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Zinc in PDB 5u5q: 12 Subunit Rna Polymerase II at Room Temperature Collected Using Sfx

Enzymatic activity of 12 Subunit Rna Polymerase II at Room Temperature Collected Using Sfx

All present enzymatic activity of 12 Subunit Rna Polymerase II at Room Temperature Collected Using Sfx:
2.7.7.6;

Protein crystallography data

The structure of 12 Subunit Rna Polymerase II at Room Temperature Collected Using Sfx, PDB code: 5u5q was solved by D.A.Bushnell, D.Oberthur, V.Mariani, O.Yefanov, A.Tolstikova, A.Barty, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.61 / 3.80
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 223.400, 396.800, 287.900, 90.00, 90.00, 90.00
R / Rfree (%) 21.8 / 27.1

Other elements in 5u5q:

The structure of 12 Subunit Rna Polymerase II at Room Temperature Collected Using Sfx also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the 12 Subunit Rna Polymerase II at Room Temperature Collected Using Sfx (pdb code 5u5q). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the 12 Subunit Rna Polymerase II at Room Temperature Collected Using Sfx, PDB code: 5u5q:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 5u5q

Go back to Zinc Binding Sites List in 5u5q
Zinc binding site 1 out of 8 in the 12 Subunit Rna Polymerase II at Room Temperature Collected Using Sfx


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of 12 Subunit Rna Polymerase II at Room Temperature Collected Using Sfx within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1801

b:0.9
occ:1.00
 SG A:CYS110 2.4 0.2 1.0
SG A:CYS148 2.5 0.4 1.0
SG A:CYS167 2.6 0.8 1.0
CB A:CYS110 3.2 0.5 1.0
O A:CYS167 3.3 0.9 1.0
SG A:CYS107 3.5 0.3 1.0
CB A:CYS167 3.6 0.8 1.0
CB A:CYS148 3.6 0.0 1.0
CB A:CYS107 3.6 0.0 1.0
O A:MET108 3.7 0.0 1.0
C A:CYS167 4.0 0.7 1.0
N A:CYS110 4.1 0.8 1.0
O A:GLY166 4.1 0.3 1.0
CA A:CYS110 4.2 0.3 1.0
N A:GLY111 4.4 0.3 1.0
CA A:CYS167 4.4 0.2 1.0
O A:CYS107 4.7 0.2 1.0
C A:CYS107 4.7 0.2 1.0
CA A:CYS107 4.8 0.8 1.0
C A:CYS110 4.8 0.2 1.0
N A:GLY168 4.9 0.1 1.0
C A:MET108 5.0 0.7 1.0

Zinc binding site 2 out of 8 in 5u5q

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Zinc binding site 2 out of 8 in the 12 Subunit Rna Polymerase II at Room Temperature Collected Using Sfx


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of 12 Subunit Rna Polymerase II at Room Temperature Collected Using Sfx within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1802

b:0.2
occ:1.00
 NE2 A:HIS80 2.0 0.0 1.0
CB A:CYS67 2.4 0.0 1.0
SG A:CYS77 2.4 0.2 1.0
SG A:CYS67 2.6 0.2 1.0
SG A:CYS70 2.8 0.7 1.0
CD2 A:HIS80 2.9 0.8 1.0
CE1 A:HIS80 3.1 0.5 1.0
CB A:CYS70 3.4 0.4 1.0
CB A:CYS77 3.4 0.9 1.0
O A:CYS67 3.5 0.7 1.0
CA A:CYS67 3.7 0.7 1.0
C A:CYS67 4.0 0.1 1.0
O A:GLN71 4.1 0.4 1.0
N A:GLN71 4.1 0.1 1.0
CG A:HIS80 4.1 0.1 1.0
ND1 A:HIS80 4.2 0.6 1.0
C A:CYS70 4.4 0.3 1.0
CA A:CYS70 4.5 0.7 1.0
CA A:CYS77 4.5 0.4 1.0
NE2 A:GLN68 4.5 1.0 1.0
CA A:GLN71 4.6 0.4 1.0
C A:GLN71 4.8 0.5 1.0
N A:CYS67 4.8 0.7 1.0

