Atomistry » Zinc » PDB 3hjt-3hqh » 3hkz
Atomistry »
  Zinc »
    PDB 3hjt-3hqh »
      3hkz »

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

Go back to Zinc Binding Sites List in 3hkz
Zinc binding site 1 out of 10 in the The X-Ray Crystal Structure of Rna Polymerase From Archaea


Mono view


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

Go back to Zinc Binding Sites List in 3hkz
Zinc binding site 2 out of 10 in the The X-Ray Crystal Structure of Rna Polymerase From Archaea


Mono view


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

Go back to Zinc Binding Sites List in 3hkz
Zinc binding site 3 out of 10 in the The X-Ray Crystal Structure of Rna Polymerase From Archaea


Mono view


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

Go back to Zinc Binding Sites List in 3hkz
Zinc binding site 4 out of 10 in the The X-Ray Crystal Structure of Rna Polymerase From Archaea


Mono view


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

Go back to Zinc Binding Sites List in 3hkz
Zinc binding site 5 out of 10 in the The X-Ray Crystal Structure of Rna Polymerase From Archaea


Mono view


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

Go back to Zinc Binding Sites List in 3hkz
Zinc binding site 6 out of 10 in the The X-Ray Crystal Structure of Rna Polymerase From Archaea


Mono view


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

Go back to Zinc Binding Sites List in 3hkz
Zinc binding site 7 out of 10 in the The X-Ray Crystal Structure of Rna Polymerase From Archaea


Mono view


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

Go back to Zinc Binding Sites List in 3hkz
Zinc binding site 8 out of 10 in the The X-Ray Crystal Structure of Rna Polymerase From Archaea


Mono view


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

Go back to Zinc Binding Sites List in 3hkz
Zinc binding site 9 out of 10 in the The X-Ray Crystal Structure of Rna Polymerase From Archaea


Mono view


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

Go back to Zinc Binding Sites List in 3hkz
Zinc binding site 10 out of 10 in the The X-Ray Crystal Structure of Rna Polymerase From Archaea


Mono view


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: Wed Dec 16 04:24:09 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy