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Zinc in PDB 2pmz: Archaeal Rna Polymerase From Sulfolobus Solfataricus

Enzymatic activity of Archaeal Rna Polymerase From Sulfolobus Solfataricus

All present enzymatic activity of Archaeal Rna Polymerase From Sulfolobus Solfataricus:
2.7.7.6;

Protein crystallography data

The structure of Archaeal Rna Polymerase From Sulfolobus Solfataricus, PDB code: 2pmz 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) 39.79 / 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 (%) 27.4 / 34.3

Other elements in 2pmz:

The structure of Archaeal Rna Polymerase From Sulfolobus Solfataricus 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 Archaeal Rna Polymerase From Sulfolobus Solfataricus (pdb code 2pmz). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Archaeal Rna Polymerase From Sulfolobus Solfataricus, PDB code: 2pmz:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 2pmz

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Zinc binding site 1 out of 8 in the Archaeal Rna Polymerase From Sulfolobus Solfataricus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Archaeal Rna Polymerase From Sulfolobus Solfataricus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1002

b:87.7
occ:1.00
OD1 A:ASN63 2.2 0.1 1.0
CE1 A:HIS71 2.6 74.2 1.0
SG A:CYS68 2.6 80.6 1.0
NE2 A:HIS71 2.7 73.6 1.0
SG A:CYS58 2.9 82.5 1.0
CG A:ASN63 3.3 0.1 1.0
CD A:PRO59 3.6 74.7 1.0
CB A:CYS68 3.8 79.3 1.0
CG A:PRO59 3.8 74.8 1.0
ND1 A:HIS71 3.8 74.1 1.0
SG A:CYS61 3.9 0.2 1.0
CB A:CYS61 3.9 0.5 1.0
CA A:CYS68 3.9 89.6 1.0
CD2 B:TYR1070 3.9 0.6 1.0
CD2 A:HIS71 4.0 73.9 1.0
CD A:PRO69 4.1 28.0 1.0
CG B:TYR1070 4.2 0.1 1.0
CE2 B:TYR1070 4.2 0.6 1.0
ND2 A:ASN63 4.2 0.1 1.0
CB A:ASN63 4.3 0.6 1.0
CG A:HIS71 4.6 74.0 1.0
CB A:CYS58 4.6 84.3 1.0
OD1 B:ASP1071 4.6 0.2 1.0
C A:CYS68 4.6 89.0 1.0
CG A:PRO69 4.7 27.6 1.0
N A:PRO69 4.7 57.0 1.0
CB B:TYR1070 4.7 0.7 1.0
CD1 B:TYR1070 4.7 0.9 1.0
CZ B:TYR1070 4.7 0.9 1.0
N A:PRO59 4.8 0.4 1.0
CA B:TYR1070 4.9 0.6 1.0
CE1 B:TYR1070 4.9 0.0 1.0

Zinc binding site 2 out of 8 in 2pmz

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Zinc binding site 2 out of 8 in the Archaeal Rna Polymerase From Sulfolobus Solfataricus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Archaeal Rna Polymerase From Sulfolobus Solfataricus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2001

b:91.5
occ:1.00
SG B:CYS1061 2.8 53.7 1.0
SG B:CYS1064 2.8 73.0 1.0
SG B:CYS1079 2.8 0.3 1.0
CB B:CYS1061 3.3 54.3 1.0
CB B:ILE1081 3.4 59.8 1.0
CG1 B:ILE1081 3.5 59.8 1.0
CD1 B:ILE1081 3.5 34.9 1.0
N B:ILE1081 3.9 0.7 1.0
C B:PRO1080 4.0 73.7 1.0
O B:CYS1064 4.1 82.0 1.0
CB B:CYS1079 4.1 0.2 1.0
NZ B:LYS1085 4.1 0.1 1.0
N B:PRO1080 4.2 74.3 1.0
CA B:ILE1081 4.2 0.3 1.0
O B:PRO1080 4.3 73.8 1.0
CB B:CYS1064 4.4 72.8 1.0
CA B:PRO1080 4.4 74.0 1.0
C B:CYS1064 4.5 82.0 1.0
O B:ILE1081 4.5 1.0 1.0
N B:CYS1064 4.5 80.9 1.0
C B:CYS1079 4.5 0.2 1.0
OG B:SER1086 4.6 83.8 1.0
CB B:PRO1080 4.6 92.9 1.0
CG2 B:ILE1081 4.6 59.5 1.0
CD B:PRO1080 4.7 93.0 1.0
CA B:CYS1061 4.7 58.1 1.0
CA B:CYS1064 4.7 81.5 1.0
C B:ILE1081 4.8 0.0 1.0
CE B:LYS1085 4.9 0.9 1.0
CA B:CYS1079 5.0 0.3 1.0

