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Zinc in PDB 5x50: Rna Polymerase II From Komagataella Pastoris (Type-2 Crystal)

Enzymatic activity of Rna Polymerase II From Komagataella Pastoris (Type-2 Crystal)

All present enzymatic activity of Rna Polymerase II From Komagataella Pastoris (Type-2 Crystal):
2.7.7.6;

Protein crystallography data

The structure of Rna Polymerase II From Komagataella Pastoris (Type-2 Crystal), PDB code: 5x50 was solved by H.Ehara, T.Umehara, S.Sekine, S.Yokoyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.70 / 4.29
Space group P 31
Cell size a, b, c (Å), α, β, γ (°) 211.750, 211.750, 132.280, 90.00, 90.00, 120.00
R / Rfree (%) 23.5 / 29.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Rna Polymerase II From Komagataella Pastoris (Type-2 Crystal) (pdb code 5x50). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Rna Polymerase II From Komagataella Pastoris (Type-2 Crystal), PDB code: 5x50:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 5x50

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Zinc binding site 1 out of 8 in the Rna Polymerase II From Komagataella Pastoris (Type-2 Crystal)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Rna Polymerase II From Komagataella Pastoris (Type-2 Crystal) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1801

b:0.4
occ:1.00
 SG A:CYS107 2.6 0.2 1.0
SG A:CYS168 2.7 0.1 1.0
O A:GLY167 2.7 0.6 1.0
O A:CYS168 2.8 0.2 1.0
CB A:CYS110 2.8 0.0 1.0
CB A:CYS148 2.9 0.2 1.0
SG A:CYS148 3.0 0.6 1.0
O A:MET108 3.0 0.1 1.0
CB A:CYS107 3.7 1.0 1.0
SG A:CYS110 3.8 0.3 1.0
C A:CYS168 3.8 0.5 1.0
N A:CYS110 3.8 0.8 1.0
C A:GLY167 3.9 0.4 1.0
CA A:CYS110 4.0 0.0 1.0
CB A:CYS168 4.0 1.0 1.0
C A:MET108 4.2 0.5 1.0
CA A:CYS168 4.3 0.8 1.0
CA A:CYS148 4.4 0.6 1.0
C A:ASN109 4.4 0.8 1.0
N A:CYS168 4.6 0.5 1.0
O A:CYS148 4.6 0.9 1.0
N A:MET108 4.6 0.8 1.0
C A:CYS107 4.7 0.4 1.0
CB A:ASN109 4.7 0.5 1.0
ND2 A:ASN170 4.8 0.4 1.0
N A:GLY111 4.8 0.2 1.0
CA A:CYS107 4.8 1.0 1.0
N A:GLY169 4.9 0.3 1.0
C A:CYS110 4.9 1.0 1.0
O A:ASN109 5.0 0.8 1.0
CA A:ASN109 5.0 0.6 1.0
N A:CYS148 5.0 0.8 1.0

Zinc binding site 2 out of 8 in 5x50

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Zinc binding site 2 out of 8 in the Rna Polymerase II From Komagataella Pastoris (Type-2 Crystal)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Rna Polymerase II From Komagataella Pastoris (Type-2 Crystal) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1802

b:1.0
occ:1.00
 O A:CYS70 2.4 0.2 1.0
SG A:CYS67 2.5 0.6 1.0
SG A:CYS70 2.7 0.9 1.0
O A:GLY71 3.2 0.6 1.0
C A:CYS70 3.3 0.1 1.0
CB A:CYS70 3.5 0.2 1.0
CB A:CYS67 3.7 0.5 1.0
CG A:GLU72 3.8 0.3 1.0
C A:GLY71 4.0 0.6 1.0
O A:CYS67 4.0 0.5 1.0
CA A:CYS70 4.0 0.2 1.0
NE2 A:HIS80 4.1 0.3 1.0
N A:GLY71 4.1 0.3 1.0
CB A:GLU72 4.2 0.7 1.0
CB A:CYS77 4.3 0.7 1.0
CA A:CYS77 4.4 0.7 1.0
CA A:GLY71 4.5 0.2 1.0
CE1 A:HIS80 4.5 0.8 1.0
N A:CYS70 4.7 0.2 1.0
O B:ALA1173 4.8 0.4 1.0
C A:CYS67 4.8 0.9 1.0
N A:GLU72 4.8 0.8 1.0
CD A:PRO78 4.9 0.4 1.0
SG A:CYS77 4.9 0.2 1.0
CA A:CYS67 4.9 0.3 1.0

