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Zinc in PDB 5x4z: Rna Polymerase II From Komagataella Pastoris (Type-1 Crystal)

Enzymatic activity of Rna Polymerase II From Komagataella Pastoris (Type-1 Crystal)

All present enzymatic activity of Rna Polymerase II From Komagataella Pastoris (Type-1 Crystal):
2.7.7.6;

Protein crystallography data

The structure of Rna Polymerase II From Komagataella Pastoris (Type-1 Crystal), PDB code: 5x4z 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) 49.82 / 7.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 155.048, 160.351, 254.354, 90.00, 105.43, 90.00
R / Rfree (%) 35.3 / 35.7

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Zinc atom in the Rna Polymerase II From Komagataella Pastoris (Type-1 Crystal) (pdb code 5x4z). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 16 binding sites of Zinc where determined in the Rna Polymerase II From Komagataella Pastoris (Type-1 Crystal), PDB code: 5x4z:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 16 in 5x4z

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Zinc binding site 1 out of 16 in the Rna Polymerase II From Komagataella Pastoris (Type-1 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-1 Crystal) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1801

b:0.4
occ:1.00
 SG A:CYS148 2.6 0.6 1.0
CB A:CYS110 2.6 0.9 1.0
SG A:CYS110 2.9 0.2 1.0
SG A:CYS107 2.9 0.7 1.0
SG A:CYS168 3.1 0.4 1.0
O A:GLY167 3.5 0.7 1.0
CB A:CYS107 3.5 0.1 1.0
O A:CYS168 3.5 0.9 1.0
CB A:CYS148 3.6 0.7 1.0
O A:MET108 3.7 0.8 1.0
CA A:CYS110 4.0 0.1 1.0
N A:CYS110 4.3 0.8 1.0
N A:GLY111 4.4 0.7 1.0
C A:CYS168 4.6 0.7 1.0
CB A:CYS168 4.7 0.8 1.0
C A:GLY167 4.7 0.2 1.0
C A:CYS110 4.7 0.3 1.0
C A:CYS107 4.7 0.6 1.0
CA A:CYS107 4.8 0.4 1.0
C A:MET108 4.8 0.2 1.0
O A:CYS107 4.9 0.7 1.0
N A:MET108 5.0 0.8 1.0
CA A:CYS148 5.0 0.6 1.0

Zinc binding site 2 out of 16 in 5x4z

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Zinc binding site 2 out of 16 in the Rna Polymerase II From Komagataella Pastoris (Type-1 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-1 Crystal) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1802

b:0.4
occ:1.00
 NE2 A:HIS80 2.0 0.5 1.0
CD2 A:HIS80 2.5 0.5 1.0
SG A:CYS67 2.6 0.3 1.0
SG A:CYS70 2.7 0.8 1.0
SG A:CYS77 3.0 0.3 1.0
CE1 A:HIS80 3.3 0.1 1.0
CG A:HIS80 3.8 0.9 1.0
O A:CYS67 3.9 0.5 1.0
CB A:CYS77 3.9 0.8 1.0
CB A:CYS70 4.1 0.2 1.0
CB A:CYS67 4.1 0.5 1.0
ND1 A:HIS80 4.1 0.4 1.0
O A:CYS70 4.2 0.0 1.0
O A:PRO78 4.4 0.5 1.0
CA A:CYS77 4.7 0.6 1.0
C A:CYS70 4.8 0.9 1.0
O A:GLY71 4.8 0.1 1.0
C A:CYS67 4.9 0.6 1.0
NE2 A:GLN68 4.9 0.2 1.0

Zinc binding site 3 out of 16 in 5x4z

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Zinc binding site 3 out of 16 in the Rna Polymerase II From Komagataella Pastoris (Type-1 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-1 Crystal) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1301

b:0.3
occ:1.00
 SG B:CYS1166 1.8 0.1 1.0
SG B:CYS1185 2.2 0.8 1.0
N B:CYS1166 2.2 0.9 1.0
SG B:CYS1163 2.4 0.4 1.0
CB B:CYS1166 2.4 1.0 1.0
CA B:CYS1166 2.7 0.9 1.0
O B:CYS1166 3.2 0.5 1.0
CB B:CYS1185 3.3 0.7 1.0
C B:CYS1166 3.4 0.9 1.0
C B:ILE1165 3.4 0.4 1.0
CB B:CYS1163 3.5 0.5 1.0
CB B:ILE1165 3.7 0.8 1.0
CA B:ILE1165 4.0 0.9 1.0
CG2 B:ILE1165 4.0 0.7 1.0
O D:ALA15 4.0 0.2 1.0
CA D:ALA15 4.2 0.6 1.0
N B:ILE1165 4.3 0.7 1.0
O B:ILE1165 4.4 0.1 1.0
SG B:CYS1182 4.5 0.9 1.0
C D:ALA15 4.6 0.4 1.0
N B:GLY1167 4.6 0.0 1.0
CA B:CYS1185 4.7 0.1 1.0
N D:ALA15 4.9 0.0 1.0
CA B:CYS1163 4.9 0.1 1.0

