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Zinc in PDB 4qiw: Crystal Structure of Euryarchaeal Rna Polymerase From Thermococcus Kodakarensis

Enzymatic activity of Crystal Structure of Euryarchaeal Rna Polymerase From Thermococcus Kodakarensis

All present enzymatic activity of Crystal Structure of Euryarchaeal Rna Polymerase From Thermococcus Kodakarensis:
2.7.7.6;

Protein crystallography data

The structure of Crystal Structure of Euryarchaeal Rna Polymerase From Thermococcus Kodakarensis, PDB code: 4qiw was solved by S.-H.Jun, K.S.Murakami, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.73 / 3.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 112.975, 206.606, 365.157, 90.00, 90.00, 90.00
R / Rfree (%) 27.7 / 31.6

Other elements in 4qiw:

The structure of Crystal Structure of Euryarchaeal Rna Polymerase From Thermococcus Kodakarensis also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Zinc Binding Sites:

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

Zinc binding site 1 out of 10 in 4qiw

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Zinc binding site 1 out of 10 in the Crystal Structure of Euryarchaeal Rna Polymerase From Thermococcus Kodakarensis


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Stereo pair view

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

b:0.7
occ:1.00
 NE2 A:HIS73 2.6 0.7 1.0
CE1 A:HIS73 2.7 0.7 1.0
SG A:CYS70 2.8 0.8 1.0
SG A:CYS60 2.9 0.8 1.0
SG A:CYS63 3.4 0.5 1.0
CD2 A:HIS73 3.5 0.6 1.0
ND1 A:HIS73 3.6 0.8 1.0
O A:PRO71 3.9 0.3 1.0
CG A:HIS73 4.0 0.2 1.0
CB A:CYS60 4.1 0.4 1.0
CA A:GLY52 4.4 0.5 1.0
CB A:CYS70 4.5 0.2 1.0
CG2 A:VAL53 4.7 0.3 1.0
O A:LEU51 4.7 0.3 1.0
N A:VAL53 4.8 0.7 1.0
CB A:ALA65 4.8 0.3 1.0
O A:CYS70 4.8 1.0 1.0
C A:PRO71 4.8 0.3 1.0
C A:CYS70 4.8 0.1 1.0
O A:ALA65 4.9 0.0 1.0

Zinc binding site 2 out of 10 in 4qiw

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Zinc binding site 2 out of 10 in the Crystal Structure of Euryarchaeal Rna Polymerase From Thermococcus Kodakarensis


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A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Euryarchaeal Rna Polymerase From Thermococcus Kodakarensis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1003

b:0.7
occ:1.00
 SG A:CYS150 1.4 0.5 1.0
SG A:CYS100 1.9 0.6 1.0
CB A:CYS150 2.0 0.5 1.0
CB A:CYS103 2.0 0.8 1.0
SG A:CYS103 2.5 0.5 1.0
SG A:CYS147 2.5 0.6 1.0
N A:CYS150 2.9 0.4 1.0
CA A:CYS150 3.0 0.3 1.0
CA A:CYS103 3.2 0.9 1.0
CB A:CYS100 3.2 0.1 1.0
N A:CYS103 3.4 0.1 1.0
C A:HIS149 3.4 0.0 1.0
O A:HIS149 3.7 0.4 1.0
CB A:CYS147 4.0 0.8 1.0
O A:ARG101 4.0 0.5 1.0
C A:CYS150 4.0 0.3 1.0
CZ A:PHE155 4.0 0.5 1.0
O A:CYS150 4.1 0.3 1.0
CD A:PRO153 4.3 0.1 1.0
CA A:HIS149 4.4 0.1 1.0
C A:CYS103 4.4 0.7 1.0
C A:GLU102 4.5 1.0 1.0
CA A:CYS100 4.5 0.2 1.0
N A:HIS149 4.6 0.3 1.0
CE2 A:PHE155 4.6 0.7 1.0
C A:CYS100 4.6 0.3 1.0
N A:GLY104 4.7 0.4 1.0
C A:ARG101 4.8 0.7 1.0
O A:CYS100 4.9 0.8 1.0
CB A:HIS149 5.0 0.3 1.0
N A:ARG101 5.0 0.6 1.0

Zinc binding site 3 out of 10 in 4qiw

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Zinc binding site 3 out of 10 in the Crystal Structure of Euryarchaeal Rna Polymerase From Thermococcus Kodakarensis