Zinc binding site 3 out of 8 in 5x50

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Zinc binding site 3 out of 8 in the Rna Polymerase II From Komagataella Pastoris (Type-2 Crystal)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Rna Polymerase II From Komagataella Pastoris (Type-2 Crystal) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1301

b:0.0
occ:1.00
 SG B:CYS1182 2.3 0.9 1.0
SG B:CYS1166 2.4 99.7 1.0
CB B:CYS1185 2.7 0.8 1.0
SG B:CYS1163 3.0 0.3 1.0
O B:CYS1182 3.2 0.7 1.0
CB B:CYS1182 3.6 0.5 1.0
SG B:CYS1185 3.8 0.2 1.0
CA B:CYS1185 3.9 0.7 1.0
CB B:CYS1166 3.9 0.8 1.0
CB B:CYS1163 4.0 0.8 1.0
C B:CYS1182 4.1 0.2 1.0
C B:CYS1185 4.1 0.8 1.0
N B:CYS1166 4.2 0.2 1.0
N B:CYS1185 4.2 0.1 1.0
O B:ARG1183 4.4 0.6 1.0
CB B:ASN1187 4.5 0.8 1.0
O B:CYS1185 4.5 0.0 1.0
CA B:CYS1182 4.5 0.7 1.0
N B:LYS1186 4.6 0.4 1.0
O B:CYS1166 4.6 1.0 1.0
CA B:CYS1166 4.6 0.0 1.0
CB B:ILE1165 4.8 0.1 1.0
N B:ASN1187 4.9 0.3 1.0

Zinc binding site 4 out of 8 in 5x50

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Zinc binding site 4 out of 8 in the Rna Polymerase II From Komagataella Pastoris (Type-2 Crystal)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Rna Polymerase II From Komagataella Pastoris (Type-2 Crystal) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:0.6
occ:1.00
 SG C:CYS94 2.4 0.4 1.0
SG C:CYS87 2.6 0.5 1.0
O C:SER82 2.7 0.1 1.0
CB C:SER82 2.7 0.4 1.0
CA C:SER82 2.8 0.3 1.0
CA C:TYR90 2.9 0.9 1.0
O C:ASP89 3.1 0.1 1.0
C C:SER82 3.1 0.2 1.0
OG C:SER82 3.3 0.4 1.0
N C:TYR90 3.4 0.9 1.0
C C:ASP89 3.4 1.0 1.0
CB C:CYS85 3.4 0.2 1.0
C C:TYR90 3.6 0.2 1.0
O C:CYS87 3.7 0.8 1.0
SG C:CYS85 3.8 0.6 1.0
CB C:CYS94 3.8 0.4 1.0
CB C:TYR90 3.8 0.0 1.0
N C:CYS91 3.9 0.0 1.0
N C:SER82 4.2 0.2 1.0
CB C:CYS87 4.3 0.6 1.0
O C:CYS85 4.4 0.8 1.0
O C:TYR90 4.4 0.5 1.0
N C:ARG83 4.4 0.6 1.0
C C:CYS87 4.5 0.0 1.0
CA C:CYS85 4.6 0.7 1.0
CA C:ASP89 4.7 1.0 1.0
C C:CYS85 4.8 0.7 1.0
CA C:CYS87 4.8 0.5 1.0
N C:ASP89 4.9 1.0 1.0
N C:CYS87 4.9 0.5 1.0
SG C:CYS91 4.9 0.9 1.0
N C:CYS85 4.9 1.0 1.0

Zinc binding site 5 out of 8 in 5x50

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Zinc binding site 5 out of 8 in the Rna Polymerase II From Komagataella Pastoris (Type-2 Crystal)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Rna Polymerase II From Komagataella Pastoris (Type-2 Crystal) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:1.0
occ:1.00
 SG I:CYS7 2.7 0.3 1.0
O I:LEU8 2.7 0.6 1.0
SG I:CYS32 3.0 0.6 1.0
SG I:CYS10 3.0 0.6 1.0
N I:CYS10 3.1 0.0 1.0
CB I:GLU9 3.8 0.1 1.0
SG I:CYS29 3.8 0.7 1.0
CA I:CYS10 3.8 0.1 1.0
C I:LEU8 3.9 0.7 1.0
CD1 I:TYR34 3.9 0.9 1.0
CB I:TYR34 4.0 0.6 1.0
CB I:CYS10 4.0 0.5 1.0
C I:CYS10 4.0 0.3 1.0
C I:GLU9 4.2 0.1 1.0
N I:ASN11 4.3 0.6 1.0
CB I:CYS29 4.3 0.7 1.0
CB I:CYS7 4.3 0.4 1.0
O I:CYS7 4.4 0.6 1.0
CA I:GLU9 4.4 0.1 1.0
CG I:TYR34 4.4 0.8 1.0
CB I:CYS32 4.4 0.5 1.0
O I:CYS10 4.5 0.3 1.0
CG I:GLU9 4.5 0.5 1.0
C I:CYS7 4.6 0.7 1.0
N I:GLU9 4.6 0.5 1.0
N I:LEU8 4.9 0.1 1.0
CE1 I:TYR34 5.0 0.0 1.0

