Magnesium in PDB 8b4l: Crystal Structure of A Selenomethionine-Labeled Hydropyrene Synthase (M75L Variant) in Its Closed Conformation

The structure of Crystal Structure of A Selenomethionine-Labeled Hydropyrene Synthase (M75L Variant) in Its Closed Conformation, PDB code: 8b4l was solved by C.P.O.Helmer, R.Driller, B.Loll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.11 / 3.39
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	80.698, 176.688, 185.651, 90, 90, 90
R / Rfree (%)	23.8 / 27.5

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of A Selenomethionine-Labeled Hydropyrene Synthase (M75L Variant) in Its Closed Conformation (pdb code 8b4l). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 16 binding sites of Magnesium where determined in the Crystal Structure of A Selenomethionine-Labeled Hydropyrene Synthase (M75L Variant) in Its Closed Conformation, PDB code: 8b4l:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 16 in the Crystal Structure of A Selenomethionine-Labeled Hydropyrene Synthase (M75L Variant) in Its Closed Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of A Selenomethionine-Labeled Hydropyrene Synthase (M75L Variant) in Its Closed Conformation within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg401 b:96.7 occ:1.00 OD2 E:ASP82 2.1 119.4 1.0 O15 E:AHD404 2.2 132.4 1.0 CG E:ASP82 2.9 119.5 1.0 OD1 E:ASP82 3.0 123.9 1.0 OE1 E:GLU160 3.0 117.6 1.0 O17 E:AHD404 3.3 112.8 1.0 P14 E:AHD404 3.3 144.4 1.0 MG E:MG403 3.5 117.3 1.0 CD E:GLU160 3.9 113.4 1.0 OE2 E:GLU160 4.0 113.3 1.0 NE2 E:GLN238 4.0 101.6 1.0 OD1 E:ASP87 4.1 112.8 1.0 O16 E:AHD404 4.2 114.2 1.0 CD1 E:ILE86 4.3 110.6 1.0 CG2 E:ILE86 4.3 93.8 1.0 CB E:ASP82 4.3 103.4 1.0 O E:GLY182 4.6 104.0 1.0 C7 E:AHD404 4.6 137.8 1.0 OD2 E:ASP87 4.6 124.6 1.0 C8 E:AHD404 4.7 141.7 1.0 CG E:ASP87 4.8 112.1 1.0 CB E:ILE86 4.9 89.3 1.0 O E:ASP82 4.9 110.6 1.0

Magnesium binding site 2 out of 16 in the Crystal Structure of A Selenomethionine-Labeled Hydropyrene Synthase (M75L Variant) in Its Closed Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of A Selenomethionine-Labeled Hydropyrene Synthase (M75L Variant) in Its Closed Conformation within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg402 b:108.0 occ:1.00 OG E:SER229 2.1 81.1 1.0 OE1 E:GLU233 2.1 106.0 1.0 OD1 E:ASN225 2.2 110.8 1.0 O10 E:AHD404 2.3 129.4 1.0 O16 E:AHD404 2.4 114.2 1.0 CD E:GLU233 3.0 100.1 1.0 CB E:SER229 3.2 94.8 1.0 CG E:ASN225 3.3 95.3 1.0 P9 E:AHD404 3.5 145.1 1.0 OE2 E:GLU233 3.5 86.7 1.0 P14 E:AHD404 3.6 144.4 1.0 O E:ASN225 3.6 79.4 1.0 C8 E:AHD404 3.9 141.7 1.0 O13 E:AHD404 3.9 131.4 1.0 OD1 E:ASP226 3.9 99.0 1.0 ND2 E:ASN225 3.9 96.8 1.0 C E:ASN225 4.0 76.1 1.0 NH2 E:ARG179 4.0 107.2 1.0 CG E:GLU233 4.2 88.2 1.0 O11 E:AHD404 4.2 132.5 1.0 CA E:ASP226 4.3 81.6 1.0 N E:ASP226 4.3 74.4 1.0 O15 E:AHD404 4.4 132.4 1.0 CB E:ASN225 4.4 76.1 1.0 CA E:SER229 4.5 90.3 1.0 O12 E:AHD404 4.6 128.8 1.0 O17 E:AHD404 4.7 112.8 1.0 CA E:ASN225 4.8 76.6 1.0 O E:SER229 4.8 74.5 1.0 C E:SER229 4.9 85.6 1.0 N E:SER229 4.9 86.8 1.0 ND2 E:ASN241 5.0 75.6 1.0 CG E:ASP226 5.0 86.9 1.0

