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Chlorine in PDB 5vjq: Complex Between HYHEL10 Fab Fragment Heavy Chain Mutant (I29F, S52T, Y53F) and Pekin Duck Egg Lysozyme Isoform I (Del-I)

Enzymatic activity of Complex Between HYHEL10 Fab Fragment Heavy Chain Mutant (I29F, S52T, Y53F) and Pekin Duck Egg Lysozyme Isoform I (Del-I)

All present enzymatic activity of Complex Between HYHEL10 Fab Fragment Heavy Chain Mutant (I29F, S52T, Y53F) 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, S52T, Y53F) and Pekin Duck Egg Lysozyme Isoform I (Del-I), PDB code: 5vjq 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) 49.32 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 88.650, 132.660, 199.110, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 23.5

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Complex Between HYHEL10 Fab Fragment Heavy Chain Mutant (I29F, S52T, Y53F) and Pekin Duck Egg Lysozyme Isoform I (Del-I) (pdb code 5vjq). 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, S52T, Y53F) and Pekin Duck Egg Lysozyme Isoform I (Del-I), PDB code: 5vjq:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 5vjq

Go back to Chlorine Binding Sites List in 5vjq
Chlorine binding site 1 out of 4 in the Complex Between HYHEL10 Fab Fragment Heavy Chain Mutant (I29F, S52T, Y53F) 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, S52T, Y53F) and Pekin Duck Egg Lysozyme Isoform I (Del-I) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl301

b:20.2
occ:1.00
 O B:HOH435 3.1 19.3 1.0
NZ B:LYS49 3.2 20.8 1.0
O I:HOH235 3.3 32.4 1.0
NH1 I:ARG93 3.3 22.1 1.0
O B:HOH546 3.3 20.6 1.0
CE B:LYS49 3.6 20.2 1.0
CG I:ARG93 3.8 20.3 1.0
CB A:ASP99 3.8 19.1 1.0
CD I:ARG93 3.9 21.2 1.0
CE2 B:TYR50 4.0 16.2 1.0
NH2 I:ARG97 4.1 20.5 1.0
CZ3 A:TRP98 4.2 16.9 1.0
CZ I:ARG93 4.4 22.3 1.0
OD2 A:ASP99 4.4 20.9 1.0
OH B:TYR50 4.5 17.1 1.0
NE I:ARG93 4.6 21.9 1.0
CG A:ASP99 4.6 19.6 1.0
CZ B:TYR50 4.7 16.5 1.0
O B:HOH434 4.8 21.8 1.0
CH2 A:TRP98 4.9 16.8 1.0
CD2 B:TYR50 4.9 16.1 1.0
CA A:ASP99 5.0 18.2 1.0
O A:HOH332 5.0 22.6 1.0
CZ I:ARG97 5.0 19.7 1.0

Chlorine binding site 2 out of 4 in 5vjq

Go back to Chlorine Binding Sites List in 5vjq
Chlorine binding site 2 out of 4 in the Complex Between HYHEL10 Fab Fragment Heavy Chain Mutant (I29F, S52T, Y53F) 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, S52T, Y53F) and Pekin Duck Egg Lysozyme Isoform I (Del-I) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl301

b:22.2
occ:1.00
 O D:HOH411 3.1 16.4 1.0
O3 C:GOL302 3.2 29.7 1.0
NZ D:LYS49 3.2 21.2 1.0
NH1 J:ARG93 3.3 21.4 1.0
O J:HOH341 3.4 25.6 1.0
CE D:LYS49 3.5 20.9 1.0
CG J:ARG93 3.8 18.2 1.0
CB C:ASP99 3.8 19.9 1.0
CD J:ARG93 3.9 19.3 1.0
CE2 D:TYR50 4.0 15.8 1.0
CZ3 C:TRP98 4.1 17.2 1.0
C3 C:GOL302 4.2 33.0 1.0
NH2 J:ARG97 4.2 18.9 1.0
CZ J:ARG93 4.4 21.0 1.0
O C:HOH459 4.4 41.0 1.0
OD2 C:ASP99 4.4 21.4 1.0
OH D:TYR50 4.5 16.3 1.0
NE J:ARG93 4.6 20.1 1.0
CG C:ASP99 4.6 20.4 1.0
CZ D:TYR50 4.7 16.0 1.0
O D:HOH403 4.7 22.4 1.0
O C:HOH447 4.8 22.3 1.0
CH2 C:TRP98 4.8 17.4 1.0
CE3 C:TRP98 4.9 16.8 1.0
CA C:ASP99 4.9 18.8 1.0
CD2 D:TYR50 5.0 15.6 1.0