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Euryarchaeal Rna Polymerase From Thermococcus Kodakarensis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1201

b:0.7
occ:1.00
 SG B:CYS1083 2.5 0.3 1.0
CB B:CYS1083 2.5 0.2 1.0
SG B:CYS1068 2.8 82.5 1.0
SG B:CYS1086 3.0 0.9 1.0
CB B:CYS1065 3.1 0.9 1.0
SG B:CYS1065 3.1 0.4 1.0
CB B:CYS1068 3.1 0.3 1.0
CA B:CYS1083 3.7 0.7 1.0
N B:CYS1086 3.8 0.2 1.0
CD B:PRO1084 3.8 0.2 1.0
N B:PRO1084 3.8 1.0 1.0
C B:CYS1083 3.9 0.1 1.0
N B:VAL1085 3.9 0.9 1.0
CG B:PRO1084 4.1 0.7 1.0
CB B:CYS1086 4.2 0.1 1.0
O B:HIS1070 4.3 0.3 1.0
CB B:VAL1085 4.4 0.3 1.0
CA B:VAL1085 4.5 0.6 1.0
CA B:CYS1065 4.6 0.7 1.0
O B:CYS1083 4.6 0.8 1.0
CA B:CYS1086 4.6 0.4 1.0
CA B:CYS1068 4.6 0.8 1.0
C B:VAL1085 4.6 0.2 1.0
C B:PRO1084 4.7 1.0 1.0
CA B:PRO1084 4.7 0.8 1.0
CG2 B:VAL1085 4.8 0.7 1.0
N B:CYS1083 4.8 0.8 1.0
O B:CYS1086 4.9 0.0 1.0
CB B:HIS1070 5.0 0.8 1.0

Zinc binding site 4 out of 10 in 4qiw

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Zinc binding site 4 out of 10 in the Crystal Structure of Euryarchaeal Rna Polymerase From Thermococcus Kodakarensis


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Euryarchaeal Rna Polymerase From Thermococcus Kodakarensis within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn1401

b:0.2
occ:1.00
 SG N:CYS45 1.9 0.0 1.0
N N:CYS45 2.1 0.4 1.0
SG N:CYS44 2.1 0.9 1.0
CB N:CYS10 2.3 0.1 1.0
CB N:CYS45 2.5 0.9 1.0
CA N:CYS45 2.6 0.2 1.0
C N:CYS44 3.0 0.3 1.0
CB N:CYS44 3.2 0.7 1.0
SG N:CYS10 3.2 0.0 1.0
CA N:CYS44 3.5 0.2 1.0
CA N:CYS10 3.5 0.6 1.0
N N:CYS10 3.7 0.3 1.0
O N:CYS44 3.8 1.0 1.0
N N:CYS44 3.9 0.6 1.0
C N:CYS45 4.0 0.3 1.0
CB N:ARG42 4.1 0.9 1.0
NE N:ARG42 4.2 0.6 1.0
SG N:CYS7 4.3 65.2 1.0
N N:ARG46 4.5 0.2 1.0
O N:ARG42 4.5 0.6 1.0
C N:ARG42 4.7 0.3 1.0
C N:TYR43 4.7 0.8 1.0
C N:CYS10 4.7 0.5 1.0
CB N:THR9 4.8 1.0 1.0
CD N:ARG42 4.8 0.3 1.0
C N:THR9 4.8 0.5 1.0
CG2 N:THR9 4.8 0.1 1.0
CA N:ARG42 5.0 0.9 1.0

Zinc binding site 5 out of 10 in 4qiw

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Zinc binding site 5 out of 10 in the Crystal Structure of Euryarchaeal Rna Polymerase From Thermococcus Kodakarensis


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Euryarchaeal Rna Polymerase From Thermococcus Kodakarensis within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Zn1501

b:0.0
occ:1.00
 OE2 P:GLU14 1.2 0.1 1.0
CD P:GLU14 1.4 0.4 1.0
SG P:CYS30 1.6 0.7 1.0
CG P:GLU14 2.0 0.8 1.0
OE1 P:GLU14 2.4 0.8 1.0
SG P:CYS11 2.7 0.5 1.0
CB P:CYS30 2.9 1.0 1.0
CB P:GLU14 3.4 0.4 1.0
O P:GLY12 3.5 0.7 1.0
C P:GLY12 3.8 0.0 1.0
N P:GLU14 3.9 0.4 1.0
N P:GLY12 4.0 0.4 1.0
C P:LYS13 4.0 0.7 1.0
CA P:GLU14 4.2 0.8 1.0
CA P:CYS30 4.2 0.6 1.0
O P:LYS13 4.2 0.8 1.0
CB P:CYS11 4.3 0.4 1.0
N P:LYS13 4.3 0.4 1.0
CA P:GLY12 4.5 0.7 1.0
C P:CYS11 4.6 0.4 1.0
CA P:LYS13 4.6 0.8 1.0
CA P:CYS11 4.8 0.4 1.0
N P:CYS30 4.8 0.9 1.0
N P:CYS11 4.9 0.5 1.0
C P:GLU14 4.9 0.4 1.0
N P:VAL15 4.9 0.4 1.0
SG P:CYS27 5.0 79.6 1.0

