Zinc in PDB 8q67: Crystal Structure of A Homohexameric Mcm From M. Acidophilum

The structure of Crystal Structure of A Homohexameric Mcm From M. Acidophilum, PDB code: 8q67 was solved by O.W.Noble, C.Degut, M.R.Hodgkinson, J.P.J.Chong, M.J.Plevin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	57.15 / 2.59
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	228.699, 127.488, 177.038, 90, 91.71, 90
R / Rfree (%)	23.1 / 25.3

The binding sites of Zinc atom in the Crystal Structure of A Homohexameric Mcm From M. Acidophilum (pdb code 8q67). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of A Homohexameric Mcm From M. Acidophilum, PDB code: 8q67:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Crystal Structure of A Homohexameric Mcm From M. Acidophilum


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of A Homohexameric Mcm From M. Acidophilum within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn703 b:95.2 occ:0.86 SG A:CYS137 2.3 93.9 1.0 SG A:CYS157 2.3 101.9 1.0 HB3 A:CYS154 2.4 106.9 1.0 SG A:CYS134 2.4 103.4 1.0 SG A:CYS154 2.4 102.8 1.0 HB2 A:CYS154 2.6 106.9 1.0 CB A:CYS154 2.6 89.0 1.0 HB3 A:CYS137 2.7 109.1 1.0 CB A:CYS137 3.0 90.8 1.0 H A:CYS137 3.1 119.8 1.0 H A:CYS157 3.1 109.1 1.0 HB3 A:CYS157 3.2 123.9 1.0 HB2 A:CYS134 3.2 117.7 1.0 CB A:CYS134 3.4 98.0 1.0 CB A:CYS157 3.4 103.2 1.0 HB3 A:CYS134 3.5 117.7 1.0 N A:CYS137 3.7 99.7 1.0 HB3 A:PHE136 3.7 108.0 1.0 HB2 A:CYS137 3.8 109.1 1.0 N A:CYS157 3.8 90.8 1.0 CA A:CYS137 3.9 91.1 1.0 HD2 A:PHE136 4.0 125.2 1.0 CA A:CYS154 4.1 95.9 1.0 CA A:CYS157 4.1 100.2 1.0 HB2 A:CYS157 4.2 123.9 1.0 HG1 A:THR161 4.2 113.5 1.0 H A:LYS159 4.4 114.6 1.0 H A:GLU156 4.4 110.1 1.0 HB2 A:GLU156 4.4 125.8 1.0 H A:ALA139 4.4 99.4 1.0 C A:CYS137 4.5 85.5 1.0 HB3 A:ALA139 4.5 99.2 1.0 H A:CYS154 4.5 104.5 1.0 H A:LYS158 4.6 108.7 1.0 HA A:CYS154 4.6 115.2 1.0 OG1 A:THR161 4.6 94.5 1.0 CB A:PHE136 4.7 89.9 1.0 HA A:CYS137 4.7 109.4 1.0 C A:PHE136 4.7 92.9 1.0 HB2 A:LYS159 4.7 105.8 1.0 C A:CYS157 4.8 89.5 1.0 C A:CYS154 4.8 89.2 1.0 H A:ASN138 4.8 110.8 1.0 CA A:CYS134 4.8 95.1 1.0 N A:LYS158 4.9 90.5 1.0 N A:CYS154 4.9 87.0 1.0 N A:ASN138 4.9 92.2 1.0 CD2 A:PHE136 4.9 104.3 1.0 HB2 A:ALA139 4.9 99.2 1.0 HA A:CYS134 5.0 114.2 1.0 C A:GLU156 5.0 100.6 1.0 HA A:CYS157 5.0 120.3 1.0 H A:PHE136 5.0 120.2 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of A Homohexameric Mcm From M. Acidophilum


