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Zinc in PDB 2r7z: Cisplatin Lesion Containing Rna Polymerase II Elongation Complex

Enzymatic activity of Cisplatin Lesion Containing Rna Polymerase II Elongation Complex

All present enzymatic activity of Cisplatin Lesion Containing Rna Polymerase II Elongation Complex:
2.7.7.6;

Protein crystallography data

The structure of Cisplatin Lesion Containing Rna Polymerase II Elongation Complex, PDB code: 2r7z was solved by G.E.Damsma, A.Alt, F.Brueckner, T.Carell, P.Cramer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 3.80
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 222.062, 393.123, 283.733, 90.00, 90.00, 90.00
R / Rfree (%) 21.5 / 24

Other elements in 2r7z:

The structure of Cisplatin Lesion Containing Rna Polymerase II Elongation Complex also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Platinum (Pt) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Cisplatin Lesion Containing Rna Polymerase II Elongation Complex (pdb code 2r7z). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Cisplatin Lesion Containing Rna Polymerase II Elongation Complex, PDB code: 2r7z:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 2r7z

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Zinc binding site 1 out of 8 in the Cisplatin Lesion Containing Rna Polymerase II Elongation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cisplatin Lesion Containing Rna Polymerase II Elongation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1734

b:0.4
occ:1.00
 SG A:CYS110 2.5 0.7 1.0
SG A:CYS148 2.7 0.4 1.0
SG A:CYS167 3.0 0.7 1.0
O A:CYS167 3.4 0.8 1.0
CB A:CYS110 3.5 0.3 1.0
O A:MET108 3.5 0.8 1.0
CB A:CYS148 3.7 0.2 1.0
O A:GLY166 3.7 0.5 1.0
CB A:CYS107 4.0 0.2 1.0
N A:CYS110 4.1 0.9 1.0
CA A:CYS110 4.3 0.1 1.0
C A:CYS167 4.5 0.6 1.0
N A:GLY111 4.5 0.1 1.0
SG A:CYS107 4.5 0.6 1.0
CB A:CYS167 4.6 0.3 1.0
O A:CYS107 4.6 0.7 1.0
C A:MET108 4.7 0.3 1.0
C A:CYS107 4.7 0.7 1.0
C A:CYS110 4.8 0.5 1.0
C A:GLY166 4.8 0.5 1.0
CA A:CYS107 5.0 0.4 1.0

Zinc binding site 2 out of 8 in 2r7z

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Zinc binding site 2 out of 8 in the Cisplatin Lesion Containing Rna Polymerase II Elongation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cisplatin Lesion Containing Rna Polymerase II Elongation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1735

b:65.3
occ:1.00
 NE2 A:HIS80 2.3 88.0 1.0
SG A:CYS67 2.5 0.1 1.0
SG A:CYS70 2.6 0.6 1.0
SG A:CYS77 2.7 86.3 1.0
CD2 A:HIS80 2.8 87.1 1.0
CB A:CYS70 3.0 0.1 1.0
CB A:CYS67 3.1 0.6 1.0
O A:CYS67 3.4 0.0 1.0
CE1 A:HIS80 3.4 88.1 1.0
CB A:CYS77 3.7 88.0 1.0
CG A:HIS80 4.0 87.0 1.0
C A:CYS67 4.2 0.1 1.0
CA A:CYS67 4.2 0.5 1.0
ND1 A:HIS80 4.3 86.7 1.0
NE2 A:GLN68 4.3 0.5 1.0
CA A:CYS70 4.4 0.0 1.0
O A:PRO78 4.5 84.8 1.0
OE1 A:GLN68 4.5 0.6 1.0
O A:GLN71 4.5 0.6 1.0
CD A:GLN68 4.6 0.0 1.0
C A:CYS70 4.6 0.8 1.0
CA A:CYS77 4.8 88.6 1.0
O A:CYS70 4.8 0.3 1.0

Zinc binding site 3 out of 8 in 2r7z

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Zinc binding site 3 out of 8 in the Cisplatin Lesion Containing Rna Polymerase II Elongation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cisplatin Lesion Containing Rna Polymerase II Elongation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1307

