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Zinc in PDB 2wb1: The Complete Structure of the Archaeal 13-Subunit Dna- Directed Rna Polymerase

Protein crystallography data

The structure of The Complete Structure of the Archaeal 13-Subunit Dna- Directed Rna Polymerase, PDB code: 2wb1 was solved by Y.Korkhin, U.M.Unligil, O.Littlefield, P.J.Nelson, D.I.Stuart, P.B.Sigler, S.D.Bell, N.G.A.Abrescia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.20 / 3.52
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 196.095, 211.871, 238.905, 90.00, 90.00, 90.00
R / Rfree (%) 33.3 / 38.4

Other elements in 2wb1:

The structure of The Complete Structure of the Archaeal 13-Subunit Dna- Directed Rna Polymerase 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 Complete Structure of the Archaeal 13-Subunit Dna- Directed Rna Polymerase (pdb code 2wb1). 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 Complete Structure of the Archaeal 13-Subunit Dna- Directed Rna Polymerase, PDB code: 2wb1:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in 2wb1

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Zinc binding site 1 out of 10 in the The Complete Structure of the Archaeal 13-Subunit Dna- Directed Rna Polymerase


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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 Complete Structure of the Archaeal 13-Subunit Dna- Directed Rna Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1880

b:79.3
occ:1.00
 SG A:CYS58 1.9 0.1 1.0
SG A:CYS61 2.5 0.9 1.0
SG A:CYS68 2.6 0.0 1.0
NE2 A:HIS71 2.7 0.6 1.0
CB A:CYS58 2.9 0.6 1.0
CE1 A:HIS71 3.1 0.7 1.0
O A:CYS68 3.2 0.5 1.0
CG2 A:THR60 3.2 0.3 1.0
CB A:CYS68 3.5 0.7 1.0
N A:CYS61 3.6 0.8 1.0
CD2 A:HIS71 3.6 0.4 1.0
C A:CYS68 3.9 0.0 1.0
CB A:CYS61 3.9 0.7 1.0
N A:GLY62 4.0 0.8 1.0
ND1 A:HIS71 4.0 0.8 1.0
CA A:CYS68 4.2 0.3 1.0
CA A:CYS61 4.2 0.1 1.0
CB A:THR60 4.3 0.5 1.0
CA A:CYS58 4.3 0.6 1.0
CG A:HIS71 4.4 0.4 1.0
CA A:GLY50 4.4 0.1 1.0
OG1 A:THR60 4.5 0.3 1.0
C A:THR60 4.6 0.1 1.0
N A:THR60 4.7 0.2 1.0
C A:CYS61 4.7 0.2 1.0
CA A:THR60 4.7 0.7 1.0
C A:CYS58 4.7 0.7 1.0
O A:CYS58 4.9 0.4 1.0
N A:GLY50 5.0 0.3 1.0
N A:PRO69 5.0 0.1 1.0

Zinc binding site 2 out of 10 in 2wb1

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Zinc binding site 2 out of 10 in the The Complete Structure of the Archaeal 13-Subunit Dna- Directed Rna Polymerase


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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 Complete Structure of the Archaeal 13-Subunit Dna- Directed Rna Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1881

b:79.3
occ:1.00
 N A:GLN144 2.5 0.1 1.0
SG A:CYS146 2.7 0.8 1.0
N A:VAL145 2.9 0.6 1.0
CB A:GLN144 3.0 0.3 1.0
CA A:GLN144 3.0 0.9 1.0
O A:LYS142 3.1 0.3 1.0
CB A:ALA143 3.4 0.5 1.0
C A:GLN144 3.4 0.7 1.0
C A:ALA143 3.5 0.4 1.0
N A:CYS146 3.8 0.8 1.0
CA A:ALA143 3.9 0.5 1.0
CB A:CYS146 4.0 0.1 1.0
CA A:VAL145 4.0 0.9 1.0
C A:VAL145 4.0 0.9 1.0
C A:LYS142 4.1 0.8 1.0
N A:ALA143 4.4 0.5 1.0
CG A:GLN144 4.4 0.2 1.0
SG A:CYS98 4.5 0.5 1.0
CA A:CYS146 4.5 0.6 1.0
O A:ALA143 4.5 0.1 1.0
CB A:CYS98 4.5 0.2 1.0
O A:GLN144 4.7 0.5 1.0
O A:VAL145 4.8 0.3 1.0
OE1 A:GLN144 4.8 0.4 1.0
SG A:CYS101 5.0 0.5 1.0