Magnesium binding site 3 out of 16 in the Crystal Structure of A Selenomethionine-Labeled Hydropyrene Synthase (M75L Variant) in Its Closed Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of A Selenomethionine-Labeled Hydropyrene Synthase (M75L Variant) in Its Closed Conformation within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg403 b:117.3 occ:1.00 OD1 E:ASP82 2.1 123.9 1.0 OD2 E:ASP87 2.2 124.6 1.0 O15 E:AHD404 2.4 132.4 1.0 O11 E:AHD404 2.5 132.5 1.0 CG E:ASP87 3.2 112.1 1.0 CG E:ASP82 3.3 119.5 1.0 MG E:MG401 3.5 96.7 1.0 OD1 E:ASP87 3.5 112.8 1.0 P14 E:AHD404 3.6 144.4 1.0 P9 E:AHD404 3.7 145.1 1.0 OE1 E:GLU233 3.8 106.0 1.0 OD2 E:ASP82 3.9 119.4 1.0 O16 E:AHD404 4.1 114.2 1.0 C8 E:AHD404 4.2 141.7 1.0 O E:ASP82 4.3 110.6 1.0 O10 E:AHD404 4.4 129.4 1.0 CG E:GLU233 4.4 88.2 1.0 C7 E:AHD404 4.4 137.8 1.0 CB E:ASP82 4.5 103.4 1.0 CD E:GLU233 4.5 100.1 1.0 NE2 E:GLN238 4.5 101.6 1.0 CB E:ASP87 4.5 103.6 1.0 C E:ASP82 4.7 111.6 1.0 O17 E:AHD404 4.9 112.8 1.0 O12 E:AHD404 4.9 128.8 1.0 CG E:GLN238 4.9 91.4 1.0

Magnesium binding site 4 out of 16 in the Crystal Structure of A Selenomethionine-Labeled Hydropyrene Synthase (M75L Variant) in Its Closed Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of A Selenomethionine-Labeled Hydropyrene Synthase (M75L Variant) in Its Closed Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:120.0 occ:1.00 OD1 A:ASP82 2.1 126.6 1.0 O15 A:AHD404 2.1 138.5 1.0 OD2 A:ASP82 2.2 125.5 1.0 CG A:ASP82 2.4 122.9 1.0 O16 A:AHD404 3.0 115.3 1.0 P14 A:AHD404 3.1 142.5 1.0 MG A:MG403 3.3 119.9 1.0 CG2 A:ILE86 3.5 102.5 1.0 OE1 A:GLU160 3.6 116.0 1.0 OD1 A:ASP87 3.9 107.3 1.0 CB A:ASP82 3.9 99.9 1.0 O17 A:AHD404 4.1 112.6 1.0 OD2 A:ASP87 4.1 143.9 1.0 O A:ASP82 4.2 119.8 1.0 CB A:ILE86 4.2 93.2 1.0 CD1 A:ILE86 4.2 95.4 1.0 NE2 A:GLN238 4.2 111.6 1.0 CG A:ASP87 4.4 119.3 1.0 C7 A:AHD404 4.4 129.0 1.0 CD A:GLU160 4.4 110.6 1.0 OE2 A:GLU160 4.5 115.3 1.0 C8 A:AHD404 4.5 131.4 1.0 CA A:ASP82 4.6 100.8 1.0 NH1 A:ARG179 4.6 137.9 1.0 CG1 A:ILE86 4.7 89.6 1.0 C A:ASP82 4.7 111.7 1.0 O A:GLY182 4.7 106.4 1.0 O12 A:AHD404 5.0 136.0 1.0

