Atomistry » Chlorine » PDB 5kvy-5l55 » 5l3h
Atomistry »
  Chlorine »
    PDB 5kvy-5l55 »
      5l3h »

Chlorine in PDB 5l3h: Re-Refinement of 4DD4; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15 with Standard Uncertainties

Enzymatic activity of Re-Refinement of 4DD4; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15 with Standard Uncertainties

All present enzymatic activity of Re-Refinement of 4DD4; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15 with Standard Uncertainties:
3.2.1.17;

Protein crystallography data

The structure of Re-Refinement of 4DD4; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15 with Standard Uncertainties, PDB code: 5l3h was solved by J.R.Helliwell, S.W.M.Tanley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.93 / 1.70
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.832, 78.832, 37.021, 90.00, 90.00, 90.00
R / Rfree (%) 20.2 / 24.8

Other elements in 5l3h:

The structure of Re-Refinement of 4DD4; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15 with Standard Uncertainties also contains other interesting chemical elements:

Platinum (Pt) 5 atoms
Sodium (Na) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Re-Refinement of 4DD4; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15 with Standard Uncertainties (pdb code 5l3h). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 7 binding sites of Chlorine where determined in the Re-Refinement of 4DD4; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15 with Standard Uncertainties, PDB code: 5l3h:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in 5l3h

Go back to Chlorine Binding Sites List in 5l3h
Chlorine binding site 1 out of 7 in the Re-Refinement of 4DD4; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15 with Standard Uncertainties


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Re-Refinement of 4DD4; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15 with Standard Uncertainties within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl201

b:13.4
occ:1.00
 H A:THR69 2.4 14.0 1.0
O A:HOH339 3.1 9.4 1.0
HA2 A:GLY67 3.1 14.1 1.0
O A:THR69 3.2 12.6 1.0
H A:GLY67 3.2 12.9 1.0
N A:THR69 3.2 11.7 1.0
O A:HOH369 3.3 15.0 1.0
H A:ARG68 3.5 13.1 1.0
OG A:SER72 3.5 14.0 1.0
O A:HOH304 3.5 24.4 1.0
HB A:THR69 3.5 13.7 1.0
N A:ARG68 3.5 10.9 1.0
C A:GLY67 3.6 11.9 1.0
CA A:GLY67 3.6 11.7 1.0
C A:THR69 3.6 13.3 1.0
OD1 A:ASN65 3.6 13.5 1.0
N A:GLY67 3.7 10.7 1.0
CA A:THR69 3.8 12.4 1.0
O A:HOH344 4.0 13.2 1.0
CB A:THR69 4.1 11.4 1.0
O A:GLY67 4.2 12.3 1.0
C A:ARG68 4.2 11.9 1.0
H A:ASP66 4.2 12.3 1.0
OD1 A:ASP66 4.2 9.2 1.0
CA A:ARG68 4.3 12.2 1.0
HG1 A:THR69 4.3 13.2 1.0
HA A:ARG68 4.5 14.6 1.0
N A:PRO70 4.5 12.6 1.0
HA A:PRO70 4.5 14.5 1.0
HA3 A:GLY67 4.5 14.1 1.0
H A:SER72 4.6 16.8 1.0
NA A:NA202 4.6 13.2 1.0
CB A:SER72 4.7 14.1 1.0
HA A:THR69 4.7 14.9 1.0
HB3 A:SER72 4.7 17.0 1.0
OG1 A:THR69 4.8 11.0 1.0
HA A:ASN65 4.8 13.7 1.0
O A:HOH341 4.8 13.9 0.6
C A:ASP66 4.8 10.0 1.0
CG A:ASN65 4.8 13.2 1.0
N A:ASP66 4.9 10.3 1.0
CA A:PRO70 5.0 12.1 1.0

Chlorine binding site 2 out of 7 in 5l3h

Go back to Chlorine Binding Sites List in 5l3h
Chlorine binding site 2 out of 7 in the Re-Refinement of 4DD4; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15 with Standard Uncertainties


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Re-Refinement of 4DD4; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15 with Standard Uncertainties within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl205

