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Chlorine 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:

Sodium (Na) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Complex Between HYHEL10 Fab Fragment Heavy Chain Mutant I29F and Pekin Duck Egg Lysozyme Isoform I (Del-I), PDB code: 5vjo:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 5vjo

Go back to Chlorine Binding Sites List in 5vjo
Chlorine binding site 1 out of 4 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 Chlorine with other atoms in the Cl 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
A:Cl301

b:68.5
occ:1.00
 CB A:SER28 3.6 38.7 1.0
CE2 A:TYR102 4.0 40.8 1.0
OG A:SER28 4.0 38.5 1.0
CG2 A:VAL2 4.1 52.8 1.0
OD2 A:ASP32 4.1 32.6 1.0
OH A:TYR102 4.8 43.0 1.0
CD2 A:TYR102 4.8 40.3 1.0
CZ A:TYR102 4.9 41.1 1.0
ND2 A:ASN97 4.9 35.5 1.0
CA A:SER28 4.9 38.6 1.0

Chlorine binding site 2 out of 4 in 5vjo

Go back to Chlorine Binding Sites List in 5vjo
Chlorine binding site 2 out of 4 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 Chlorine with other atoms in the Cl binding site number 2 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
B:Cl301

b:43.4
occ:1.00
 O B:HOH404 2.9 26.7 1.0
NZ B:LYS49 3.5 45.8 1.0
CE B:LYS49 3.5 45.9 1.0
NE E:ARG93 3.5 43.2 1.0
NH1 E:ARG93 3.7 43.8 1.0
CE2 B:TYR50 3.9 43.0 1.0
CB A:ASP99 4.0 36.8 1.0
CZ E:ARG93 4.1 43.3 1.0
CG E:ARG93 4.1 41.9 1.0
CZ3 A:TRP98 4.3 37.7 1.0
NH2 E:ARG97 4.4 34.4 1.0
OH B:TYR50 4.4 43.5 1.0
CD E:ARG93 4.5 43.1 1.0
OD2 A:ASP99 4.6 35.9 1.0
CZ B:TYR50 4.7 43.4 1.0
CD B:LYS49 4.7 45.7 1.0
CG A:ASP99 4.8 36.1 1.0
CD2 B:TYR50 4.9 43.5 1.0
CH2 A:TRP98 4.9 38.4 1.0
O E:ARG93 5.0 38.3 1.0

Chlorine binding site 3 out of 4 in 5vjo

Go back to Chlorine Binding Sites List in 5vjo
Chlorine binding site 3 out of 4 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 Chlorine with other atoms in the Cl binding site number 3 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
C:Cl301

b:91.8
occ:1.00
 CG2 C:THR110 3.5 50.9 1.0
CE2 C:PHE146 3.8 69.5 1.0
CZ C:PHE146 3.8 70.2 1.0
CD2 C:LEU170 4.0 63.1 1.0
OH C:TYR175 4.1 58.3 1.0
CB C:SER112 4.2 60.3 1.0
OG C:SER112 4.4 60.4 1.0
CD1 C:LEU170 4.8 63.0 1.0
O C:VAL111 4.9 58.6 1.0
CB C:THR110 5.0 50.7 1.0
CZ C:TYR175 5.0 57.8 1.0

Chlorine binding site 4 out of 4 in 5vjo

Go back to Chlorine Binding Sites List in 5vjo
Chlorine binding site 4 out of 4 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 Chlorine with other atoms in the Cl binding site number 4 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
D:Cl301

b:46.2
occ:1.00
 NZ D:LYS49 2.9 50.1 1.0
O D:HOH407 2.9 37.8 1.0
CE D:LYS49 3.5 49.1 1.0
NE F:ARG93 3.6 44.7 1.0
NH1 F:ARG93 3.6 45.2 1.0
CB C:ASP99 3.9 42.1 1.0
CE2 D:TYR50 4.0 45.2 1.0
NH2 F:ARG97 4.0 44.8 1.0
CZ F:ARG93 4.1 44.8 1.0
CG F:ARG93 4.1 44.0 1.0
CZ3 C:TRP98 4.2 42.1 1.0
OH D:TYR50 4.4 45.0 1.0
CD F:ARG93 4.5 44.8 1.0
OD2 C:ASP99 4.5 43.7 1.0
CZ D:TYR50 4.7 45.0 1.0
CG C:ASP99 4.8 43.2 1.0
CH2 C:TRP98 4.9 42.2 1.0
O F:ARG93 4.9 44.1 1.0
CD D:LYS49 4.9 48.7 1.0
CZ F:ARG97 5.0 44.6 1.0
CD2 D:TYR50 5.0 45.4 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: Fri Jul 26 18:50:50 2024

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