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Platinum in PDB 6myl: The PRP8 Intein-Cisplatin Complex

Protein crystallography data

The structure of The PRP8 Intein-Cisplatin Complex, PDB code: 6myl was solved by Z.Li, H.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.55 / 3.06
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 74.853, 74.853, 191.886, 90.00, 90.00, 90.00
R / Rfree (%) 24.3 / 29.8

Platinum Binding Sites:

The binding sites of Platinum atom in the The PRP8 Intein-Cisplatin Complex (pdb code 6myl). This binding sites where shown within 5.0 Angstroms radius around Platinum atom.
In total 9 binding sites of Platinum where determined in the The PRP8 Intein-Cisplatin Complex, PDB code: 6myl:
Jump to Platinum binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Platinum binding site 1 out of 9 in 6myl

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Platinum binding site 1 out of 9 in the The PRP8 Intein-Cisplatin Complex


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 1 of The PRP8 Intein-Cisplatin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt201

b:0.7
occ:1.00
N A:CYS1 2.2 0.7 1.0
SG A:CYS1 2.3 86.5 1.0
CB A:CYS1 2.8 80.1 1.0
CA A:CYS1 3.0 84.3 1.0
C A:ASN170 4.1 0.6 1.0
ND1 A:HIS64 4.1 83.5 1.0
O A:ASN170 4.1 0.1 1.0
C A:CYS1 4.2 74.4 1.0
OG1 A:THR61 4.3 77.1 1.0
ND2 A:ASN63 4.3 99.8 1.0
O A:CYS1 4.5 65.9 1.0
CA A:HIS64 4.5 76.0 1.0
CB A:HIS64 4.8 72.5 1.0
CG A:HIS64 4.9 84.4 1.0
CG A:ASN63 4.9 75.4 1.0
N A:HIS64 5.0 79.9 1.0
OD1 A:ASN63 5.0 73.4 1.0

Platinum binding site 2 out of 9 in 6myl

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Platinum binding site 2 out of 9 in the The PRP8 Intein-Cisplatin Complex


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 2 of The PRP8 Intein-Cisplatin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt202

b:0.3
occ:1.00
NE2 A:HIS62 2.2 84.8 1.0
CE1 A:HIS62 3.2 79.4 1.0
CD2 A:HIS62 3.2 85.8 1.0
OE1 A:GLU45 4.1 0.4 1.0
ND1 A:HIS62 4.3 78.2 1.0
OE2 A:GLU45 4.3 99.1 1.0
CG A:HIS62 4.4 85.7 1.0
OD1 A:ASN63 4.4 73.4 1.0
CD A:GLU45 4.6 98.7 1.0
CG A:ASN63 4.9 75.4 1.0

Platinum binding site 3 out of 9 in 6myl

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Platinum binding site 3 out of 9 in the The PRP8 Intein-Cisplatin Complex


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 3 of The PRP8 Intein-Cisplatin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt203

b:0.5
occ:1.00
NE2 A:HIS169 2.2 0.8 1.0
OD2 A:ASP95 2.2 0.3 1.0
CD2 A:HIS169 2.9 0.6 1.0
CE1 A:HIS169 3.2 0.0 1.0
CG A:ASP95 3.3 95.9 1.0
CG A:HIS169 4.1 85.6 1.0
CB A:ASP95 4.1 75.2 1.0
ND1 A:HIS169 4.2 87.8 1.0
OD1 A:ASP95 4.2 93.4 1.0
OG A:SER158 4.5 98.5 1.0

Platinum binding site 4 out of 9 in 6myl

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Platinum binding site 4 out of 9 in the The PRP8 Intein-Cisplatin Complex


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 4 of The PRP8 Intein-Cisplatin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Pt201

b:0.4
occ:1.00
N B:CYS1 2.2 0.9 1.0
SG B:CYS1 2.3 0.1 1.0
CB B:CYS1 2.8 0.7 1.0
O B:ASN170 2.8 0.2 1.0
CA B:CYS1 3.0 97.5 1.0
C B:ASN170 3.8 0.7 1.0
ND1 B:HIS64 4.2 97.2 1.0
C B:CYS1 4.2 95.9 1.0
ND2 B:ASN63 4.3 0.8 1.0
OG1 B:THR61 4.4 0.8 1.0
O B:CYS1 4.5 0.8 1.0
CA B:HIS64 4.6 97.0 1.0
CB B:HIS64 4.9 87.4 1.0
CG B:ASN63 5.0 0.4 1.0
CG B:HIS64 5.0 92.3 1.0

Platinum binding site 5 out of 9 in 6myl

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Platinum binding site 5 out of 9 in the The PRP8 Intein-Cisplatin Complex