b:16.6
occ:0.70
 PT A:PT203 2.3 22.3 0.7
HG23 A:THR89 2.8 17.1 1.0
HB3 A:HIS15 2.8 17.6 1.0
N A:NH3208 3.0 19.5 0.7
HN1 A:NH3208 3.0 23.4 0.7
ND1 A:HIS15 3.1 16.7 1.0
HA A:THR89 3.1 14.8 1.0
HN2 A:NH3208 3.2 23.4 0.7
HB A:VAL92 3.2 13.8 1.0
OD1 A:ASN93 3.2 17.4 1.0
HG11 A:VAL92 3.4 14.0 1.0
HG12 A:VAL92 3.6 14.0 1.0
CB A:HIS15 3.6 14.7 1.0
CG A:HIS15 3.6 15.8 1.0
CG2 A:THR89 3.7 14.3 1.0
HN3 A:NH3208 3.8 23.4 0.7
CG1 A:VAL92 3.8 11.6 1.0
O A:THR89 3.8 11.4 1.0
O A:HIS15 3.8 15.1 1.0
CA A:THR89 3.9 12.3 1.0
CB A:VAL92 4.0 11.5 1.0
HZ2 A:LYS96 4.0 17.2 1.0
HA A:HIS15 4.0 18.2 1.0
HG22 A:THR89 4.0 17.1 1.0
CG A:ASN93 4.0 15.1 1.0
CE1 A:HIS15 4.1 17.1 1.0
HD21 A:ASN93 4.1 18.7 1.0
H A:ASN93 4.2 13.6 1.0
CB A:THR89 4.2 12.7 1.0
CA A:HIS15 4.3 15.2 1.0
HB2 A:HIS15 4.3 17.6 1.0
N A:NH3207 4.3 17.1 0.7
C A:THR89 4.3 11.8 1.0
HG21 A:THR89 4.3 17.1 1.0
HE1 A:HIS15 4.4 20.6 1.0
ND2 A:ASN93 4.4 15.6 1.0
OG1 A:THR89 4.4 14.3 1.0
HG21 A:VAL92 4.5 14.0 1.0
C A:HIS15 4.5 15.1 1.0
HN1 A:NH3207 4.5 20.5 0.7
N A:ASN93 4.6 11.4 1.0
HZ1 A:LYS96 4.7 17.2 1.0
NZ A:LYS96 4.7 14.4 1.0
HG13 A:VAL92 4.7 14.0 1.0
HN2 A:NH3207 4.8 20.5 0.7
CD2 A:HIS15 4.8 15.4 1.0
CG2 A:VAL92 4.8 11.7 1.0
HN3 A:NH3207 4.8 20.5 0.7
HA A:ASN93 4.9 14.1 1.0
NE2 A:HIS15 5.0 16.9 1.0
HG1 A:THR89 5.0 17.1 1.0
HE3 A:LYS96 5.0 16.6 1.0

Chlorine binding site 3 out of 7 in 5l3h

Go back to Chlorine Binding Sites List in 5l3h
Chlorine binding site 3 out of 7 in the Re-Refinement of 4DD4; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15 with Standard Uncertainties


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Re-Refinement of 4DD4; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15 with Standard Uncertainties within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl206

b:12.9
occ:0.52
 PT A:PT204 2.3 16.4 0.5
HN2 A:NH3209 2.5 16.7 0.5
H A:ILE88 2.6 15.9 1.0
HG12 A:ILE88 2.7 15.1 1.0
N A:NH3209 2.9 13.9 0.5
HA A:ASP87 3.1 16.6 1.0
HN1 A:NH3209 3.3 16.7 0.5
HB1 A:ALA11 3.3 16.0 1.0
N A:ILE88 3.5 13.3 1.0
HG23 A:ILE88 3.5 14.3 1.0
NE2 A:HIS15 3.5 16.9 1.0
CG1 A:ILE88 3.6 12.6 1.0
HZ A:PHE3 3.6 15.7 1.0
HN3 A:NH3209 3.6 16.7 0.5
O A:HOH312 3.6 16.8 1.0
HD2 A:HIS15 3.8 18.4 1.0
OD1 A:ASP87 4.0 15.6 1.0
HG13 A:ILE88 4.0 15.1 1.0
CA A:ASP87 4.0 13.9 1.0
HH11 A:ARG14 4.0 22.2 1.0
CD2 A:HIS15 4.0 15.4 1.0
HB2 A:ALA11 4.1 16.0 1.0
CB A:ALA11 4.1 13.3 1.0
CG2 A:ILE88 4.2 12.0 1.0
C A:ASP87 4.2 12.5 1.0
O A:SER86 4.3 14.7 1.0
CB A:ILE88 4.3 12.2 1.0
CG A:ASP87 4.3 16.1 1.0
HH12 A:ARG14 4.3 22.2 1.0
CZ A:PHE3 4.4 13.1 1.0
CA A:ILE88 4.4 12.5 1.0
HD11 A:ILE88 4.4 13.2 1.0
CD1 A:ILE88 4.5 11.0 1.0
HE2 A:PHE3 4.5 15.5 1.0
HD13 A:ILE88 4.5 13.2 1.0
NH1 A:ARG14 4.5 18.5 1.0
HG21 A:ILE88 4.6 14.3 1.0
CE1 A:HIS15 4.6 17.1 1.0
H A:THR89 4.7 14.9 1.0
HB3 A:ALA11 4.7 16.0 1.0
CB A:ASP87 4.7 14.3 1.0
O A:HOH373 4.8 19.1 1.0
OD2 A:ASP87 4.8 17.9 1.0
HG1 A:THR89 4.9 17.1 1.0
CE2 A:PHE3 4.9 12.9 1.0
HA A:ALA11 4.9 15.2 1.0
HE1 A:HIS15 4.9 20.6 1.0

