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Zinc in PDB 6kf3: Cryo-Em Structure of Thermococcus Kodakarensis Rna Polymerase

Enzymatic activity of Cryo-Em Structure of Thermococcus Kodakarensis Rna Polymerase

All present enzymatic activity of Cryo-Em Structure of Thermococcus Kodakarensis Rna Polymerase:
2.7.7.6;

Other elements in 6kf3:

The structure of Cryo-Em Structure of Thermococcus Kodakarensis Rna Polymerase also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Cryo-Em Structure of Thermococcus Kodakarensis Rna Polymerase (pdb code 6kf3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Cryo-Em Structure of Thermococcus Kodakarensis Rna Polymerase, PDB code: 6kf3:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 6kf3

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Zinc binding site 1 out of 5 in the Cryo-Em Structure of Thermococcus Kodakarensis Rna Polymerase


Mono view


Stereo pair view

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

b:66.0
occ:1.00
NE2 A:HIS73 2.2 72.4 1.0
SG A:CYS60 2.5 80.7 1.0
CD2 A:HIS73 3.0 72.4 1.0
SG A:CYS70 3.2 66.2 1.0
CE1 A:HIS73 3.3 72.4 1.0
O A:PRO71 3.4 59.4 1.0
SG A:CYS63 3.7 74.7 1.0
OE2 A:GLU61 3.9 75.0 1.0
CB A:ALA65 4.0 74.2 1.0
CB A:CYS60 4.1 80.7 1.0
CG A:HIS73 4.2 72.4 1.0
ND1 A:HIS73 4.3 72.4 1.0
CG A:GLU61 4.4 75.0 1.0
C A:PRO71 4.6 59.4 1.0
CD A:GLU61 4.6 75.0 1.0
CB A:CYS70 4.7 66.2 1.0
N A:PRO71 4.9 59.4 1.0
CD A:PRO71 5.0 59.4 1.0
N A:GLU61 5.0 75.0 1.0

Zinc binding site 2 out of 5 in 6kf3

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Zinc binding site 2 out of 5 in the Cryo-Em Structure of Thermococcus Kodakarensis Rna Polymerase


Mono view


Stereo pair view

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

b:0.5
occ:1.00
ND1 A:HIS149 2.2 88.1 1.0
CG A:HIS149 2.8 88.1 1.0
SG A:CYS147 2.8 85.5 1.0
CB A:HIS149 2.9 88.1 1.0
SG A:CYS103 3.0 86.0 1.0
SG A:CYS150 3.1 86.8 1.0
CE1 A:HIS149 3.3 88.1 1.0
CG A:ARG105 3.4 77.0 1.0
CA A:HIS149 3.8 88.1 1.0
CB A:ARG105 3.9 77.0 1.0
C A:HIS149 3.9 88.1 1.0
CD2 A:HIS149 4.0 88.1 1.0
N A:HIS149 4.1 88.1 1.0
CB A:CYS103 4.1 86.0 1.0
SG A:CYS100 4.1 90.2 1.0
NE2 A:HIS149 4.2 88.1 1.0
N A:CYS150 4.3 86.8 1.0
O A:HIS149 4.3 88.1 1.0
CB A:CYS147 4.5 85.5 1.0
CB A:CYS150 4.6 86.8 1.0
CD A:ARG105 4.7 77.0 1.0
CB A:CYS100 4.9 90.2 1.0

Zinc binding site 3 out of 5 in 6kf3

Go back to Zinc Binding Sites List in 6kf3
Zinc binding site 3 out of 5 in the Cryo-Em Structure of Thermococcus Kodakarensis Rna Polymerase