Zinc binding site 3 out of 8 in 5u5q

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Zinc binding site 3 out of 8 in the 12 Subunit Rna Polymerase II at Room Temperature Collected Using Sfx


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of 12 Subunit Rna Polymerase II at Room Temperature Collected Using Sfx within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1301

b:0.4
occ:1.00
 SG B:CYS1185 2.4 0.9 1.0
SG B:CYS1166 2.4 0.5 1.0
SG B:CYS1182 2.5 0.1 1.0
CB B:CYS1185 2.5 0.6 1.0
SG B:CYS1163 2.5 0.6 1.0
CB B:CYS1166 3.5 0.1 1.0
CB B:CYS1163 3.5 0.8 1.0
N B:CYS1166 3.5 0.9 1.0
CB B:CYS1182 3.9 0.1 1.0
CA B:CYS1185 4.0 0.1 1.0
CA B:CYS1166 4.1 0.2 1.0
CB B:ILE1165 4.2 0.9 1.0
CD1 B:ILE1165 4.3 0.0 1.0
O B:CYS1166 4.4 0.2 1.0
N B:CYS1185 4.4 0.4 1.0
O B:CYS1182 4.5 0.7 1.0
C B:ILE1165 4.6 0.6 1.0
N B:ILE1165 4.7 0.2 1.0
CA B:ILE1165 4.7 0.4 1.0
C B:CYS1166 4.7 1.0 1.0
CG1 B:ILE1165 4.8 0.4 1.0
C B:CYS1185 4.9 0.6 1.0
CA B:CYS1163 5.0 0.5 1.0

Zinc binding site 4 out of 8 in 5u5q

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Zinc binding site 4 out of 8 in the 12 Subunit Rna Polymerase II at Room Temperature Collected Using Sfx


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of 12 Subunit Rna Polymerase II at Room Temperature Collected Using Sfx within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:0.3
occ:1.00
 SG C:CYS88 2.2 0.4 1.0
SG C:CYS92 2.3 0.6 1.0
SG C:CYS95 2.4 0.5 1.0
CB C:CYS95 2.9 0.5 1.0
SG C:CYS86 2.9 0.9 1.0
CB C:CYS92 3.1 0.0 1.0
N C:CYS92 3.4 0.9 1.0
CB C:CYS86 3.4 0.5 1.0
CB C:CYS88 3.6 0.0 1.0
CA C:CYS92 3.7 0.9 1.0
C C:HIS91 3.7 0.2 1.0
N C:CYS95 3.8 0.3 1.0
CA C:CYS95 3.9 0.5 1.0
CA C:HIS91 4.2 0.2 1.0
O C:HIS91 4.3 0.2 1.0
C C:CYS92 4.3 0.8 1.0
C C:LYS94 4.5 0.1 1.0
N C:CYS88 4.5 0.0 1.0
CA C:CYS88 4.6 99.5 1.0
O C:ASP90 4.7 0.6 1.0
O C:CYS92 4.7 0.7 1.0
CA C:CYS86 4.8 0.6 1.0
C C:CYS95 4.8 1.0 1.0
N C:LYS94 4.8 0.1 1.0
C C:CYS86 4.9 0.3 1.0
N C:ASP93 5.0 0.5 1.0

Zinc binding site 5 out of 8 in 5u5q

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Zinc binding site 5 out of 8 in the 12 Subunit Rna Polymerase II at Room Temperature Collected Using Sfx


