Chlorine in PDB 8cw8: Laser Off Temperature-Jump Xfel Structure of Lysozyme

Enzymatic activity of Laser Off Temperature-Jump Xfel Structure of Lysozyme

All present enzymatic activity of Laser Off Temperature-Jump Xfel Structure of Lysozyme:
3.2.1.17;

Protein crystallography data

The structure of Laser Off Temperature-Jump Xfel Structure of Lysozyme, PDB code: 8cw8 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) 28.09 / 1.57
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 79.446, 79.446, 38.159, 90, 90, 90
R / Rfree (%) 14.6 / 18.3

Other elements in 8cw8:

The structure of Laser Off Temperature-Jump Xfel Structure of Lysozyme also contains other interesting chemical elements:

Sodium (Na) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Laser Off Temperature-Jump Xfel Structure of Lysozyme (pdb code 8cw8). 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, PDB code: 8cw8:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 8cw8

Go back to Chlorine Binding Sites List in 8cw8
Chlorine binding site 1 out of 5 in the Laser Off Temperature-Jump Xfel Structure of Lysozyme


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl204

b:55.1
occ:1.00
 H A:THR69 2.4 20.2 1.0
O A:HOH352 3.1 16.6 1.0
O A:THR69 3.1 19.0 1.0
HD21 A:ASN65 3.2 27.7 1.0
N A:THR69 3.2 16.9 1.0
HD22 A:ASN65 3.3 27.7 1.0
HA2 A:GLY67 3.4 22.4 1.0
H A:GLY67 3.4 18.3 1.0
C A:THR69 3.5 18.0 1.0
H A:ARG68 3.5 21.4 0.4
H A:ARG68 3.6 22.0 0.6
ND2 A:ASN65 3.6 23.1 1.0
HB A:THR69 3.6 18.2 1.0
N A:ARG68 3.6 17.8 0.4
N A:ARG68 3.7 18.3 0.6
OG A:SER72 3.7 23.0 1.0
C A:GLY67 3.8 19.3 1.0
CA A:GLY67 3.8 18.6 1.0
CA A:THR69 3.8 16.4 1.0
N A:GLY67 3.8 15.3 1.0
HA A:PRO70 4.0 26.1 1.0
O A:HOH361 4.1 24.2 1.0
CB A:THR69 4.2 15.2 1.0
H A:ASP66 4.2 16.3 1.0
N A:PRO70 4.2 20.5 1.0
C A:ARG68 4.3 17.8 0.4
C A:ARG68 4.3 18.6 0.6
OD1 A:ASP66 4.3 13.1 1.0
CA A:ARG68 4.4 17.2 0.4
O A:GLY67 4.4 20.9 1.0
CA A:ARG68 4.4 18.5 0.6
HG1 A:THR69 4.5 18.3 1.0
H A:SER72 4.5 27.2 1.0
HA A:ARG68 4.5 20.7 0.4
HA A:ARG68 4.6 22.2 0.6
CA A:PRO70 4.6 21.8 1.0
HA A:THR69 4.7 19.7 1.0
HA3 A:GLY67 4.8 22.4 1.0
NA A:NA201 4.8 18.6 1.0
HA A:ASN65 4.8 17.0 1.0
C A:ASP66 4.9 14.8 1.0
CG A:ASN65 4.9 22.1 1.0
OG1 A:THR69 4.9 15.2 1.0
N A:ASP66 4.9 13.6 1.0

Chlorine binding site 2 out of 5 in 8cw8

Go back to Chlorine Binding Sites List in 8cw8
Chlorine binding site 2 out of 5 in the Laser Off Temperature-Jump Xfel Structure of Lysozyme