Zinc binding site 4 out of 16 in 5x4z

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Zinc binding site 4 out of 16 in the Rna Polymerase II From Komagataella Pastoris (Type-1 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-1 Crystal) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:0.4
occ:1.00
 SG C:CYS85 2.3 0.4 1.0
SG C:CYS91 2.4 0.8 1.0
SG C:CYS94 2.5 0.6 1.0
SG C:CYS87 2.5 0.3 1.0
CB C:CYS85 3.3 0.7 1.0
N C:CYS91 3.4 1.0 1.0
CB C:CYS91 3.4 0.1 1.0
CB C:CYS87 3.5 0.4 1.0
CB C:CYS94 3.6 0.7 1.0
C C:TYR90 3.7 0.0 1.0
CA C:CYS91 3.9 0.5 1.0
CA C:TYR90 4.1 0.8 1.0
N C:CYS94 4.1 1.0 1.0
O C:TYR90 4.2 0.3 1.0
O C:CYS91 4.3 0.7 1.0
C C:CYS91 4.3 0.4 1.0
CA C:CYS94 4.4 0.2 1.0
CA C:CYS87 4.6 0.5 1.0
N C:CYS87 4.6 0.9 1.0
C C:GLU93 4.6 0.7 1.0
CA C:CYS85 4.7 0.3 1.0
CB C:GLU93 4.8 0.2 1.0
O C:CYS87 4.8 0.8 1.0
N C:TYR90 4.9 0.9 1.0
C C:CYS85 5.0 0.5 1.0
N C:GLU93 5.0 0.0 1.0

Zinc binding site 5 out of 16 in 5x4z

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Zinc binding site 5 out of 16 in the Rna Polymerase II From Komagataella Pastoris (Type-1 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-1 Crystal) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:0.7
occ:1.00
 SG I:CYS32 2.3 0.1 1.0
SG I:CYS10 2.5 0.2 1.0
SG I:CYS7 2.6 0.5 1.0
SG I:CYS29 2.8 0.3 1.0
CB I:CYS29 3.5 0.7 1.0
CB I:CYS32 3.7 0.3 1.0
CB I:CYS10 4.0 0.8 1.0
N I:CYS10 4.1 0.7 1.0
O I:LEU8 4.1 0.1 1.0
CB I:CYS7 4.1 0.5 1.0
CB I:TYR34 4.3 0.2 1.0
CA I:CYS10 4.4 0.8 1.0
N I:CYS32 4.5 0.9 1.0
C I:CYS10 4.5 0.9 1.0
O I:CYS10 4.6 0.2 1.0
CA I:CYS32 4.7 0.4 1.0
CB I:GLU9 4.8 0.6 1.0
CB I:ASN12 4.9 0.6 1.0
CB I:ASN31 4.9 0.4 1.0
CA I:CYS29 5.0 0.8 1.0

Zinc binding site 6 out of 16 in 5x4z

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Zinc binding site 6 out of 16 in the Rna Polymerase II From Komagataella Pastoris (Type-1 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-1 Crystal) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:0.7
occ:1.00
 SG I:CYS106 2.6 0.7 1.0
SG I:CYS78 2.8 0.6 1.0
SG I:CYS75 2.9 0.4 1.0
CB I:CYS106 2.9 0.7 1.0
CB I:CYS78 3.2 0.6 1.0
CB I:CYS75 3.4 0.6 1.0
N I:CYS78 3.7 0.5 1.0
O I:ASN105 3.8 0.8 1.0
CB I:CYS103 4.0 0.5 1.0
SG I:CYS103 4.0 0.3 1.0
CA I:CYS78 4.0 0.4 1.0
CB I:LYS108 4.3 0.8 1.0
CA I:CYS106 4.3 0.1 1.0
C I:ASN105 4.4 0.1 1.0
N I:CYS106 4.6 0.4 1.0
CB I:GLU77 4.8 0.5 1.0
C I:GLU77 4.8 0.3 1.0
CA I:CYS75 4.9 0.1 1.0
C I:CYS78 4.9 0.0 1.0