Zinc binding site 3 out of 10 in 2wb1

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Zinc binding site 3 out of 10 in the The Complete Structure of the Archaeal 13-Subunit Dna- Directed Rna Polymerase


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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 Complete Structure of the Archaeal 13-Subunit Dna- Directed Rna Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2123

b:75.9
occ:1.00
 SG B:CYS1067 2.2 0.4 1.0
SG B:CYS1064 2.7 0.7 1.0
CG1 B:ILE1084 3.0 0.2 1.0
CB B:CYS1064 3.2 0.8 1.0
CB B:ILE1084 3.3 0.0 1.0
CB B:CYS1067 3.4 0.7 1.0
SG B:CYS1082 3.7 0.9 1.0
O B:TYR1069 4.0 0.1 1.0
N B:CYS1067 4.2 0.3 1.0
CG2 B:ILE1084 4.2 0.6 1.0
CA B:CYS1067 4.3 0.3 1.0
CD1 B:ILE1084 4.5 0.7 1.0
CB B:CYS1082 4.5 0.8 1.0
CA B:ILE1084 4.5 0.2 1.0
N B:ILE1084 4.6 0.8 1.0
N B:GLY1068 4.7 0.3 1.0
CA B:CYS1064 4.7 0.7 1.0
C B:CYS1067 4.9 0.6 1.0

Zinc binding site 4 out of 10 in 2wb1

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Zinc binding site 4 out of 10 in the The Complete Structure of the Archaeal 13-Subunit Dna- Directed Rna Polymerase


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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 Complete Structure of the Archaeal 13-Subunit Dna- Directed Rna Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn1065

b:83.6
occ:1.00
 N N:CYS45 2.2 91.5 1.0
SG N:CYS7 2.3 87.5 1.0
C N:CYS44 2.4 90.5 1.0
SG N:CYS44 2.6 97.7 1.0
CB N:CYS44 2.7 95.4 1.0
SG N:CYS10 2.7 94.5 1.0
CA N:CYS45 2.8 89.7 1.0
SG N:CYS45 2.9 94.9 1.0
O N:CYS44 3.0 87.8 1.0
CA N:CYS44 3.1 93.1 1.0
CB N:CYS45 3.2 91.4 1.0
N N:CYS10 3.4 95.8 1.0
CB N:CYS10 3.4 98.5 1.0
CB N:CYS7 3.6 87.8 1.0
CB N:THR9 3.6 92.5 1.0
CA N:CYS10 4.0 98.9 1.0
N N:CYS44 4.1 95.6 1.0
C N:CYS45 4.2 88.8 1.0
OG1 N:THR9 4.3 89.7 1.0
C N:THR9 4.3 95.9 1.0
CA N:THR9 4.4 92.7 1.0
CG2 N:THR9 4.4 96.3 1.0
N N:THR9 4.6 89.5 1.0
NH2 N:ARG47 4.6 84.3 1.0
O N:ARG42 4.6 96.2 1.0
N N:ARG46 4.7 89.9 1.0
CA N:CYS7 4.9 86.6 1.0

Zinc binding site 5 out of 10 in 2wb1

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Zinc binding site 5 out of 10 in the The Complete Structure of the Archaeal 13-Subunit Dna- Directed Rna Polymerase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of The Complete Structure of the Archaeal 13-Subunit Dna- Directed Rna Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Zn1065

b:81.8
occ:1.00
 SG O:CYS7 2.3 83.5 1.0
SG O:CYS10 2.3 90.6 1.0
N O:CYS45 2.3 86.0 1.0
SG O:CYS45 2.5 91.4 1.0
CA O:CYS45 2.6 86.4 1.0
C O:CYS44 2.7 83.6 1.0
SG O:CYS44 2.8 88.6 1.0
CB O:CYS45 2.9 89.4 1.0
CB O:CYS44 3.1 84.8 1.0
CB O:CYS10 3.2 92.0 1.0
O O:CYS44 3.3 81.6 1.0
CB O:CYS7 3.3 85.7 1.0
N O:CYS10 3.3 87.3 1.0
CA O:CYS44 3.5 83.6 1.0
CA O:CYS10 3.9 90.8 1.0
CB O:THR9 3.9 81.7 1.0
C O:CYS45 4.2 86.0 1.0
C O:THR9 4.4 85.7 1.0
N O:CYS44 4.5 85.4 1.0
CA O:THR9 4.5 82.4 1.0
OG1 O:THR9 4.6 78.9 1.0
CA O:CYS7 4.6 84.7 1.0
N O:THR9 4.7 81.3 1.0
O O:ARG42 4.7 89.5 1.0
CG2 O:THR9 4.7 82.5 1.0
N O:GLY11 4.8 91.7 1.0
N O:ARG46 4.8 85.5 1.0
C O:CYS10 4.9 92.6 1.0
C O:CYS7 4.9 84.1 1.0
OG O:SER12 4.9 94.0 1.0
NH2 O:ARG47 5.0 76.8 1.0
O O:CYS45 5.0 86.1 1.0

