Chlorine in PDB 8j81: MDM2 Bound with A Peptoid

Enzymatic activity of MDM2 Bound with A Peptoid

All present enzymatic activity of MDM2 Bound with A Peptoid:
2.3.2.27;

Protein crystallography data

The structure of MDM2 Bound with A Peptoid, PDB code: 8j81 was solved by M.Yokomine, Y.Fukuda, H.Ago, H.Matsuura, G.Ueno, S.Nagatoishi, M.Yamamoto, K.Tsumoto, M.Jumpei, S.Sando, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.21 / 1.35
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 39.521, 45.815, 63.79, 90, 90, 90
R / Rfree (%) 16.9 / 19

Chlorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Chlorine atom in the MDM2 Bound with A Peptoid (pdb code 8j81). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 11 binding sites of Chlorine where determined in the MDM2 Bound with A Peptoid, PDB code: 8j81:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 11 in 8j81

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Chlorine binding site 1 out of 11 in the MDM2 Bound with A Peptoid


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of MDM2 Bound with A Peptoid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl201

b:14.5
occ:1.00
 CL4 A:UAC201 0.0 14.5 1.0
C39 A:UAC201 1.8 12.6 1.0
C41 A:UAC201 2.7 13.1 1.0
C38 A:UAC201 2.7 13.5 1.0
CZ A:PHE86 3.8 15.4 1.0
CE2 A:PHE86 3.9 16.0 1.0
CB A:LEU57 3.9 12.9 1.0
CD1 A:ILE61 3.9 14.3 1.0
C35 A:UAC201 4.0 12.1 1.0
C37 A:UAC201 4.0 13.3 1.0
CD1 A:LEU57 4.0 16.0 1.0
CG2 A:ILE99 4.1 16.2 1.0
CD1 A:ILE103 4.3 15.1 1.0
CZ A:PHE91 4.4 13.9 1.0
CG A:LEU57 4.4 13.0 1.0
C36 A:UAC201 4.5 12.4 1.0
CD2 A:LEU57 4.6 16.7 1.0
CE1 A:PHE91 4.7 14.8 1.0
C51 A:UAC201 4.8 23.6 1.0
CG1 A:ILE103 4.9 13.8 1.0

Chlorine binding site 2 out of 11 in 8j81

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Chlorine binding site 2 out of 11 in the MDM2 Bound with A Peptoid


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of MDM2 Bound with A Peptoid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl202

b:23.5
occ:1.00
 N A:THR26 3.3 24.1 1.0
N A:MET50 3.4 16.3 0.4
N A:MET50 3.4 16.3 0.6
N A:LYS51 3.4 15.7 1.0
CB A:MET50 3.8 19.1 0.6
CA A:GLU25 3.8 27.0 1.0
CB A:THR49 3.8 15.3 1.0
CB A:MET50 3.8 19.1 0.4
O A:THR26 3.9 21.9 1.0
CA A:MET50 3.9 16.2 0.6
CA A:MET50 4.0 16.3 0.4
C A:GLU25 4.1 30.3 1.0
CB A:LYS51 4.1 22.8 1.0
C A:MET50 4.1 15.9 0.4
C A:MET50 4.2 15.9 0.6
C A:THR49 4.2 14.5 1.0
CB A:GLU25 4.2 32.4 1.0
CA A:THR26 4.3 21.5 1.0
CA A:THR49 4.4 15.4 1.0
CA A:LYS51 4.4 16.4 1.0
OG1 A:THR49 4.4 17.2 1.0
CB A:THR26 4.4 24.3 1.0
C A:THR26 4.5 20.8 1.0
CG2 A:THR49 4.7 19.8 1.0
OG1 A:THR26 4.8 29.9 1.0
CG A:MET50 4.9 17.1 0.6
N A:GLU25 4.9 37.2 1.0

Chlorine binding site 3 out of 11 in 8j81

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Chlorine binding site 3 out of 11 in the MDM2 Bound with A Peptoid


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of MDM2 Bound with A Peptoid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl203

b:18.8
occ:1.00
 O A:HOH327 3.1 23.2 1.0
N A:VAL109 3.3 16.2 1.0
CA A:VAL108 3.8 15.4 0.5
CA A:VAL108 3.9 15.4 0.5
CG2 A:VAL109 3.9 19.0 1.0
CB A:VAL109 4.0 16.3 1.0
C A:VAL108 4.0 16.7 0.5
C A:VAL108 4.1 16.6 0.5
CA A:VAL109 4.2 16.7 1.0
O A:LEU107 4.2 14.4 1.0
CB A:VAL108 4.4 18.4 0.5
CG1 A:VAL108 4.5 19.2 0.5
CG1 A:VAL108 4.6 17.0 0.5
CB A:VAL108 4.7 19.6 0.5
O A:VAL109 4.8 20.3 1.0
N A:VAL108 4.8 14.4 0.5
N A:VAL108 4.9 14.4 0.5
O A:HOH355 4.9 19.8 1.0
C A:LEU107 4.9 13.7 1.0