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of 12 Subunit Rna Polymerase II at Room Temperature Collected Using Sfx within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:0.6
occ:1.00
 SG I:CYS10 2.3 0.8 1.0
SG I:CYS7 2.4 0.5 1.0
SG I:CYS32 2.5 0.4 1.0
CB I:CYS7 2.7 0.8 1.0
SG I:CYS29 2.9 0.4 1.0
CB I:CYS29 3.3 0.7 1.0
CB I:CYS32 3.6 0.2 1.0
CB I:CYS10 3.8 0.2 1.0
N I:CYS10 3.9 0.5 1.0
N I:CYS32 4.2 0.4 1.0
CA I:CYS7 4.2 0.7 1.0
N I:ASN11 4.3 0.5 1.0
CB I:TYR34 4.3 0.3 1.0
CA I:CYS10 4.3 0.5 1.0
CA I:CYS32 4.5 0.5 1.0
C I:CYS10 4.6 0.9 1.0
OD1 I:ASN12 4.7 0.3 1.0
CA I:CYS29 4.7 0.8 1.0
OD1 I:ASP9 4.8 0.9 1.0
C I:CYS7 4.9 1.0 1.0
CB I:ASP9 4.9 0.1 1.0
N I:TYR34 4.9 0.0 1.0
CD1 I:TYR34 4.9 0.3 1.0
C I:ASP9 4.9 0.6 1.0
CG I:TYR34 4.9 0.6 1.0
N I:ASN12 5.0 0.7 1.0
N I:CYS7 5.0 0.5 1.0

Zinc binding site 6 out of 8 in 5u5q

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Zinc binding site 6 out of 8 in the 12 Subunit Rna Polymerase II at Room Temperature Collected Using Sfx


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of 12 Subunit Rna Polymerase II at Room Temperature Collected Using Sfx within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:0.3
occ:1.00
 SG I:CYS106 2.3 0.6 1.0
CB I:CYS75 2.6 0.9 1.0
SG I:CYS75 3.2 0.1 1.0
SG I:CYS78 3.4 0.6 1.0
CA I:CYS75 3.5 0.0 1.0
CD I:PRO76 3.5 0.9 1.0
CB I:CYS103 3.5 0.1 1.0
CB I:HIS108 3.6 0.4 1.0
SG I:CYS103 3.9 0.8 1.0
N I:PRO76 4.0 0.1 1.0
CB I:CYS106 4.0 1.0 1.0
CD2 I:HIS108 4.1 0.4 1.0
N I:LYS77 4.1 1.0 1.0
O I:HIS108 4.1 0.5 1.0
CG I:HIS108 4.2 0.8 1.0
C I:CYS75 4.2 0.5 1.0
N I:CYS78 4.3 0.3 1.0
CB I:LYS77 4.3 0.5 1.0
N I:HIS108 4.4 0.9 1.0
CA I:HIS108 4.4 0.1 1.0
C I:HIS108 4.6 0.9 1.0
CG I:LYS77 4.7 0.6 1.0
CA I:LYS77 4.7 0.4 1.0
N I:CYS75 4.7 0.1 1.0
CE1 I:PHE110 4.8 0.2 1.0
CD1 I:PHE110 4.8 0.3 1.0
CG I:PRO76 4.8 1.0 1.0
CB I:CYS78 4.9 0.3 1.0
C I:LYS77 5.0 0.7 1.0

Zinc binding site 7 out of 8 in 5u5q

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Zinc binding site 7 out of 8 in the 12 Subunit Rna Polymerase II at Room Temperature Collected Using Sfx


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of 12 Subunit Rna Polymerase II at Room Temperature Collected Using Sfx within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:0.7
occ:1.00
 SG J:CYS10 2.4 0.9 1.0
SG J:CYS45 2.5 0.4 1.0
CB J:CYS10 2.6 0.1 1.0
N J:CYS46 2.6 0.5 1.0
CB J:CYS46 2.6 0.6 1.0
SG J:CYS46 2.8 0.4 1.0
SG J:CYS7 2.9 0.3 1.0
CA J:CYS46 3.0 0.3 1.0
C J:CYS45 3.3 0.8 1.0
CB J:CYS7 3.4 0.7 1.0
CB J:CYS45 3.4 1.0 1.0
N J:CYS10 3.5 0.2 1.0
OG J:SER9 3.6 0.3 1.0
CA J:CYS10 3.6 0.2 1.0
NE J:ARG43 3.9 0.8 1.0
CA J:CYS45 3.9 0.1 1.0
O J:CYS45 4.0 0.8 1.0
NH2 J:ARG43 4.3 0.9 1.0
N J:GLY11 4.3 0.6 1.0
C J:CYS46 4.5 0.1 1.0
C J:CYS10 4.5 0.1 1.0
CZ J:ARG43 4.5 0.8 1.0
N J:CYS45 4.7 0.9 1.0
CD J:ARG43 4.8 0.1 1.0
C J:SER9 4.8 1.0 1.0
CB J:SER9 4.9 0.8 1.0
CA J:CYS7 4.9 0.5 1.0
CG J:ARG43 5.0 0.2 1.0

Zinc binding site 8 out of 8 in 5u5q

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Zinc binding site 8 out of 8 in the 12 Subunit Rna Polymerase II at Room Temperature Collected Using Sfx


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of 12 Subunit Rna Polymerase II at Room Temperature Collected Using Sfx within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:0.5
occ:1.00
 SG L:CYS31 2.4 0.8 1.0
SG L:CYS48 2.4 0.6 1.0
SG L:CYS34 2.5 0.9 1.0
SG L:CYS51 2.6 0.6 1.0
CB L:CYS34 3.1 0.7 1.0
CB L:CYS48 3.2 0.2 1.0
CB L:CYS31 3.2 0.5 1.0
N L:CYS34 4.0 0.8 1.0
CB L:CYS51 4.0 0.1 1.0
N L:CYS51 4.1 0.6 1.0
CA L:CYS34 4.2 0.2 1.0
CB L:ASP50 4.3 0.1 1.0
OG L:SER36 4.3 0.9 1.0
O L:CYS51 4.4 1.0 1.0
CA L:CYS51 4.5 0.1 1.0
C L:ASP50 4.7 0.8 1.0
CA L:CYS48 4.7 0.8 1.0
CA L:CYS31 4.7 0.3 1.0
C L:CYS51 4.7 0.1 1.0
O L:GLY52 4.8 0.5 1.0
OD2 L:ASP50 4.9 0.1 1.0
CA L:ASP50 4.9 0.1 1.0
C L:CYS34 4.9 0.2 1.0
N L:ASP50 4.9 0.4 1.0

Reference:

D.Oberthuer, J.Knoska, M.O.Wiedorn, K.R.Beyerlein, D.A.Bushnell, E.G.Kovaleva, M.Heymann, L.Gumprecht, R.A.Kirian, A.Barty, V.Mariani, A.Tolstikova, L.Adriano, S.Awel, M.Barthelmess, K.Dorner, P.L.Xavier, O.Yefanov, D.R.James, G.Nelson, D.Wang, G.Calvey, Y.Chen, A.Schmidt, M.Szczepek, S.Frielingsdorf, O.Lenz, E.Snell, P.J.Robinson, B.Sarler, G.Belsak, M.Macek, F.Wilde, A.Aquila, S.Boutet, M.Liang, M.S.Hunter, P.Scheerer, J.D.Lipscomb, U.Weierstall, R.D.Kornberg, J.C.Spence, L.Pollack, H.N.Chapman, S.Bajt. Double-Flow Focused Liquid Injector For Efficient Serial Femtosecond Crystallography. Sci Rep V. 7 44628 2017.
ISSN: ESSN 2045-2322
PubMed: 28300169
DOI: 10.1038/SREP44628
Page generated: Mon Oct 28 09:07:24 2024

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