Zinc in PDB 6kf9: 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;

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

Magnesium

(Mg)

1 atom

The binding sites of Zinc atom in the Cryo-Em Structure of Thermococcus Kodakarensis Rna Polymerase (pdb code 6kf9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Cryo-Em Structure of Thermococcus Kodakarensis Rna Polymerase, PDB code: 6kf9:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 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:74.7 occ:1.00 NE2 A:HIS73 2.5 45.2 1.0 SG A:CYS60 2.8 81.8 1.0 SG A:CYS70 3.1 74.6 1.0 CD2 A:HIS73 3.2 45.2 1.0 O A:PRO71 3.5 56.2 1.0 CE1 A:HIS73 3.6 45.2 1.0 SG A:CYS63 3.7 94.4 1.0 OE2 A:GLU61 4.0 78.3 1.0 CB A:ALA65 4.0 88.7 1.0 CB A:CYS60 4.4 81.8 1.0 CG A:HIS73 4.5 45.2 1.0 CG A:GLU61 4.5 78.3 1.0 ND1 A:HIS73 4.6 45.2 1.0 C A:PRO71 4.7 56.2 1.0 CB A:CYS70 4.7 74.6 1.0 CD A:GLU61 4.7 78.3 1.0 N A:PRO71 5.0 56.2 1.0

Zinc binding site 2 out of 6 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 SG A:CYS100 2.5 90.8 1.0 SG A:CYS147 2.5 99.7 1.0 SG A:CYS150 2.5 0.6 1.0 SG A:CYS103 2.5 92.3 1.0 ND1 A:HIS149 3.2 95.7 1.0 CB A:CYS100 3.3 90.8 1.0 CB A:CYS147 3.9 99.7 1.0 CB A:CYS103 3.9 92.3 1.0 CG A:HIS149 4.0 95.7 1.0 CB A:HIS149 4.0 95.7 1.0 CB A:CYS150 4.1 0.6 1.0 CE1 A:HIS149 4.2 95.7 1.0 CB A:ARG105 4.3 89.3 1.0 N A:CYS150 4.4 0.6 1.0 C A:HIS149 4.5 95.7 1.0 CG A:ARG105 4.6 89.3 1.0 CA A:HIS149 4.6 95.7 1.0 N A:HIS149 4.6 95.7 1.0 CA A:CYS100 4.7 90.8 1.0 O A:CYS100 4.8 90.8 1.0 O A:ARG101 4.9 91.5 1.0 CA A:CYS150 4.9 0.6 1.0 C A:CYS100 4.9 90.8 1.0 O A:HIS149 4.9 95.7 1.0 N A:ARG105 5.0 89.3 1.0

Zinc binding site 3 out of 6 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:0.7 occ:1.00 SG B:CYS1068 2.4 62.1 1.0 SG B:CYS1065 2.5 53.0 1.0 SG B:CYS1083 2.5 68.0 1.0 CB B:CYS1068 2.8 62.1 1.0 N B:CYS1068 3.4 62.1 1.0 CB B:CYS1065 3.5 53.0 1.0 SG B:CYS1086 3.6 71.2 1.0 CA B:CYS1068 3.7 62.1 1.0 CB B:CYS1083 3.8 68.0 1.0 CD B:GLU1088 4.1 85.5 1.0 OE1 B:GLU1088 4.2 85.5 1.0 OE2 B:GLU1088 4.3 85.5 1.0 C B:SER1067 4.4 59.5 1.0 CG B:GLU1088 4.5 85.5 1.0 N B:SER1067 4.6 59.5 1.0 CB B:CYS1086 4.7 71.2 1.0 N B:CYS1086 4.8 71.2 1.0 C B:CYS1068 4.8 62.1 1.0 CA B:CYS1065 4.9 53.0 1.0 CA B:SER1067 5.0 59.5 1.0 N B:GLY1069 5.0 51.2 1.0 N B:GLU1066 5.0 60.6 1.0