Chlorine binding site 4 out of 11 in 8j81

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Chlorine binding site 4 out of 11 in the MDM2 Bound with A Peptoid


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of MDM2 Bound with A Peptoid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl204

b:16.7
occ:1.00
 OH A:TYR56 3.1 15.7 1.0
N A:GLN44 3.2 16.9 1.0
CE2 A:TYR48 3.7 16.0 1.0
CG A:LYS45 3.8 19.0 1.0
CE2 A:TYR56 3.8 13.8 1.0
CZ A:TYR56 3.8 13.2 1.0
CE A:LYS45 3.8 20.0 1.0
CA A:ALA43 3.9 16.0 1.0
N A:LYS45 4.0 18.5 1.0
C A:ALA43 4.0 16.6 1.0
CA A:GLN44 4.1 18.1 1.0
CB A:GLN44 4.1 21.3 1.0
CB A:ALA43 4.2 15.9 1.0
CD A:LYS45 4.3 20.7 1.0
CB A:LYS45 4.3 20.3 1.0
C A:GLN44 4.4 22.9 1.0
CD2 A:TYR48 4.5 15.4 1.0
CG A:GLN44 4.5 24.5 1.0
OH A:TYR48 4.5 18.1 1.0
CZ A:TYR48 4.6 15.8 1.0
CA A:LYS45 4.8 17.7 1.0

Chlorine binding site 5 out of 11 in 8j81

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Chlorine binding site 5 out of 11 in the MDM2 Bound with A Peptoid


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of MDM2 Bound with A Peptoid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl205

b:16.2
occ:0.74
 O A:HOH341 3.1 15.5 1.0
N A:LEU33 3.3 12.6 1.0
O A:HOH379 3.3 40.9 1.0
O A:HOH382 3.5 41.1 1.0
CB A:LEU33 3.7 13.9 1.0
N A:PRO32 3.7 13.6 1.0
CB A:LYS31 3.8 13.8 1.0
CD A:PRO32 3.8 16.0 1.0
CG A:LEU33 3.9 17.5 1.0
CA A:LEU33 4.1 13.0 1.0
C A:LYS31 4.2 13.1 1.0
CD1 A:LEU33 4.2 20.5 1.0
C A:PRO32 4.2 13.2 1.0
CA A:PRO32 4.3 14.6 1.0
CB A:PRO32 4.4 16.9 1.0
CA A:LYS31 4.6 14.4 1.0
CG A:PRO32 4.6 18.0 1.0
O A:LYS31 4.8 13.6 1.0
N A:LEU34 4.9 11.9 1.0
CD A:LYS31 4.9 17.2 1.0
CG A:LYS31 4.9 15.4 1.0

Chlorine binding site 6 out of 11 in 8j81

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Chlorine binding site 6 out of 11 in the MDM2 Bound with A Peptoid


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of MDM2 Bound with A Peptoid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl206

b:18.6
occ:0.65
 CL A:CL206 0.0 18.6 0.7
CL A:CL206 1.4 21.3 0.3
O A:HOH340 3.2 17.3 1.0
O A:HOH334 3.2 20.4 1.0
CA A:PHE55 3.7 12.8 1.0
C44 A:UAC201 3.8 20.1 1.0
C45 A:UAC201 4.0 20.7 1.0
N A:PHE55 4.2 12.5 1.0
CD1 A:PHE55 4.2 13.0 1.0
C33 A:UAC201 4.2 14.8 1.0
CB A:PHE55 4.2 13.3 1.0
O A:LEU54 4.4 12.9 1.0
N34 A:UAC201 4.4 14.2 1.0
C A:LEU54 4.5 13.1 1.0
CG A:PHE55 4.7 13.1 1.0
N6 A:UAC201 4.8 19.1 1.0
C A:PHE55 4.9 12.2 1.0
O A:PHE55 4.9 11.6 1.0

Chlorine binding site 7 out of 11 in 8j81

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Chlorine binding site 7 out of 11 in the MDM2 Bound with A Peptoid


