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Chlorine in PDB 2d4k: Monoclinic Hen Egg-White Lysozyme Crystallized at 313K

Enzymatic activity of Monoclinic Hen Egg-White Lysozyme Crystallized at 313K

All present enzymatic activity of Monoclinic Hen Egg-White Lysozyme Crystallized at 313K:
3.2.1.17;

Protein crystallography data

The structure of Monoclinic Hen Egg-White Lysozyme Crystallized at 313K, PDB code: 2d4k was solved by K.Harata, T.Akiba, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.70 / 1.15
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 27.217, 63.484, 59.189, 90.00, 92.93, 90.00
R / Rfree (%) 13.3 / 16.4

Other elements in 2d4k:

The structure of Monoclinic Hen Egg-White Lysozyme Crystallized at 313K also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Monoclinic Hen Egg-White Lysozyme Crystallized at 313K (pdb code 2d4k). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Monoclinic Hen Egg-White Lysozyme Crystallized at 313K, PDB code: 2d4k:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 2d4k

Go back to Chlorine Binding Sites List in 2d4k
Chlorine binding site 1 out of 4 in the Monoclinic Hen Egg-White Lysozyme Crystallized at 313K


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Monoclinic Hen Egg-White Lysozyme Crystallized at 313K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl405

b:38.2
occ:0.50
 O A:HOH404 1.6 26.3 0.5
O A:HOH403 1.8 17.4 0.5
OD1 A:ASN65 2.7 45.3 1.0
OG A:SER72 2.9 45.2 1.0
N A:GLY67 2.9 24.3 1.0
N A:ASP66 3.3 19.2 1.0
OD1 A:ASP66 3.3 18.7 1.0
CB A:SER72 3.5 45.2 1.0
O A:HOH402 3.5 43.8 1.0
CA A:GLY67 3.6 27.9 1.0
CG A:ASN65 3.7 36.6 1.0
N A:ARG68 3.7 27.9 1.0
N A:THR69 3.7 20.8 1.0
C A:ASP66 3.8 23.5 1.0
C A:GLY67 3.9 33.1 1.0
CA A:ASN65 3.9 21.6 1.0
NA A:NA401 3.9 21.8 1.0
CB A:THR69 4.0 18.5 1.0
C A:ASN65 4.1 20.1 1.0
CA A:ASP66 4.1 18.8 1.0
O A:THR69 4.1 24.0 1.0
OG1 A:THR69 4.3 17.1 1.0
CB A:ASN65 4.4 29.2 1.0
CA A:THR69 4.4 17.2 1.0
CG A:ASP66 4.4 16.3 1.0
ND2 A:ASN65 4.6 53.3 1.0
C A:ARG68 4.7 25.6 1.0
O A:CYS64 4.7 19.8 1.0
C A:THR69 4.7 18.4 1.0
CB A:ASP66 4.8 17.7 1.0
CA A:ARG68 4.8 29.4 1.0
O A:GLY67 4.8 46.5 1.0
O A:ASP66 4.9 26.8 1.0

Chlorine binding site 2 out of 4 in 2d4k

Go back to Chlorine Binding Sites List in 2d4k
Chlorine binding site 2 out of 4 in the Monoclinic Hen Egg-White Lysozyme Crystallized at 313K


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Monoclinic Hen Egg-White Lysozyme Crystallized at 313K within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Cl409

