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

The structure of The Complete Structure of the Archaeal 13-Subunit Dna-Directed Rna Polymerase, PDB code: 2waq 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)	42.78 / 3.35
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	193.501, 212.620, 128.998, 90.00, 90.00, 90.00
R / Rfree (%)	27.1 / 34.1

The structure of The Complete Structure of the Archaeal 13-Subunit Dna-Directed Rna Polymerase also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Iron	(Fe)	3 atoms

The binding sites of Zinc atom in the The Complete Structure of the Archaeal 13-Subunit Dna-Directed Rna Polymerase (pdb code 2waq). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the The Complete Structure of the Archaeal 13-Subunit Dna-Directed Rna Polymerase, PDB code: 2waq:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 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 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:Zn1300 b:58.7 occ:1.00 NE2 A:HIS71 2.1 87.0 1.0 SG A:CYS68 2.3 90.6 1.0 SG A:CYS58 2.5 0.8 1.0 O A:CYS68 2.7 89.5 1.0 SG A:CYS61 2.8 0.8 1.0 CE1 A:HIS71 3.0 87.5 1.0 CD2 A:HIS71 3.0 87.0 1.0 CB A:CYS58 3.1 0.7 1.0 CB A:CYS68 3.3 89.8 1.0 C A:CYS68 3.5 89.3 1.0 CA A:CYS68 3.9 89.3 1.0 ND1 A:HIS71 4.1 87.8 1.0 CG A:HIS71 4.1 87.5 1.0 CA A:GLY50 4.2 91.9 1.0 CG2 A:THR60 4.4 0.6 1.0 CB A:CYS61 4.5 0.6 1.0 N A:PRO69 4.5 83.0 1.0 CA A:CYS58 4.6 0.9 1.0 N A:GLY50 4.8 92.5 1.0 CA A:PRO69 4.9 82.9 1.0 C A:PRO69 5.0 83.4 1.0 O A:PRO69 5.0 83.7 1.0 N A:CYS61 5.0 0.8 1.0

Zinc binding site 2 out of 9 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 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:Zn1350 b:58.7 occ:1.00 SG A:CYS98 2.3 0.7 1.0 SG A:CYS101 2.6 0.9 1.0 CB A:CYS98 2.7 0.9 1.0 SG A:CYS146 2.9 0.3 1.0 O A:VAL145 3.0 0.2 1.0 C A:VAL145 3.3 0.8 1.0 N A:VAL145 3.3 0.7 1.0 CB A:CYS101 3.6 0.3 1.0 CA A:VAL145 3.8 0.6 1.0 CG1 A:VAL145 3.8 0.6 1.0 CA A:CYS98 3.9 0.1 1.0 N A:CYS146 4.0 0.9 1.0 CB A:CYS146 4.2 0.8 1.0 CA A:CYS146 4.3 0.0 1.0 CB A:GLN144 4.4 0.6 1.0 C A:GLN144 4.4 0.6 1.0 N A:GLN144 4.5 0.5 1.0 CB A:VAL145 4.5 0.5 1.0 O A:GLY102 4.6 0.2 1.0 CA A:GLN144 4.6 0.5 1.0 O A:CYS98 4.7 0.5 1.0 O A:LYS142 4.8 0.4 1.0 C A:CYS98 4.8 0.3 1.0 CA A:CYS101 4.8 0.3 1.0 N A:CYS101 4.9 0.6 1.0 N A:CYS98 4.9 0.6 1.0 N A:GLY102 5.0 0.2 1.0