Zinc binding site 6 out of 10 in 4qiw

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Zinc binding site 6 out of 10 in the Crystal Structure of Euryarchaeal Rna Polymerase From Thermococcus Kodakarensis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Euryarchaeal Rna Polymerase From Thermococcus Kodakarensis within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1102

b:0.9
occ:1.00
 NE2 I:HIS73 2.6 0.6 1.0
SG I:CYS70 2.8 0.4 1.0
CE1 I:HIS73 2.8 0.2 1.0
SG I:CYS63 2.9 0.5 1.0
SG I:CYS60 2.9 0.6 1.0
CD2 I:HIS73 3.7 0.8 1.0
ND1 I:HIS73 3.8 0.5 1.0
CB I:CYS60 4.0 0.0 1.0
O I:PRO71 4.2 0.8 1.0
CB I:ALA65 4.2 0.8 1.0
CG I:HIS73 4.3 0.3 1.0
CB I:CYS63 4.5 0.1 1.0
CB I:CYS70 4.5 0.9 1.0
O I:ALA65 4.6 0.6 1.0
O I:GLY64 4.6 0.5 1.0
CG2 I:VAL53 4.8 0.0 1.0
C I:CYS70 4.9 0.7 1.0
CA I:CYS70 5.0 0.8 1.0
N I:GLU61 5.0 0.4 1.0

Zinc binding site 7 out of 10 in 4qiw

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Zinc binding site 7 out of 10 in the Crystal Structure of Euryarchaeal Rna Polymerase From Thermococcus Kodakarensis


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Euryarchaeal Rna Polymerase From Thermococcus Kodakarensis within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1103

b:0.1
occ:1.01
 SG I:CYS147 2.2 0.0 1.0
SG I:CYS100 2.3 0.2 1.0
CB I:CYS103 2.5 0.1 1.0
CB I:CYS100 2.8 0.3 1.0
SG I:CYS103 2.8 0.6 1.0
CB I:CYS147 2.8 0.3 1.0
SG I:CYS150 2.9 0.6 1.0
N I:CYS150 3.1 0.8 1.0
CB I:CYS150 3.2 0.7 1.0
C I:HIS149 3.5 0.1 1.0
CA I:CYS103 3.7 1.0 1.0
CA I:CYS150 3.7 0.8 1.0
N I:HIS149 3.9 0.5 1.0
CA I:HIS149 4.0 0.3 1.0
O I:HIS149 4.0 0.5 1.0
CA I:CYS147 4.2 0.3 1.0
N I:CYS103 4.2 0.9 1.0
CA I:CYS100 4.3 0.2 1.0
N I:ALA152 4.3 0.3 1.0
CZ I:PHE155 4.4 0.1 1.0
C I:CYS147 4.4 0.6 1.0
CA I:ALA152 4.4 0.7 1.0
CB I:HIS149 4.5 0.2 1.0
CE2 I:PHE155 4.5 0.6 1.0
CB I:ALA152 4.6 0.6 1.0
C I:CYS150 4.6 0.2 1.0
CB I:ARG105 4.7 0.2 1.0
N I:ARG105 4.7 0.1 1.0
O I:CYS147 4.7 0.9 1.0
N I:GLY104 4.8 0.4 1.0
C I:CYS103 4.8 0.8 1.0
N I:PRO148 4.8 0.8 1.0
N I:CYS147 4.9 0.6 1.0
C I:CYS100 5.0 0.8 1.0

Zinc binding site 8 out of 10 in 4qiw

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Zinc binding site 8 out of 10 in the Crystal Structure of Euryarchaeal Rna Polymerase From Thermococcus Kodakarensis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Euryarchaeal Rna Polymerase From Thermococcus Kodakarensis within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn1301

b:0.8
occ:1.01
 SG J:CYS1065 2.1 0.9 1.0
CB J:CYS1068 2.2 0.9 1.0
SG J:CYS1086 2.7 0.7 1.0
SG J:CYS1068 3.1 0.1 1.0
CB J:CYS1086 3.3 0.3 1.0
CB J:CYS1065 3.4 0.1 1.0
SG J:CYS1083 3.4 0.2 1.0
CA J:CYS1068 3.4 0.2 1.0
OE1 J:GLU1090 3.7 0.1 1.0
N J:CYS1086 3.7 0.6 1.0
N J:CYS1068 3.7 0.5 1.0
CB J:VAL1085 4.1 0.4 1.0
CA J:CYS1086 4.1 0.7 1.0
CB J:CYS1083 4.2 0.8 1.0
C J:VAL1085 4.5 0.0 1.0
C J:SER1067 4.5 0.1 1.0
CA J:VAL1085 4.7 0.0 1.0
CD J:GLU1090 4.7 0.4 1.0
N J:VAL1085 4.7 0.8 1.0
C J:CYS1068 4.7 0.7 1.0
CB J:GLU1090 4.7 0.4 1.0
CA J:CYS1065 4.8 0.8 1.0
CG2 J:VAL1085 4.8 0.9 1.0
CG1 J:VAL1085 4.9 0.2 1.0
CG J:GLU1090 4.9 0.1 1.0

