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Zinc in PDB 3hkz: The X-Ray Crystal Structure of Rna Polymerase From Archaea

Enzymatic activity of The X-Ray Crystal Structure of Rna Polymerase From Archaea

All present enzymatic activity of The X-Ray Crystal Structure of Rna Polymerase From Archaea:
2.7.7.6;

Protein crystallography data

The structure of The X-Ray Crystal Structure of Rna Polymerase From Archaea, PDB code: 3hkz was solved by K.S.Murakami, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 3.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 125.820, 201.235, 196.050, 90.00, 100.92, 90.00
R / Rfree (%) 26.5 / 34.1

Other elements in 3hkz:

The structure of The X-Ray Crystal Structure of Rna Polymerase From Archaea also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Iron (Fe) 6 atoms

Zinc Binding Sites:

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

Zinc binding site 1 out of 10 in 3hkz

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Zinc binding site 1 out of 10 in the The X-Ray Crystal Structure of Rna Polymerase From Archaea


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The X-Ray Crystal Structure of Rna Polymerase From Archaea within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:46.7
occ:1.00
 SG A:CYS68 2.0 79.4 1.0
NE2 A:HIS71 2.3 74.6 1.0
OD1 A:ASN63 2.4 95.8 1.0
CE1 A:HIS71 2.5 74.9 1.0
SG A:CYS58 2.5 90.2 1.0
CB A:CYS68 3.3 75.5 1.0
CD A:PRO59 3.4 0.7 1.0
CD2 A:HIS71 3.5 76.2 1.0
CG A:ASN63 3.6 97.0 1.0
CA A:CYS68 3.6 74.6 1.0
ND1 A:HIS71 3.7 75.8 1.0
CD2 B:TYR1070 3.8 0.4 1.0
CB A:CYS61 3.9 0.4 1.0
CB A:CYS58 3.9 95.2 1.0
SG A:CYS61 4.0 0.9 1.0
CG A:PRO59 4.1 0.6 1.0
CD A:PRO69 4.1 72.1 1.0
CG A:HIS71 4.2 77.7 1.0
CB A:ASN63 4.4 98.0 1.0
C A:CYS68 4.5 73.2 1.0
CE2 B:TYR1070 4.5 0.2 1.0
ND2 A:ASN63 4.5 96.0 1.0
N A:PRO69 4.6 72.5 1.0
CB B:TYR1070 4.6 0.2 1.0
CG B:TYR1070 4.6 0.3 1.0
N A:PRO59 4.8 0.4 1.0
N A:CYS68 4.8 75.0 1.0
CG A:PRO69 4.9 71.5 1.0
CA B:TYR1070 5.0 0.6 1.0

Zinc binding site 2 out of 10 in 3hkz

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Zinc binding site 2 out of 10 in the The X-Ray Crystal Structure of Rna Polymerase From Archaea


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The X-Ray Crystal Structure of Rna Polymerase From Archaea within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1002

b:69.9
occ:1.00
 SG A:CYS98 2.1 89.0 1.0
SG A:CYS146 2.3 0.1 1.0
CB A:CYS98 2.5 90.2 1.0
N A:VAL145 3.1 0.8 1.0
CB A:GLN144 3.3 0.9 1.0
CA A:CYS98 3.3 90.2 1.0
N A:CYS146 3.4 0.6 1.0
SG A:CYS101 3.5 89.5 1.0
C A:VAL145 3.6 0.5 1.0
CB A:CYS146 3.6 0.7 1.0
CA A:CYS146 3.8 0.6 1.0
CA A:GLN144 3.9 0.9 1.0
CA A:VAL145 3.9 0.2 1.0
N A:GLN144 3.9 0.6 1.0
C A:GLN144 3.9 0.3 1.0
CG1 A:VAL145 3.9 0.1 1.0
O A:CYS98 4.0 90.7 1.0
C A:CYS98 4.1 90.7 1.0
CG A:GLN144 4.2 0.8 1.0
CB A:CYS101 4.3 90.7 1.0
O A:VAL145 4.3 0.5 1.0
O A:LYS142 4.3 0.5 1.0
N A:CYS98 4.4 90.2 1.0
CB A:VAL145 4.5 0.2 1.0

Zinc binding site 3 out of 10 in 3hkz

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Zinc binding site 3 out of 10 in the The X-Ray Crystal Structure of Rna Polymerase From Archaea


