Chlorine in PDB 8cvu: 20NS Temperature-Jump (Light) Xfel Structure of Lysozyme

Enzymatic activity of 20NS Temperature-Jump (Light) Xfel Structure of Lysozyme

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

Protein crystallography data

The structure of 20NS Temperature-Jump (Light) Xfel Structure of Lysozyme, PDB code: 8cvu 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) 31.62 / 1.57
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 79.523, 79.523, 38.233, 90, 90, 90
R / Rfree (%) 15.1 / 17.2

Other elements in 8cvu:

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

Chlorine binding site 1 out of 5 in 8cvu

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

b:39.2
occ:0.97
 H A:THR69 2.4 21.5 1.0
O A:HOH348 3.0 16.8 1.0
O A:THR69 3.1 19.3 1.0
N A:THR69 3.2 17.9 1.0
HD21 A:ASN65 3.2 29.2 1.0
HD22 A:ASN65 3.3 29.2 1.0
H A:GLY67 3.3 19.4 1.0
HA2 A:GLY67 3.4 23.4 1.0
C A:THR69 3.5 18.9 1.0
H A:ARG68 3.5 22.1 0.4
H A:ARG68 3.5 22.5 0.6
HB A:THR69 3.6 21.0 1.0
ND2 A:ASN65 3.6 24.4 1.0
N A:ARG68 3.6 18.4 0.4
N A:ARG68 3.6 18.8 0.6
OG A:SER72 3.7 23.6 1.0
C A:GLY67 3.8 20.0 1.0
CA A:GLY67 3.8 19.5 1.0
N A:GLY67 3.8 16.1 1.0
CA A:THR69 3.8 17.7 1.0
HA A:PRO70 4.0 26.6 1.0
O A:HOH354 4.0 23.0 1.0
CB A:THR69 4.2 17.5 1.0
H A:ASP66 4.2 17.9 1.0
N A:PRO70 4.2 20.8 1.0
C A:ARG68 4.2 18.5 0.4
C A:ARG68 4.3 19.3 0.6
OD1 A:ASP66 4.3 14.7 1.0
CA A:ARG68 4.4 17.8 0.4
CA A:ARG68 4.4 18.9 0.6
O A:GLY67 4.5 21.7 1.0
HG1 A:THR69 4.5 20.1 1.0
HA A:ARG68 4.5 21.4 0.4
H A:SER72 4.6 28.4 1.0
HA A:ARG68 4.6 22.8 0.6
CA A:PRO70 4.6 22.1 1.0
HA A:THR69 4.7 21.2 1.0
HA3 A:GLY67 4.7 23.4 1.0
NA A:NA201 4.8 20.3 1.0
HA A:ASN65 4.8 18.4 1.0
C A:ASP66 4.9 15.8 1.0
OG1 A:THR69 4.9 16.7 1.0
CG A:ASN65 4.9 23.0 1.0
N A:ASP66 4.9 14.9 1.0

Chlorine binding site 2 out of 5 in 8cvu

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Chlorine binding site 2 out of 5 in the 20NS Temperature-Jump (Light) 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 20NS Temperature-Jump (Light) Xfel Structure of Lysozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl205

b:105.5
occ:1.00
 HE1 A:HIS15 2.5 31.7 1.0
HH22 A:ARG14 2.5 32.7 0.5
O A:HOH377 2.6 26.8 1.0
HH21 A:ARG14 2.8 32.7 0.5
NH2 A:ARG14 2.9 27.3 0.5
OD1 A:ASP87 3.1 30.8 1.0
CE1 A:HIS15 3.2 26.4 1.0
HG1 A:THR89 3.3 28.9 1.0
NE2 A:HIS15 3.6 26.8 1.0
CG A:ASP87 3.6 30.2 1.0
O A:HOH301 3.6 48.9 1.0
H A:ILE88 3.8 23.2 0.6
H A:ILE88 3.8 23.2 0.4
HA A:ASP87 3.8 26.6 1.0
OD2 A:ASP87 3.9 34.0 1.0
OG1 A:THR89 3.9 24.1 1.0
CZ A:ARG14 4.1 26.9 0.5
HG12 A:ILE88 4.2 24.7 1.0
H A:THR89 4.5 22.8 1.0
ND1 A:HIS15 4.5 26.9 1.0
HH12 A:ARG14 4.5 32.0 0.5
N A:ILE88 4.5 19.4 0.6
N A:ILE88 4.5 19.4 0.4
CA A:ASP87 4.6 22.1 1.0
CB A:ASP87 4.6 26.7 1.0
NH1 A:ARG14 4.7 26.7 0.5
HB2 A:ASP87 4.8 32.0 1.0
HD1 A:HIS15 4.8 32.3 1.0
HE A:ARG14 4.8 32.0 0.5
HG13 A:ILE88 4.8 24.7 1.0
CD2 A:HIS15 4.9 26.1 1.0
NE A:ARG14 4.9 26.6 0.5
HB1 A:ALA11 5.0 21.4 1.0
C A:ASP87 5.0 19.9 1.0
N A:THR89 5.0 19.0 1.0
CG1 A:ILE88 5.0 20.6 1.0