Zinc binding site 6 out of 10 in 2wb1

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Zinc binding site 6 out of 10 in the The Complete Structure of the Archaeal 13-Subunit Dna- Directed Rna Polymerase


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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 Complete Structure of the Archaeal 13-Subunit Dna- Directed Rna Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Zn1049

b:87.5
occ:1.00
 SG P:CYS29 1.4 0.6 1.0
SG P:CYS26 2.1 0.3 1.0
OG1 P:THR12 3.0 0.1 1.0
CB P:CYS29 3.2 0.8 1.0
CB P:CYS9 3.4 0.5 1.0
CB P:CYS26 3.6 0.5 1.0
SG P:CYS9 3.6 0.2 1.0
O P:THR12 3.6 0.1 1.0
O P:TYR28 3.7 0.8 1.0
OG1 P:THR14 3.9 0.4 1.0
CA P:CYS29 4.0 0.2 1.0
CB P:THR12 4.1 0.1 1.0
C P:TYR28 4.3 0.6 1.0
O P:PRO27 4.3 0.8 1.0
N P:CYS29 4.5 0.9 1.0
CB P:THR14 4.6 0.2 1.0
C P:THR12 4.7 0.3 1.0
CA P:CYS26 4.8 0.6 1.0
C P:CYS26 4.9 0.2 1.0
CA P:CYS9 4.9 97.5 1.0
CA P:THR12 5.0 0.6 1.0

Zinc binding site 7 out of 10 in 2wb1

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Zinc binding site 7 out of 10 in the The Complete Structure of the Archaeal 13-Subunit Dna- Directed Rna Polymerase


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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 Complete Structure of the Archaeal 13-Subunit Dna- Directed Rna Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Zn2123

b:76.8
occ:1.00
 SG R:CYS1082 2.6 0.9 1.0
CB R:ILE1084 2.7 0.3 1.0
CG1 R:ILE1084 2.9 0.2 1.0
SG R:CYS1064 3.1 0.2 1.0
CB R:CYS1064 3.4 0.5 1.0
SG R:CYS1067 3.4 0.3 1.0
CA R:ILE1084 3.7 0.0 1.0
CB R:CYS1082 3.7 0.1 1.0
N R:ILE1084 3.7 0.6 1.0
CG2 R:ILE1084 3.8 0.9 1.0
C R:ILE1084 4.4 0.1 1.0
CD1 R:ILE1084 4.4 0.8 1.0
O R:TYR1069 4.5 0.2 1.0
CB R:CYS1067 4.5 0.7 1.0
N R:HIS1085 4.8 0.5 1.0
C R:PRO1083 4.9 0.1 1.0
O R:ILE1084 4.9 0.4 1.0
CA R:CYS1064 4.9 0.2 1.0
CA R:CYS1082 5.0 0.8 1.0
N R:PRO1083 5.0 0.8 1.0

Zinc binding site 8 out of 10 in 2wb1

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Zinc binding site 8 out of 10 in the The Complete Structure of the Archaeal 13-Subunit Dna- Directed Rna Polymerase


