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

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

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

Protein crystallography data

The structure of 20NS Temperature-Jump (DARK1) Xfel Structure of Lysozyme, PDB code: 8cvv 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 (°) 79.439, 79.439, 38.192, 90, 90, 90
R / Rfree (%) 14.5 / 17

Other elements in 8cvv:

The structure of 20NS 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 20NS Temperature-Jump (DARK1) Xfel Structure of Lysozyme (pdb code 8cvv). 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 (DARK1) Xfel Structure of Lysozyme, PDB code: 8cvv:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 8cvv

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

b:36.0
occ:0.97
 H A:THR69 2.4 20.1 1.0
O A:HOH356 3.1 16.1 1.0
O A:THR69 3.1 19.2 1.0
HD21 A:ASN65 3.2 29.5 1.0
N A:THR69 3.2 16.8 1.0
HD22 A:ASN65 3.3 29.5 1.0
H A:GLY67 3.3 18.7 1.0
HA2 A:GLY67 3.4 23.0 1.0
H A:ARG68 3.5 19.9 0.4
C A:THR69 3.5 17.9 1.0
H A:ARG68 3.5 20.3 0.6
ND2 A:ASN65 3.6 24.6 1.0
N A:ARG68 3.6 16.6 0.4
HB A:THR69 3.6 19.4 1.0
N A:ARG68 3.6 16.9 0.6
C A:GLY67 3.7 19.3 1.0
OG A:SER72 3.8 22.5 1.0
CA A:GLY67 3.8 19.2 1.0
N A:GLY67 3.8 15.6 1.0
CA A:THR69 3.8 16.0 1.0
HA A:PRO70 4.0 25.6 1.0
O A:HOH357 4.0 22.9 1.0
CB A:THR69 4.2 16.2 1.0
N A:PRO70 4.2 19.9 1.0
C A:ARG68 4.2 17.6 0.4
H A:ASP66 4.2 17.6 1.0
C A:ARG68 4.3 19.0 0.6
OD1 A:ASP66 4.3 13.7 1.0
CA A:ARG68 4.4 16.3 0.4
O A:GLY67 4.4 21.4 1.0
CA A:ARG68 4.4 17.9 0.6
HA A:ARG68 4.5 19.5 0.4
HA A:ARG68 4.6 21.5 0.6
H A:SER72 4.6 26.4 1.0
HG1 A:THR69 4.6 19.3 1.0
CA A:PRO70 4.6 21.3 1.0
HA3 A:GLY67 4.7 23.0 1.0
HA A:THR69 4.7 19.2 1.0
NA A:NA201 4.8 17.7 1.0
HA A:ASN65 4.8 17.6 1.0
C A:ASP66 4.9 15.2 1.0
CG A:ASN65 4.9 23.2 1.0
OG1 A:THR69 4.9 16.1 1.0
N A:ASP66 4.9 14.6 1.0

Chlorine binding site 2 out of 5 in 8cvv

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Chlorine binding site 2 out of 5 in the 20NS 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 20NS Temperature-Jump (DARK1) Xfel Structure of Lysozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl205

b:86.8
occ:1.00
 HE1 A:HIS15 2.5 33.1 1.0
HH22 A:ARG14 2.6 35.3 0.4
O A:HOH379 2.6 25.2 1.0
HH21 A:ARG14 2.8 35.3 0.4
NH2 A:ARG14 2.9 29.4 0.4
OD1 A:ASP87 3.1 29.6 1.0
O A:HOH301 3.1 46.1 1.0
CE1 A:HIS15 3.2 27.6 1.0
HG1 A:THR89 3.3 26.8 1.0
NE2 A:HIS15 3.5 27.7 1.0
CG A:ASP87 3.6 30.0 1.0
H A:ILE88 3.8 20.9 0.4
H A:ILE88 3.8 20.7 0.6
HA A:ASP87 3.8 24.7 1.0
OD2 A:ASP87 3.9 35.1 1.0
OG1 A:THR89 3.9 22.3 1.0
CZ A:ARG14 4.1 28.6 0.4
HG12 A:ILE88 4.2 22.8 1.0
H A:THR89 4.4 20.4 1.0
ND1 A:HIS15 4.4 27.4 1.0
N A:ILE88 4.5 17.4 0.4
N A:ILE88 4.5 17.2 0.6
HH12 A:ARG14 4.5 34.5 0.4
CA A:ASP87 4.5 20.6 1.0
CB A:ASP87 4.5 26.1 1.0
NH1 A:ARG14 4.7 28.7 0.4
HB2 A:ASP87 4.7 31.3 1.0
HD1 A:HIS15 4.8 32.9 1.0
HE A:ARG14 4.8 34.2 0.4
CD2 A:HIS15 4.9 26.4 1.0
HG13 A:ILE88 4.9 22.8 1.0
C A:ASP87 4.9 17.9 1.0
N A:THR89 4.9 17.0 1.0
HB1 A:ALA11 4.9 21.6 1.0
NE A:ARG14 4.9 28.5 0.4
CG1 A:ILE88 5.0 19.0 1.0