Chlorine binding site 3 out of 5 in 8cvu

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

b:22.8
occ:1.00
 HH A:TYR23 2.4 17.5 1.0
OH A:TYR23 3.0 14.6 1.0
HE2 A:TYR23 3.2 15.8 1.0
HA3 A:GLY104 3.4 16.1 1.0
O A:HOH351 3.4 21.8 1.0
CE2 A:TYR23 3.7 13.2 1.0
CZ A:TYR23 3.7 13.3 1.0
HA2 A:GLY104 4.0 16.1 1.0
CA A:GLY104 4.1 13.4 1.0
N A:GLY104 4.7 14.7 1.0
O A:ARG21 4.7 19.9 0.5
O A:ARG21 4.7 19.9 0.5
O A:HOH313 4.8 22.9 1.0
H A:MET105 4.8 14.6 1.0
H A:GLY104 4.8 17.6 1.0
CD2 A:TYR23 4.9 12.7 1.0
CE1 A:TYR23 4.9 12.4 1.0

Chlorine binding site 4 out of 5 in 8cvu

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

b:37.8
occ:1.00
 H A:GLY26 2.3 16.2 1.0
HG A:SER24 2.5 23.1 1.0
HB2 A:SER24 2.9 20.7 1.0
HA A:GLN121 2.9 28.7 1.0
HA3 A:GLY26 3.0 15.5 1.0
N A:GLY26 3.1 13.5 1.0
OG A:SER24 3.1 19.3 1.0
HD11 A:ILE124 3.3 32.1 1.0
HG23 A:VAL120 3.4 24.7 1.0
CB A:SER24 3.5 17.2 1.0
CA A:GLY26 3.5 12.9 1.0
HD13 A:ILE124 3.6 32.1 1.0
HG2 A:GLN121 3.6 40.2 1.0
CA A:GLN121 3.8 23.9 1.0
HG12 A:ILE124 3.8 29.5 1.0
H A:LEU25 3.9 17.9 1.0
CD1 A:ILE124 3.9 26.8 1.0
HB2 A:GLN121 3.9 33.9 1.0
N A:LEU25 4.0 14.9 1.0
N A:GLN121 4.1 22.0 1.0
HA2 A:GLY26 4.1 15.5 1.0
HB3 A:SER24 4.1 20.7 1.0
HB3 A:LEU25 4.2 19.6 1.0
C A:SER24 4.2 15.0 1.0
CB A:GLN121 4.2 28.3 1.0
C A:LEU25 4.2 13.2 1.0
H A:ASN27 4.3 13.3 1.0
CG A:GLN121 4.3 33.5 1.0
CG1 A:ILE124 4.3 24.6 1.0
O A:VAL120 4.4 18.9 1.0
CG2 A:VAL120 4.4 20.6 1.0
C A:VAL120 4.4 20.4 1.0
CA A:SER24 4.5 15.7 1.0
H A:GLN121 4.5 26.4 1.0
CA A:LEU25 4.5 14.5 1.0
C A:GLY26 4.6 12.0 1.0
O A:SER24 4.7 15.0 1.0
N A:ASN27 4.7 11.1 1.0
HG3 A:GLN121 4.7 40.2 1.0
HD12 A:ILE124 4.7 32.1 1.0
HG21 A:VAL120 4.8 24.7 1.0
HG22 A:VAL120 4.8 24.7 1.0
HG23 A:ILE124 4.9 26.5 1.0
CB A:LEU25 4.9 16.4 1.0
HG13 A:ILE124 4.9 29.5 1.0
C A:GLN121 4.9 22.0 1.0
HB A:VAL120 4.9 23.8 1.0
HA A:SER24 5.0 18.9 1.0

Chlorine binding site 5 out of 5 in 8cvu

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

b:120.7
occ:1.00
 HZ2 A:LYS33 2.5 32.1 1.0
HE2 A:PHE38 2.8 17.5 1.0
HD3 A:LYS33 3.3 25.2 1.0
NZ A:LYS33 3.4 26.7 1.0
HZ3 A:TRP123 3.5 26.4 1.0
HE2 A:LYS33 3.6 29.3 1.0
CE2 A:PHE38 3.7 14.6 1.0
HB2 A:ARG5 3.7 26.2 1.0
HZ3 A:LYS33 3.8 32.1 1.0
CE A:LYS33 3.9 24.4 1.0
HZ1 A:LYS33 3.9 32.1 1.0
HD3 A:ARG5 3.9 27.1 1.0
CD A:LYS33 4.1 21.0 1.0
HD2 A:PHE38 4.3 16.4 1.0
HZ A:PHE38 4.4 17.5 1.0
CZ3 A:TRP123 4.4 22.0 1.0
CD2 A:PHE38 4.4 13.6 1.0
CZ A:PHE38 4.5 14.6 1.0
HD2 A:LYS33 4.6 25.2 1.0
CB A:ARG5 4.7 21.8 1.0
HE3 A:LYS33 4.8 29.3 1.0
CD A:ARG5 4.9 22.6 1.0
HG2 A:LYS33 4.9 20.9 1.0
HH2 A:TRP123 4.9 27.1 1.0
O A:HOH372 5.0 51.0 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 08:09:46 2024

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