Chlorine in PDB 8cw1: 20US Temperature-Jump (DARK1) Xfel Structure of Lysozyme

Enzymatic activity of 20US Temperature-Jump (DARK1) Xfel Structure of Lysozyme

All present enzymatic activity of 20US Temperature-Jump (DARK1) Xfel Structure of Lysozyme:
3.2.1.17;

Protein crystallography data

The structure of 20US Temperature-Jump (DARK1) Xfel Structure of Lysozyme, PDB code: 8cw1 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 (°) 79.443, 79.443, 38.198, 90, 90, 90
R / Rfree (%) 14.8 / 16.8

Other elements in 8cw1:

The structure of 20US Temperature-Jump (DARK1) 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 20US Temperature-Jump (DARK1) Xfel Structure of Lysozyme (pdb code 8cw1). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the 20US Temperature-Jump (DARK1) Xfel Structure of Lysozyme, PDB code: 8cw1:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 8cw1

Go back to Chlorine Binding Sites List in 8cw1
Chlorine binding site 1 out of 5 in the 20US Temperature-Jump (DARK1) 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 20US Temperature-Jump (DARK1) Xfel Structure of Lysozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl204

b:35.2
occ:0.97
 H A:THR69 2.4 19.6 1.0
O A:HOH354 3.1 15.7 1.0
HD21 A:ASN65 3.1 28.8 1.0
O A:THR69 3.2 19.6 1.0
HD22 A:ASN65 3.2 28.8 1.0
N A:THR69 3.2 16.3 1.0
H A:GLY67 3.3 18.8 1.0
HA2 A:GLY67 3.4 22.3 1.0
H A:ARG68 3.5 20.1 0.4
ND2 A:ASN65 3.5 24.0 1.0
C A:THR69 3.5 18.4 1.0
H A:ARG68 3.5 20.3 0.6
HB A:THR69 3.6 18.9 1.0
N A:ARG68 3.6 16.7 0.4
N A:ARG68 3.6 16.9 0.6
C A:GLY67 3.7 18.9 1.0
N A:GLY67 3.7 15.6 1.0
OG A:SER72 3.8 22.8 1.0
CA A:GLY67 3.8 18.6 1.0
CA A:THR69 3.8 16.3 1.0
O A:HOH359 4.0 22.7 1.0
HA A:PRO70 4.0 26.5 1.0
H A:ASP66 4.2 16.8 1.0
CB A:THR69 4.2 15.8 1.0
C A:ARG68 4.3 17.1 0.4
N A:PRO70 4.3 20.6 1.0
C A:ARG68 4.3 17.9 0.6
OD1 A:ASP66 4.3 13.9 1.0
CA A:ARG68 4.4 16.7 0.4
O A:GLY67 4.4 21.4 1.0
CA A:ARG68 4.4 17.7 0.6
HA A:ARG68 4.5 20.1 0.4
HG1 A:THR69 4.5 18.6 1.0
HA A:ARG68 4.6 21.2 0.6
H A:SER72 4.6 27.0 1.0
CA A:PRO70 4.6 22.1 1.0
HA3 A:GLY67 4.7 22.3 1.0
HA A:THR69 4.8 19.5 1.0
NA A:NA201 4.8 19.1 1.0
HA A:ASN65 4.8 16.6 1.0
CG A:ASN65 4.8 22.1 1.0
C A:ASP66 4.8 15.1 1.0
N A:ASP66 4.8 14.0 1.0
OG1 A:THR69 4.9 15.5 1.0
O A:HOH350 5.0 43.4 1.0