Zinc binding site 6 out of 8 in 5x50

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Zinc binding site 6 out of 8 in the Rna Polymerase II From Komagataella Pastoris (Type-2 Crystal)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Rna Polymerase II From Komagataella Pastoris (Type-2 Crystal) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:0.9
occ:1.00
 O I:ASN105 2.2 0.8 1.0
C I:ASN105 2.6 0.1 1.0
CB I:CYS106 2.7 0.8 1.0
SG I:CYS78 2.8 0.6 1.0
SG I:CYS75 2.9 0.1 1.0
SG I:CYS106 3.2 0.3 1.0
N I:CYS106 3.2 1.0 1.0
CB I:CYS75 3.2 0.2 1.0
SG I:CYS103 3.5 0.2 1.0
CA I:CYS106 3.5 0.9 1.0
CA I:ASN105 3.6 0.5 1.0
CB I:CYS78 3.6 0.3 1.0
CB I:ASN105 3.7 0.5 1.0
CB I:CYS103 3.8 0.8 1.0
N I:CYS78 4.0 0.6 1.0
N I:ASN105 4.0 0.8 1.0
CA I:CYS78 4.3 0.4 1.0
O I:CYS103 4.6 0.9 1.0
C I:CYS106 4.7 0.3 1.0
CA I:CYS75 4.7 0.1 1.0
N I:LYS107 4.8 0.7 1.0
OG I:SER80 4.8 0.1 1.0
C I:CYS103 4.8 0.9 1.0
N I:HIS79 4.9 0.4 1.0
CA I:CYS103 4.9 0.3 1.0
C I:CYS78 4.9 0.3 1.0

Zinc binding site 7 out of 8 in 5x50

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Zinc binding site 7 out of 8 in the Rna Polymerase II From Komagataella Pastoris (Type-2 Crystal)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Rna Polymerase II From Komagataella Pastoris (Type-2 Crystal) within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:0.8
occ:1.00
 N J:CYS45 2.0 0.5 1.0
CA J:CYS45 2.2 0.4 1.0
C J:CYS44 2.4 0.9 1.0
CB J:CYS45 2.6 0.6 1.0
SG J:CYS7 2.6 0.1 1.0
SG J:CYS10 2.7 0.6 1.0
O J:CYS44 2.8 0.3 1.0
SG J:CYS44 2.9 0.1 1.0
CB J:CYS44 3.4 0.9 1.0
CB J:CYS7 3.5 0.8 1.0
CA J:CYS44 3.5 0.1 1.0
SG J:CYS45 3.5 0.3 1.0
CB J:CYS10 3.6 0.1 1.0
C J:CYS45 3.7 0.1 1.0
N J:CYS10 3.7 0.5 1.0
CB J:SER9 4.1 0.0 1.0
CA J:CYS10 4.2 0.5 1.0
N J:ARG46 4.4 0.2 1.0
O J:CYS45 4.4 0.8 1.0
N J:CYS44 4.5 0.6 1.0
C J:SER9 4.7 1.0 1.0
OG J:SER9 4.8 0.1 1.0
CA J:SER9 4.8 0.1 1.0
N J:GLY11 4.8 0.2 1.0
CA J:CYS7 4.9 0.2 1.0
O J:ARG42 5.0 0.5 1.0

Zinc binding site 8 out of 8 in 5x50

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Zinc binding site 8 out of 8 in the Rna Polymerase II From Komagataella Pastoris (Type-2 Crystal)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Rna Polymerase II From Komagataella Pastoris (Type-2 Crystal) within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:1.0
occ:1.00
 CB L:CYS50 2.4 0.3 1.0
SG L:CYS36 2.4 0.9 1.0
O L:CYS53 2.7 0.1 1.0
CB L:CYS53 2.7 0.7 1.0
SG L:CYS33 2.8 0.3 1.0
SG L:CYS50 3.0 0.9 1.0
CA L:CYS53 3.2 0.3 1.0
C L:CYS53 3.3 0.6 1.0
N L:CYS53 3.3 0.6 1.0
CB L:CYS33 3.6 0.8 1.0
CA L:CYS50 3.8 0.0 1.0
SG L:CYS53 3.8 0.1 1.0
C L:GLU52 4.1 0.3 1.0
C L:CYS50 4.1 0.0 1.0
CB L:CYS36 4.2 0.8 1.0
N L:CYS50 4.4 0.7 1.0
O L:HIS55 4.4 0.1 1.0
O L:CYS50 4.5 0.9 1.0
N L:LYS51 4.5 0.7 1.0
N L:GLY54 4.6 0.2 1.0
N L:CYS36 4.6 0.1 1.0
N L:GLU52 4.6 0.3 1.0
O L:GLU52 4.7 0.9 1.0
O L:CYS36 4.7 0.8 1.0
CA L:GLU52 4.8 0.3 1.0
CA L:CYS36 4.9 0.2 1.0
CB L:GLU52 4.9 0.6 1.0

Reference:

H.Ehara, T.Umehara, S.I.Sekine, S.Yokoyama. Crystal Structure of Rna Polymerase II From Komagataella Pastoris Biochem. Biophys. Res. V. 487 230 2017COMMUN..
ISSN: ESSN 1090-2104
PubMed: 28412353
DOI: 10.1016/J.BBRC.2017.04.039
Page generated: Mon Oct 28 14:49:08 2024

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