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of A Homohexameric Mcm From M. Acidophilum within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn703 b:152.1 occ:1.00 SG B:CYS157 2.3 159.2 1.0 SG B:CYS154 2.5 143.5 1.0 SG B:CYS134 2.5 128.9 1.0 SG B:CYS137 2.5 149.2 1.0 H B:CYS157 2.8 160.9 1.0 HB2 B:CYS154 2.8 163.4 1.0 CB B:CYS154 2.9 136.1 1.0 HB2 B:CYS134 3.0 154.5 1.0 H B:CYS137 3.0 156.2 1.0 HB3 B:CYS154 3.0 163.4 1.0 CB B:CYS134 3.1 128.6 1.0 HB2 B:CYS157 3.2 162.2 1.0 HB3 B:CYS134 3.2 154.5 1.0 CB B:CYS157 3.3 135.1 1.0 HB3 B:CYS137 3.5 160.0 1.0 HB2 B:GLU156 3.5 164.6 1.0 N B:CYS157 3.5 134.0 1.0 CB B:CYS137 3.6 133.2 1.0 N B:CYS137 3.8 130.1 1.0 HB3 B:PHE136 4.0 154.8 1.0 CA B:CYS157 4.0 135.7 1.0 HB3 B:CYS157 4.1 162.2 1.0 HG23 B:THR161 4.2 158.7 1.0 H B:GLU156 4.2 174.5 1.0 CA B:CYS137 4.3 132.1 1.0 H B:PHE136 4.3 168.3 1.0 HB2 B:CYS137 4.4 160.0 1.0 CA B:CYS154 4.4 136.8 1.0 CB B:GLU156 4.4 137.1 1.0 HG21 B:THR161 4.5 158.7 1.0 HG1 B:THR161 4.5 164.7 1.0 HB2 B:PHE136 4.5 154.8 1.0 CA B:CYS134 4.6 128.0 1.0 C B:GLU156 4.6 137.5 1.0 CB B:PHE136 4.6 128.9 1.0 H B:LYS158 4.7 167.6 1.0 HA B:CYS154 4.8 164.2 1.0 HB3 B:GLU156 4.8 164.6 1.0 HA B:CYS157 4.8 163.0 1.0 CG2 B:THR161 4.8 132.1 1.0 N B:GLU156 4.8 145.3 1.0 CA B:GLU156 4.8 137.1 1.0 C B:PHE136 4.9 134.4 1.0 H B:CYS154 4.9 166.1 1.0 HA B:CYS134 4.9 153.7 1.0 C B:CYS157 4.9 139.6 1.0 HD23 B:LEU162 4.9 151.4 1.0 H B:ALA139 4.9 158.1 1.0 HD2 B:PRO155 4.9 157.4 1.0 H B:ASN138 4.9 160.5 1.0 HB3 B:ALA139 5.0 151.7 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of A Homohexameric Mcm From M. Acidophilum


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of A Homohexameric Mcm From M. Acidophilum within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn703 b:107.7 occ:0.90 HB3 C:CYS157 1.8 134.8 1.0 CB C:CYS157 2.4 112.2 1.0 SG C:CYS137 2.4 98.8 1.0 SG C:CYS157 2.4 122.0 1.0 SG C:CYS154 2.4 107.7 1.0 SG C:CYS134 2.5 112.8 1.0 H C:CYS157 2.8 131.3 1.0 H C:CYS137 3.0 129.9 1.0 HB3 C:CYS154 3.0 118.7 1.0 HB3 C:CYS137 3.1 119.4 1.0 HB2 C:CYS157 3.1 134.8 1.0 CB C:CYS154 3.1 98.8 1.0 HB2 C:CYS154 3.2 118.7 1.0 HB2 C:CYS134 3.2 120.2 1.0 CB C:CYS137 3.3 99.4 1.0 CB C:CYS134 3.4 100.1 1.0 N C:CYS157 3.4 109.3 1.0 CA C:CYS157 3.4 105.8 1.0 HB3 C:CYS134 3.5 120.2 1.0 HB3 C:PHE136 3.7 131.3 1.0 N C:CYS137 3.8 108.1 1.0 HG1 C:THR161 3.9 130.1 1.0 HB2 C:CYS137 4.1 119.4 1.0 HA C:CYS157 4.1 127.0 1.0 H C:LYS158 4.1 123.0 1.0 CA C:CYS137 4.1 100.1 1.0 HD2 C:PHE136 4.2 146.5 1.0 C C:CYS157 4.3 102.3 1.0 HB3 C:ALA139 4.3 115.4 1.0 OG1 C:THR161 4.3 108.3 1.0 H C:LYS159 4.4 129.6 1.0 N C:LYS158 4.5 102.5 1.0 CA C:CYS154 4.6 97.1 1.0 HG2 C:GLU156 4.6 129.4 1.0 H C:GLU156 4.6 130.2 1.0 H C:ALA139 4.6 116.0 1.0 C C:GLU156 4.7 111.4 1.0 CB C:PHE136 4.7 109.3 1.0 H C:PHE136 4.7 132.3 1.0 CA C:CYS134 4.8 101.0 1.0 HB2 C:ALA139 4.8 115.4 1.0 HD23 C:LEU162 4.8 115.0 1.0 CD2 C:PHE136 4.8 122.0 1.0 C C:PHE136 4.9 108.1 1.0 H C:ASN138 4.9 136.1 1.0 HA C:CYS137 4.9 120.2 1.0 C C:CYS137 4.9 113.3 1.0 HB2 C:GLU156 4.9 122.8 1.0 HG3 C:LYS159 5.0 130.0 1.0 HA C:CYS154 5.0 116.7 1.0 HA C:CYS134 5.0 121.3 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of A Homohexameric Mcm From M. Acidophilum