Zinc binding site 9 out of 10 in 4qiw

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Zinc binding site 9 out of 10 in the Crystal Structure of Euryarchaeal Rna Polymerase From Thermococcus Kodakarensis


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of Euryarchaeal Rna Polymerase From Thermococcus Kodakarensis within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Zn1601

b:0.4
occ:1.00
 N V:CYS10 2.6 0.1 1.0
C V:CYS44 2.7 0.1 1.0
N V:CYS45 2.7 0.3 1.0
SG V:CYS10 2.7 0.4 1.0
O V:CYS44 2.9 0.3 1.0
SG V:CYS7 2.9 76.7 1.0
CB V:CYS10 3.0 80.9 1.0
CB V:THR9 3.0 0.6 1.0
CA V:CYS45 3.1 0.6 1.0
SG V:CYS44 3.1 0.2 1.0
CB V:CYS44 3.1 0.1 1.0
SG V:CYS45 3.1 57.9 1.0
CA V:CYS10 3.3 95.8 1.0
C V:THR9 3.5 0.5 1.0
CA V:CYS44 3.5 0.5 1.0
CA V:THR9 3.5 0.3 1.0
N V:THR9 3.6 0.8 1.0
CB V:CYS45 3.7 0.8 1.0
CG2 V:THR9 3.7 0.1 1.0
OG1 V:THR9 4.0 0.6 1.0
NH2 V:ARG47 4.1 89.2 1.0
C V:CYS45 4.4 0.9 1.0
C V:CYS10 4.5 90.7 1.0
N V:CYS44 4.6 0.1 1.0
O V:THR9 4.6 0.9 1.0
CB V:CYS7 4.6 90.4 1.0
C V:PHE8 4.7 0.3 1.0
N V:GLY11 4.7 0.8 1.0
N V:PHE8 4.8 88.2 1.0
CZ V:ARG47 4.8 90.2 1.0

Zinc binding site 10 out of 10 in 4qiw

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Zinc binding site 10 out of 10 in the Crystal Structure of Euryarchaeal Rna Polymerase From Thermococcus Kodakarensis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of Euryarchaeal Rna Polymerase From Thermococcus Kodakarensis within 5.0Å range:
probe atom residue distance (Å) B Occ
W:Zn1701

b:94.1
occ:1.00
 CB W:CYS30 1.9 0.6 1.0
OE2 W:GLU14 2.0 0.2 1.0
CD W:GLU14 2.1 0.3 1.0
SG W:CYS11 2.2 0.2 1.0
SG W:CYS30 2.5 0.1 1.0
CG W:GLU14 2.6 0.4 1.0
OE1 W:GLU14 2.7 0.1 1.0
CA W:CYS30 3.3 1.0 1.0
N W:CYS30 3.8 1.0 1.0
CB W:CYS11 4.0 0.1 1.0
SG W:CYS27 4.1 0.8 1.0
CB W:GLU14 4.1 0.6 1.0
O W:GLY12 4.3 0.5 1.0
N W:GLY12 4.4 0.7 1.0
C W:TYR29 4.4 0.5 1.0
C W:CYS30 4.5 0.4 1.0
CB W:SER32 4.6 0.2 1.0
O W:TYR29 4.6 0.2 1.0
C W:GLY12 4.7 0.5 1.0
CB W:CYS27 4.8 0.3 1.0
CA W:CYS11 4.8 0.2 1.0
N W:GLU14 4.8 0.1 1.0
C W:CYS11 4.9 0.2 1.0
N W:CYS11 4.9 0.6 1.0
CA W:GLU14 4.9 0.5 1.0
O W:CYS30 5.0 0.0 1.0

Reference:

S.-H.Jun, A.Hirata, T.Kanai, T.J.Santangelo, T.Imanaka, K.S.Murakami. The X-Ray Crystal Structure of the Euryarchaeal Rna Polymerase in An Open Clamp Configuration Nat.Commun. 2014.
Page generated: Sun Oct 27 06:35:31 2024

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