b:71.5
occ:1.00
 SG B:CYS1163 2.3 80.8 1.0
SG B:CYS1182 2.5 97.7 1.0
SG B:CYS1166 2.5 74.2 1.0
SG B:CYS1185 2.6 0.7 1.0
CB B:CYS1185 2.7 0.5 1.0
CB B:CYS1163 2.8 81.8 1.0
O B:CYS1182 3.8 0.6 1.0
CB B:CYS1166 4.0 76.7 1.0
N B:CYS1166 4.0 78.7 1.0
CB B:CYS1182 4.1 0.0 1.0
O B:CYS1166 4.1 81.7 1.0
CA B:CYS1185 4.2 0.3 1.0
CA B:CYS1163 4.3 81.5 1.0
OG1 B:THR1170 4.4 77.8 1.0
CG2 B:ILE1165 4.4 84.0 1.0
CA B:CYS1166 4.5 78.5 1.0
CB B:ILE1165 4.6 83.7 1.0
N B:CYS1185 4.7 0.2 1.0
C B:CYS1166 4.8 80.3 1.0
CB B:THR1170 4.8 76.9 1.0
C B:CYS1182 4.8 0.2 1.0
C B:CYS1185 4.9 0.8 1.0

Zinc binding site 4 out of 8 in 2r7z

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Zinc binding site 4 out of 8 in the Cisplatin Lesion Containing Rna Polymerase II Elongation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Cisplatin Lesion Containing Rna Polymerase II Elongation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn319

b:60.7
occ:1.00
 SG C:CYS86 2.3 72.7 1.0
SG C:CYS95 2.5 90.1 1.0
SG C:CYS88 2.6 84.6 1.0
SG C:CYS92 2.8 96.2 1.0
CB C:CYS86 3.1 75.5 1.0
N C:CYS92 3.1 99.0 1.0
CB C:CYS95 3.3 90.2 1.0
CB C:CYS92 3.6 98.2 1.0
C C:HIS91 3.7 0.1 1.0
CB C:CYS88 3.7 84.9 1.0
O C:CYS92 3.7 97.8 1.0
CA C:CYS92 3.8 98.3 1.0
CA C:HIS91 3.8 0.3 1.0
N C:CYS95 4.0 88.8 1.0
C C:CYS92 4.1 98.3 1.0
O C:CYS86 4.1 80.8 1.0
CA C:CYS95 4.2 88.7 1.0
CA C:CYS86 4.4 79.1 1.0
C C:CYS86 4.5 80.0 1.0
O C:HIS91 4.6 0.1 1.0
N C:CYS88 4.6 83.0 1.0
C C:LYS94 4.6 88.9 1.0
CA C:CYS88 4.7 85.4 1.0
N C:HIS91 4.7 0.2 1.0
CB C:LYS94 4.8 90.1 1.0
CB C:HIS91 4.8 99.7 1.0
N C:LYS94 4.9 92.9 1.0
O C:CYS88 5.0 88.3 1.0
C C:CYS95 5.0 87.2 1.0

Zinc binding site 5 out of 8 in 2r7z

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Zinc binding site 5 out of 8 in the Cisplatin Lesion Containing Rna Polymerase II Elongation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Cisplatin Lesion Containing Rna Polymerase II Elongation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn203

b:0.2
occ:1.00
 SG I:CYS7 2.4 0.7 1.0
SG I:CYS32 2.4 0.9 1.0
SG I:CYS10 2.4 0.8 1.0
SG I:CYS29 2.7 0.8 1.0
CB I:CYS29 3.2 1.0 1.0
CB I:CYS7 3.6 0.7 1.0
CB I:CYS32 3.8 0.8 1.0
CB I:CYS10 3.9 0.5 1.0
CB I:TYR34 4.1 94.1 1.0
N I:CYS10 4.2 0.4 1.0
O I:ARG8 4.2 0.1 1.0
CA I:CYS10 4.3 0.7 1.0
N I:CYS32 4.3 0.0 1.0
C I:CYS10 4.4 0.0 1.0
N I:ASN11 4.6 0.1 1.0
CA I:CYS29 4.6 0.9 1.0
OD2 I:ASP9 4.7 0.6 1.0
CA I:CYS32 4.7 0.6 1.0
CB I:THR31 4.7 1.0 1.0
O I:CYS10 4.9 0.9 1.0
N I:ASN12 4.9 0.7 1.0
N I:TYR34 4.9 0.5 1.0
CA I:CYS7 5.0 0.8 1.0
CG I:TYR34 5.0 91.9 1.0

