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Chlorine in PDB 5l3i: Re-Refinement of 4DD6; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15

Enzymatic activity of Re-Refinement of 4DD6; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15

All present enzymatic activity of Re-Refinement of 4DD6; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15:
3.2.1.17;

Protein crystallography data

The structure of Re-Refinement of 4DD6; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15, PDB code: 5l3i was solved by J.R.Helliwell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 18.39 / 1.70
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.016, 78.016, 37.071, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 21.2

Other elements in 5l3i:

The structure of Re-Refinement of 4DD6; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15 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 4DD6; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15 (pdb code 5l3i). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Re-Refinement of 4DD6; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15, PDB code: 5l3i:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 5l3i

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Chlorine binding site 1 out of 6 in the Re-Refinement of 4DD6; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15


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 4DD6; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl205

b:20.0
occ:0.60
PT A:PT203 2.3 27.7 0.6
HG23 A:THR89 2.7 23.4 1.0
ND1 A:HIS15 2.8 19.9 1.0
HN1 A:NH3207 2.8 22.1 0.6
HB3 A:HIS15 2.9 17.5 1.0
HB A:VAL92 3.0 15.2 1.0
N A:NH3207 3.0 18.4 0.6
HA A:THR89 3.2 16.2 1.0
HD21 A:ASN93 3.5 33.6 1.0
ND2 A:ASN93 3.5 28.0 1.0
HD22 A:ASN93 3.5 33.6 1.0
HG12 A:VAL92 3.5 16.1 1.0
HN2 A:NH3207 3.5 22.1 0.6
CG A:HIS15 3.5 15.6 1.0
HG11 A:VAL92 3.6 16.1 1.0
CG2 A:THR89 3.6 19.5 1.0
CB A:HIS15 3.6 14.6 1.0
O A:THR89 3.7 13.0 1.0
CE1 A:HIS15 3.7 20.9 1.0
HG21 A:THR89 3.7 23.4 1.0
HN3 A:NH3207 3.7 22.1 0.6
CG1 A:VAL92 3.8 13.4 1.0
CB A:VAL92 3.8 12.7 1.0
H A:ASN93 3.9 13.3 1.0
HE1 A:HIS15 3.9 25.0 1.0
CA A:THR89 4.0 13.5 1.0
O A:HIS15 4.0 18.1 1.0
HZ1 A:LYS96 4.0 25.4 1.0
CG A:ASN93 4.0 27.5 1.0
HA A:HIS15 4.2 19.9 1.0
N A:ASN93 4.2 11.1 1.0
C A:THR89 4.2 15.3 1.0
HG22 A:THR89 4.3 23.4 1.0
CB A:THR89 4.3 18.0 1.0
N A:NH3206 4.3 14.7 0.6
HB2 A:HIS15 4.4 17.5 1.0
CA A:HIS15 4.4 16.6 1.0
HB2 A:ASN93 4.5 21.0 1.0
HG22 A:VAL92 4.5 18.2 1.0
HN3 A:NH3206 4.5 17.6 0.6
HN1 A:NH3206 4.5 17.6 0.6
HA A:ASN93 4.5 15.8 1.0
OD1 A:ASN93 4.5 34.2 1.0
CB A:ASN93 4.6 17.5 1.0
CD2 A:HIS15 4.7 21.0 1.0
C A:HIS15 4.7 16.3 1.0
OG1 A:THR89 4.7 20.1 1.0
CA A:ASN93 4.7 13.2 1.0
CG2 A:VAL92 4.7 15.1 1.0
C A:VAL92 4.7 12.0 1.0
NE2 A:HIS15 4.7 19.3 1.0
NZ A:LYS96 4.8 21.1 1.0
HG13 A:VAL92 4.8 16.1 1.0
HZ2 A:LYS96 4.8 25.4 1.0
CA A:VAL92 4.9 11.0 1.0
HE3 A:LYS96 4.9 18.3 1.0

Chlorine binding site 2 out of 6 in 5l3i

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Chlorine binding site 2 out of 6 in the Re-Refinement of 4DD6; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15


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 4DD6; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl209

