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Chlorine in PDB 8cwb: Laser Off Temperature-Jump Xfel Structure of Lysozyme Bound to N,N'- Diacetylchitobiose

Enzymatic activity of Laser Off Temperature-Jump Xfel Structure of Lysozyme Bound to N,N'- Diacetylchitobiose

All present enzymatic activity of Laser Off Temperature-Jump Xfel Structure of Lysozyme Bound to N,N'- Diacetylchitobiose:
3.2.1.17;

Protein crystallography data

The structure of Laser Off Temperature-Jump Xfel Structure of Lysozyme Bound to N,N'- Diacetylchitobiose, PDB code: 8cwb was solved by A.M.Wolff, M.C.Thompson, J.S.Fraser, E.Nango, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.74 / 1.51
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 77.061, 77.061, 37.223, 90, 90, 90
R / Rfree (%) 13.6 / 16.8

Other elements in 8cwb:

The structure of Laser Off Temperature-Jump Xfel Structure of Lysozyme Bound to N,N'- Diacetylchitobiose also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Laser Off Temperature-Jump Xfel Structure of Lysozyme Bound to N,N'- Diacetylchitobiose (pdb code 8cwb). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Laser Off Temperature-Jump Xfel Structure of Lysozyme Bound to N,N'- Diacetylchitobiose, PDB code: 8cwb:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 8cwb

Go back to Chlorine Binding Sites List in 8cwb
Chlorine binding site 1 out of 5 in the Laser Off Temperature-Jump Xfel Structure of Lysozyme Bound to N,N'- Diacetylchitobiose


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Laser Off Temperature-Jump Xfel Structure of Lysozyme Bound to N,N'- Diacetylchitobiose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl204

b:26.5
occ:1.00
 H A:THR69 2.4 19.1 1.0
O A:HOH335 3.0 16.5 1.0
H A:GLY67 3.1 19.4 1.0
O A:HOH383 3.2 40.4 1.0
HA2 A:GLY67 3.2 23.5 1.0
N A:THR69 3.2 15.9 1.0
O A:THR69 3.3 18.1 1.0
H A:ARG68 3.4 20.2 1.0
OD1 A:ASN65 3.5 23.6 1.0
N A:ARG68 3.5 16.8 1.0
C A:THR69 3.5 16.4 1.0
CA A:GLY67 3.6 19.6 1.0
N A:GLY67 3.6 16.2 1.0
C A:GLY67 3.6 19.1 1.0
HB A:THR69 3.7 17.7 1.0
CA A:THR69 3.8 15.7 1.0
OG A:SER72 3.9 17.8 1.0
O A:HOH371 4.0 18.9 1.0
HA A:PRO70 4.0 22.9 1.0
H A:ASP66 4.1 16.2 1.0
OD1 A:ASP66 4.2 13.8 1.0
N A:PRO70 4.2 17.6 1.0
C A:ARG68 4.2 19.4 1.0
CB A:THR69 4.2 14.7 1.0
O A:GLY67 4.3 22.7 1.0
CA A:ARG68 4.3 18.3 1.0
HG1 A:THR69 4.4 16.8 1.0
HA A:ARG68 4.5 22.0 1.0
HA3 A:GLY67 4.6 23.5 1.0
CA A:PRO70 4.6 19.1 1.0
HA A:ASN65 4.6 16.9 1.0
H A:SER72 4.7 23.4 1.0
CG A:ASN65 4.7 21.4 1.0
C A:ASP66 4.7 15.1 1.0
N A:ASP66 4.7 13.5 1.0
HA A:THR69 4.7 18.9 1.0
NA A:NA201 4.8 15.7 1.0
HD3 A:PRO70 4.8 25.4 1.0
OG1 A:THR69 4.8 14.0 1.0

Chlorine binding site 2 out of 5 in 8cwb

Go back to Chlorine Binding Sites List in 8cwb
Chlorine binding site 2 out of 5 in the Laser Off Temperature-Jump Xfel Structure of Lysozyme Bound to N,N'- Diacetylchitobiose


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Laser Off Temperature-Jump Xfel Structure of Lysozyme Bound to N,N'- Diacetylchitobiose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl205