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl205

b:99.7
occ:1.00
 HH22 A:ARG14 2.2 34.1 0.4
HE1 A:HIS15 2.4 29.5 1.0
HH21 A:ARG14 2.4 34.1 0.4
NH2 A:ARG14 2.6 28.4 0.4
O A:HOH379 2.8 25.6 1.0
CE1 A:HIS15 3.1 24.6 1.0
OD1 A:ASP87 3.4 32.3 1.0
NE2 A:HIS15 3.5 24.6 1.0
HG1 A:THR89 3.6 28.3 1.0
CZ A:ARG14 3.8 27.8 0.4
CG A:ASP87 3.8 31.5 1.0
H A:ILE88 4.1 23.2 0.4
H A:ILE88 4.1 23.2 0.6
OD2 A:ASP87 4.1 35.1 1.0
HA A:ASP87 4.1 27.1 1.0
OG1 A:THR89 4.2 23.6 1.0
HH12 A:ARG14 4.3 33.1 0.4
ND1 A:HIS15 4.4 25.2 1.0
HG12 A:ILE88 4.4 24.7 1.0
HE A:ARG14 4.5 33.1 0.4
NH1 A:ARG14 4.5 27.6 0.4
NE A:ARG14 4.6 27.6 0.4
HD1 A:HIS15 4.7 30.3 1.0
H A:THR89 4.7 22.3 1.0
N A:ILE88 4.8 19.4 0.4
N A:ILE88 4.8 19.4 0.6
CB A:ASP87 4.8 27.5 1.0
HE A:ARG14 4.8 37.0 0.6
CA A:ASP87 4.8 22.6 1.0
CD2 A:HIS15 4.9 24.0 1.0
HB1 A:ALA11 4.9 20.9 1.0
HB2 A:ASP87 4.9 33.0 1.0
HG13 A:ILE88 5.0 24.7 1.0

Chlorine binding site 3 out of 5 in 8cw8

Go back to Chlorine Binding Sites List in 8cw8
Chlorine binding site 3 out of 5 in the Laser Off Temperature-Jump Xfel Structure of Lysozyme


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl206

b:21.8
occ:1.00
 HH A:TYR23 2.4 14.9 1.0
OH A:TYR23 3.0 12.4 1.0
HE2 A:TYR23 3.1 14.7 1.0
O A:HOH355 3.4 23.6 1.0
HA3 A:GLY104 3.4 13.9 1.0
CE2 A:TYR23 3.7 12.2 1.0
CZ A:TYR23 3.7 11.8 1.0
HA2 A:GLY104 4.0 13.9 1.0
CA A:GLY104 4.1 11.6 1.0
O A:ARG21 4.7 19.2 0.5
O A:ARG21 4.7 19.3 0.5
N A:GLY104 4.7 13.4 1.0
H A:MET105 4.8 12.8 1.0
O A:HOH323 4.8 23.0 1.0
CD2 A:TYR23 4.9 12.2 1.0
H A:GLY104 4.9 16.1 1.0
CE1 A:TYR23 4.9 11.6 1.0

Chlorine binding site 4 out of 5 in 8cw8

Go back to Chlorine Binding Sites List in 8cw8
Chlorine binding site 4 out of 5 in the Laser Off Temperature-Jump Xfel Structure of Lysozyme


