Zinc in PDB 7yh1: Roadblock From Candidatus Prometheoarchaeum Syntrophicum Strain Mk-D1

The structure of Roadblock From Candidatus Prometheoarchaeum Syntrophicum Strain Mk-D1, PDB code: 7yh1 was solved by R.C.Robinson, L.T.Tran, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.94 / 2.69
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	48.338, 53.574, 59.856, 76.65, 75.32, 80.61
R / Rfree (%)	22.2 / 26.5

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc atom in the Roadblock From Candidatus Prometheoarchaeum Syntrophicum Strain Mk-D1 (pdb code 7yh1). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the Roadblock From Candidatus Prometheoarchaeum Syntrophicum Strain Mk-D1, PDB code: 7yh1:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in the Roadblock From Candidatus Prometheoarchaeum Syntrophicum Strain Mk-D1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Roadblock From Candidatus Prometheoarchaeum Syntrophicum Strain Mk-D1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn201 b:42.6 occ:0.83 NE2 D:HIS19 2.1 90.3 1.0 CD2 D:HIS19 2.9 83.8 1.0 CE1 D:HIS19 3.2 90.1 1.0 O D:ARG76 3.6 45.6 1.0 CA D:THR94 3.9 73.6 1.0 O D:THR93 4.0 40.0 1.0 CG D:HIS19 4.1 81.5 1.0 CG2 D:THR94 4.2 63.0 1.0 ND1 D:HIS19 4.2 87.1 1.0 CB D:THR94 4.5 70.7 1.0 N D:THR94 4.5 69.7 1.0 C D:THR93 4.5 40.6 1.0 CH2 D:TRP38 4.6 69.8 1.0 CZ2 D:TRP38 4.6 74.0 1.0 C D:ARG76 4.8 47.8 1.0 C D:THR94 4.9 81.6 1.0

Zinc binding site 2 out of 12 in the Roadblock From Candidatus Prometheoarchaeum Syntrophicum Strain Mk-D1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Roadblock From Candidatus Prometheoarchaeum Syntrophicum Strain Mk-D1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn202 b:67.7 occ:0.55 NE2 A:HIS50 2.1 101.1 1.0 CE1 D:HIS50 2.2 99.5 1.0 ZN A:ZN201 2.3 56.9 0.5 OE1 B:GLU42 2.3 95.3 1.0 CD2 A:HIS50 2.8 98.1 1.0 NE2 D:HIS50 2.9 94.5 1.0 OE2 B:GLU42 3.0 97.2 1.0 CD B:GLU42 3.0 90.7 1.0 CE1 A:HIS50 3.2 99.9 1.0 ND1 D:HIS50 3.2 94.8 1.0 CD1 D:ILE54 3.5 59.8 1.0 CG1 D:ILE54 3.7 56.3 1.0 CG A:HIS50 4.0 96.7 1.0 ND1 A:HIS50 4.1 99.5 1.0 CD2 D:HIS50 4.2 93.1 1.0 CG D:HIS50 4.3 88.0 1.0 CD1 A:ILE54 4.4 77.0 1.0 CG B:GLU42 4.5 80.6 1.0

Zinc binding site 3 out of 12 in the Roadblock From Candidatus Prometheoarchaeum Syntrophicum Strain Mk-D1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Roadblock From Candidatus Prometheoarchaeum Syntrophicum Strain Mk-D1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn203 b:49.2 occ:0.87 O D:PHE115 1.8 80.1 1.0 C D:PHE115 2.8 76.7 1.0 OXT D:PHE115 3.1 78.4 1.0 CD2 D:PHE115 4.1 61.4 1.0 CA D:PHE115 4.1 71.2 1.0 CB D:PHE115 4.5 68.9 1.0 CG D:PHE115 4.7 64.8 1.0 CE2 D:PHE115 5.0 59.9 1.0

Zinc binding site 4 out of 12 in the Roadblock From Candidatus Prometheoarchaeum Syntrophicum Strain Mk-D1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Roadblock From Candidatus Prometheoarchaeum Syntrophicum Strain Mk-D1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn204 b:107.2 occ:0.80 O D:HOH314 2.5 68.5 1.0 O D:HOH309 2.6 56.2 1.0 O D:HOH307 2.7 66.8 1.0 ND1 D:HIS19 2.7 87.1 1.0 O D:HOH316 2.9 58.6 1.0 CG D:HIS19 3.6 81.5 1.0 CE1 D:HIS19 3.6 90.1 1.0 CA D:HIS19 3.8 64.7 1.0 CB D:HIS19 3.8 70.0 1.0 O D:HIS19 4.2 72.5 1.0 C D:HIS19 4.5 66.0 1.0 CG D:PRO36 4.7 69.7 1.0 NE2 D:HIS19 4.7 90.3 1.0 CD2 D:HIS19 4.7 83.8 1.0 CB D:PRO36 4.8 71.7 1.0 O D:ILE18 4.8 62.4 1.0 N D:HIS19 4.9 60.5 1.0