b:34.5
occ:1.00
HZ2 A:LYS33 2.6 34.5 1.0
HE2 A:PHE38 2.8 23.7 1.0
HZ3 A:TRP123 3.2 25.1 1.0
HD3 A:ARG5 3.2 24.1 1.0
HD3 A:LYS33 3.4 24.2 1.0
NZ A:LYS33 3.5 28.8 1.0
HB2 A:ARG5 3.5 21.0 1.0
CE2 A:PHE38 3.7 19.8 1.0
HE2 A:LYS33 3.7 30.6 1.0
HZ1 A:LYS33 3.8 34.5 1.0
PT A:PT218 3.9 28.9 0.1
CE A:LYS33 4.0 25.5 1.0
HZ3 A:LYS33 4.0 34.5 1.0
CZ3 A:TRP123 4.1 20.9 1.0
CD A:ARG5 4.2 20.1 1.0
CD A:LYS33 4.2 20.2 1.0
H23 A:DMS201 4.2 28.5 1.0
HZ A:PHE38 4.2 20.1 1.0
HE A:ARG5 4.3 23.9 1.0
CZ A:PHE38 4.4 16.8 1.0
CB A:ARG5 4.4 17.5 1.0
H12 A:DMS201 4.5 36.8 1.0
HD2 A:PHE38 4.5 22.7 1.0
CD2 A:PHE38 4.6 18.9 1.0
HE3 A:TRP123 4.6 20.6 1.0
NE A:ARG5 4.7 19.9 1.0
HD2 A:LYS33 4.7 24.2 1.0
CG A:ARG5 4.7 17.6 1.0
HD2 A:ARG5 4.7 24.1 1.0
HG3 A:ARG5 4.7 21.1 1.0
H22 A:DMS201 4.8 28.5 1.0
CE3 A:TRP123 4.8 17.2 1.0
HB3 A:ARG5 4.8 21.0 1.0
HH2 A:TRP123 4.9 19.9 1.0
HE3 A:LYS33 4.9 30.6 1.0
C2 A:DMS201 5.0 23.7 1.0

Chlorine binding site 3 out of 6 in 5l3i

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Chlorine binding site 3 out of 6 in the Re-Refinement of 4DD6; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15


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 4DD6; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl210

b:13.8
occ:1.00
OH A:TYR23 3.0 10.4 1.0
HE2 A:TYR23 3.2 12.5 1.0
O A:HOH310 3.3 12.6 1.0
HA3 A:GLY104 3.4 13.6 1.0
HH A:TYR23 3.5 12.5 0.0
CZ A:TYR23 3.7 9.1 1.0
CE2 A:TYR23 3.7 10.4 1.0
CA A:GLY104 4.2 11.3 1.0
HA2 A:GLY104 4.2 13.6 1.0
O A:ARG21 4.5 12.4 1.0
N A:GLY104 4.7 12.6 1.0
H A:MET105 4.8 10.7 1.0
HB3 A:ARG21 4.8 16.2 1.0
CE1 A:TYR23 4.9 8.1 1.0
CD2 A:TYR23 4.9 9.6 1.0
H A:GLY104 4.9 15.1 1.0

Chlorine binding site 4 out of 6 in 5l3i

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Chlorine binding site 4 out of 6 in the Re-Refinement of 4DD6; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15


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 4DD6; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl211

b:18.8
occ:1.00
H A:GLY26 2.3 13.6 1.0
HG A:SER24 2.7 13.4 0.0
HA A:GLN121 2.8 21.1 1.0
HA3 A:GLY26 2.9 12.2 1.0
HB2 A:SER24 2.9 13.6 1.0
OG A:SER24 3.0 11.2 1.0
N A:GLY26 3.1 11.3 1.0
HD12 A:ILE124 3.3 31.5 1.0
HG23 A:VAL120 3.4 17.8 1.0
HD13 A:ILE124 3.4 31.5 1.0
CB A:SER24 3.4 11.4 1.0
CA A:GLY26 3.5 10.1 1.0
HG2 A:GLN121 3.5 33.3 1.0
CA A:GLN121 3.7 17.6 1.0
HG12 A:ILE124 3.7 21.8 1.0
CD1 A:ILE124 3.7 26.2 1.0
HB2 A:GLN121 3.9 25.0 1.0
N A:GLN121 4.0 16.4 1.0
HA2 A:GLY26 4.0 12.2 1.0
HB3 A:SER24 4.1 13.6 1.0
H A:LEU25 4.1 14.1 1.0
CB A:GLN121 4.1 20.8 1.0
N A:LEU25 4.1 11.8 1.0
HB3 A:LEU25 4.2 18.6 1.0
H A:ASN27 4.2 10.7 1.0
CG A:GLN121 4.3 27.8 1.0
C A:LEU25 4.3 13.5 1.0
C A:SER24 4.3 12.8 1.0
CG1 A:ILE124 4.3 18.2 1.0
CG2 A:VAL120 4.3 14.8 1.0
H A:GLN121 4.4 19.7 1.0
C A:VAL120 4.4 15.6 1.0
O A:VAL120 4.4 16.1 1.0
CA A:SER24 4.5 10.8 1.0
HG22 A:VAL120 4.5 17.8 1.0
C A:GLY26 4.6 10.0 1.0
HD11 A:ILE124 4.6 31.5 1.0
CA A:LEU25 4.6 10.4 1.0
HG3 A:GLN121 4.7 33.3 1.0
N A:ASN27 4.7 8.9 1.0
O A:SER24 4.8 11.7 1.0
HG21 A:VAL120 4.8 17.8 1.0
C A:GLN121 4.8 16.0 1.0
HG22 A:ILE124 4.8 22.5 1.0
HG13 A:ILE124 4.9 21.8 1.0
HG23 A:ILE124 4.9 22.5 1.0
CB A:LEU25 4.9 15.5 1.0
HB A:VAL120 4.9 16.3 1.0
HA A:SER24 4.9 12.9 1.0