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of MDM2 Bound with A Peptoid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl206

b:21.3
occ:0.35
 CL A:CL206 0.0 21.3 0.3
CL A:CL206 1.4 18.6 0.7
O A:HOH334 3.1 20.4 1.0
C33 A:UAC201 3.2 14.8 1.0
O A:HOH340 3.2 17.3 1.0
N34 A:UAC201 3.2 14.2 1.0
C45 A:UAC201 3.2 20.7 1.0
O A:LEU54 3.4 12.9 1.0
C A:LEU54 3.6 13.1 1.0
CA A:PHE55 3.6 12.8 1.0
C44 A:UAC201 3.6 20.1 1.0
N A:PHE55 3.7 12.5 1.0
CB A:LEU54 4.1 15.1 1.0
N6 A:UAC201 4.2 19.1 1.0
C5 A:UAC201 4.2 19.6 1.0
CA A:LEU54 4.5 13.1 1.0
CB A:PHE55 4.5 13.3 1.0
C35 A:UAC201 4.5 12.1 1.0
C32 A:UAC201 4.6 14.1 1.0
C A:PHE55 4.7 12.2 1.0
O A:PHE55 4.8 11.6 1.0
C29 A:UAC201 5.0 19.3 1.0

Chlorine binding site 8 out of 11 in 8j81

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Chlorine binding site 8 out of 11 in the MDM2 Bound with A Peptoid


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of MDM2 Bound with A Peptoid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl207

b:30.2
occ:0.46
 CL A:CL207 0.0 30.2 0.5
CL A:CL207 1.7 50.0 0.5
O A:HOH337 3.6 21.3 1.0
OH A:TYR60 3.7 17.7 1.0
NZ A:LYS64 3.9 25.1 1.0
CD2 A:LEU81 4.0 20.2 1.0
CB A:LEU81 4.2 16.0 1.0
CE1 A:TYR60 4.6 15.5 1.0
CZ A:TYR60 4.6 15.5 1.0
CG A:LEU81 4.8 16.3 1.0

Chlorine binding site 9 out of 11 in 8j81

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Chlorine binding site 9 out of 11 in the MDM2 Bound with A Peptoid


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of MDM2 Bound with A Peptoid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl207

b:50.0
occ:0.54
 CL A:CL207 0.0 50.0 0.5
CL A:CL207 1.7 30.2 0.5
O A:HOH374 3.6 42.8 1.0
CB A:SER40 4.1 19.1 1.0
OG A:SER40 4.2 18.3 1.0
CE A:LYS36 4.5 14.7 1.0
CD2 A:LEU81 4.5 20.2 1.0
OH A:TYR60 4.6 17.7 1.0
CE1 A:TYR60 4.7 15.5 1.0
O A:HOH336 4.8 32.3 1.0
CG A:LYS36 4.8 13.8 1.0
O A:LYS36 4.9 14.3 1.0
CD A:LYS36 5.0 14.1 1.0

Chlorine binding site 10 out of 11 in 8j81

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Chlorine binding site 10 out of 11 in the MDM2 Bound with A Peptoid


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of MDM2 Bound with A Peptoid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl208

b:28.5
occ:0.41
 CL A:CL208 0.0 28.5 0.4
CL A:CL208 1.0 30.8 0.6
N A:ARG97 3.3 17.9 1.0
N A:HIS96 3.5 16.9 1.0
CB A:HIS96 3.6 21.1 1.0
O A:HOH314 3.8 24.0 1.0
CA A:HIS96 3.9 17.6 1.0
CB A:ARG97 4.0 20.6 1.0
C A:HIS96 4.1 19.3 1.0
O A:LYS94 4.1 22.8 1.0
CG A:HIS96 4.2 27.8 1.0
CA A:ARG97 4.3 20.0 1.0
C A:GLU95 4.4 17.3 0.8
C A:GLU95 4.4 17.4 0.2
ND1 A:HIS96 4.4 39.8 1.0
CA A:GLU95 4.7 17.5 0.2
CA A:GLU95 4.8 17.5 0.8
O A:HOH369 4.9 33.4 1.0

Reference:

M.Yokomine, M.Jumpei, Y.Fukuda, T.Ueda, K.Takeuchi, K.Suzuki, S.Maeda, H.Ago, H.Matsuura, G.Ueno, M.Yamamoto, A.Senoo, S.Nagatoishi, K.Tsumoto, S.Sando. A Structural and Physicochemical Study of How A Peptoid Binds to A Protein To Be Published.
Page generated: Tue Jul 30 10:56:12 2024

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