b:70.5
occ:1.00
 H A:ILE88 2.4 23.6 1.0
HG12 A:ILE88 2.5 23.1 1.0
HE1 A:HIS15 2.7 33.1 1.0
HH21 A:ARG14 2.9 34.8 0.5
HA A:ASP87 3.1 28.4 1.0
HH22 A:ARG14 3.1 34.8 0.5
N A:ILE88 3.3 19.7 1.0
NH2 A:ARG14 3.4 29.0 0.5
HH12 A:ARG14 3.4 37.4 0.6
CG1 A:ILE88 3.5 19.3 1.0
CE1 A:HIS15 3.6 27.6 1.0
HB1 A:ALA11 3.6 21.9 1.0
OD1 A:ASP87 3.7 29.1 1.0
HG13 A:ILE88 3.7 23.1 1.0
HG23 A:ILE88 3.8 23.3 1.0
HZ A:PHE3 3.9 22.7 1.0
O A:HOH325 3.9 34.0 1.0
CA A:ASP87 3.9 23.7 1.0
NH1 A:ARG14 4.0 31.2 0.6
C A:ASP87 4.0 21.8 1.0
H A:THR89 4.1 21.7 1.0
HB2 A:ALA11 4.2 21.9 1.0
HH22 A:ARG14 4.2 38.7 0.6
CA A:ILE88 4.2 15.9 1.0
CB A:ILE88 4.2 17.0 1.0
HG1 A:THR89 4.3 27.9 1.0
HD1 A:HIS15 4.3 33.1 1.0
HD13 A:ILE88 4.3 25.2 1.0
CG A:ASP87 4.3 31.6 1.0
ND1 A:HIS15 4.4 27.6 1.0
O A:SER86 4.4 25.8 1.0
CB A:ALA11 4.4 18.3 1.0
CD1 A:ILE88 4.4 21.0 1.0
HH11 A:ARG14 4.4 37.4 0.6
HD11 A:ILE88 4.5 25.2 1.0
CG2 A:ILE88 4.5 19.4 1.0
N A:THR89 4.6 18.1 1.0
NE2 A:HIS15 4.6 29.9 1.0
CZ A:ARG14 4.7 27.6 0.5
CB A:ASP87 4.7 27.6 1.0
CZ A:PHE3 4.7 18.9 1.0
NH2 A:ARG14 4.8 32.3 0.6
C A:ILE88 4.8 17.0 1.0
CZ A:ARG14 4.8 30.6 0.6
HE2 A:PHE3 4.8 21.9 1.0
OG1 A:THR89 4.8 23.3 1.0
N A:ASP87 5.0 22.8 1.0
HB3 A:ALA11 5.0 21.9 1.0
HB2 A:ASP87 5.0 33.1 1.0

Chlorine binding site 3 out of 5 in 8cwb

Go back to Chlorine Binding Sites List in 8cwb
Chlorine binding site 3 out of 5 in the Laser Off Temperature-Jump Xfel Structure of Lysozyme Bound to N,N'- Diacetylchitobiose


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Laser Off Temperature-Jump Xfel Structure of Lysozyme Bound to N,N'- Diacetylchitobiose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl206

b:22.2
occ:1.00
 HH A:TYR23 2.1 18.3 1.0
OH A:TYR23 2.9 15.3 1.0
O A:HOH357 3.0 28.1 1.0
HE2 A:TYR23 3.0 15.8 1.0
HA3 A:GLY104 3.2 17.1 1.0
O A:HOH342 3.5 21.9 1.0
CE2 A:TYR23 3.6 13.2 1.0
CZ A:TYR23 3.6 13.2 1.0
HA2 A:GLY104 3.9 17.1 1.0
CA A:GLY104 4.0 14.2 1.0
O A:HOH319 4.4 29.1 1.0
O A:ARG21 4.4 20.7 1.0
N A:GLY104 4.5 15.5 1.0
H A:MET105 4.6 12.5 1.0
H A:GLY104 4.6 18.6 1.0
CD2 A:TYR23 4.7 11.5 1.0
HB3 A:ARG21 4.7 27.9 1.0
CE1 A:TYR23 4.8 12.4 1.0
O A:HOH341 4.9 29.6 1.0

Chlorine binding site 4 out of 5 in 8cwb

Go back to Chlorine Binding Sites List in 8cwb
Chlorine binding site 4 out of 5 in the Laser Off Temperature-Jump Xfel Structure of Lysozyme Bound to N,N'- Diacetylchitobiose


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Laser Off Temperature-Jump Xfel Structure of Lysozyme Bound to N,N'- Diacetylchitobiose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl207