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of A Homohexameric Mcm From M. Acidophilum within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn703 b:68.5 occ:0.90 SG D:CYS154 2.1 69.7 1.0 SG D:CYS137 2.2 76.7 1.0 SG D:CYS134 2.5 72.3 1.0 SG D:CYS157 2.6 68.6 1.0 H D:CYS157 2.7 87.7 1.0 HB2 D:CYS154 2.8 83.1 1.0 CB D:CYS154 2.8 69.2 1.0 HB3 D:CYS154 2.8 83.1 1.0 HB3 D:CYS157 2.8 88.0 1.0 HB2 D:CYS134 3.0 88.8 1.0 CB D:CYS134 3.2 73.9 1.0 CB D:CYS157 3.2 73.2 1.0 HB3 D:CYS137 3.2 84.5 1.0 H D:CYS137 3.2 86.8 1.0 HB3 D:CYS134 3.3 88.8 1.0 CB D:CYS137 3.4 70.3 1.0 N D:CYS157 3.5 73.0 1.0 HB2 D:GLU156 3.6 101.5 1.0 HB3 D:ALA139 3.9 84.5 1.0 HG1 D:THR161 3.9 99.4 1.0 N D:CYS137 4.0 72.3 1.0 CA D:CYS157 4.0 68.4 1.0 H D:ALA139 4.0 84.9 1.0 HB3 D:PHE136 4.0 92.8 1.0 HB2 D:CYS157 4.0 88.0 1.0 H D:GLU156 4.1 95.6 1.0 HB2 D:CYS137 4.1 84.5 1.0 CA D:CYS137 4.2 70.5 1.0 CA D:CYS154 4.3 80.9 1.0 OG1 D:THR161 4.3 82.7 1.0 HB2 D:ALA139 4.4 84.5 1.0 HD2 D:PHE136 4.4 89.2 1.0 CB D:GLU156 4.6 84.5 1.0 H D:PHE136 4.6 103.8 1.0 CB D:ALA139 4.6 70.3 1.0 HA D:CYS154 4.6 97.2 1.0 H D:LYS158 4.6 94.1 1.0 C D:GLU156 4.7 77.2 1.0 H D:ASN138 4.7 100.8 1.0 CA D:CYS134 4.7 76.7 1.0 HA D:CYS157 4.7 82.2 1.0 HG3 D:GLU156 4.7 85.3 1.0 N D:GLU156 4.8 79.6 1.0 H D:LYS159 4.8 82.2 1.0 N D:ALA139 4.8 70.7 1.0 C D:CYS137 4.8 77.4 1.0 HD23 D:LEU162 4.9 82.6 1.0 C D:CYS154 4.9 80.3 1.0 HA D:CYS134 4.9 92.1 1.0 C D:CYS157 4.9 67.9 1.0 CA D:GLU156 4.9 80.4 1.0 N D:ASN138 4.9 83.9 1.0 H D:CYS154 4.9 84.6 1.0 CB D:PHE136 5.0 77.2 1.0 HD21 D:LEU162 5.0 82.6 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of A Homohexameric Mcm From M. Acidophilum