b:29.5
occ:1.00
 O N:HOH407 3.0 22.2 1.0
O N:THR269 3.3 19.8 1.0
N N:THR269 3.4 20.3 1.0
OD1 N:ASN265 3.4 31.8 1.0
N N:GLY267 3.5 20.7 1.0
CA N:GLY267 3.6 24.5 1.0
N N:ARG268 3.6 21.2 1.0
C N:THR269 3.6 18.1 1.0
OG N:SER272 3.7 18.6 1.0
C N:GLY267 3.7 23.5 1.0
CA N:THR269 4.0 17.8 1.0
O N:HOH408 4.0 23.5 1.0
OD2 N:ASP266 4.1 18.0 1.0
CB N:THR269 4.2 20.0 1.0
N N:PRO270 4.3 20.3 1.0
C N:ARG268 4.5 21.9 1.0
O N:GLY267 4.5 31.0 1.0
CA N:ARG268 4.6 25.0 1.0
CG N:ASN265 4.6 25.3 1.0
C N:ASP266 4.6 19.9 1.0
N N:ASP266 4.7 15.6 1.0
CA N:PRO270 4.7 22.6 1.0
NA N:NA406 4.8 16.6 1.0
OG1 N:THR269 4.9 18.8 1.0
CB N:SER272 5.0 17.5 1.0

Chlorine binding site 3 out of 4 in 2d4k

Go back to Chlorine Binding Sites List in 2d4k
Chlorine binding site 3 out of 4 in the Monoclinic Hen Egg-White Lysozyme Crystallized at 313K


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Monoclinic Hen Egg-White Lysozyme Crystallized at 313K within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Cl410

b:30.0
occ:1.00
 O N:HOH500 3.1 38.0 0.8
NE1 N:TRP263 3.3 13.9 1.0
O N:HOH541 3.4 23.4 0.4
O N:HOH421 3.8 21.9 1.0
CD1 N:TRP262 4.0 21.1 1.0
CD1 N:TRP263 4.1 12.9 1.0
CE2 N:TRP263 4.3 13.4 1.0
CB N:ASN259 4.7 18.1 1.0
CZ2 N:TRP263 4.7 16.8 1.0
CG N:TRP262 4.8 18.1 1.0
NE1 N:TRP262 4.8 25.3 1.0
O N:HOH645 5.0 37.0 0.6

Chlorine binding site 4 out of 4 in 2d4k

Go back to Chlorine Binding Sites List in 2d4k
Chlorine binding site 4 out of 4 in the Monoclinic Hen Egg-White Lysozyme Crystallized at 313K


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Monoclinic Hen Egg-White Lysozyme Crystallized at 313K within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Cl411

b:17.6
occ:1.00
 N N:GLY226 3.0 11.9 1.0
OG N:SER224 3.1 17.5 1.0
CB N:SER224 3.5 15.3 1.0
CA N:GLY226 3.5 11.8 1.0
CA N:GLN321 3.8 16.7 1.0
N N:LEU225 4.0 12.4 1.0
CB N:GLN321 4.1 20.5 1.0
N N:GLN321 4.1 14.8 1.0
C N:LEU225 4.1 11.1 1.0
C N:SER224 4.2 12.1 1.0
CD1 N:ILE324 4.2 31.9 1.0
CG N:GLN321 4.2 37.1 1.0
O N:VAL320 4.3 14.9 1.0
C N:VAL320 4.4 13.3 1.0
CA N:SER224 4.5 13.1 1.0
CA N:LEU225 4.5 11.2 1.0
O N:HOH593 4.5 34.8 0.5
CG1 N:ILE324 4.5 24.1 1.0
CG2 N:VAL320 4.5 19.9 1.0
CD N:GLN321 4.6 49.0 1.0
O N:SER224 4.6 13.0 1.0
C N:GLY226 4.7 11.3 1.0
OE1 N:GLN321 4.7 82.8 1.0
CB N:LEU225 4.7 13.7 1.0
N N:ASN227 4.8 10.6 1.0
C N:GLN321 5.0 15.2 1.0

Reference:

K.Harata, T.Akiba. Structural Phase Transition of Monoclinic Crystals of Hen Egg-White Lysozyme Acta Crystallogr.,Sect.D V. 62 375 2006.
ISSN: ISSN 0907-4449
PubMed: 16552138
DOI: 10.1107/S0907444906001314
Page generated: Sat Dec 12 09:02:50 2020

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