Magnesium binding site 5 out of 16 in the Crystal Structure of A Selenomethionine-Labeled Hydropyrene Synthase (M75L Variant) in Its Closed Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of A Selenomethionine-Labeled Hydropyrene Synthase (M75L Variant) in Its Closed Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:111.3 occ:1.00 OE1 A:GLU233 2.1 97.6 1.0 OG A:SER229 2.2 87.7 1.0 O10 A:AHD404 2.2 120.6 1.0 OD1 A:ASN225 2.2 111.5 1.0 O17 A:AHD404 2.4 112.6 1.0 CD A:GLU233 3.0 98.6 1.0 CB A:SER229 3.2 89.2 1.0 NH2 A:ARG179 3.3 121.5 1.0 CG A:ASN225 3.3 93.0 1.0 OE2 A:GLU233 3.5 95.4 1.0 P9 A:AHD404 3.5 122.9 1.0 O A:ASN225 3.6 68.6 1.0 OD1 A:ASP226 3.7 97.8 1.0 P14 A:AHD404 3.7 142.5 1.0 ND2 A:ASN225 3.9 106.7 1.0 C8 A:AHD404 4.0 131.4 1.0 C A:ASN225 4.0 76.0 1.0 O13 A:AHD404 4.0 130.8 1.0 O12 A:AHD404 4.2 136.0 1.0 CG A:GLU233 4.2 86.3 1.0 CA A:ASP226 4.3 88.9 1.0 N A:ASP226 4.3 79.2 1.0 CZ A:ARG179 4.4 118.0 1.0 CB A:ASN225 4.4 78.7 1.0 O15 A:AHD404 4.5 138.5 1.0 CA A:SER229 4.6 85.3 1.0 O11 A:AHD404 4.6 119.2 1.0 O16 A:AHD404 4.8 115.3 1.0 CG A:ASP226 4.8 87.7 1.0 CA A:ASN225 4.8 77.8 1.0 O A:SER229 4.9 77.5 1.0 ND2 A:ASN241 4.9 87.5 1.0 C A:SER229 5.0 83.4 1.0 NH1 A:ARG179 5.0 137.9 1.0 N A:SER229 5.0 83.3 1.0

Magnesium binding site 6 out of 16 in the Crystal Structure of A Selenomethionine-Labeled Hydropyrene Synthase (M75L Variant) in Its Closed Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of A Selenomethionine-Labeled Hydropyrene Synthase (M75L Variant) in Its Closed Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:119.9 occ:1.00 OD2 A:ASP87 2.1 143.9 1.0 OD2 A:ASP82 2.2 125.5 1.0 O15 A:AHD404 2.2 138.5 1.0 O12 A:AHD404 2.4 136.0 1.0 CG A:ASP87 3.2 119.3 1.0 MG A:MG401 3.3 120.0 1.0 CG A:ASP82 3.4 122.9 1.0 P14 A:AHD404 3.4 142.5 1.0 P9 A:AHD404 3.6 122.9 1.0 OD1 A:ASP87 3.7 107.3 1.0 C8 A:AHD404 3.8 131.4 1.0 C7 A:AHD404 3.9 129.0 1.0 O A:ASP82 4.1 119.8 1.0 O17 A:AHD404 4.1 112.6 1.0 OD1 A:ASP82 4.2 126.6 1.0 CB A:ASP82 4.3 99.9 1.0 OE1 A:GLU233 4.4 97.6 1.0 C A:ASP82 4.4 111.7 1.0 O10 A:AHD404 4.5 120.6 1.0 CB A:ASP87 4.5 99.3 1.0 O16 A:AHD404 4.6 115.3 1.0 O11 A:AHD404 4.7 119.2 1.0 N A:ASP83 4.8 98.1 1.0 CA A:ASP83 4.9 98.9 1.0

