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Sodium in PDB 3agi: High Resolution X-Ray Analysis of Arg-Lysozyme Complex in the Presence of 500 Mm Arg

Enzymatic activity of High Resolution X-Ray Analysis of Arg-Lysozyme Complex in the Presence of 500 Mm Arg

All present enzymatic activity of High Resolution X-Ray Analysis of Arg-Lysozyme Complex in the Presence of 500 Mm Arg:
3.2.1.17;

Protein crystallography data

The structure of High Resolution X-Ray Analysis of Arg-Lysozyme Complex in the Presence of 500 Mm Arg, PDB code: 3agi was solved by L.Ito, K.Shiraki, K.Hasegawa, S.Baba, T.Kumasaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.02 / 1.20
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.033, 78.033, 37.752, 90.00, 90.00, 90.00
R / Rfree (%) 13.7 / 16.7

Other elements in 3agi:

The structure of High Resolution X-Ray Analysis of Arg-Lysozyme Complex in the Presence of 500 Mm Arg also contains other interesting chemical elements:

Chlorine (Cl) 8 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the High Resolution X-Ray Analysis of Arg-Lysozyme Complex in the Presence of 500 Mm Arg (pdb code 3agi). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the High Resolution X-Ray Analysis of Arg-Lysozyme Complex in the Presence of 500 Mm Arg, PDB code: 3agi:

Sodium binding site 1 out of 1 in 3agi

Go back to Sodium Binding Sites List in 3agi
Sodium binding site 1 out of 1 in the High Resolution X-Ray Analysis of Arg-Lysozyme Complex in the Presence of 500 Mm Arg


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of High Resolution X-Ray Analysis of Arg-Lysozyme Complex in the Presence of 500 Mm Arg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na134

b:10.8
occ:1.00
 O A:SER60 2.4 10.1 1.0
O A:ARG73 2.4 13.2 1.0
O A:CYS64 2.4 9.2 1.0
O A:HOH215 2.4 13.2 1.0
O A:HOH197 2.5 11.1 1.0
OG A:SER72 2.5 14.0 1.0
CB A:SER72 3.3 13.4 1.0
C A:ARG73 3.5 13.7 1.0
C A:CYS64 3.5 8.1 1.0
C A:SER60 3.5 9.4 1.0
CA A:ASN65 3.9 9.9 1.0
N A:ARG73 4.0 14.3 1.0
CA A:SER60 4.1 9.0 1.0
N A:ASN65 4.1 9.0 1.0
C A:SER72 4.2 14.3 1.0
CB A:SER60 4.2 9.3 1.0
CA A:ARG73 4.3 15.0 1.0
N A:ASN74 4.3 12.7 1.0
CA A:SER72 4.4 15.4 1.0
N A:CYS64 4.4 8.9 1.0
O A:HOH318 4.5 28.2 1.0
CA A:ASN74 4.6 11.8 1.0
C A:ARG61 4.6 11.8 1.0
N A:ARG61 4.6 10.2 1.0
CA A:CYS64 4.6 9.1 1.0
O A:SER72 4.6 16.1 1.0
N A:ASP66 4.6 9.5 1.0
OD1 A:ASN65 4.6 13.5 1.0
CB A:THR69 4.7 11.9 1.0
CB A:ASN74 4.7 12.9 1.0
CL A:CL135 4.7 16.7 1.0
O A:ARG61 4.7 12.8 1.0
N A:TRP62 4.8 10.4 1.0
CB A:ASN65 4.8 11.5 1.0
CA A:ARG61 4.8 9.7 0.7
C A:ASN65 4.9 8.6 1.0
O A:THR69 5.0 14.2 1.0

Reference:

L.Ito, K.Shiraki, T.Matsuura, M.Okumura, K.Hasegawa, S.Baba, H.Yamaguchi, T.Kumasaka. High-Resolution X-Ray Analysis Reveals Binding of Arginine to Aromatic Residues of Lysozyme Surface: Implication of Suppression of Protein Aggregation By Arginine Protein Eng.Des.Sel. V. 24 269 2011.
ISSN: ISSN 1741-0126
PubMed: 21084280
DOI: 10.1093/PROTEIN/GZQ101
Page generated: Tue Dec 15 06:02:09 2020

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