Zinc binding site 3 out of 8 in 2pmz

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Zinc binding site 3 out of 8 in the Archaeal Rna Polymerase From Sulfolobus Solfataricus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Archaeal Rna Polymerase From Sulfolobus Solfataricus within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn1001

b:93.9
occ:1.00
CB N:CYS10 2.4 72.4 1.0
SG N:CYS45 2.5 63.0 1.0
N N:CYS45 2.6 75.8 1.0
N N:CYS10 2.6 0.9 1.0
C N:CYS44 2.7 0.3 1.0
SG N:CYS44 2.7 0.3 1.0
CB N:CYS44 2.8 0.9 1.0
CA N:CYS45 3.0 75.1 1.0
CB N:CYS45 3.0 63.1 1.0
SG N:CYS7 3.0 86.2 1.0
SG N:CYS10 3.0 71.9 1.0
CA N:CYS10 3.1 0.9 1.0
O N:CYS44 3.1 0.3 1.0
CA N:CYS44 3.3 0.9 1.0
CB N:THR9 3.6 72.2 1.0
C N:THR9 3.8 66.5 1.0
CB N:CYS7 4.0 86.1 1.0
CA N:THR9 4.2 65.6 1.0
C N:CYS10 4.2 0.7 1.0
N N:GLY11 4.3 90.2 1.0
CG2 N:THR9 4.4 72.0 1.0
N N:CYS44 4.4 0.8 1.0
OG1 N:THR9 4.5 71.8 1.0
C N:CYS45 4.5 74.6 1.0
N N:THR9 4.6 64.9 1.0
O N:THR9 4.8 66.7 1.0
O N:CYS7 4.9 46.6 1.0

Zinc binding site 4 out of 8 in 2pmz

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Zinc binding site 4 out of 8 in the Archaeal Rna Polymerase From Sulfolobus Solfataricus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Archaeal Rna Polymerase From Sulfolobus Solfataricus within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Zn1001

b:0.4
occ:1.00
OG1 P:THR12 2.4 0.7 1.0
SG P:CYS29 2.5 0.1 1.0
SG P:CYS9 2.6 0.8 1.0
CB P:CYS9 2.7 0.6 1.0
CB P:CYS29 2.7 0.5 1.0
SG P:CYS26 2.8 89.9 1.0
O P:PRO27 3.6 87.5 1.0
CB P:THR12 3.7 0.8 1.0
O P:THR12 4.0 0.8 1.0
CA P:CYS29 4.0 93.9 1.0
CB P:CYS26 4.2 90.2 1.0
N P:CYS29 4.2 94.4 1.0
CA P:CYS9 4.3 63.8 1.0
CG P:PRO27 4.3 1.0 1.0
OE2 P:GLU16 4.3 0.8 1.0
CG2 P:THR12 4.5 0.0 1.0
CD P:PRO27 4.6 0.9 1.0
C P:PRO27 4.7 87.4 1.0
O P:TRP10 4.7 0.5 1.0
N P:PRO27 4.7 86.7 1.0
CA P:THR12 4.8 0.2 1.0
O P:CYS29 4.8 93.3 1.0
C P:THR12 4.8 0.7 1.0
CB P:THR14 4.9 0.4 1.0
N P:CYS9 4.9 63.7 1.0
C P:CYS29 4.9 93.3 1.0
OG1 P:THR14 4.9 0.6 1.0
C P:CYS9 5.0 63.8 1.0