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 5 of The PRP8 Intein-Cisplatin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Pt202

b:0.5
occ:1.00
NE2 B:HIS62 2.2 0.8 1.0
CE1 B:HIS62 2.7 0.7 1.0
OD1 B:ASN63 3.3 0.9 1.0
CD2 B:HIS62 3.3 0.8 1.0
CG B:ASN63 3.5 0.4 1.0
CB B:ASN63 3.8 0.1 1.0
ND1 B:HIS62 3.8 0.5 1.0
ND2 B:ASN63 4.0 0.8 1.0
CG B:HIS62 4.2 1.0 1.0
N B:ASN63 4.8 0.9 1.0
CA B:ASN63 4.9 0.6 1.0
OE1 B:GLU45 5.0 0.2 1.0

Platinum binding site 6 out of 9 in 6myl

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Platinum binding site 6 out of 9 in the The PRP8 Intein-Cisplatin Complex


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 6 of The PRP8 Intein-Cisplatin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Pt203

b:0.7
occ:1.00
NE2 B:HIS169 2.2 0.7 1.0
OD2 B:ASP95 2.2 0.5 1.0
CD2 B:HIS169 2.7 0.3 1.0
CG B:ASP95 3.3 0.9 1.0
CE1 B:HIS169 3.4 0.6 1.0
OG B:SER158 3.8 0.3 1.0
CG B:HIS169 3.9 0.9 1.0
OD1 B:ASP95 4.0 0.9 1.0
ND1 B:HIS169 4.3 0.6 1.0
CB B:ASP95 4.3 93.0 1.0
O B:ASP157 4.4 97.4 1.0
NH2 B:ARG93 4.5 0.5 1.0
CD2 B:LEU159 4.7 89.3 1.0

Platinum binding site 7 out of 9 in 6myl

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Platinum binding site 7 out of 9 in the The PRP8 Intein-Cisplatin Complex


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 7 of The PRP8 Intein-Cisplatin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Pt201

b:0.2
occ:1.00
N C:CYS1 2.2 0.5 1.0
SG C:CYS1 2.2 0.8 1.0
CB C:CYS1 2.9 0.6 1.0
CA C:CYS1 3.1 92.4 1.0
O C:ASN170 4.0 0.3 1.0
C C:ASN170 4.0 0.5 1.0
C C:CYS1 4.3 87.8 1.0
ND2 C:ASN63 4.5 0.2 1.0
ND1 C:HIS64 4.5 95.1 1.0
OG1 C:THR61 4.6 96.0 1.0
O C:CYS1 4.7 83.0 1.0
CA C:GLY151 5.0 91.1 1.0

Platinum binding site 8 out of 9 in 6myl

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Platinum binding site 8 out of 9 in the The PRP8 Intein-Cisplatin Complex


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 8 of The PRP8 Intein-Cisplatin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Pt202

b:0.8
occ:1.00
NE2 C:HIS62 2.2 1.0 1.0
CE1 C:HIS62 2.6 1.0 1.0
CD2 C:HIS62 3.5 0.4 1.0
ND1 C:HIS62 3.9 0.5 1.0
OD1 C:ASN63 3.9 0.6 1.0
CG C:ASN63 4.0 0.0 1.0
CB C:ASN63 4.2 0.3 1.0
CG C:HIS62 4.3 98.6 1.0
ND2 C:ASN63 4.5 0.2 1.0

Platinum binding site 9 out of 9 in 6myl

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Platinum binding site 9 out of 9 in the The PRP8 Intein-Cisplatin Complex


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 9 of The PRP8 Intein-Cisplatin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Pt203

b:0.8
occ:1.00
OD2 C:ASP95 2.2 98.2 1.0
NE2 C:HIS169 2.2 0.0 1.0
CD2 C:HIS169 2.9 0.4 1.0
CG C:ASP95 3.3 0.1 1.0
CE1 C:HIS169 3.4 0.8 1.0
OD1 C:ASP95 4.0 0.1 1.0
OG C:SER158 4.1 0.6 1.0
CG C:HIS169 4.2 0.2 1.0
CB C:ASP95 4.2 88.2 1.0
ND1 C:HIS169 4.3 0.1 1.0
O C:ASP157 4.6 0.9 1.0
NH2 C:ARG93 4.7 0.6 1.0

Reference:

Z.Li, B.Fu, C.M.Green, Y.Lang, T.S.Owen, J.Zhang, X.Li, B.P.Callahan, S.Chaturvedi, M.Belfort, H.Li. Cisplatin Inhibits PRP8 Intein Splicing and Protects Mice From Challenge of Cryptococcus Neoformans To Be Published.
Page generated: Wed Dec 16 02:05:40 2020

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