Chlorine in PDB 5swk: Crystal Structure of P53 Epitope-Scaffold Based on A Inhibitor of Cysteine Proteases in Complex with Human MDM2

Protein crystallography data

The structure of Crystal Structure of P53 Epitope-Scaffold Based on A Inhibitor of Cysteine Proteases in Complex with Human MDM2, PDB code: 5swk was solved by P.Jimenez-Sandoval, L.G.Brieba, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.99 / 1.92
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 87.361, 87.361, 160.840, 90.00, 90.00, 90.00
R / Rfree (%) 22.1 / 24.9

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of P53 Epitope-Scaffold Based on A Inhibitor of Cysteine Proteases in Complex with Human MDM2 (pdb code 5swk). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 7 binding sites of Chlorine where determined in the Crystal Structure of P53 Epitope-Scaffold Based on A Inhibitor of Cysteine Proteases in Complex with Human MDM2, PDB code: 5swk:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in 5swk

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Chlorine binding site 1 out of 7 in the Crystal Structure of P53 Epitope-Scaffold Based on A Inhibitor of Cysteine Proteases in Complex with Human MDM2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of P53 Epitope-Scaffold Based on A Inhibitor of Cysteine Proteases in Complex with Human MDM2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl201

b:59.9
occ:1.00
 N A:THR47 3.3 38.6 1.0
N A:ASP46 3.3 47.4 1.0
CB A:LYS45 3.6 46.7 1.0
OG1 A:THR47 3.8 45.7 1.0
CB A:THR47 3.9 43.4 1.0
CA A:ASP46 4.0 45.4 1.0
C A:ASP46 4.1 44.0 1.0
CA A:THR47 4.1 40.0 1.0
CB A:ASP46 4.1 48.8 1.0
CA A:LYS45 4.3 42.0 1.0
C A:LYS45 4.3 46.9 1.0
O A:THR47 4.4 41.3 1.0
CG A:LYS45 4.7 45.1 1.0
C A:THR47 4.8 38.4 1.0

Chlorine binding site 2 out of 7 in 5swk

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Chlorine binding site 2 out of 7 in the Crystal Structure of P53 Epitope-Scaffold Based on A Inhibitor of Cysteine Proteases in Complex with Human MDM2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of P53 Epitope-Scaffold Based on A Inhibitor of Cysteine Proteases in Complex with Human MDM2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl202

b:54.6
occ:1.00
 NE2 A:HIS73 3.3 28.2 1.0
O C:HOH322 3.4 36.7 1.0
NE2 A:GLN71 3.5 24.9 1.0
O C:HOH341 3.8 37.8 1.0
NZ A:LYS94 3.9 41.1 1.0
CD2 A:HIS73 4.0 26.6 1.0
CG A:GLN71 4.1 24.6 1.0
CE1 A:HIS73 4.3 26.9 1.0
CD A:GLN71 4.3 24.3 1.0
CB A:GLN71 4.7 24.5 1.0
CE A:LYS94 4.7 37.2 1.0
O C:HOH319 4.8 46.9 1.0
O A:HOH315 4.9 33.3 1.0

Chlorine binding site 3 out of 7 in 5swk

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Chlorine binding site 3 out of 7 in the Crystal Structure of P53 Epitope-Scaffold Based on A Inhibitor of Cysteine Proteases in Complex with Human MDM2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of P53 Epitope-Scaffold Based on A Inhibitor of Cysteine Proteases in Complex with Human MDM2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl202

b:61.8
occ:1.00
 N B:ASP46 3.3 41.9 1.0
N B:THR47 3.5 38.7 1.0
CB B:LYS45 3.9 43.3 1.0
OG1 B:THR47 3.9 41.8 1.0
CA B:ASP46 4.0 39.5 1.0
CB B:THR47 4.0 39.3 1.0
CB B:ASP46 4.0 44.2 1.0
C B:ASP46 4.1 38.5 1.0
C B:LYS45 4.2 43.4 1.0
CA B:LYS45 4.2 44.3 1.0
CA B:THR47 4.3 35.3 1.0
CG B:LYS45 4.6 47.8 1.0
O B:THR47 4.6 34.3 1.0
CG B:ASP46 4.7 49.0 1.0
OD2 B:ASP46 4.8 56.1 1.0
CD B:LYS45 4.9 48.6 1.0
C B:THR47 5.0 36.2 1.0

