Zinc in PDB 6kf4: 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 6kf4). 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: 6kf4:
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:0.3 occ:1.00 NE2 A:HIS73 2.3 90.5 1.0 SG A:CYS60 2.8 0.8 1.0 SG A:CYS70 3.1 98.7 1.0 CD2 A:HIS73 3.2 90.5 1.0 CE1 A:HIS73 3.4 90.5 1.0 SG A:CYS63 3.4 0.1 1.0 OE2 A:GLU61 3.6 0.4 1.0 O A:PRO71 4.2 92.1 1.0 CB A:CYS60 4.3 0.8 1.0 CG A:GLU61 4.3 0.4 1.0 CG A:HIS73 4.4 90.5 1.0 CD A:GLU61 4.4 0.4 1.0 ND1 A:HIS73 4.4 90.5 1.0 CB A:ALA65 4.7 0.5 1.0 CB A:CYS70 4.8 98.7 1.0 N A:GLU61 5.0 0.4 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:0.9 occ:1.00 C A:HIS149 2.4 0.8 1.0 SG A:CYS150 2.5 0.7 1.0 O A:HIS149 2.5 0.8 1.0 CB A:CYS103 2.7 93.2 1.0 N A:CYS150 2.7 0.7 1.0 CB A:HIS149 2.9 0.8 1.0 SG A:CYS147 2.9 1.0 1.0 CA A:HIS149 2.9 0.8 1.0 CB A:CYS150 3.2 0.7 1.0 SG A:CYS103 3.3 93.2 1.0 N A:HIS149 3.3 0.8 1.0 CA A:CYS150 3.5 0.7 1.0 CA A:CYS103 4.1 93.2 1.0 CB A:CYS147 4.2 1.0 1.0 CG A:HIS149 4.3 0.8 1.0 SG A:CYS100 4.5 0.4 1.0 N A:CYS103 4.6 93.2 1.0 C A:PRO148 4.7 0.3 1.0 C A:CYS150 4.8 0.7 1.0 ND1 A:HIS149 4.9 0.8 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:0.5 occ:1.00 SG B:CYS1068 2.4 82.8 1.0 SG B:CYS1065 2.5 73.5 1.0 SG B:CYS1086 2.5 98.7 1.0 SG B:CYS1083 2.9 99.5 1.0 CB B:CYS1068 3.1 82.8 1.0 CB B:CYS1065 3.2 73.5 1.0 CB B:CYS1083 3.6 99.5 1.0 N B:CYS1086 3.8 98.7 1.0 CB B:CYS1086 3.9 98.7 1.0 CA B:CYS1068 4.3 82.8 1.0 O B:CYS1086 4.3 98.7 1.0 CA B:CYS1086 4.3 98.7 1.0 N B:CYS1068 4.4 82.8 1.0 N B:VAL1085 4.5 85.3 1.0 CB B:VAL1085 4.6 85.3 1.0 CA B:CYS1065 4.7 73.5 1.0 CA B:CYS1083 4.8 99.5 1.0 C B:VAL1085 4.8 85.3 1.0 C B:CYS1083 4.8 99.5 1.0 C B:CYS1086 4.8 98.7 1.0 CA B:VAL1085 4.9 85.3 1.0 OE1 B:GLU1090 4.9 0.2 1.0 N B:PRO1084 5.0 87.6 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:68.3 occ:1.00 C N:CYS44 2.2 27.8 1.0 SG N:CYS10 2.3 12.9 1.0 CB N:CYS44 2.4 27.8 1.0 N N:CYS45 2.4 23.2 1.0 O N:CYS44 2.5 27.8 1.0 SG N:CYS44 2.6 27.8 1.0 CA N:CYS44 2.8 27.8 1.0 SG N:CYS7 3.1 17.8 1.0 CA N:CYS45 3.1 23.2 1.0 CB N:CYS10 3.6 12.9 1.0 N N:CYS10 3.7 12.9 1.0 N N:CYS44 3.9 27.8 1.0 CB N:THR9 4.1 18.6 1.0 CB N:CYS45 4.1 23.2 1.0 CB N:CYS7 4.2 17.8 1.0 CA N:CYS10 4.3 12.9 1.0 C N:CYS45 4.4 23.2 1.0 SG N:CYS45 4.5 23.2 1.0 N N:THR9 4.6 18.6 1.0 C N:THR9 4.7 18.6 1.0 CG2 N:THR9 4.7 18.6 1.0 CA N:THR9 4.7 18.6 1.0 C N:TYR43 4.9 25.8 1.0 OG1 N:THR9 4.9 18.6 1.0 O N:CYS10 5.0 12.9 1.0 N N:ARG46 5.0 19.4 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:89.6 occ:1.00 OE1 P:GLU14 2.2 77.1 1.0 SG P:CYS30 2.5 74.3 1.0 SG P:CYS11 2.7 58.0 1.0 SG P:CYS27 2.9 71.2 1.0 CD P:GLU14 3.0 77.1 1.0 O P:GLY12 3.4 65.9 1.0 CB P:GLU14 3.6 77.1 1.0 CB P:CYS30 3.6 74.3 1.0 CG P:GLU14 3.7 77.1 1.0 CB P:CYS11 3.8 58.0 1.0 OE2 P:GLU14 3.8 77.1 1.0 CB P:CYS27 4.1 71.2 1.0 C P:GLY12 4.1 65.9 1.0 N P:GLY12 4.1 65.9 1.0 N P:CYS30 4.2 74.3 1.0 CA P:CYS30 4.6 74.3 1.0 N P:GLU14 4.6 77.1 1.0 CA P:GLY12 4.6 65.9 1.0 CA P:GLU14 4.7 77.1 1.0 C P:LYS13 4.9 68.1 1.0 C P:CYS11 4.9 58.0 1.0 N P:LYS13 4.9 68.1 1.0 CA P:CYS11 5.0 58.0 1.0 CD2 P:TYR29 5.0 72.5 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:0.5 occ:1.00 CG2 G:THR119 2.6 0.8 1.0 CB G:CYS117 2.8 0.5 1.0 SG G:CYS140 2.9 98.2 1.0 N G:GLY118 3.2 0.9 1.0 OG1 G:THR119 3.2 0.8 1.0 CB G:THR119 3.4 0.8 1.0 N G:THR119 3.5 0.8 1.0 C G:CYS117 3.5 0.5 1.0 CB G:LYS142 3.5 0.9 1.0 NE2 G:HIS122 3.5 0.8 1.0 CA G:CYS117 3.6 0.5 1.0 C G:GLY118 3.7 0.9 1.0 CD2 G:HIS122 3.8 0.8 1.0 CD G:LYS142 3.9 0.9 1.0 SG G:CYS117 4.0 0.5 1.0 CA G:GLY118 4.0 0.9 1.0 CA G:THR119 4.0 0.8 1.0 O G:CYS117 4.2 0.5 1.0 CG G:LYS142 4.2 0.9 1.0 O G:GLY118 4.4 0.9 1.0 CB G:CYS140 4.4 98.2 1.0 CE1 G:HIS122 4.6 0.8 1.0 CA G:LYS142 4.6 0.9 1.0 SG G:CYS137 4.7 0.5 1.0 N G:LYS142 4.7 0.9 1.0 CB G:CYS137 4.9 0.5 1.0 N G:CYS117 5.0 0.5 1.0 O G:GLY121 5.0 0.9 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.