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The X-Ray Crystal Structure of Rna Polymerase From Archaea within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2001

b:66.6
occ:1.00
 SG B:CYS1064 1.7 93.4 1.0
SG B:CYS1079 2.4 0.8 1.0
SG B:CYS1061 2.5 79.5 1.0
CB B:CYS1061 3.1 81.2 1.0
CB B:CYS1064 3.5 92.3 1.0
CB B:ILE1081 3.5 0.9 1.0
CG1 B:ILE1081 3.8 0.1 1.0
N B:ILE1081 3.8 0.3 1.0
O B:CYS1064 3.8 91.8 1.0
CB B:CYS1079 3.9 0.9 1.0
C B:CYS1064 4.1 91.8 1.0
CA B:CYS1064 4.1 92.1 1.0
CD1 B:ILE1081 4.1 99.5 1.0
CA B:ILE1081 4.1 0.5 1.0
N B:CYS1064 4.1 92.2 1.0
O B:ILE1081 4.2 0.5 1.0
OG B:SER1086 4.3 0.5 1.0
NZ B:LYS1085 4.6 0.3 1.0
CA B:CYS1061 4.6 81.3 1.0
C B:PRO1080 4.6 0.4 1.0
C B:ILE1081 4.7 0.6 1.0
CG2 B:ILE1081 4.8 0.4 1.0
CB B:SER1086 4.9 0.7 1.0
N B:GLY1065 5.0 91.5 1.0

Zinc binding site 4 out of 10 in 3hkz

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Zinc binding site 4 out of 10 in the The X-Ray Crystal Structure of Rna Polymerase From Archaea


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The X-Ray Crystal Structure of Rna Polymerase From Archaea within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn1001

b:56.1
occ:1.00
 SG N:CYS45 1.6 83.9 1.0
SG N:CYS44 2.5 91.2 1.0
SG N:CYS10 2.5 77.8 1.0
CB N:CYS10 2.6 74.9 1.0
CB N:CYS45 2.7 86.7 1.0
N N:CYS45 2.8 88.4 1.0
N N:CYS10 2.9 73.0 1.0
SG N:CYS7 2.9 64.9 1.0
C N:CYS44 3.0 89.3 1.0
CA N:CYS45 3.0 87.4 1.0
CB N:CYS44 3.1 90.2 1.0
CA N:CYS10 3.3 74.6 1.0
O N:CYS44 3.4 89.3 1.0
CA N:CYS44 3.6 90.0 1.0
CB N:CYS7 3.7 66.4 1.0
CB N:THR9 3.9 69.8 1.0
C N:THR9 4.1 71.4 1.0
C N:CYS10 4.3 74.8 1.0
N N:GLY11 4.4 75.3 1.0
CG2 N:THR9 4.5 69.7 1.0
CA N:THR9 4.5 70.2 1.0
C N:CYS45 4.5 87.6 1.0
N N:CYS44 4.6 90.5 1.0
OG1 N:THR9 4.8 69.2 1.0
N N:THR9 4.8 69.3 1.0

Zinc binding site 5 out of 10 in 3hkz

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Zinc binding site 5 out of 10 in the The X-Ray Crystal Structure of Rna Polymerase From Archaea


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of The X-Ray Crystal Structure of Rna Polymerase From Archaea within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Zn1001

b:33.8
occ:1.00
 SG P:CYS9 2.3 89.3 1.0
OG1 P:THR12 2.4 0.2 1.0
SG P:CYS29 2.5 0.5 1.0
SG P:CYS26 2.6 97.2 1.0
CB P:CYS9 2.8 88.1 1.0
CB P:CYS29 3.0 0.6 1.0
CB P:CYS26 3.6 98.9 1.0
O P:PRO27 3.7 0.5 1.0
CB P:THR12 3.8 1.0 1.0
O P:THR12 3.9 0.3 1.0
OE2 P:GLU16 4.1 0.2 1.0
CA P:CYS29 4.2 0.6 1.0
O P:TRP10 4.2 97.7 1.0
N P:CYS29 4.3 0.8 1.0
CA P:CYS9 4.3 88.2 1.0
CD P:PRO27 4.4 0.9 1.0
CG2 P:THR12 4.5 0.9 1.0
CG P:PRO27 4.7 0.3 1.0
CA P:THR12 4.7 0.6 1.0
N P:PRO27 4.7 0.7 1.0
C P:PRO27 4.8 0.4 1.0
C P:THR12 4.8 100.0 1.0
N P:THR12 4.8 0.8 1.0
CB P:THR14 4.9 97.5 1.0
O P:CYS29 4.9 0.7 1.0
OG1 P:THR14 5.0 97.4 1.0
CA P:CYS26 5.0 99.2 1.0
C P:CYS9 5.0 90.4 1.0