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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 Complete Structure of the Archaeal 13-Subunit Dna- Directed Rna Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
W:Zn1880

b:81.1
occ:1.00
 NE2 W:HIS71 1.7 0.8 1.0
O W:CYS68 2.4 0.2 1.0
CE1 W:HIS71 2.5 0.3 1.0
CD2 W:HIS71 2.6 0.8 1.0
SG W:CYS58 2.8 0.6 1.0
SG W:CYS68 3.1 1.0 1.0
C W:CYS68 3.2 99.7 1.0
SG W:CYS61 3.2 0.2 1.0
ND1 W:HIS71 3.5 0.4 1.0
CG2 W:THR60 3.6 0.1 1.0
CG W:HIS71 3.6 0.6 1.0
CB W:CYS68 3.6 0.1 1.0
CA W:GLY50 3.8 0.2 1.0
CA W:CYS68 3.8 99.8 1.0
CB W:CYS58 3.9 0.6 1.0
N W:PRO69 4.0 97.9 1.0
CA W:PRO69 4.3 97.7 1.0
N W:GLY50 4.4 0.2 1.0
C W:PRO69 4.6 98.4 1.0
N W:CYS61 4.6 0.6 1.0
CB W:CYS61 4.7 0.3 1.0
O W:PRO69 4.8 98.5 1.0
CB W:THR60 4.8 0.8 1.0
C W:GLY50 4.8 0.2 1.0
OG1 W:THR60 4.8 0.4 1.0
N W:VAL51 4.9 0.7 1.0
CB W:HIS71 5.0 0.5 1.0

Zinc binding site 9 out of 10 in 2wb1

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Zinc binding site 9 out of 10 in the The Complete Structure of the Archaeal 13-Subunit Dna- Directed Rna Polymerase


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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 Complete Structure of the Archaeal 13-Subunit Dna- Directed Rna Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
W:Zn1881

b:81.1
occ:1.00
 SG W:CYS146 2.9 0.7 1.0
SG W:CYS98 3.0 0.0 1.0
SG W:CYS101 3.0 0.5 1.0
N W:VAL145 3.3 0.9 1.0
CB W:CYS98 3.4 0.1 1.0
CB W:GLN144 3.6 0.2 1.0
C W:VAL145 3.9 0.6 1.0
CB W:CYS101 4.0 0.2 1.0
CG1 W:VAL145 4.1 0.9 1.0
N W:CYS146 4.1 0.9 1.0
CA W:VAL145 4.1 0.1 1.0
CA W:GLN144 4.2 0.9 1.0
C W:GLN144 4.2 0.5 1.0
O W:VAL145 4.2 0.1 1.0
N W:GLN144 4.2 0.6 1.0
CB W:CYS146 4.4 0.1 1.0
CA W:CYS146 4.6 0.2 1.0
CA W:CYS98 4.6 0.0 1.0
CG W:GLN144 4.7 0.7 1.0
CB W:VAL145 4.7 0.5 1.0
O W:GLY102 4.7 0.7 1.0
OE1 W:GLN144 4.8 0.3 1.0
O W:LYS142 4.9 0.1 1.0

Zinc binding site 10 out of 10 in 2wb1

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Zinc binding site 10 out of 10 in the The Complete Structure of the Archaeal 13-Subunit Dna- Directed Rna Polymerase


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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 Complete Structure of the Archaeal 13-Subunit Dna- Directed Rna Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Zn1049

b:91.7
occ:1.00
 SG X:CYS29 1.7 0.1 1.0
OG1 X:THR12 1.9 0.8 1.0
SG X:CYS9 2.7 0.1 1.0
SG X:CYS26 3.1 0.3 1.0
CB X:CYS9 3.1 0.1 1.0
O X:THR12 3.2 0.3 1.0
CB X:THR12 3.3 0.9 1.0
CB X:CYS29 3.4 0.8 1.0
C X:THR12 4.0 0.5 1.0
CA X:THR12 4.1 0.0 1.0
CA X:CYS29 4.1 1.0 1.0
O X:TYR28 4.1 0.1 1.0
OG1 X:THR14 4.2 0.9 1.0
CG2 X:THR12 4.3 0.3 1.0
CB X:CYS26 4.3 0.5 1.0
N X:THR12 4.4 0.6 1.0
CA X:CYS9 4.5 99.9 1.0
O X:TRP10 4.6 0.5 1.0
C X:TYR28 4.9 0.5 1.0
N X:CYS29 4.9 0.3 1.0
C X:CYS9 4.9 0.0 1.0

Reference:

Y.Korkhin, U.M.Unligil, O.Littlefield, P.J.Nelson, D.I.Stuart, P.B.Sigler, S.D.Bell, N.G.A.Abrescia. Evolution of Complex Rna Polymerase: the Complete Archaeal Rna Polymerase Structure Plos Biol. V. 7 E102 2009.
ISSN: ISSN 1544-9173
PubMed: 19419240
DOI: 10.1371/JOURNAL.PBIO.1000102
Page generated: Thu Oct 17 04:49:31 2024

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