide Binding Modes in Human Lysozyme Co-Crystallized with Hexa-N-Acetyl- Chitohexaose at pH 4.0

All present enzymatic activity of Structural Changes of the Active Site Cleft and Different Saccharide Binding Modes in Human Lysozyme Co-Crystallized with Hexa-N-Acetyl- Chitohexaose at pH 4.0:
3.2.1.17;

Protein crystallography data

The structure of Structural Changes of the Active Site Cleft and Different Saccharide Binding Modes in Human Lysozyme Co-Crystallized with Hexa-N-Acetyl- Chitohexaose at pH 4.0, PDB code: 1lzs was solved by M.Matsushima, H.Song, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 6.00 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.990, 162.250, 32.520, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Sodium Binding Sites:

The binding sites of Sodium atom in the Structural Changes of the Active Site Cleft and Different Saccharide Binding Modes in Human Lysozyme Co-Crystallized with Hexa-N-Acetyl- Chitohexaose at pH 4.0 (pdb code 1lzs). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structural Changes of the Active Site Cleft and Different Saccharide Binding Modes in Human Lysozyme Co-Crystallized with Hexa-N-Acetyl- Chitohexaose at pH 4.0, PDB code: 1lzs:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 1lzs

Go back to Sodium Binding Sites List in 1lzs
Sodium binding site 1 out of 2 in the Structural Changes of the Active Site Cleft and Different Saccharide Binding Modes in Human Lysozyme Co-Crystallized with Hexa-N-Acetyl- Chitohexaose at pH 4.0


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structural Changes of the Active Site Cleft and Different Saccharide Binding Modes in Human Lysozyme Co-Crystallized with Hexa-N-Acetyl- Chitohexaose at pH 4.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na131

b:21.3
occ:1.00
O A:SER61 2.3 15.8 1.0
O A:HOH395 2.4 18.0 1.0
O A:CYS65 2.5 15.8 1.0
O A:VAL74 2.5 21.5 1.0
O A:HOH370 2.5 23.5 1.0
CB A:ALA73 3.1 25.5 1.0
C A:SER61 3.5 16.1 1.0
C A:VAL74 3.6 22.1 1.0
C A:CYS65 3.6 14.5 1.0
N A:VAL74 3.8 24.6 1.0
CA A:ASN66 3.9 15.6 1.0
C A:ALA73 4.1 25.9 1.0
O A:ARG62 4.1 18.5 1.0
CA A:ALA73 4.1 26.7 1.0
CA A:SER61 4.2 14.9 1.0
N A:ASN66 4.2 14.9 1.0
O A:HOH424 4.2 20.9 1.0
C A:ARG62 4.2 17.8 1.0
CA A:VAL74 4.3 22.9 1.0
N A:CYS65 4.3 14.0 1.0
CB A:SER61 4.4 11.1 1.0
N A:ASN75 4.4 20.1 1.0
OD1 A:ASN66 4.5 19.3 1.0
N A:ARG62 4.5 17.9 1.0
N A:ASP67 4.5 16.0 1.0
CA A:ARG62 4.6 18.5 1.0
CA A:CYS65 4.7 13.9 1.0
CA A:ASN75 4.7 18.6 1.0
N A:TYR63 4.7 17.7 1.0
CB A:ASN75 4.7 17.7 1.0
C A:ASN66 4.8 16.2 1.0
CB A:ASN66 4.8 15.8 1.0
O A:ALA73 4.8 26.9 1.0
O A:HOH429 4.9 31.2 1.0
CB A:THR70 4.9 22.2 1.0
N A:TRP64 5.0 16.9 1.0

Sodium binding site 2 out of 2 in 1lzs

Go back to Sodium Binding Sites List in 1lzs
Sodium binding site 2 out of 2 in the Structural Changes of the Active Site Cleft and Different Saccharide Binding Modes in Human Lysozyme Co-Crystallized with Hexa-N-Acetyl- Chitohexaose at pH 4.0


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structural Changes of the Active Site Cleft and Different Saccharide Binding Modes in Human Lysozyme Co-Crystallized with Hexa-N-Acetyl- Chitohexaose at pH 4.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na131

b:18.6
occ:1.00
O B:SER61 2.3 15.5 1.0
O B:VAL74 2.3 20.2 1.0
O B:CYS65 2.4 14.3 1.0
O B:HOH364 2.5 20.9 1.0
O B:HOH418 2.7 15.4 1.0
CB B:ALA73 3.2 21.1 1.0
C B:CYS65 3.4 15.1 1.0
C B:VAL74 3.4 21.1 1.0
C B:SER61 3.5 14.2 1.0
N B:VAL74 3.8 20.2 1.0
CA B:ASN66 3.9 16.8 1.0
N B:ASN66 4.0 15.6 1.0
C B:ALA73 4.1 21.1 1.0
N B:CYS65 4.2 13.3 1.0
C B:ARG62 4.2 14.9 1.0
O B:ARG62 4.2 14.2 1.0
CA B:VAL74 4.2 21.4 1.0
CA B:SER61 4.2 12.5 1.0
CA B:ALA73 4.3 20.6 1.0
N B:ASN75 4.3 21.1 1.0
CA B:CYS65 4.4 13.4 1.0
N B:ARG62 4.4 15.1 1.0
CA B:ASN75 4.5 20.1 1.0
O B:HOH366 4.5 16.9 1.0
CA B:ARG62 4.5 14.8 1.0
CB B:ASN75 4.5 20.5 1.0
CB B:SER61 4.5 10.7 1.0
N B:TYR63 4.6 12.5 1.0
O B:ALA73 4.7 21.6 1.0
N B:ASP67 4.7 15.2 1.0
OD1 B:ASN66 4.8 21.1 1.0
CB B:ASN66 4.8 18.6 1.0
C B:ASN66 4.8 15.2 1.0
N B:TRP64 4.9 14.5 1.0
C B:TYR63 4.9 15.6 1.0
O B:HOH549 5.0 39.6 1.0

Reference:

H.Song, K.Inaka, K.Maenaka, M.Matsushima. Structural Changes of Active Site Cleft and Different Saccharide Binding Modes in Human Lysozyme Co-Crystallized with Hexa-N-Acetyl-Chitohexaose at pH 4.0. J.Mol.Biol. V. 244 522 1994.
ISSN: ISSN 0022-2836
PubMed: 7990138
DOI: 10.1006/JMBI.1994.1750
Page generated: Tue Dec 15 05:29:35 2020

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