Zinc binding site 6 out of 10 in 3hkz

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Zinc binding site 6 out of 10 in the The X-Ray Crystal Structure of Rna Polymerase From Archaea


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of The X-Ray Crystal Structure of Rna Polymerase From Archaea within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1001

b:57.1
occ:1.00
 OD1 I:ASN63 2.4 95.8 1.0
CE1 I:HIS71 2.5 74.8 1.0
NE2 I:HIS71 2.6 74.7 1.0
SG I:CYS68 2.8 79.5 1.0
SG I:CYS58 3.3 90.4 1.0
CD2 J:TYR1070 3.4 0.5 1.0
SG I:CYS61 3.5 0.0 1.0
CB I:CYS61 3.6 0.4 1.0
CG I:ASN63 3.6 97.0 1.0
ND1 I:HIS71 3.6 75.7 1.0
CD I:PRO59 3.7 0.5 1.0
CD2 I:HIS71 3.8 76.3 1.0
CB I:CYS68 3.9 75.6 1.0
CB J:TYR1070 4.0 0.3 1.0
CA I:CYS68 4.0 74.7 1.0
CD I:PRO69 4.0 72.1 1.0
CG J:TYR1070 4.1 0.3 1.0
CG I:PRO59 4.2 0.5 1.0
CE2 J:TYR1070 4.3 0.1 1.0
CG I:HIS71 4.3 77.7 1.0
ND2 I:ASN63 4.3 96.0 1.0
CA J:TYR1070 4.4 0.7 1.0
CB I:CYS58 4.6 95.2 1.0
CB I:ASN63 4.6 97.9 1.0
N I:PRO69 4.7 72.5 1.0
CG I:PRO69 4.7 71.5 1.0
C I:CYS68 4.8 73.2 1.0

Zinc binding site 7 out of 10 in 3hkz

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Zinc binding site 7 out of 10 in the The X-Ray Crystal Structure of Rna Polymerase From Archaea


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of The X-Ray Crystal Structure of Rna Polymerase From Archaea within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1002

b:78.7
occ:1.00
 SG I:CYS98 2.5 89.0 1.0
SG I:CYS146 2.6 0.0 1.0
CB I:CYS98 2.7 90.2 1.0
CB I:GLN144 2.9 0.9 1.0
N I:VAL145 3.0 0.9 1.0
CA I:CYS98 3.5 90.4 1.0
CA I:GLN144 3.5 1.0 1.0
SG I:CYS101 3.6 89.5 1.0
N I:CYS146 3.6 0.7 1.0
N I:GLN144 3.6 0.6 1.0
C I:GLN144 3.7 0.3 1.0
CG I:GLN144 3.8 0.8 1.0
C I:VAL145 3.8 0.6 1.0
CA I:VAL145 3.9 0.3 1.0
CB I:CYS146 4.0 0.6 1.0
CG1 I:VAL145 4.0 0.1 1.0
CA I:CYS146 4.2 0.6 1.0
CB I:CYS101 4.3 90.7 1.0
O I:LYS142 4.3 0.6 1.0
O I:CYS98 4.4 90.9 1.0
C I:CYS98 4.4 90.8 1.0
N I:CYS98 4.5 90.2 1.0
O I:VAL145 4.6 0.6 1.0
CB I:VAL145 4.6 0.2 1.0
O I:GLN144 4.8 0.2 1.0
C I:ALA143 4.9 0.3 1.0

Zinc binding site 8 out of 10 in 3hkz

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Zinc binding site 8 out of 10 in the The X-Ray Crystal Structure of Rna Polymerase From Archaea