Chlorine binding site 3 out of 5 in 8cvv

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

b:21.3
occ:1.00
 HH A:TYR23 2.4 16.0 1.0
OH A:TYR23 3.0 13.3 1.0
HE2 A:TYR23 3.2 14.8 1.0
HA3 A:GLY104 3.4 15.2 1.0
O A:HOH353 3.4 21.4 1.0
CE2 A:TYR23 3.7 12.3 1.0
CZ A:TYR23 3.7 12.0 1.0
HA2 A:GLY104 4.0 15.2 1.0
CA A:GLY104 4.1 12.7 1.0
O A:ARG21 4.7 18.9 0.5
O A:ARG21 4.7 18.9 0.5
N A:GLY104 4.7 14.1 1.0
O A:HOH318 4.8 22.1 1.0
H A:MET105 4.8 13.1 1.0
H A:GLY104 4.8 17.0 1.0
CD2 A:TYR23 4.9 11.5 1.0
CE1 A:TYR23 4.9 12.3 1.0
HB3 A:ARG21 5.0 26.9 0.5

Chlorine binding site 4 out of 5 in 8cvv

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Chlorine binding site 4 out of 5 in the 20NS 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 20NS Temperature-Jump (DARK1) 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 15.7 1.0
HG A:SER24 2.5 22.0 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 19.6 1.0
N A:GLY26 3.1 13.1 1.0
OG A:SER24 3.1 18.3 1.0
HD11 A:ILE124 3.4 30.1 1.0
HG23 A:VAL120 3.4 23.0 1.0
CA A:GLY26 3.5 12.3 1.0
CB A:SER24 3.5 16.3 1.0
HG2 A:GLN121 3.6 40.5 1.0
HD13 A:ILE124 3.7 30.1 1.0
HG12 A:ILE124 3.7 27.5 1.0
CA A:GLN121 3.7 22.6 1.0
HB2 A:GLN121 3.8 33.0 1.0
H A:LEU25 3.9 17.1 1.0
CD1 A:ILE124 3.9 25.1 1.0
N A:LEU25 4.0 14.3 1.0
N A:GLN121 4.0 20.5 1.0
CB A:GLN121 4.1 27.5 1.0
HA2 A:GLY26 4.1 14.8 1.0
HB3 A:LEU25 4.2 19.2 1.0
HB3 A:SER24 4.2 19.6 1.0
C A:SER24 4.2 14.0 1.0
C A:LEU25 4.2 12.1 1.0
H A:ASN27 4.3 12.7 1.0
CG1 A:ILE124 4.3 22.9 1.0
CG A:GLN121 4.3 33.8 1.0
O A:VAL120 4.3 17.0 1.0
CG2 A:VAL120 4.3 19.2 1.0
H A:GLN121 4.4 24.6 1.0
C A:VAL120 4.4 19.1 1.0
CA A:SER24 4.5 15.3 1.0
CA A:LEU25 4.6 13.5 1.0
C A:GLY26 4.6 11.6 1.0
O A:SER24 4.7 14.0 1.0
HG22 A:VAL120 4.7 23.0 1.0
HG3 A:GLN121 4.7 40.5 1.0
N A:ASN27 4.7 10.6 1.0
HG21 A:VAL120 4.8 23.0 1.0
HD12 A:ILE124 4.8 30.1 1.0
HG13 A:ILE124 4.8 27.5 1.0
CB A:LEU25 4.9 16.0 1.0
C A:GLN121 4.9 20.6 1.0
HB A:VAL120 4.9 22.1 1.0
HG23 A:ILE124 4.9 24.2 1.0

Chlorine binding site 5 out of 5 in 8cvv

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Chlorine binding site 5 out of 5 in the 20NS 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 20NS Temperature-Jump (DARK1) Xfel Structure of Lysozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl208

b:110.0
occ:1.00
 HZ2 A:LYS33 2.5 34.1 1.0
HE2 A:PHE38 2.8 16.0 1.0
HD3 A:LYS33 3.3 26.0 1.0
NZ A:LYS33 3.4 28.4 1.0
HZ3 A:TRP123 3.5 26.0 1.0
HE2 A:LYS33 3.6 31.2 1.0
CE2 A:PHE38 3.7 13.4 1.0
HB2 A:ARG5 3.7 25.6 1.0
HZ3 A:LYS33 3.8 34.1 1.0
CE A:LYS33 3.9 26.0 1.0
HD3 A:ARG5 3.9 24.8 1.0
HZ1 A:LYS33 3.9 34.1 1.0
CD A:LYS33 4.1 21.7 1.0
HD2 A:PHE38 4.3 16.0 1.0
HZ A:PHE38 4.3 17.4 1.0
CZ3 A:TRP123 4.4 21.7 1.0
CZ A:PHE38 4.4 14.5 1.0
CD2 A:PHE38 4.4 13.3 1.0
O A:HOH376 4.6 42.8 1.0
HD2 A:LYS33 4.7 26.0 1.0
CB A:ARG5 4.7 21.3 1.0
HE3 A:LYS33 4.8 31.2 1.0
CD A:ARG5 4.8 20.7 1.0
HG2 A:LYS33 4.8 21.4 1.0
HH2 A:TRP123 4.9 26.4 1.0
HE A:ARG5 5.0 27.9 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 22:38:30 2023

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