Zinc binding site 5 out of 8 in 2pmz

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Zinc binding site 5 out of 8 in the Archaeal Rna Polymerase From Sulfolobus Solfataricus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Archaeal Rna Polymerase From Sulfolobus Solfataricus within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Zn1002

b:89.3
occ:1.00
OD1 Q:ASN63 2.2 70.9 1.0
CE1 Q:HIS71 2.5 79.6 1.0
NE2 Q:HIS71 2.8 79.2 1.0
SG Q:CYS68 2.8 0.5 1.0
SG Q:CYS58 3.2 97.0 1.0
CG Q:ASN63 3.4 71.2 1.0
ND1 Q:HIS71 3.7 79.5 1.0
CD Q:PRO59 3.7 0.9 1.0
CD2 R:TYR1070 3.9 0.5 1.0
CG Q:PRO59 3.9 0.1 1.0
SG Q:CYS61 3.9 0.4 1.0
CB Q:CYS61 4.0 0.5 1.0
CB Q:CYS68 4.0 0.4 1.0
CA Q:CYS68 4.0 72.6 1.0
CD Q:PRO69 4.0 57.8 1.0
CD2 Q:HIS71 4.0 79.3 1.0
CG R:TYR1070 4.2 1.0 1.0
CE2 R:TYR1070 4.2 0.4 1.0
ND2 Q:ASN63 4.2 70.4 1.0
CB Q:ASN63 4.5 71.8 1.0
CG Q:PRO69 4.5 57.5 1.0
CG Q:HIS71 4.5 79.5 1.0
OD1 R:ASP1071 4.5 0.8 1.0
CB R:TYR1070 4.6 0.3 1.0
N Q:PRO69 4.6 62.2 1.0
C Q:CYS68 4.7 71.8 1.0
CD1 R:TYR1070 4.7 0.8 1.0
CZ R:TYR1070 4.7 0.8 1.0
CB Q:CYS58 4.8 98.8 1.0
CA R:TYR1070 4.8 88.5 1.0
CE1 R:TYR1070 4.9 1.0 1.0
N Q:PRO59 5.0 0.7 1.0

Zinc binding site 6 out of 8 in 2pmz

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Zinc binding site 6 out of 8 in the Archaeal Rna Polymerase From Sulfolobus Solfataricus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Archaeal Rna Polymerase From Sulfolobus Solfataricus within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Zn2001

b:0.0
occ:1.00
SG R:CYS1064 2.6 0.5 1.0
SG R:CYS1061 2.7 62.0 1.0
SG R:CYS1079 3.1 0.3 1.0
CB R:CYS1061 3.2 62.6 1.0
CB R:ILE1081 3.5 80.2 1.0
CD1 R:ILE1081 3.5 54.7 1.0
CG1 R:ILE1081 3.5 80.3 1.0
O R:CYS1064 3.9 0.6 1.0
N R:ILE1081 4.0 1.0 1.0
NZ R:LYS1085 4.1 0.0 1.0
C R:PRO1080 4.1 79.5 1.0
CB R:CYS1064 4.2 0.3 1.0
CB R:CYS1079 4.2 0.1 1.0
CA R:ILE1081 4.3 0.6 1.0
C R:CYS1064 4.3 0.5 1.0
N R:PRO1080 4.4 80.0 1.0
N R:CYS1064 4.4 0.5 1.0
O R:PRO1080 4.4 79.5 1.0
CA R:CYS1064 4.5 0.1 1.0
OG R:SER1086 4.6 0.1 1.0
CA R:PRO1080 4.6 79.8 1.0
CG2 R:ILE1081 4.6 80.3 1.0
O R:ILE1081 4.6 0.1 1.0
CA R:CYS1061 4.7 97.0 1.0
CB R:PRO1080 4.7 0.1 1.0
C R:CYS1079 4.7 0.6 1.0
CD R:PRO1080 4.8 0.3 1.0
CE R:LYS1085 4.8 0.2 1.0
C R:ILE1081 4.9 0.3 1.0