Zinc binding site 7 out of 16 in 5x4z

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Zinc binding site 7 out of 16 in the Rna Polymerase II From Komagataella Pastoris (Type-1 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-1 Crystal) within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:0.7
occ:1.00
 SG J:CYS10 2.4 0.8 1.0
SG J:CYS7 2.4 0.3 1.0
SG J:CYS44 2.4 0.3 1.0
N J:CYS45 2.7 0.4 1.0
CB J:CYS45 2.7 1.0 1.0
CA J:CYS45 2.9 0.8 1.0
SG J:CYS45 3.1 0.3 1.0
CB J:CYS7 3.1 0.3 1.0
C J:CYS44 3.3 0.3 1.0
CB J:CYS10 3.6 0.8 1.0
CB J:CYS44 3.6 0.5 1.0
N J:CYS10 3.8 0.5 1.0
O J:CYS44 4.0 0.6 1.0
CA J:CYS44 4.0 1.0 1.0
CA J:CYS10 4.2 0.6 1.0
C J:CYS45 4.4 0.4 1.0
NE J:ARG42 4.5 0.4 1.0
CB J:SER9 4.5 0.2 1.0
NH2 J:ARG42 4.5 0.5 1.0
N J:GLY11 4.5 0.9 1.0
CA J:CYS7 4.6 0.7 1.0
CZ J:ARG42 4.7 0.5 1.0
O J:ARG42 4.8 0.4 1.0
N J:CYS44 4.8 0.3 1.0
C J:CYS10 4.8 0.9 1.0
C J:SER9 4.9 0.6 1.0
CE J:MET48 5.0 0.9 1.0
C J:CYS7 5.0 0.5 1.0

Zinc binding site 8 out of 16 in 5x4z

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Zinc binding site 8 out of 16 in the Rna Polymerase II From Komagataella Pastoris (Type-1 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-1 Crystal) within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:0.4
occ:1.00
 SG L:CYS36 2.5 0.3 1.0
SG L:CYS50 2.6 0.9 1.0
CB L:CYS50 2.7 0.0 1.0
CB L:CYS53 3.1 0.4 1.0
SG L:CYS33 3.1 0.2 1.0
O L:CYS53 3.7 0.2 1.0
CB L:CYS33 3.7 0.1 1.0
SG L:CYS53 3.7 0.4 1.0
N L:CYS53 3.8 0.7 1.0
CA L:CYS53 3.8 0.3 1.0
CA L:CYS50 4.1 0.1 1.0
C L:CYS53 4.2 0.3 1.0
CB L:CYS36 4.3 0.7 1.0
C L:CYS50 4.5 0.7 1.0
C L:GLU52 4.6 0.9 1.0
O L:CYS36 4.6 0.0 1.0
N L:LYS51 4.7 0.4 1.0
N L:GLU52 4.9 0.8 1.0
N L:CYS50 4.9 0.1 1.0
CG L:HIS38 5.0 1.0 1.0
CB L:GLU52 5.0 0.2 1.0

Zinc binding site 9 out of 16 in 5x4z

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Zinc binding site 9 out of 16 in the Rna Polymerase II From Komagataella Pastoris (Type-1 Crystal)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Rna Polymerase II From Komagataella Pastoris (Type-1 Crystal) within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn1801

b:0.6
occ:1.00
 SG M:CYS148 2.6 0.8 1.0
CB M:CYS110 2.6 0.1 1.0
SG M:CYS110 2.9 0.4 1.0
SG M:CYS107 2.9 0.9 1.0
SG M:CYS168 3.1 0.6 1.0
O M:GLY167 3.5 0.8 1.0
CB M:CYS107 3.5 0.3 1.0
O M:CYS168 3.5 0.1 1.0
CB M:CYS148 3.6 0.9 1.0
O M:MET108 3.7 0.9 1.0
CA M:CYS110 4.0 0.3 1.0
N M:CYS110 4.3 0.9 1.0
N M:GLY111 4.4 0.8 1.0
C M:CYS168 4.6 0.8 1.0
CB M:CYS168 4.7 1.0 1.0
C M:GLY167 4.7 0.4 1.0
C M:CYS110 4.7 0.5 1.0
C M:CYS107 4.7 0.8 1.0
CA M:CYS107 4.8 0.6 1.0
C M:MET108 4.8 0.3 1.0
O M:CYS107 4.9 0.9 1.0
N M:MET108 5.0 0.9 1.0
CA M:CYS148 5.0 0.8 1.0

Zinc binding site 10 out of 16 in 5x4z

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Zinc binding site 10 out of 16 in the Rna Polymerase II From Komagataella Pastoris (Type-1 Crystal)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Rna Polymerase II From Komagataella Pastoris (Type-1 Crystal) within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn1802

b:0.6
occ:1.00
 NE2 M:HIS80 2.1 0.7 1.0
SG M:CYS70 2.9 0.0 1.0
CD2 M:HIS80 2.9 0.6 1.0
SG M:CYS77 3.0 0.5 1.0
SG M:CYS67 3.1 0.5 1.0
CE1 M:HIS80 3.3 0.3 1.0
CB M:CYS77 3.6 0.9 1.0
O M:CYS70 3.9 0.2 1.0
CB M:CYS70 4.0 0.4 1.0
CG M:HIS80 4.1 0.1 1.0
CA M:CYS77 4.3 0.8 1.0
O M:PRO78 4.3 0.7 1.0
ND1 M:HIS80 4.3 0.6 1.0
O M:CYS67 4.4 0.7 1.0
CB M:CYS67 4.6 0.7 1.0
C M:CYS70 4.7 0.1 1.0
O M:GLY71 4.8 0.3 1.0
C M:CYS77 4.8 0.8 1.0
CA M:CYS70 5.0 0.3 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 14:48:30 2024

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