Zinc binding site 6 out of 8 in 2r7z

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Zinc binding site 6 out of 8 in the Cisplatin Lesion Containing Rna Polymerase II Elongation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Cisplatin Lesion Containing Rna Polymerase II Elongation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn204

b:0.2
occ:1.00
 SG I:CYS106 2.5 0.6 1.0
SG I:CYS78 2.8 0.5 1.0
CB I:CYS75 3.0 0.9 1.0
SG I:CYS75 3.1 0.5 1.0
N I:CYS78 3.6 0.3 1.0
CB I:HIS108 3.6 0.1 1.0
CB I:CYS78 3.8 0.9 1.0
CB I:CYS103 3.9 0.1 1.0
CB I:CYS106 3.9 0.4 1.0
CA I:CYS78 4.2 0.3 1.0
SG I:CYS103 4.3 0.5 1.0
CB I:LYS77 4.4 0.1 1.0
N I:LYS77 4.4 0.4 1.0
CG I:HIS108 4.5 0.1 1.0
CA I:CYS75 4.5 0.1 1.0
C I:LYS77 4.5 0.2 1.0
CA I:LYS77 4.7 1.0 1.0
N I:HIS108 4.7 0.5 1.0
CD2 I:HIS108 4.7 0.3 1.0
CA I:HIS108 4.8 0.3 1.0
CD I:PRO76 4.9 0.9 1.0
C I:CYS75 4.9 1.0 1.0
C I:CYS78 4.9 0.5 1.0
N I:PRO76 4.9 0.6 1.0

Zinc binding site 7 out of 8 in 2r7z

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Zinc binding site 7 out of 8 in the Cisplatin Lesion Containing Rna Polymerase II Elongation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Cisplatin Lesion Containing Rna Polymerase II Elongation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:68.5
occ:1.00
 SG J:CYS10 2.4 83.0 1.0
SG J:CYS45 2.7 0.5 1.0
SG J:CYS46 2.7 0.3 1.0
N J:CYS46 2.7 95.2 1.0
SG J:CYS7 2.8 75.7 1.0
CB J:CYS46 2.9 97.4 1.0
CB J:CYS10 2.9 79.1 1.0
CA J:CYS46 3.2 96.6 1.0
CB J:CYS45 3.4 96.3 1.0
N J:CYS10 3.4 79.3 1.0
C J:CYS45 3.5 94.4 1.0
CB J:CYS7 3.6 77.6 1.0
CA J:CYS10 3.8 78.8 1.0
NE J:ARG43 3.9 94.0 1.0
CA J:CYS45 4.0 94.7 1.0
CB J:SER9 4.3 78.5 1.0
CG J:ARG43 4.3 94.9 1.0
O J:CYS45 4.3 93.5 1.0
NH2 J:ARG43 4.5 93.9 1.0
C J:SER9 4.5 79.3 1.0
CZ J:ARG43 4.5 94.6 1.0
C J:CYS46 4.6 96.7 1.0
CD J:ARG43 4.7 93.6 1.0
N J:GLY11 4.7 78.2 1.0
N J:CYS45 4.7 93.7 1.0
C J:CYS10 4.8 77.5 1.0
CA J:SER9 4.8 78.1 1.0
O J:ARG43 4.9 93.3 1.0

Zinc binding site 8 out of 8 in 2r7z

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Zinc binding site 8 out of 8 in the Cisplatin Lesion Containing Rna Polymerase II Elongation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Cisplatin Lesion Containing Rna Polymerase II Elongation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn105

b:0.3
occ:1.00
 SG L:CYS34 2.4 0.9 1.0
SG L:CYS48 2.5 0.7 1.0
CB L:CYS48 2.6 0.8 1.0
CB L:CYS51 2.7 0.6 1.0
SG L:CYS31 2.9 0.7 1.0
O L:CYS51 3.1 0.1 1.0
CB L:CYS31 3.2 0.0 1.0
CA L:CYS51 3.6 0.6 1.0
C L:CYS51 3.7 0.2 1.0
N L:CYS51 3.8 0.0 1.0
SG L:CYS51 3.8 0.6 1.0
CB L:CYS34 4.1 0.0 1.0
CA L:CYS48 4.1 0.7 1.0
C L:CYS48 4.5 0.3 1.0
O L:CYS34 4.6 0.6 1.0
CA L:CYS31 4.6 0.1 1.0
N L:LYS49 4.7 0.6 1.0
N L:CYS48 4.8 0.2 1.0
O L:LYS49 4.9 0.0 1.0
C L:ASP50 4.9 0.2 1.0
N L:CYS34 4.9 0.9 1.0
CA L:CYS34 5.0 0.4 1.0
OG L:SER36 5.0 0.2 1.0
N L:GLY52 5.0 0.7 1.0

Reference:

G.E.Damsma, A.Alt, F.Brueckner, T.Carell, P.Cramer. Mechanism of Transcriptional Stalling at Cisplatin-Damaged Dna. Nat.Struct.Mol.Biol. V. 14 1127 2007.
ISSN: ISSN 1545-9993
PubMed: 17994106
DOI: 10.1038/NSMB1314
Page generated: Wed Dec 16 03:51:40 2020

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