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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

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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

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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

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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

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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

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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: Sat Dec 12 11:58:11 2020

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