Mono view


Stereo pair view

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

b:0.2
occ:1.00
SG B:CYS1083 2.5 81.1 1.0
CG B:GLU1088 2.6 81.3 1.0
N B:GLU1088 2.9 81.3 1.0
SG B:CYS1086 2.9 78.0 1.0
CB B:GLU1088 2.9 81.3 1.0
CD B:GLU1088 3.2 81.3 1.0
CB B:CYS1083 3.4 81.1 1.0
CA B:GLU1088 3.4 81.3 1.0
OE1 B:GLU1088 3.5 81.3 1.0
N B:GLY1087 3.7 74.2 1.0
C B:GLY1087 3.7 74.2 1.0
SG B:CYS1065 3.8 80.6 1.0
OE2 B:GLU1088 3.9 81.3 1.0
C B:CYS1086 3.9 78.0 1.0
CA B:GLY1087 4.0 74.2 1.0
O B:CYS1083 4.1 81.1 1.0
CB B:CYS1086 4.2 78.0 1.0
O B:CYS1086 4.4 78.0 1.0
CA B:CYS1083 4.4 81.1 1.0
CA B:CYS1086 4.4 78.0 1.0
SG B:CYS1068 4.4 61.1 1.0
N B:CYS1086 4.4 78.0 1.0
C B:GLU1088 4.6 81.3 1.0
C B:CYS1083 4.6 81.1 1.0
O B:GLY1087 4.6 74.2 1.0
N B:CYS1083 4.6 81.1 1.0
O B:GLU1088 4.9 81.3 1.0

Zinc binding site 4 out of 5 in 6kf3

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Zinc binding site 4 out of 5 in the Cryo-Em Structure of Thermococcus Kodakarensis Rna Polymerase


Mono view


Stereo pair view

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

b:89.0
occ:1.00
O N:CYS44 2.2 3.9 1.0
C N:CYS44 2.3 3.9 1.0
SG N:CYS10 2.4 11.7 1.0
CB N:CYS44 2.5 3.9 1.0
CA N:CYS44 2.8 3.9 1.0
N N:CYS45 2.9 11.7 1.0
SG N:CYS7 3.0 11.7 1.0
SG N:CYS44 3.2 3.9 1.0
N N:CYS10 3.5 11.7 1.0
CB N:CYS10 3.7 11.7 1.0
CA N:CYS45 3.7 11.7 1.0
CB N:THR9 3.8 11.7 1.0
CB N:CYS7 4.0 11.7 1.0
N N:CYS44 4.1 3.9 1.0
CA N:CYS10 4.2 11.7 1.0
N N:THR9 4.3 11.7 1.0
CG2 N:THR9 4.4 11.7 1.0
CA N:THR9 4.4 11.7 1.0
C N:THR9 4.4 11.7 1.0
OG1 N:THR9 4.7 11.7 1.0
C N:CYS45 4.7 11.7 1.0
CB N:CYS45 4.8 11.7 1.0
O N:CYS10 4.8 11.7 1.0
NH2 N:ARG47 4.9 5.0 1.0
SG N:CYS45 5.0 11.7 1.0

Zinc binding site 5 out of 5 in 6kf3

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Zinc binding site 5 out of 5 in the Cryo-Em Structure of Thermococcus Kodakarensis Rna Polymerase


Mono view


Stereo pair view

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

b:0.8
occ:1.00
SG P:CYS11 2.5 31.5 1.0
SG P:CYS30 2.5 54.9 1.0
SG P:CYS27 2.5 48.4 1.0
CG2 P:VAL15 2.7 39.2 1.0
CB P:CYS30 3.2 54.9 1.0
CB P:VAL15 3.7 39.2 1.0
O P:GLY12 3.7 28.3 1.0
CB P:CYS27 3.7 48.4 1.0
N P:CYS30 3.8 54.9 1.0
CB P:CYS11 4.0 31.5 1.0
CA P:CYS30 4.1 54.9 1.0
O P:LYS13 4.1 39.0 1.0
N P:VAL15 4.1 39.2 1.0
CD2 P:LEU17 4.4 39.9 1.0
CA P:VAL15 4.4 39.2 1.0
CD2 P:TYR29 4.8 42.5 1.0
C P:LYS13 4.8 39.0 1.0
O P:VAL15 4.8 39.2 1.0
CB P:TYR29 4.9 42.5 1.0
C P:GLY12 4.9 28.3 1.0
CG1 P:VAL15 4.9 39.2 1.0
C P:TYR29 4.9 42.5 1.0
C P:VAL15 4.9 39.2 1.0

Reference:

S.-H.Jun, J.Hyun, H.Jeong, J.S.Cha, H.Kim, M.S.Bartlett, H.-S.Cho, K.S.Murakami. Cryo-Em Structure of Thermococcus Kodakarensis Rna Polymerase To Be Published.
Page generated: Wed Dec 16 12:06:46 2020

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