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of The X-Ray Crystal Structure of Rna Polymerase From Archaea within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn2001

b:1.0
occ:1.00
 SG J:CYS1064 1.6 93.4 1.0
SG J:CYS1079 2.4 1.0 1.0
SG J:CYS1061 2.5 79.3 1.0
CB J:CYS1061 3.0 81.2 1.0
CB J:CYS1064 3.3 92.4 1.0
O J:CYS1064 3.6 91.8 1.0
CB J:ILE1081 3.7 1.0 1.0
C J:CYS1064 3.9 91.9 1.0
CA J:CYS1064 3.9 92.2 1.0
CG1 J:ILE1081 3.9 0.1 1.0
N J:ILE1081 4.0 0.3 1.0
CB J:CYS1079 4.0 0.1 1.0
N J:CYS1064 4.0 92.2 1.0
CD1 J:ILE1081 4.3 99.5 1.0
CA J:ILE1081 4.3 0.5 1.0
OG J:SER1086 4.3 0.7 1.0
O J:ILE1081 4.4 0.5 1.0
CA J:CYS1061 4.5 81.4 1.0
N J:GLY1065 4.7 91.5 1.0
NZ J:LYS1085 4.7 0.3 1.0
C J:PRO1080 4.8 0.4 1.0
C J:ILE1081 4.9 0.6 1.0
CG2 J:ILE1081 5.0 0.3 1.0
CB J:SER1086 5.0 0.7 1.0

Zinc binding site 9 out of 10 in 3hkz

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Zinc binding site 9 out of 10 in the The X-Ray Crystal Structure of Rna Polymerase From Archaea


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of The X-Ray Crystal Structure of Rna Polymerase From Archaea within 5.0Å range:
probe atom residue distance (Å) B Occ
W:Zn1001

b:63.9
occ:1.00
 SG W:CYS45 2.1 84.0 1.0
SG W:CYS44 2.5 91.3 1.0
C W:CYS44 2.6 89.3 1.0
CB W:CYS44 2.6 90.2 1.0
N W:CYS45 2.6 88.4 1.0
SG W:CYS7 2.8 64.7 1.0
CB W:CYS10 2.8 74.9 1.0
N W:CYS10 3.0 73.1 1.0
O W:CYS44 3.0 89.4 1.0
CB W:CYS45 3.0 86.7 1.0
SG W:CYS10 3.0 77.9 1.0
CA W:CYS45 3.0 87.4 1.0
CA W:CYS44 3.2 90.0 1.0
CA W:CYS10 3.5 74.6 1.0
CB W:THR9 3.5 69.9 1.0
CB W:CYS7 4.0 66.3 1.0
C W:THR9 4.0 71.4 1.0
CG2 W:THR9 4.0 69.8 1.0
CA W:THR9 4.2 70.2 1.0
N W:CYS44 4.3 90.5 1.0
OG1 W:THR9 4.4 69.3 1.0
C W:CYS10 4.6 74.8 1.0
C W:CYS45 4.6 87.7 1.0
N W:THR9 4.6 69.4 1.0
N W:GLY11 4.7 75.3 1.0

Zinc binding site 10 out of 10 in 3hkz

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Zinc binding site 10 out of 10 in the The X-Ray Crystal Structure of Rna Polymerase From Archaea


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of The X-Ray Crystal Structure of Rna Polymerase From Archaea within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Zn1001

b:54.9
occ:1.00
 OG1 X:THR12 2.1 0.2 1.0
SG X:CYS29 2.1 0.4 1.0
SG X:CYS9 2.3 89.0 1.0
CB X:CYS29 2.7 0.6 1.0
SG X:CYS26 2.8 97.2 1.0
CB X:CYS9 2.9 88.1 1.0
CB X:THR12 3.5 0.1 1.0
O X:PRO27 3.8 0.6 1.0
O X:TRP10 3.9 97.7 1.0
CB X:CYS26 3.9 98.9 1.0
O X:THR12 3.9 0.4 1.0
CA X:CYS29 4.0 0.6 1.0
N X:CYS29 4.2 0.8 1.0
CG2 X:THR12 4.3 0.8 1.0
CA X:CYS9 4.4 88.2 1.0
CA X:THR12 4.5 0.8 1.0
N X:THR12 4.5 0.8 1.0
OE2 X:GLU16 4.6 0.2 1.0
C X:THR12 4.7 0.1 1.0
CD X:PRO27 4.8 0.9 1.0
C X:CYS29 4.9 0.7 1.0
C X:PRO27 4.9 0.5 1.0
O X:CYS29 5.0 0.6 1.0
C X:CYS9 5.0 90.4 1.0

Reference:

A.Hirata, B.J.Klein, K.S.Murakami. The X-Ray Crystal Structure of Rna Polymerase From Archaea. Nature V. 451 851 2008.
ISSN: ISSN 0028-0836
PubMed: 18235446
DOI: 10.1038/NATURE06530
Page generated: Sat Oct 26 06:23:57 2024

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