Magnesium binding site 7 out of 16 in the Crystal Structure of A Selenomethionine-Labeled Hydropyrene Synthase (M75L Variant) in Its Closed Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of A Selenomethionine-Labeled Hydropyrene Synthase (M75L Variant) in Its Closed Conformation within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:127.8 occ:1.00 OD1 B:ASP82 2.1 146.1 1.0 O17 B:AHD404 2.2 145.8 1.0 OD2 B:ASP82 2.2 161.6 1.0 CG B:ASP82 2.4 149.9 1.0 MG B:MG403 3.2 139.1 1.0 O15 B:AHD404 3.2 131.1 1.0 P14 B:AHD404 3.3 140.7 1.0 OD1 B:ASP87 3.6 131.1 1.0 OE1 B:GLU160 3.7 116.4 1.0 OD2 B:ASP87 3.9 141.0 1.0 NE2 B:GLN238 3.9 122.5 1.0 CB B:ASP82 3.9 125.8 1.0 CG2 B:ILE86 4.2 131.9 1.0 CG B:ASP87 4.2 138.1 1.0 O16 B:AHD404 4.2 128.3 1.0 CD1 B:ILE86 4.4 124.6 1.0 C7 B:AHD404 4.5 147.3 1.0 O B:ASP82 4.6 139.0 1.0 C8 B:AHD404 4.6 141.2 1.0 CB B:ILE86 4.6 138.2 1.0 CA B:ASP82 4.7 120.3 1.0 CD B:GLU160 4.8 118.7 1.0 O11 B:AHD404 4.9 154.4 1.0 C B:ASP82 5.0 128.1 1.0

Magnesium binding site 8 out of 16 in the Crystal Structure of A Selenomethionine-Labeled Hydropyrene Synthase (M75L Variant) in Its Closed Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of A Selenomethionine-Labeled Hydropyrene Synthase (M75L Variant) in Its Closed Conformation within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:113.3 occ:1.00 OE1 B:GLU233 2.1 111.6 1.0 OG B:SER229 2.2 120.9 1.0 OD1 B:ASN225 2.2 132.1 1.0 O16 B:AHD404 2.3 128.3 1.0 O10 B:AHD404 2.4 143.7 1.0 CD B:GLU233 3.0 126.7 1.0 CG B:ASN225 3.3 117.9 1.0 CB B:SER229 3.4 125.5 1.0 NH2 B:ARG179 3.4 106.1 1.0 OD1 B:ASP226 3.4 116.4 1.0 O B:ASN225 3.5 107.0 1.0 OE2 B:GLU233 3.5 121.2 1.0 P14 B:AHD404 3.6 140.7 1.0 P9 B:AHD404 3.6 154.8 1.0 C B:ASN225 3.8 99.6 1.0 CA B:ASP226 4.0 110.1 1.0 ND2 B:ASN225 4.0 113.1 1.0 C8 B:AHD404 4.0 141.2 1.0 N B:ASP226 4.0 104.3 1.0 O13 B:AHD404 4.1 128.6 1.0 O11 B:AHD404 4.2 154.4 1.0 CG B:GLU233 4.2 128.8 1.0 O17 B:AHD404 4.3 145.8 1.0 CB B:ASN225 4.4 97.9 1.0 CG B:ASP226 4.5 114.1 1.0 CZ B:ARG179 4.6 102.5 1.0 CA B:SER229 4.6 110.2 1.0 O15 B:AHD404 4.7 131.1 1.0 CA B:ASN225 4.7 94.2 1.0 ND2 B:ASN241 4.8 104.8 1.0 O12 B:AHD404 4.8 143.9 1.0 O B:SER229 4.8 118.0 1.0 C B:SER229 4.9 107.5 1.0 CB B:ASP226 4.9 103.7 1.0 N B:SER229 4.9 108.8 1.0 C B:ASP226 4.9 99.7 1.0

Magnesium binding site 9 out of 16 in the Crystal Structure of A Selenomethionine-Labeled Hydropyrene Synthase (M75L Variant) in Its Closed Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of A Selenomethionine-Labeled Hydropyrene Synthase (M75L Variant) in Its Closed Conformation within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg403 b:139.1 occ:1.00 OD2 B:ASP87 2.1 141.0 1.0 OD2 B:ASP82 2.1 161.6 1.0 O17 B:AHD404 2.3 145.8 1.0 O11 B:AHD404 2.4 154.4 1.0 MG B:MG401 3.2 127.8 1.0 CG B:ASP87 3.3 138.1 1.0 CG B:ASP82 3.4 149.9 1.0 P14 B:AHD404 3.6 140.7 1.0 P9 B:AHD404 3.7 154.8 1.0 OD1 B:ASP87 3.8 131.1 1.0 C8 B:AHD404 4.0 141.2 1.0 C7 B:AHD404 4.1 147.3 1.0 NH1 B:ARG313 4.1 145.2 1.0 OD1 B:ASP82 4.2 146.1 1.0 OE1 B:GLU233 4.2 111.6 1.0 O16 B:AHD404 4.2 128.3 1.0 CB B:ASP82 4.4 125.8 1.0 O B:ASP82 4.4 139.0 1.0 O10 B:AHD404 4.5 143.7 1.0 CB B:ASP87 4.5 134.2 1.0 NH2 B:ARG313 4.6 132.9 1.0 O15 B:AHD404 4.7 131.1 1.0 C B:ASP82 4.7 128.1 1.0 O12 B:AHD404 4.7 143.9 1.0 CZ B:ARG313 4.8 143.3 1.0 CG B:GLU233 4.8 128.8 1.0 CD B:GLU233 4.9 126.7 1.0 NE2 B:GLN238 5.0 122.5 1.0

Magnesium binding site 10 out of 16 in the Crystal Structure of A Selenomethionine-Labeled Hydropyrene Synthase (M75L Variant) in Its Closed Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of A Selenomethionine-Labeled Hydropyrene Synthase (M75L Variant) in Its Closed Conformation within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg401 b:138.9 occ:1.00 OD1 C:ASP82 2.1 142.2 1.0 O15 C:AHD404 2.1 142.8 1.0 OD2 C:ASP82 2.2 151.0 1.0 CG C:ASP82 2.4 141.5 1.0 MG C:MG403 3.2 132.9 1.0 P14 C:AHD404 3.3 150.3 1.0 OD1 C:ASP87 3.3 117.0 1.0 O16 C:AHD404 3.3 139.1 1.0 OD2 C:ASP87 3.5 145.8 1.0 OE1 C:GLU160 3.7 120.7 1.0 CG C:ASP87 3.8 132.9 1.0 CB C:ASP82 3.9 117.1 1.0 NE2 C:GLN238 4.0 133.0 1.0 CG2 C:ILE86 4.1 125.1 1.0 O C:ASP82 4.2 125.8 1.0 O17 C:AHD404 4.3 137.0 1.0 CD1 C:ILE86 4.3 135.2 1.0 CB C:ILE86 4.4 143.7 1.0 C7 C:AHD404 4.5 140.0 1.0 C8 C:AHD404 4.6 133.0 1.0 CA C:ASP82 4.6 122.2 1.0 CD C:GLU160 4.7 118.6 1.0 C C:ASP82 4.7 124.1 1.0 O12 C:AHD404 4.8 139.1 1.0 OE2 C:GLU160 4.9 104.0 1.0 CG1 C:ILE86 5.0 129.5 1.0

C.P.O.Helmer, R.Driller, B.Loll. Crystal Structure of S Hydropyrene Synthase in Its Closed Conformation To Be Published.