Chlorine binding site 3 out of 4 in 5vjq

Go back to Chlorine Binding Sites List in 5vjq
Chlorine binding site 3 out of 4 in the Complex Between HYHEL10 Fab Fragment Heavy Chain Mutant (I29F, S52T, Y53F) 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, S52T, Y53F) and Pekin Duck Egg Lysozyme Isoform I (Del-I) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl301

b:24.6
occ:1.00
 O F:HOH411 3.0 19.3 1.0
NH1 K:ARG93 3.2 26.9 1.0
O F:HOH487 3.2 26.8 1.0
NZ F:LYS49 3.3 22.8 1.0
O K:HOH211 3.3 27.0 1.0
CG K:ARG93 3.6 26.3 1.0
CB E:ASP99 3.7 22.1 1.0
CD K:ARG93 3.7 26.7 1.0
CE2 F:TYR50 4.0 21.1 1.0
CE F:LYS49 4.1 22.2 1.0
CZ3 E:TRP98 4.2 22.0 1.0
CZ K:ARG93 4.3 27.3 1.0
NH2 K:ARG97 4.3 23.7 1.0
OD2 E:ASP99 4.4 23.6 1.0
CD F:LYS49 4.4 22.2 1.0
NE K:ARG93 4.4 26.9 1.0
OH F:TYR50 4.5 21.8 1.0
CG E:ASP99 4.6 22.6 1.0
CZ F:TYR50 4.7 21.4 1.0
O E:HOH436 4.9 26.0 1.0
CA E:ASP99 4.9 21.2 1.0
CH2 E:TRP98 4.9 22.3 1.0
O E:HOH442 4.9 29.9 1.0
CD2 F:TYR50 4.9 20.8 1.0
O K:ARG93 4.9 25.4 1.0
CE3 E:TRP98 5.0 21.5 1.0

Chlorine binding site 4 out of 4 in 5vjq

Go back to Chlorine Binding Sites List in 5vjq
Chlorine binding site 4 out of 4 in the Complex Between HYHEL10 Fab Fragment Heavy Chain Mutant (I29F, S52T, Y53F) 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, S52T, Y53F) and Pekin Duck Egg Lysozyme Isoform I (Del-I) within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cl301

b:30.0
occ:1.00
 NZ H:LYS49 3.1 22.5 1.0
O H:HOH414 3.1 18.9 1.0
O H:HOH436 3.2 24.3 1.0
O L:HOH215 3.4 32.1 1.0
NH1 L:ARG93 3.5 29.4 1.0
CE H:LYS49 3.5 22.5 1.0
CG L:ARG93 3.8 26.6 1.0
CB G:ASP99 3.8 21.2 1.0
CD L:ARG93 3.9 27.6 1.0
CE2 H:TYR50 4.0 20.4 1.0
CZ3 G:TRP98 4.2 20.7 1.0
NH2 L:ARG97 4.3 25.9 1.0
OH H:TYR50 4.5 20.8 1.0
CZ L:ARG93 4.5 29.8 1.0
OD2 G:ASP99 4.5 22.9 1.0
NE L:ARG93 4.7 29.1 1.0
CZ H:TYR50 4.7 20.7 1.0
CG G:ASP99 4.7 21.4 1.0
O G:HOH343 4.7 29.2 1.0
O H:HOH426 4.8 24.8 1.0
CD2 H:TYR50 4.9 20.5 1.0
CA G:ASP99 4.9 20.3 1.0
CH2 G:TRP98 4.9 21.2 1.0
CD H:LYS49 5.0 22.0 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: Sat Jul 12 09:54:13 2025

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