Chlorine binding site 4 out of 7 in 5l3h

Go back to Chlorine Binding Sites List in 5l3h
Chlorine binding site 4 out of 7 in the Re-Refinement of 4DD4; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15 with Standard Uncertainties


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Re-Refinement of 4DD4; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15 with Standard Uncertainties within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl210

b:20.9
occ:1.00
 HD22 A:ASN65 2.4 16.2 1.0
HB3 A:PRO79 2.7 14.0 1.0
O A:HOH362 3.1 13.9 1.0
HB3 A:ASN65 3.2 13.9 1.0
HA A:PRO79 3.2 12.6 1.0
ND2 A:ASN65 3.2 13.5 1.0
CB A:PRO79 3.6 11.7 1.0
HD21 A:ASN65 3.7 16.2 1.0
CA A:PRO79 3.7 10.5 1.0
HD3 A:PRO79 3.8 14.6 1.0
N A:PRO79 3.9 11.4 1.0
CB A:ASN65 4.0 11.6 1.0
CG A:ASN65 4.1 13.2 1.0
CD A:PRO79 4.3 12.2 1.0
HB2 A:PRO79 4.3 14.0 1.0
O A:ASN65 4.3 10.0 1.0
CG A:PRO79 4.3 12.8 1.0
HG3 A:PRO79 4.4 15.4 1.0
HD21 A:ASN74 4.5 14.5 1.0
C A:ILE78 4.5 11.5 1.0
HB2 A:ASN65 4.6 13.9 1.0
O A:ILE78 4.6 10.7 1.0
HD22 A:ASN74 4.8 14.5 1.0
ND2 A:ASN74 4.9 12.1 1.0
H A:ASN65 4.9 12.6 1.0
C A:ASN65 5.0 9.9 1.0

Chlorine binding site 5 out of 7 in 5l3h

Go back to Chlorine Binding Sites List in 5l3h
Chlorine binding site 5 out of 7 in the Re-Refinement of 4DD4; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15 with Standard Uncertainties


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Re-Refinement of 4DD4; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15 with Standard Uncertainties within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl211

b:23.4
occ:1.00
 HZ3 A:LYS33 2.6 15.7 1.0
HE2 A:PHE38 2.8 14.5 1.0
HZ3 A:TRP123 3.1 15.1 1.0
HD3 A:LYS33 3.3 14.2 1.0
HD3 A:ARG5 3.4 16.9 1.0
HB2 A:ARG5 3.4 15.6 1.0
NZ A:LYS33 3.5 13.1 1.0
CE2 A:PHE38 3.6 12.1 1.0
HE2 A:LYS33 3.7 14.7 1.0
PT A:PT217 3.7 20.7 0.1
HZ1 A:LYS33 3.9 15.7 1.0
CE A:LYS33 4.0 12.2 1.0
HZ2 A:LYS33 4.0 15.7 1.0
CZ3 A:TRP123 4.1 12.6 1.0
CD A:LYS33 4.1 11.8 1.0
HD2 A:PHE38 4.3 13.4 1.0
CD A:ARG5 4.3 14.1 1.0
HZ A:PHE38 4.3 12.8 1.0
CB A:ARG5 4.4 13.0 1.0
CD2 A:PHE38 4.4 11.2 1.0
CZ A:PHE38 4.4 10.7 1.0
HE A:ARG5 4.5 17.2 1.0
HD2 A:LYS33 4.6 14.2 1.0
HE3 A:TRP123 4.7 13.5 1.0
HH2 A:TRP123 4.7 14.1 1.0
HG3 A:ARG5 4.7 15.8 1.0
CG A:ARG5 4.8 13.2 1.0
HB3 A:ARG5 4.8 15.6 1.0
NE A:ARG5 4.9 14.3 1.0
CE3 A:TRP123 4.9 11.2 1.0
CH2 A:TRP123 4.9 11.7 1.0
HE3 A:LYS33 4.9 14.7 1.0
HD2 A:ARG5 5.0 16.9 1.0

Chlorine binding site 6 out of 7 in 5l3h

Go back to Chlorine Binding Sites List in 5l3h
Chlorine binding site 6 out of 7 in the Re-Refinement of 4DD4; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15 with Standard Uncertainties