Zinc binding site 3 out of 9 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 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 A:Zn1360 b:58.7 occ:1.00 OE2 C:GLU80 2.0 50.2 1.0 CD2 A:HIS426 2.7 45.2 1.0 NE2 A:HIS426 2.7 45.4 1.0 CG A:HIS426 2.7 45.2 1.0 CD C:GLU80 2.7 50.4 1.0 ND1 A:HIS426 2.8 45.3 1.0 CE1 A:HIS426 2.8 45.5 1.0 OE1 C:GLU80 2.9 50.6 1.0 CB A:HIS426 3.6 45.0 1.0 CG2 A:THR488 4.1 42.9 1.0 CG C:GLU80 4.2 50.4 1.0 NE A:ARG490 4.3 45.5 1.0 NH2 A:ARG490 4.3 45.3 1.0 CB A:ARG490 4.3 45.5 1.0 CZ A:ARG490 4.4 45.4 1.0 CD1 A:ILE495 4.4 41.4 1.0 CA A:HIS426 4.9 45.1 1.0 CD A:ARG490 5.0 45.7 1.0

Zinc binding site 4 out of 9 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 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 B:Zn1300 b:62.1 occ:1.00 SG B:CYS1064 2.1 89.5 1.0 SG B:CYS1067 2.4 85.8 1.0 CB B:CYS1064 3.2 88.4 1.0 SG B:CYS1082 3.3 95.0 1.0 CB B:CYS1067 3.7 86.2 1.0 CG1 B:ILE1084 3.8 93.8 1.0 OG B:SER1089 3.9 96.5 1.0 N B:CYS1067 4.0 86.4 1.0 CB B:ILE1084 4.0 94.3 1.0 CA B:CYS1067 4.4 86.1 1.0 CB B:CYS1082 4.5 94.0 1.0 O B:TYR1069 4.5 80.6 1.0 CA B:CYS1064 4.6 88.0 1.0 N B:GLY1068 4.7 82.3 1.0 CB B:GLN1066 4.8 93.3 1.0 CG2 B:ILE1084 4.8 95.2 1.0 N B:GLN1066 5.0 92.0 1.0

Zinc binding site 5 out of 9 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 B:Zn1400 b:62.1 occ:1.00 ND1 B:HIS570 2.2 86.0 1.0 NH2 B:ARG174 3.0 87.4 1.0 CG B:HIS570 3.1 86.1 1.0 CE1 B:HIS570 3.1 86.2 1.0 OE1 B:GLU622 3.1 76.8 1.0 CZ B:ARG174 3.2 87.0 1.0 NH1 B:ARG174 3.4 86.9 1.0 CB B:HIS570 3.4 85.9 1.0 NE B:ARG174 3.9 86.9 1.0 OD1 B:ASN572 3.9 81.3 1.0 NE2 B:HIS570 4.0 86.5 1.0 CD2 B:HIS570 4.1 86.4 1.0 N B:GLY527 4.2 88.3 1.0 CG2 B:ILE524 4.3 91.5 1.0 CD B:GLU622 4.4 76.7 1.0 CA B:GLY527 4.6 88.5 1.0 CA B:HIS570 4.6 86.8 1.0 CD B:ARG174 4.8 86.6 1.0 CG B:ASN572 4.8 80.7 1.0 ND2 B:ASN572 4.9 80.2 1.0 CB B:ILE524 4.9 92.4 1.0

Zinc binding site 6 out of 9 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 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 B:Zn1500 b:62.1 occ:1.00 NE2 B:HIS696 2.9 50.8 1.0 CD2 B:HIS696 3.4 51.0 1.0 ND1 B:HIS997 3.6 46.7 1.0 CD B:ARG694 3.7 50.7 1.0 CG B:HIS997 3.8 47.0 1.0 CB B:HIS997 3.8 47.2 1.0 CE1 B:HIS696 4.0 50.9 1.0 CG B:ARG694 4.1 51.0 1.0 CE1 B:HIS997 4.3 46.6 1.0 CD2 B:HIS997 4.5 47.0 1.0 CG B:HIS696 4.7 51.3 1.0 CE1 B:PHE757 4.7 51.3 1.0 NE2 B:HIS997 4.8 46.8 1.0 CB B:ARG694 4.8 51.2 1.0 CG2 B:THR420 4.8 50.9 1.0 NE B:ARG694 4.9 50.6 1.0 ND1 B:HIS696 5.0 51.2 1.0