Zinc binding site 5 out of 12 in the Roadblock From Candidatus Prometheoarchaeum Syntrophicum Strain Mk-D1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Roadblock From Candidatus Prometheoarchaeum Syntrophicum Strain Mk-D1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:56.9 occ:0.48 OE2 B:GLU42 2.0 97.2 1.0 NE2 D:HIS50 2.1 94.5 1.0 CE1 A:HIS50 2.2 99.9 1.0 NE2 A:HIS50 2.2 101.1 1.0 ZN D:ZN202 2.3 67.7 0.6 CE1 D:HIS50 2.6 99.5 1.0 CD B:GLU42 2.9 90.7 1.0 OE1 B:GLU42 3.2 95.3 1.0 CD2 D:HIS50 3.4 93.1 1.0 ND1 A:HIS50 3.5 99.5 1.0 CD2 A:HIS50 3.6 98.1 1.0 ND1 D:HIS50 3.9 94.8 1.0 CD1 A:ILE54 4.1 77.0 1.0 CG A:HIS50 4.2 96.7 1.0 CG B:GLU42 4.3 80.6 1.0 CG D:HIS50 4.3 88.0 1.0 CG1 A:ILE54 4.3 68.2 1.0 CB B:GLU42 4.7 71.3 1.0

Zinc binding site 6 out of 12 in the Roadblock From Candidatus Prometheoarchaeum Syntrophicum Strain Mk-D1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Roadblock From Candidatus Prometheoarchaeum Syntrophicum Strain Mk-D1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:41.3 occ:0.73 NE2 A:HIS19 2.1 84.1 1.0 CD2 A:HIS19 2.9 81.7 1.0 CE1 A:HIS19 3.3 84.8 1.0 O A:ARG76 3.7 55.3 1.0 CG2 A:THR94 4.0 66.5 1.0 CG A:HIS19 4.1 80.5 1.0 O A:THR93 4.2 56.8 1.0 CA A:THR94 4.2 66.2 1.0 ND1 A:HIS19 4.2 83.5 1.0 CB A:THR94 4.6 69.0 1.0 C A:THR93 4.7 56.5 1.0 N A:THR94 4.7 60.0 1.0 CH2 A:TRP38 4.8 57.3 1.0 C A:ARG76 4.9 55.4 1.0 CZ2 A:TRP38 4.9 60.4 1.0

Zinc binding site 7 out of 12 in the Roadblock From Candidatus Prometheoarchaeum Syntrophicum Strain Mk-D1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Roadblock From Candidatus Prometheoarchaeum Syntrophicum Strain Mk-D1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:39.0 occ:0.65 O A:PHE115 1.9 90.1 1.0 OXT A:PHE115 2.1 84.7 1.0 C A:PHE115 2.3 82.9 1.0 O A:HOH313 2.8 45.2 1.0 CA A:PHE115 3.8 77.4 1.0 CD1 A:PHE115 4.1 67.3 1.0 CB A:PHE115 4.3 75.4 1.0 CG A:PHE115 4.6 70.0 1.0 N A:PHE115 4.6 70.5 1.0 CE1 A:PHE115 5.0 63.1 1.0

Zinc binding site 8 out of 12 in the Roadblock From Candidatus Prometheoarchaeum Syntrophicum Strain Mk-D1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Roadblock From Candidatus Prometheoarchaeum Syntrophicum Strain Mk-D1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn204 b:96.8 occ:0.80 O A:HOH314 2.3 58.5 1.0 ND1 A:HIS19 2.4 83.5 1.0 CE1 A:HIS19 3.2 84.8 1.0 CG A:HIS19 3.5 80.5 1.0 CA A:HIS19 3.7 65.8 1.0 CB A:HIS19 3.9 71.9 1.0 NE2 A:HIS19 4.3 84.1 1.0 O A:HIS19 4.3 63.6 1.0 O A:ILE18 4.5 65.3 1.0 CD2 A:HIS19 4.5 81.7 1.0 C A:HIS19 4.5 63.1 1.0 N A:HIS19 4.7 65.0 1.0 C A:ILE18 5.0 63.4 1.0

Zinc binding site 9 out of 12 in the Roadblock From Candidatus Prometheoarchaeum Syntrophicum Strain Mk-D1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Roadblock From Candidatus Prometheoarchaeum Syntrophicum Strain Mk-D1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:108.6 occ:0.72 O B:HOH310 2.3 74.0 1.0 ND1 B:HIS19 2.8 85.8 1.0 CE1 B:HIS19 3.4 89.6 1.0 CG B:HIS19 3.7 81.3 1.0 O B:HIS19 3.9 76.0 1.0 CA B:HIS19 4.0 67.1 1.0 CB B:HIS19 4.1 72.2 1.0 NE2 B:HIS19 4.4 87.5 1.0 C B:HIS19 4.4 67.5 1.0 CD2 B:HIS19 4.6 84.0 1.0 CG B:PRO36 4.7 57.6 1.0

Zinc binding site 10 out of 12 in the Roadblock From Candidatus Prometheoarchaeum Syntrophicum Strain Mk-D1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Roadblock From Candidatus Prometheoarchaeum Syntrophicum Strain Mk-D1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn202 b:76.3 occ:0.55 NE2 B:HIS50 2.0 103.7 1.0 ZN C:ZN201 2.1 71.8 0.6 CE1 C:HIS50 2.2 120.6 1.0 NE2 C:HIS50 2.6 118.9 1.0 CD2 B:HIS50 2.9 100.1 1.0 CD1 B:ILE54 3.0 58.0 1.0 CE1 B:HIS50 3.1 99.9 1.0 ND1 C:HIS50 3.4 116.2 1.0 CD2 C:HIS50 3.9 118.0 1.0 CG1 B:ILE54 4.0 57.4 1.0 CG B:HIS50 4.1 94.8 1.0 ND1 B:HIS50 4.2 98.4 1.0 CG C:HIS50 4.3 111.1 1.0 CD1 C:ILE54 5.0 67.2 1.0

R.C.Robinson, L.T.Tran. Roadblock From Candidatus Prometheoarchaeum Syntrophicum Strain Mk-D1 To Be Published.