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl207

b:32.5
occ:1.00
 H A:GLY26 2.3 16.4 1.0
HG A:SER24 2.6 21.3 1.0
HA A:GLN121 2.9 27.1 1.0
HA3 A:GLY26 3.0 14.8 1.0
HB2 A:SER24 3.0 19.4 1.0
N A:GLY26 3.0 13.6 1.0
OG A:SER24 3.1 17.8 1.0
HD11 A:ILE124 3.4 31.1 1.0
HG23 A:VAL120 3.4 24.7 1.0
CA A:GLY26 3.5 12.3 1.0
CB A:SER24 3.5 16.1 1.0
HG2 A:GLN121 3.6 39.4 1.0
HD13 A:ILE124 3.6 31.1 1.0
HG12 A:ILE124 3.7 28.5 1.0
CA A:GLN121 3.7 22.6 1.0
HB2 A:GLN121 3.8 33.6 1.0
CD1 A:ILE124 3.9 25.9 1.0
H A:LEU25 3.9 17.1 1.0
N A:LEU25 4.0 14.2 1.0
N A:GLN121 4.1 21.0 1.0
HA2 A:GLY26 4.1 14.8 1.0
CB A:GLN121 4.1 28.0 1.0
HB3 A:LEU25 4.2 18.0 1.0
C A:SER24 4.2 14.4 1.0
C A:LEU25 4.2 12.7 1.0
HB3 A:SER24 4.2 19.4 1.0
CG A:GLN121 4.3 32.8 1.0
H A:ASN27 4.3 12.3 1.0
CG1 A:ILE124 4.3 23.7 1.0
O A:VAL120 4.3 17.8 1.0
C A:VAL120 4.4 19.5 1.0
CG2 A:VAL120 4.4 20.6 1.0
H A:GLN121 4.4 25.2 1.0
CA A:SER24 4.5 14.6 1.0
CA A:LEU25 4.5 13.6 1.0
C A:GLY26 4.6 11.8 1.0
HG3 A:GLN121 4.6 39.4 1.0
O A:SER24 4.7 14.9 1.0
HG21 A:VAL120 4.7 24.7 1.0
N A:ASN27 4.7 10.3 1.0
HD12 A:ILE124 4.8 31.1 1.0
HG13 A:ILE124 4.8 28.5 1.0
HG22 A:VAL120 4.8 24.7 1.0
CB A:LEU25 4.8 15.0 1.0
C A:GLN121 4.9 20.1 1.0
HG23 A:ILE124 4.9 25.1 1.0
HB A:VAL120 5.0 23.8 1.0
HG21 A:ILE124 5.0 25.1 1.0

Chlorine binding site 5 out of 5 in 8cw8

Go back to Chlorine Binding Sites List in 8cw8
Chlorine binding site 5 out of 5 in the Laser Off Temperature-Jump Xfel Structure of Lysozyme


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl208

b:104.0
occ:1.00
 HE2 A:PHE38 2.8 17.4 1.0
HZ2 A:LYS33 2.8 33.6 1.0
HZ3 A:TRP123 3.3 24.9 1.0
O A:HOH385 3.4 35.2 1.0
HB2 A:ARG5 3.4 25.4 1.0
HD3 A:LYS33 3.5 25.2 1.0
HD3 A:ARG5 3.6 26.4 1.0
CE2 A:PHE38 3.6 14.5 1.0
NZ A:LYS33 3.7 28.0 1.0
HE2 A:LYS33 3.8 30.0 1.0
HZ3 A:LYS33 4.0 33.6 1.0
CE A:LYS33 4.1 25.0 1.0
HZ A:PHE38 4.2 16.3 1.0
HZ1 A:LYS33 4.2 33.6 1.0
CD A:LYS33 4.2 21.0 1.0
CZ3 A:TRP123 4.2 20.8 1.0
CB A:ARG5 4.3 21.2 1.0
CZ A:PHE38 4.4 13.6 1.0
HD2 A:PHE38 4.4 15.6 1.0
CD A:ARG5 4.5 22.0 1.0
CD2 A:PHE38 4.5 13.0 1.0
O A:HOH371 4.5 43.6 1.0
HE A:ARG5 4.6 27.9 1.0
HB3 A:ARG5 4.6 25.4 1.0
HG3 A:ARG5 4.8 25.5 1.0
CG A:ARG5 4.8 21.3 1.0
HD2 A:LYS33 4.8 25.2 1.0
HE3 A:TRP123 4.9 23.9 1.0
HH2 A:TRP123 4.9 25.6 1.0
H A:ARG5 5.0 22.6 1.0
HG2 A:LYS33 5.0 20.5 1.0
NE A:ARG5 5.0 23.3 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 Apr 4 22:39:46 2023

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