Zinc binding site 7 out of 8 in 2pmz

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Zinc binding site 7 out of 8 in the Archaeal Rna Polymerase From Sulfolobus Solfataricus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Archaeal Rna Polymerase From Sulfolobus Solfataricus within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Zn1001

b:93.9
occ:1.00
SG Y:CYS45 2.5 99.4 1.0
N Y:CYS45 2.5 0.6 1.0
CB Y:CYS10 2.5 0.0 1.0
C Y:CYS44 2.6 0.0 1.0
N Y:CYS10 2.7 0.5 1.0
SG Y:CYS7 2.8 61.9 1.0
SG Y:CYS44 2.8 0.7 1.0
CA Y:CYS45 2.9 0.8 1.0
CB Y:CYS44 2.9 0.2 1.0
O Y:CYS44 2.9 1.0 1.0
CB Y:CYS45 3.0 99.5 1.0
SG Y:CYS10 3.1 0.6 1.0
CA Y:CYS10 3.2 0.5 1.0
CA Y:CYS44 3.3 0.6 1.0
CB Y:THR9 3.6 0.8 1.0
C Y:THR9 3.8 87.8 1.0
CB Y:CYS7 4.0 61.8 1.0
CA Y:THR9 4.2 86.9 1.0
C Y:CYS10 4.3 0.3 1.0
CG2 Y:THR9 4.3 0.7 1.0
N Y:CYS44 4.4 0.5 1.0
N Y:GLY11 4.4 86.5 1.0
C Y:CYS45 4.4 0.3 1.0
OG1 Y:THR9 4.4 0.5 1.0
N Y:THR9 4.6 86.2 1.0
O Y:CYS7 4.8 63.8 1.0
O Y:THR9 4.9 88.0 1.0

Zinc binding site 8 out of 8 in 2pmz

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Zinc binding site 8 out of 8 in the Archaeal Rna Polymerase From Sulfolobus Solfataricus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Archaeal Rna Polymerase From Sulfolobus Solfataricus within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Zn1001

b:0.8
occ:1.00
SG Z:CYS29 2.4 81.5 1.0
OG1 Z:THR12 2.5 0.0 1.0
SG Z:CYS9 2.6 0.1 1.0
CB Z:CYS29 2.6 81.0 1.0
SG Z:CYS26 2.7 86.6 1.0
CB Z:CYS9 2.8 0.9 1.0
O Z:PRO27 3.5 0.3 1.0
CB Z:THR12 3.8 0.3 1.0
CA Z:CYS29 3.9 0.3 1.0
N Z:CYS29 4.1 0.9 1.0
CB Z:CYS26 4.1 86.9 1.0
O Z:THR12 4.1 0.8 1.0
CG Z:PRO27 4.3 86.8 1.0
CA Z:CYS9 4.4 0.7 1.0
OE2 Z:GLU16 4.4 0.6 1.0
CG2 Z:THR12 4.5 0.5 1.0
C Z:PRO27 4.6 0.3 1.0
CD Z:PRO27 4.6 86.7 1.0
N Z:PRO27 4.7 0.5 1.0
O Z:TRP10 4.7 0.1 1.0
O Z:CYS29 4.7 0.6 1.0
C Z:CYS29 4.8 0.7 1.0
CA Z:THR12 4.8 0.1 1.0
C Z:THR12 4.9 0.8 1.0
CB Z:THR14 5.0 81.7 1.0
N Z:CYS9 5.0 0.6 1.0
OG1 Z:THR14 5.0 81.8 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: Wed Dec 16 03:48:40 2020

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