Chlorine binding site 5 out of 6 in 5l3i

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Chlorine binding site 5 out of 6 in the Re-Refinement of 4DD6; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15


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 4DD6; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl212

b:14.4
occ:0.50
PT A:PT204 2.2 17.2 0.5
H A:ILE88 2.7 22.3 1.0
OD1 A:ASP87 2.9 25.0 1.0
HN2 A:NH3208 2.9 13.7 0.5
NE2 A:HIS15 2.9 19.3 1.0
HN3 A:NH3208 3.0 13.7 0.5
HA A:ASP87 3.1 19.1 1.0
H A:THR89 3.1 20.6 1.0
N A:NH3208 3.2 11.4 0.5
HG12 A:ILE88 3.3 14.3 1.0
N A:ILE88 3.3 18.6 1.0
OG1 A:THR89 3.4 20.1 1.0
CG A:ASP87 3.4 27.4 1.0
HH22 A:ARG14 3.4 26.0 1.0
HE1 A:HIS15 3.5 25.0 1.0
CE1 A:HIS15 3.5 20.9 1.0
HG13 A:ILE88 3.6 14.3 1.0
N A:THR89 3.7 17.2 1.0
HH12 A:ARG14 3.7 26.1 1.0
HG1 A:THR89 3.8 24.1 0.0
CA A:ASP87 3.8 15.9 1.0
C A:ASP87 3.9 17.7 1.0
CG1 A:ILE88 3.9 11.9 1.0
OD2 A:ASP87 3.9 27.5 1.0
CD2 A:HIS15 4.0 21.0 1.0
HN1 A:NH3208 4.1 13.7 0.5
CB A:ASP87 4.1 20.3 1.0
CA A:ILE88 4.2 15.8 1.0
NH2 A:ARG14 4.3 21.7 1.0
HD2 A:HIS15 4.3 25.1 1.0
C A:ILE88 4.3 15.6 1.0
HA A:THR89 4.5 16.2 1.0
CA A:THR89 4.5 13.5 1.0
CB A:THR89 4.5 18.0 1.0
HB2 A:ASP87 4.5 24.4 1.0
NH1 A:ARG14 4.5 21.8 1.0
CB A:ILE88 4.6 13.3 1.0
ND1 A:HIS15 4.7 19.9 1.0
HG23 A:ILE88 4.8 19.1 1.0
HB2 A:ALA11 4.8 16.8 1.0
HH21 A:ARG14 4.8 26.0 1.0
HB A:THR89 4.8 21.6 1.0
CZ A:ARG14 4.9 20.4 1.0
O A:ASP87 4.9 17.5 1.0
HB3 A:ASP87 4.9 24.4 1.0
CG A:HIS15 5.0 15.6 1.0
HD12 A:ILE88 5.0 20.2 1.0

Chlorine binding site 6 out of 6 in 5l3i

Go back to Chlorine Binding Sites List in 5l3i
Chlorine binding site 6 out of 6 in the Re-Refinement of 4DD6; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15


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 4DD6; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl217

b:16.9
occ:1.00
H A:THR69 2.5 16.4 1.0
O A:HOH327 3.2 9.6 1.0
HA2 A:GLY67 3.3 15.0 1.0
N A:THR69 3.3 13.6 1.0
H A:ARG68 3.4 14.3 1.0
O A:THR69 3.4 14.3 1.0
H A:GLY67 3.4 14.3 1.0
N A:ARG68 3.6 11.9 1.0
OG A:SER72 3.6 18.1 1.0
C A:GLY67 3.6 14.5 1.0
OD1 A:ASN65 3.7 15.0 1.0
CA A:GLY67 3.7 12.5 1.0
HB A:THR69 3.7 20.2 1.0
C A:THR69 3.8 15.6 1.0
N A:GLY67 3.8 11.9 1.0
O A:HOH336 3.9 12.8 1.0
CA A:THR69 4.0 15.5 1.0
O A:GLY67 4.2 14.2 1.0
H A:ASP66 4.3 12.7 1.0
C A:ARG68 4.3 16.2 1.0
CB A:THR69 4.4 16.9 1.0
CA A:ARG68 4.4 12.9 1.0
OD1 A:ASP66 4.4 11.2 1.0
HA A:PRO70 4.5 20.1 1.0
HA A:ARG68 4.5 15.5 1.0
N A:PRO70 4.6 18.0 1.0
NA A:NA202 4.6 12.0 1.0
HA3 A:GLY67 4.7 15.0 1.0
H A:SER72 4.7 24.3 1.0
O A:HOH325 4.8 11.5 0.5
CB A:SER72 4.8 18.9 1.0
HA A:ASN65 4.8 15.0 1.0
CG A:ASN65 4.9 11.7 1.0
HB3 A:SER72 4.9 22.7 1.0
HA A:THR69 4.9 18.6 1.0
C A:ASP66 4.9 11.4 1.0
N A:ASP66 5.0 10.5 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: Wed Oct 28 12:44:11 2020

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