Zinc binding site 4 out of 6 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:86.5 occ:1.00 O N:CYS44 2.2 29.9 1.0 C N:CYS44 2.3 29.9 1.0 SG N:CYS10 2.4 23.6 1.0 CB N:CYS44 2.5 29.9 1.0 SG N:CYS7 2.8 19.7 1.0 CA N:CYS44 2.8 29.9 1.0 N N:CYS45 2.9 28.9 1.0 SG N:CYS44 3.2 29.9 1.0 N N:CYS10 3.6 23.6 1.0 CA N:CYS45 3.7 28.9 1.0 CB N:CYS10 3.8 23.6 1.0 CB N:THR9 4.0 20.9 1.0 CB N:CYS7 4.0 19.7 1.0 N N:CYS44 4.1 29.9 1.0 N N:THR9 4.3 20.9 1.0 CA N:CYS10 4.3 23.6 1.0 CA N:THR9 4.5 20.9 1.0 C N:THR9 4.5 20.9 1.0 CG2 N:THR9 4.5 20.9 1.0 C N:CYS45 4.7 28.9 1.0 CB N:CYS45 4.8 28.9 1.0 NH2 N:ARG47 4.8 20.8 1.0 OG1 N:THR9 4.8 20.9 1.0 O N:CYS10 4.9 23.6 1.0 NE N:ARG47 4.9 20.8 1.0 SG N:CYS45 4.9 28.9 1.0 N N:PHE8 5.0 19.6 1.0

Zinc binding site 5 out of 6 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:0.9 occ:1.00 SG P:CYS30 2.5 66.2 1.0 SG P:CYS27 2.5 64.1 1.0 SG P:CYS11 2.5 57.3 1.0 CG2 P:VAL15 2.8 63.2 1.0 CB P:CYS30 3.2 66.2 1.0 CB P:CYS27 3.6 64.1 1.0 CB P:VAL15 3.7 63.2 1.0 N P:CYS30 3.9 66.2 1.0 O P:GLY12 3.9 60.0 1.0 CB P:CYS11 4.0 57.3 1.0 N P:VAL15 4.1 63.2 1.0 CA P:CYS30 4.1 66.2 1.0 O P:LYS13 4.3 57.0 1.0 CD2 P:LEU17 4.4 61.3 1.0 CA P:VAL15 4.4 63.2 1.0 O P:VAL15 4.7 63.2 1.0 C P:VAL15 4.8 63.2 1.0 CD2 P:TYR29 4.9 67.4 1.0

Zinc binding site 6 out of 6 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 6 of Cryo-Em Structure of Thermococcus Kodakarensis Rna Polymerase within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn201 b:0.8 occ:1.00 SG G:CYS117 2.5 0.1 1.0 CB G:CYS117 2.7 0.1 1.0 SG G:CYS140 2.7 0.6 1.0 CB G:CYS137 3.2 0.0 1.0 SG G:CYS137 3.3 0.0 1.0 NE2 G:HIS122 3.5 0.3 1.0 CD2 G:HIS122 3.5 0.3 1.0 CB G:LYS142 3.6 0.4 1.0 CA G:CYS117 3.8 0.1 1.0 O G:LYS142 3.8 0.4 1.0 N G:LYS142 4.0 0.4 1.0 CA G:LYS142 4.1 0.4 1.0 C G:LYS142 4.3 0.4 1.0 CG2 G:THR119 4.3 0.8 1.0 CB G:CYS140 4.5 0.6 1.0 OG1 G:THR119 4.6 0.8 1.0 C G:CYS117 4.6 0.1 1.0 N G:GLY118 4.6 0.3 1.0 CA G:CYS137 4.6 0.0 1.0 CG G:LYS142 4.7 0.4 1.0 CE1 G:HIS122 4.8 0.3 1.0 O G:HIS122 4.9 0.3 1.0 CG G:HIS122 4.9 0.3 1.0 N G:GLY141 4.9 0.9 1.0 CD G:LYS142 4.9 0.4 1.0 N G:CYS117 5.0 0.1 1.0

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.