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of A Homohexameric Mcm From M. Acidophilum within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn703 b:127.2 occ:0.93 HB3 E:CYS157 1.9 163.5 1.0 SG E:CYS154 2.4 124.3 1.0 SG E:CYS137 2.4 122.7 1.0 SG E:CYS134 2.4 138.3 1.0 SG E:CYS157 2.5 139.0 1.0 CB E:CYS157 2.5 136.2 1.0 H E:CYS157 2.5 167.1 1.0 HB2 E:CYS134 2.7 154.5 1.0 HB3 E:CYS154 2.9 157.1 1.0 HB2 E:CYS154 3.0 157.1 1.0 CB E:CYS154 3.0 130.8 1.0 CB E:CYS134 3.0 128.6 1.0 H E:CYS137 3.1 152.9 1.0 N E:CYS157 3.1 139.1 1.0 HB3 E:CYS134 3.2 154.5 1.0 HB2 E:CYS157 3.3 163.5 1.0 CA E:CYS157 3.4 133.6 1.0 HB3 E:CYS137 3.4 151.1 1.0 CB E:CYS137 3.5 125.8 1.0 N E:CYS137 3.7 127.3 1.0 HG1 E:THR161 3.8 158.9 1.0 HB3 E:PHE136 3.9 165.8 1.0 HB3 E:ALA139 3.9 141.8 1.0 HA E:CYS157 4.1 160.4 1.0 HB2 E:GLU156 4.1 156.8 1.0 CA E:CYS137 4.1 129.9 1.0 C E:CYS157 4.2 130.9 1.0 OG1 E:THR161 4.3 132.3 1.0 C E:GLU156 4.3 134.3 1.0 H E:PHE136 4.3 166.9 1.0 HB2 E:CYS137 4.3 151.1 1.0 H E:ALA139 4.3 143.0 1.0 HB2 E:ALA139 4.3 141.8 1.0 H E:LYS159 4.4 160.2 1.0 H E:LYS158 4.4 158.8 1.0 CA E:CYS154 4.4 129.8 1.0 CA E:CYS134 4.4 124.4 1.0 CB E:ALA139 4.6 118.1 1.0 N E:LYS158 4.6 132.3 1.0 HA E:CYS134 4.6 149.4 1.0 H E:GLU156 4.6 157.2 1.0 HD23 E:LEU162 4.6 145.9 1.0 C E:CYS137 4.7 129.4 1.0 HD2 E:PHE136 4.7 164.1 1.0 O E:CYS154 4.7 127.3 1.0 C E:PHE136 4.8 129.0 1.0 CB E:PHE136 4.8 138.1 1.0 O E:CYS157 4.8 130.1 1.0 C E:CYS154 4.8 131.4 1.0 CA E:GLU156 4.8 133.5 1.0 CB E:GLU156 4.8 130.6 1.0 HA E:CYS154 4.8 155.9 1.0 N E:GLU156 4.9 130.9 1.0 O E:LYS159 4.9 131.5 1.0 HD21 E:LEU162 5.0 145.9 1.0 H E:ASN138 5.0 146.8 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of A Homohexameric Mcm From M. Acidophilum


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 A Homohexameric Mcm From M. Acidophilum within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn703 b:118.3 occ:0.76 HB3 F:CYS157 1.8 145.1 1.0 SG F:CYS137 2.4 115.6 1.0 SG F:CYS157 2.4 121.2 1.0 CB F:CYS157 2.4 120.8 1.0 SG F:CYS154 2.5 132.5 1.0 SG F:CYS134 2.5 124.6 1.0 HB2 F:CYS157 3.0 145.1 1.0 H F:CYS137 3.1 149.4 1.0 H F:CYS157 3.1 155.8 1.0 HB2 F:CYS134 3.2 146.4 1.0 HB3 F:CYS154 3.3 145.6 1.0 HB2 F:CYS154 3.3 145.6 1.0 CB F:CYS154 3.3 121.2 1.0 CB F:CYS134 3.3 122.0 1.0 HB3 F:CYS137 3.3 138.2 1.0 HB3 F:CYS134 3.4 146.4 1.0 CB F:CYS137 3.4 115.1 1.0 HB3 F:PHE136 3.6 144.0 1.0 CA F:CYS157 3.6 128.1 1.0 N F:CYS157 3.7 129.7 1.0 N F:CYS137 3.7 124.4 1.0 CA F:CYS137 4.1 115.8 1.0 HB3 F:ALA139 4.2 134.3 1.0 HG1 F:THR161 4.2 151.3 1.0 HB2 F:CYS137 4.2 138.2 1.0 H F:PHE136 4.3 142.2 1.0 HA F:CYS157 4.3 153.8 1.0 OG1 F:THR161 4.3 126.0 1.0 HB2 F:GLU156 4.4 147.8 1.0 C F:CYS157 4.4 129.9 1.0 H F:ALA139 4.5 143.3 1.0 HB2 F:ALA139 4.5 134.3 1.0 HD1 F:PHE136 4.5 146.4 1.0 CB F:PHE136 4.6 119.9 1.0 C F:PHE136 4.6 122.8 1.0 CA F:CYS134 4.7 123.2 1.0 CA F:CYS154 4.7 122.1 1.0 C F:CYS137 4.7 115.4 1.0 H F:LYS158 4.8 155.3 1.0 CB F:ALA139 4.8 111.8 1.0 H F:LYS159 4.9 158.3 1.0 O F:CYS157 4.9 126.0 1.0 C F:GLU156 4.9 125.0 1.0 N F:LYS158 4.9 129.3 1.0 HA F:CYS134 4.9 147.9 1.0 H F:ASN138 4.9 142.5 1.0 HA F:CYS137 4.9 139.1 1.0 H F:GLU156 5.0 152.4 1.0 N F:PHE136 5.0 118.4 1.0 CA F:PHE136 5.0 120.2 1.0

O.W.Noble, C.Degut, M.R.Hodgkinson, J.P.J.Chong, M.J.Plevin. Fundamental Steps of Minichromosome Maintenance Complex Assembly Are Conserved From Archaea to Eukaryotes To Be Published.