Chlorine binding site 4 out of 7 in 5swk

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Chlorine binding site 4 out of 7 in the Crystal Structure of P53 Epitope-Scaffold Based on A Inhibitor of Cysteine Proteases in Complex with Human MDM2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of P53 Epitope-Scaffold Based on A Inhibitor of Cysteine Proteases in Complex with Human MDM2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl203

b:55.5
occ:1.00
 O B:HOH329 3.0 31.3 1.0
O D:HOH349 3.2 28.9 1.0
CG B:MET62 3.7 23.7 1.0
SD A:MET62 3.7 29.2 1.0
CB B:MET62 3.7 18.9 1.0
CB D:ALA88 4.2 20.4 1.0
OE1 B:GLN59 4.4 26.3 1.0
CE A:MET62 4.5 27.4 1.0
O A:HOH304 4.6 22.0 1.0
CE B:MET62 4.6 21.5 1.0
O B:HOH311 4.6 26.0 1.0
CA D:ALA88 4.7 21.1 1.0
O D:HOH337 4.7 30.7 1.0
O B:GLY58 4.7 19.1 1.0
CD2 D:PHE87 4.8 21.2 1.0
CE2 D:PHE87 4.9 23.1 1.0
SD B:MET62 4.9 27.7 1.0
O C:HOH331 4.9 25.0 1.0
CG A:MET62 5.0 23.6 1.0
O C:HOH339 5.0 27.5 1.0

Chlorine binding site 5 out of 7 in 5swk

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Chlorine binding site 5 out of 7 in the Crystal Structure of P53 Epitope-Scaffold Based on A Inhibitor of Cysteine Proteases in Complex with Human MDM2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of P53 Epitope-Scaffold Based on A Inhibitor of Cysteine Proteases in Complex with Human MDM2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl204

b:66.0
occ:1.00
 OE1 B:GLU95 3.0 47.0 1.0
CD B:LYS98 3.4 44.1 1.0
CB B:LYS98 3.8 30.7 1.0
CD B:GLU95 4.0 42.7 1.0
CG B:LYS98 4.0 32.8 1.0
O2 B:SO4201 4.1 29.0 0.5
CE B:LYS98 4.5 43.9 1.0
CB B:GLU95 4.6 28.5 1.0
O4 B:SO4201 4.6 37.7 0.5
CG B:GLU95 4.7 32.6 1.0
NZ B:LYS98 4.7 43.4 1.0
O3 B:SO4201 4.7 41.6 0.5
OE2 B:GLU95 4.7 48.6 1.0
S B:SO4201 4.7 33.8 0.5
CA B:LYS98 4.9 24.8 1.0

Chlorine binding site 6 out of 7 in 5swk

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Chlorine binding site 6 out of 7 in the Crystal Structure of P53 Epitope-Scaffold Based on A Inhibitor of Cysteine Proteases in Complex with Human MDM2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of P53 Epitope-Scaffold Based on A Inhibitor of Cysteine Proteases in Complex with Human MDM2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl205

b:52.3
occ:1.00
 NE2 B:HIS73 3.4 22.8 1.0
O D:HOH309 3.5 35.8 1.0
NE2 B:GLN71 3.6 23.2 1.0
NZ B:LYS94 3.8 43.0 1.0
O D:HOH347 4.0 34.5 1.0
CD2 B:HIS73 4.1 23.2 1.0
CG B:GLN71 4.3 19.4 1.0
CD B:GLN71 4.4 24.3 1.0
CE1 B:HIS73 4.4 26.5 1.0
CE B:LYS94 4.8 33.7 1.0
O D:HOH338 4.9 32.8 1.0

Chlorine binding site 7 out of 7 in 5swk

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Chlorine binding site 7 out of 7 in the Crystal Structure of P53 Epitope-Scaffold Based on A Inhibitor of Cysteine Proteases in Complex with Human MDM2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of P53 Epitope-Scaffold Based on A Inhibitor of Cysteine Proteases in Complex with Human MDM2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl201

b:62.8
occ:1.00
 N D:THR11 3.4 32.4 1.0
CA D:THR10 3.7 36.4 1.0
CB D:THR10 3.8 34.3 1.0
C D:THR10 4.0 36.1 1.0
CB D:THR11 4.2 35.0 1.0
OG1 D:THR11 4.3 37.8 1.0
CA D:THR11 4.4 33.2 1.0
CG2 D:THR10 4.4 36.0 1.0
O D:THR11 4.5 36.6 1.0
O D:ASN9 4.7 37.2 1.0
C D:THR11 5.0 36.8 1.0
N D:THR10 5.0 38.6 1.0

Reference:

P.Jimenez-Sandoval, E.A.Madrigal-Carrillo, H.A.Santamaria-Suarez, D.Maturana, I.Renteria-Gonzalez, C.G.Benitez-Cardoza, A.Torres-Larios, L.G.Brieba. Mimicking A P53-MDM2 Interaction Based on A Stable Immunoglobulin-Like Domain Scaffold. Proteins V. 86 802 2018.
ISSN: ESSN 1097-0134
PubMed: 29696695
DOI: 10.1002/PROT.25519
Page generated: Sat Dec 12 12:26:40 2020

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