Chlorine binding site 2 out of 5 in 8cw1

Go back to Chlorine Binding Sites List in 8cw1
Chlorine binding site 2 out of 5 in the 20US Temperature-Jump (DARK1) 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 20US Temperature-Jump (DARK1) Xfel Structure of Lysozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl205

b:95.7
occ:1.00
 HE1 A:HIS15 2.5 31.4 1.0
HH22 A:ARG14 2.5 34.2 0.4
O A:HOH380 2.6 25.9 1.0
HH21 A:ARG14 2.7 34.2 0.4
NH2 A:ARG14 2.8 28.5 0.4
CE1 A:HIS15 3.2 26.2 1.0
OD1 A:ASP87 3.3 29.9 1.0
O A:HOH301 3.3 46.2 1.0
HG1 A:THR89 3.5 28.8 1.0
NE2 A:HIS15 3.6 26.2 1.0
CG A:ASP87 3.7 30.1 1.0
H A:ILE88 3.8 22.2 0.6
H A:ILE88 3.8 22.1 0.4
HA A:ASP87 3.8 25.5 1.0
OD2 A:ASP87 3.9 34.6 1.0
CZ A:ARG14 4.0 27.4 0.4
OG1 A:THR89 4.1 24.0 1.0
HG12 A:ILE88 4.2 24.3 1.0
ND1 A:HIS15 4.4 26.6 1.0
HH12 A:ARG14 4.5 32.3 0.4
N A:ILE88 4.5 18.5 0.6
N A:ILE88 4.5 18.4 0.4
H A:THR89 4.5 22.2 1.0
CA A:ASP87 4.6 21.2 1.0
CB A:ASP87 4.6 26.2 1.0
NH1 A:ARG14 4.7 26.9 0.4
HE A:ARG14 4.7 32.7 0.4
HD1 A:HIS15 4.8 31.9 1.0
HB2 A:ASP87 4.8 31.4 1.0
NE A:ARG14 4.8 27.2 0.4
HG13 A:ILE88 4.9 24.3 1.0
HB1 A:ALA11 4.9 21.8 1.0
O A:HOH353 4.9 48.9 1.0
CD2 A:HIS15 4.9 24.9 1.0
CG1 A:ILE88 5.0 20.2 1.0
C A:ASP87 5.0 18.6 1.0

Chlorine binding site 3 out of 5 in 8cw1

Go back to Chlorine Binding Sites List in 8cw1
Chlorine binding site 3 out of 5 in the 20US Temperature-Jump (DARK1) 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 20US Temperature-Jump (DARK1) Xfel Structure of Lysozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl206

b:22.3
occ:1.00
 HH A:TYR23 2.4 16.4 1.0
OH A:TYR23 3.0 13.7 1.0
HE2 A:TYR23 3.2 14.7 1.0
HA3 A:GLY104 3.4 15.0 1.0
O A:HOH356 3.4 21.0 1.0
CE2 A:TYR23 3.7 12.2 1.0
CZ A:TYR23 3.7 11.9 1.0
HA2 A:GLY104 4.0 15.0 1.0
CA A:GLY104 4.1 12.5 1.0
N A:GLY104 4.7 13.7 1.0
O A:ARG21 4.7 17.9 0.5
O A:ARG21 4.7 19.0 0.5
H A:MET105 4.8 13.4 1.0
H A:GLY104 4.8 16.5 1.0
O A:HOH323 4.8 22.2 1.0
CD2 A:TYR23 4.9 12.2 1.0
CE1 A:TYR23 4.9 12.7 1.0

Chlorine binding site 4 out of 5 in 8cw1

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Chlorine binding site 4 out of 5 in the 20US Temperature-Jump (DARK1) 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 20US Temperature-Jump (DARK1) Xfel Structure of Lysozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl207