Zinc binding site 7 out of 9 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 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 C:Zn1000 b:58.6 occ:1.00 NE2 C:HIS353 1.9 75.6 1.0 CE1 C:HIS353 2.8 76.1 1.0 CD2 C:HIS353 2.9 75.3 1.0 OE2 C:GLU348 3.2 70.2 1.0 OE1 C:GLU348 3.8 70.2 1.0 CD C:GLU348 3.8 69.9 1.0 ND1 C:HIS353 3.9 76.2 1.0 CG C:HIS353 4.0 75.7 1.0 CB C:ARG331 4.8 70.3 1.0 O C:ARG331 4.8 71.7 1.0

Zinc binding site 8 out of 9 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 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 N:Zn100 b:63.1 occ:1.00 SG N:CYS10 2.1 66.6 1.0 SG N:CYS7 2.3 64.4 1.0 SG N:CYS45 2.4 67.1 1.0 SG N:CYS44 2.6 64.0 1.0 N N:CYS45 2.7 65.9 1.0 CB N:CYS10 2.8 66.5 1.0 CA N:CYS45 3.0 66.3 1.0 N N:CYS10 3.0 64.9 1.0 CB N:CYS45 3.1 67.1 1.0 C N:CYS44 3.1 63.4 1.0 CB N:CYS7 3.3 65.1 1.0 CB N:CYS44 3.3 63.0 1.0 CA N:CYS10 3.5 65.7 1.0 O N:CYS44 3.6 62.9 1.0 CA N:CYS44 3.8 63.1 1.0 CB N:THR9 3.9 61.0 1.0 C N:THR9 4.1 61.7 1.0 CA N:THR9 4.4 61.0 1.0 C N:CYS45 4.5 66.6 1.0 N N:THR9 4.5 61.0 1.0 N N:GLY11 4.6 67.4 1.0 C N:CYS10 4.6 66.1 1.0 NH2 N:ARG47 4.6 62.1 1.0 CG2 N:THR9 4.6 60.8 1.0 N N:CYS44 4.7 63.8 1.0 CA N:CYS7 4.7 64.7 1.0 NE N:ARG42 4.7 70.5 1.0 OG1 N:THR9 4.8 60.6 1.0 C N:CYS7 4.9 64.1 1.0

Zinc binding site 9 out of 9 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 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 P:Zn50 b:71.1 occ:1.00 SG P:CYS29 1.6 0.1 1.0 SG P:CYS9 2.4 85.8 1.0 OG1 P:THR12 2.5 99.4 1.0 SG P:CYS26 2.7 0.2 1.0 CB P:CYS29 3.0 0.9 1.0 CB P:CYS9 3.0 86.0 1.0 O P:THR12 3.6 99.3 1.0 CB P:CYS26 3.7 0.5 1.0 CB P:THR12 3.9 100.0 1.0 CA P:CYS29 4.0 0.4 1.0 O P:TRP10 4.2 82.9 1.0 C P:THR12 4.5 99.6 1.0 CA P:CYS9 4.5 85.5 1.0 O P:TYR28 4.5 0.4 1.0 CA P:THR12 4.6 99.8 1.0 CB P:TYR31 4.8 93.3 1.0 N P:THR12 4.8 99.3 1.0 N P:TRP10 4.8 82.0 1.0 CG2 P:THR12 4.9 0.3 1.0 N P:CYS29 4.9 0.9 1.0

Y.Korkhin, U.M.Unligil, O.Littlefield, P.J.Nelson, D.I.Stuart, P.B.Sigler, S.D.Bell, N.G.Abrescia. Evolution of Complex Rna Polymerases: the Complete Archaeal Rna Polymerase Structure. Plos Biol. V. 7 00102 2009.
ISSN: ESSN 1545-7885
PubMed: 19419240
DOI: 10.1371/JOURNAL.PBIO.1000102