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Sodium in PDB 5vjo: Complex Between HYHEL10 Fab Fragment Heavy Chain Mutant I29F and Pekin Duck Egg Lysozyme Isoform I (Del-I)

Enzymatic activity of Complex Between HYHEL10 Fab Fragment Heavy Chain Mutant I29F and Pekin Duck Egg Lysozyme Isoform I (Del-I)

All present enzymatic activity of Complex Between HYHEL10 Fab Fragment Heavy Chain Mutant I29F and Pekin Duck Egg Lysozyme Isoform I (Del-I):
3.2.1.18;

Protein crystallography data

The structure of Complex Between HYHEL10 Fab Fragment Heavy Chain Mutant I29F and Pekin Duck Egg Lysozyme Isoform I (Del-I), PDB code: 5vjo was solved by D.B.Langley, D.Christ, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.49 / 2.43
Space group P 21 2 21
Cell size a, b, c (Å), α, β, γ (°) 89.020, 102.910, 133.980, 90.00, 90.00, 90.00
R / Rfree (%) 26.2 / 29.6

Other elements in 5vjo:

The structure of Complex Between HYHEL10 Fab Fragment Heavy Chain Mutant I29F and Pekin Duck Egg Lysozyme Isoform I (Del-I) also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Complex Between HYHEL10 Fab Fragment Heavy Chain Mutant I29F and Pekin Duck Egg Lysozyme Isoform I (Del-I) (pdb code 5vjo). 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 Complex Between HYHEL10 Fab Fragment Heavy Chain Mutant I29F and Pekin Duck Egg Lysozyme Isoform I (Del-I), PDB code: 5vjo:

Sodium binding site 1 out of 1 in 5vjo

Go back to Sodium Binding Sites List in 5vjo
Sodium binding site 1 out of 1 in the Complex Between HYHEL10 Fab Fragment Heavy Chain Mutant I29F and Pekin Duck Egg Lysozyme Isoform I (Del-I)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Complex Between HYHEL10 Fab Fragment Heavy Chain Mutant I29F and Pekin Duck Egg Lysozyme Isoform I (Del-I) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na201

b:61.9
occ:1.00
 OG E:SER72 2.2 48.6 1.0
O E:HOH306 2.3 45.2 1.0
O E:HOH301 2.4 56.2 1.0
O E:CYS64 2.5 50.8 1.0
O E:SER60 2.6 47.7 1.0
CB E:SER72 3.2 48.9 1.0
C E:CYS64 3.5 50.0 1.0
CA E:ASP65 3.6 51.9 1.0
C E:SER60 3.8 48.0 1.0
N E:LYS73 3.9 47.6 1.0
N E:ASN74 3.9 42.8 1.0
N E:ASP65 3.9 50.9 1.0
C E:SER72 4.3 47.9 1.0
N E:ASP66 4.3 53.1 1.0
CA E:SER72 4.3 48.6 1.0
CA E:SER60 4.4 47.7 1.0
CB E:SER60 4.5 48.5 1.0
OD1 E:ASP65 4.5 52.9 1.0
C E:ASP65 4.5 52.7 1.0
CB E:ASP65 4.5 52.3 1.0
CA E:ASN74 4.6 41.5 1.0
CB E:ASN74 4.6 41.7 1.0
CB E:THR69 4.7 50.9 1.0
C E:LYS73 4.7 45.5 1.0
CA E:CYS64 4.7 48.0 1.0
N E:CYS64 4.8 46.3 1.0
CA E:LYS73 4.8 46.8 1.0
N E:ARG61 4.9 48.6 1.0
C E:ARG61 4.9 48.2 1.0
CG E:ASP65 4.9 53.6 1.0
OG1 E:THR69 5.0 50.7 1.0
O E:ARG61 5.0 48.7 1.0

Reference:

D.L.Burnett, D.B.Langley, P.Schofield, J.R.Hermes, T.D.Chan, J.Jackson, K.Bourne, J.H.Reed, K.Patterson, B.T.Porebski, R.Brink, D.Christ, C.C.Goodnow. Germinal Center Antibody Mutation Trajectories Are Determined By Rapid Self/Foreign Discrimination. Science V. 360 223 2018.
ISSN: ESSN 1095-9203
PubMed: 29650674
DOI: 10.1126/SCIENCE.AAO3859
Page generated: Tue Oct 8 00:51:20 2024

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