b:37.4
occ:1.00
 H A:GLY26 2.3 15.2 1.0
HG A:SER24 2.5 21.9 1.0
HA A:GLN121 2.9 26.6 1.0
HB2 A:SER24 2.9 19.3 1.0
HA3 A:GLY26 3.0 14.6 1.0
N A:GLY26 3.1 12.7 1.0
OG A:SER24 3.1 18.3 1.0
HD11 A:ILE124 3.3 32.4 1.0
HG23 A:VAL120 3.4 23.4 1.0
CB A:SER24 3.5 16.1 1.0
CA A:GLY26 3.5 12.2 1.0
HD13 A:ILE124 3.6 32.4 1.0
HG2 A:GLN121 3.7 39.9 1.0
HG12 A:ILE124 3.7 28.7 1.0
CA A:GLN121 3.7 22.2 1.0
CD1 A:ILE124 3.8 27.0 1.0
H A:LEU25 3.9 18.2 1.0
HB2 A:GLN121 3.9 32.6 1.0
N A:LEU25 4.0 15.1 1.0
N A:GLN121 4.1 20.3 1.0
HA2 A:GLY26 4.1 14.6 1.0
HB3 A:LEU25 4.1 18.7 1.0
HB3 A:SER24 4.2 19.3 1.0
C A:SER24 4.2 14.4 1.0
CB A:GLN121 4.2 27.2 1.0
C A:LEU25 4.2 12.2 1.0
H A:ASN27 4.2 13.0 1.0
CG1 A:ILE124 4.3 23.9 1.0
O A:VAL120 4.4 17.6 1.0
CG A:GLN121 4.4 33.2 1.0
CG2 A:VAL120 4.4 19.5 1.0
H A:GLN121 4.4 24.4 1.0
C A:VAL120 4.4 18.8 1.0
CA A:SER24 4.5 14.7 1.0
CA A:LEU25 4.5 13.7 1.0
C A:GLY26 4.6 11.3 1.0
O A:SER24 4.6 14.6 1.0
HD12 A:ILE124 4.7 32.4 1.0
N A:ASN27 4.7 10.8 1.0
HG22 A:VAL120 4.8 23.4 1.0
HG3 A:GLN121 4.8 39.9 1.0
HG21 A:VAL120 4.8 23.4 1.0
HG13 A:ILE124 4.8 28.7 1.0
CB A:LEU25 4.8 15.6 1.0
HG23 A:ILE124 4.9 25.2 1.0
C A:GLN121 4.9 20.3 1.0
HB A:VAL120 5.0 22.7 1.0
HA A:SER24 5.0 17.6 1.0

Chlorine binding site 5 out of 5 in 8cw1

Go back to Chlorine Binding Sites List in 8cw1
Chlorine binding site 5 out of 5 in the 20US Temperature-Jump (DARK1) 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 20US Temperature-Jump (DARK1) Xfel Structure of Lysozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl208

b:119.9
occ:1.00
 HZ2 A:LYS33 2.3 37.3 1.0
HE2 A:PHE38 2.9 16.9 1.0
NZ A:LYS33 3.1 31.1 1.0
HD3 A:LYS33 3.1 27.5 1.0
HE2 A:LYS33 3.4 33.8 1.0
HZ3 A:TRP123 3.4 26.5 1.0
HZ3 A:LYS33 3.5 37.3 1.0
CE A:LYS33 3.6 28.2 1.0
CE2 A:PHE38 3.6 14.1 1.0
HZ1 A:LYS33 3.7 37.3 1.0
O A:HOH382 3.7 43.4 1.0
CD A:LYS33 3.8 22.9 1.0
HB2 A:ARG5 3.9 24.9 1.0
HD3 A:ARG5 4.1 25.0 1.0
HD2 A:PHE38 4.3 16.0 1.0
CZ3 A:TRP123 4.3 22.1 1.0
HZ A:PHE38 4.3 17.0 1.0
CZ A:PHE38 4.4 14.2 1.0
CD2 A:PHE38 4.4 13.3 1.0
HD2 A:LYS33 4.4 27.5 1.0
HE3 A:LYS33 4.6 33.8 1.0
HG2 A:LYS33 4.7 21.0 1.0
HH2 A:TRP123 4.7 27.1 1.0
CB A:ARG5 4.9 20.7 1.0
CG A:LYS33 4.9 17.5 1.0
O A:HOH374 4.9 43.1 1.0
CD A:ARG5 5.0 20.8 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 08:10:18 2024

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