b:29.9
occ:1.00
 H A:GLY26 2.2 15.1 1.0
HG3 A:GLN121 2.6 43.4 1.0
HA A:GLN121 2.7 24.4 1.0
HB2 A:SER24 2.9 21.0 1.0
OG A:SER24 3.0 19.9 1.0
HA3 A:GLY26 3.0 13.6 1.0
N A:GLY26 3.0 12.6 1.0
HD13 A:ILE124 3.0 30.2 1.0
HE22 A:GLN121 3.2 51.1 1.0
HG23 A:VAL120 3.4 24.3 1.0
CB A:SER24 3.4 17.5 1.0
CG A:GLN121 3.4 36.2 1.0
CA A:GLY26 3.5 11.3 1.0
HG A:SER24 3.5 23.9 1.0
HG12 A:ILE124 3.5 27.6 1.0
CA A:GLN121 3.5 20.3 1.0
NE2 A:GLN121 3.7 42.6 1.0
HD11 A:ILE124 3.7 30.2 1.0
CD1 A:ILE124 3.7 25.2 1.0
H A:LEU25 3.8 16.6 1.0
CD A:GLN121 3.9 41.7 1.0
N A:LEU25 3.9 13.9 1.0
CB A:GLN121 3.9 25.8 1.0
N A:GLN121 4.0 18.0 1.0
HB3 A:LEU25 4.0 16.7 1.0
C A:SER24 4.1 14.2 1.0
HB3 A:SER24 4.1 21.0 1.0
HA2 A:GLY26 4.1 13.6 1.0
C A:LEU25 4.1 12.9 1.0
CG1 A:ILE124 4.1 23.0 1.0
HG2 A:GLN121 4.1 43.4 1.0
HB3 A:GLN121 4.1 31.0 1.0
H A:ASN27 4.2 13.7 1.0
HE21 A:GLN121 4.3 51.1 1.0
O A:VAL120 4.3 16.2 1.0
CG2 A:VAL120 4.3 20.2 1.0
C A:VAL120 4.3 16.9 1.0
H A:GLN121 4.3 21.6 1.0
CA A:SER24 4.3 15.7 1.0
CA A:LEU25 4.4 13.3 1.0
C A:GLY26 4.5 10.2 1.0
HG23 A:ILE124 4.6 26.9 1.0
O A:SER24 4.6 15.6 1.0
HG21 A:VAL120 4.6 24.3 1.0
HD12 A:ILE124 4.6 30.2 1.0
N A:ASN27 4.7 11.4 1.0
HG13 A:ILE124 4.7 27.6 1.0
C A:GLN121 4.7 18.9 1.0
CB A:LEU25 4.7 13.9 1.0
HA A:SER24 4.8 18.8 1.0
HG22 A:VAL120 4.8 24.3 1.0
HB2 A:GLN121 4.8 31.0 1.0
HB A:VAL120 4.9 21.3 1.0
OE1 A:GLN121 4.9 42.3 1.0
O A:GLN121 4.9 20.6 1.0

Chlorine binding site 5 out of 5 in 8cwb

Go back to Chlorine Binding Sites List in 8cwb
Chlorine binding site 5 out of 5 in the Laser Off Temperature-Jump Xfel Structure of Lysozyme Bound to N,N'- Diacetylchitobiose


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Laser Off Temperature-Jump Xfel Structure of Lysozyme Bound to N,N'- Diacetylchitobiose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl208

b:96.4
occ:1.00
 HE2 A:PHE38 2.6 19.9 1.0
HZ2 A:LYS33 3.1 37.1 1.0
HZ1 A:LYS33 3.2 37.1 1.0
HD3 A:LYS33 3.4 25.8 1.0
CE2 A:PHE38 3.5 16.6 1.0
NZ A:LYS33 3.5 30.9 1.0
HB2 A:ARG5 3.6 20.9 1.0
HD2 A:PHE38 3.8 17.9 1.0
HZ3 A:TRP123 4.0 27.4 1.0
CD2 A:PHE38 4.1 14.9 1.0
O A:HOH365 4.1 35.8 1.0
HD3 A:ARG5 4.1 21.4 1.0
CD A:LYS33 4.2 21.5 1.0
HZ3 A:LYS33 4.2 37.1 1.0
CE A:LYS33 4.3 27.4 1.0
HE2 A:LYS33 4.3 32.8 1.0
O A:HOH309 4.4 26.8 1.0
CZ A:PHE38 4.4 14.8 1.0
HZ A:PHE38 4.5 17.7 1.0
HD2 A:LYS33 4.5 25.8 1.0
CB A:ARG5 4.5 17.4 1.0
H A:ARG5 4.6 20.4 1.0
O A:HOH354 4.7 28.5 1.0
HB3 A:ARG5 4.8 20.9 1.0
CZ3 A:TRP123 4.9 22.8 1.0
HE A:ARG5 5.0 23.8 1.0
CD A:ARG5 5.0 17.8 1.0

Reference:

A.M.Wolff, E.Nango, I.D.Young, A.S.Brewster, M.Kubo, T.Nomura, M.Sugahara, S.Owada, B.A.Barad, K.Ito, A.Bhowmick, S.Carbajo, T.Hino, J.M.Holton, D.Im, L.J.O'riordan, T.Tanaka, R.Tanaka, R.G.Sierra, F.Yumoto, K.Tono, S.Iwata, N.K.Sauter, J.S.Fraser, M.C.Thompson. Mapping Protein Dynamics at High-Resolution with Temperature-Jump X-Ray Crystallography Biorxiv 2022.
DOI: 10.1101/2022.06.10.495662
Page generated: Tue Jul 30 08:13:49 2024

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