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Re-Refinement of 4DD4; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15 with Standard Uncertainties within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl212

b:12.9
occ:1.00
 OH A:TYR23 3.0 8.4 1.0
HE2 A:TYR23 3.2 11.4 1.0
HA3 A:GLY104 3.4 12.7 1.0
O A:HOH327 3.4 9.5 1.0
HH A:TYR23 3.5 10.1 1.0
CZ A:TYR23 3.7 9.9 1.0
CE2 A:TYR23 3.7 9.5 1.0
HA2 A:GLY104 4.1 12.7 1.0
CA A:GLY104 4.1 10.6 1.0
O A:ARG21 4.6 9.9 1.0
N A:GLY104 4.7 11.2 1.0
H A:MET105 4.8 11.7 1.0
H A:GLY104 4.9 13.5 1.0
CE1 A:TYR23 4.9 9.3 1.0
CD2 A:TYR23 4.9 9.6 1.0
HB3 A:ARG21 5.0 15.8 1.0

Chlorine binding site 7 out of 7 in 5l3h

Go back to Chlorine Binding Sites List in 5l3h
Chlorine binding site 7 out of 7 in the Re-Refinement of 4DD4; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15 with Standard Uncertainties


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Re-Refinement of 4DD4; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15 with Standard Uncertainties within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl213

b:16.9
occ:1.00
 H A:GLY26 2.4 11.2 1.0
HA A:GLN121 2.7 16.7 1.0
HG A:SER24 2.8 12.7 1.0
HB2 A:SER24 2.9 13.3 1.0
HA3 A:GLY26 2.9 12.1 1.0
HD11 A:ILE124 3.0 20.1 1.0
OG A:SER24 3.1 10.6 1.0
N A:GLY26 3.2 9.4 1.0
HD13 A:ILE124 3.2 20.1 1.0
CB A:SER24 3.5 11.1 1.0
HG23 A:VAL120 3.5 15.5 1.0
CA A:GLY26 3.5 10.1 1.0
CD1 A:ILE124 3.5 16.8 1.0
CA A:GLN121 3.6 13.9 1.0
HG12 A:ILE124 3.6 17.5 1.0
HG2 A:GLN121 3.6 21.4 1.0
HB2 A:GLN121 3.7 19.2 1.0
CB A:GLN121 4.0 16.0 1.0
H A:LEU25 4.0 13.0 1.0
N A:GLN121 4.0 14.1 1.0
HB3 A:SER24 4.1 13.3 1.0
HA2 A:GLY26 4.1 12.1 1.0
CG1 A:ILE124 4.1 14.6 1.0
N A:LEU25 4.1 10.8 1.0
CG A:GLN121 4.3 17.8 1.0
H A:ASN27 4.3 10.3 1.0
HB3 A:LEU25 4.3 14.1 1.0
O A:VAL120 4.4 11.4 1.0
C A:LEU25 4.4 10.9 1.0
C A:SER24 4.4 10.9 1.0
HD12 A:ILE124 4.4 20.1 1.0
C A:VAL120 4.4 13.2 1.0
CG2 A:VAL120 4.4 12.9 1.0
H A:GLN121 4.4 16.9 1.0
CA A:SER24 4.5 11.1 1.0
HG3 A:GLN121 4.6 21.4 1.0
HG21 A:VAL120 4.6 15.5 1.0
C A:GLY26 4.6 10.1 1.0
HG13 A:ILE124 4.7 17.5 1.0
HG21 A:ILE124 4.7 16.2 1.0
CA A:LEU25 4.7 10.3 1.0
N A:ASN27 4.7 8.6 1.0
C A:GLN121 4.8 14.9 1.0
HG23 A:ILE124 4.8 16.2 1.0
HB A:VAL120 4.9 13.8 1.0
O A:HOH366 4.9 14.8 1.0
O A:SER24 4.9 9.2 1.0
HB3 A:GLN121 5.0 19.2 1.0
O A:GLN121 5.0 14.3 1.0
CB A:LEU25 5.0 11.8 1.0
HG22 A:VAL120 5.0 15.5 1.0
HA A:SER24 5.0 13.3 1.0

Reference:

J.R.Helliwell, A.M.M.Schreurs, L.M.J.Kroon-Batenburg, S.Tanley. Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15 with Ligand Distances and Angles, and Their Standard Uncertainties, and Also Reporting A Split Occupancy Effect Arxiv 2016.
DOI: 10.3927/45371856
Page generated: Fri Jul 26 11:01:26 2024

Last articles

Zn in 2YRC
Zn in 2YQP
Zn in 2YR2
Zn in 2YQL
Zn in 2YPT
Zn in 2YPA
Zn in 2YPU
Zn in 2YNW
Zn in 2YNT
Zn in 2YNV
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy