Magnesium in PDB 7yua: Structural Insight Into A Metal-Dependent Mutase Mtdl Revealing An Arginine Residue Covalently Mediated Interconversion Between Nucleotide-Based Furanose and Pyranose

The structure of Structural Insight Into A Metal-Dependent Mutase Mtdl Revealing An Arginine Residue Covalently Mediated Interconversion Between Nucleotide-Based Furanose and Pyranose, PDB code: 7yua was solved by C.B.Chi, M.Ma, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.92 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	58.843, 155.155, 94.636, 90, 97.45, 90
R / Rfree (%)	17.9 / 24.4

Pages:

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

Binding sites:

The binding sites of Magnesium atom in the Structural Insight Into A Metal-Dependent Mutase Mtdl Revealing An Arginine Residue Covalently Mediated Interconversion Between Nucleotide-Based Furanose and Pyranose (pdb code 7yua). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 11 binding sites of Magnesium where determined in the Structural Insight Into A Metal-Dependent Mutase Mtdl Revealing An Arginine Residue Covalently Mediated Interconversion Between Nucleotide-Based Furanose and Pyranose, PDB code: 7yua:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 11 in the Structural Insight Into A Metal-Dependent Mutase Mtdl Revealing An Arginine Residue Covalently Mediated Interconversion Between Nucleotide-Based Furanose and Pyranose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structural Insight Into A Metal-Dependent Mutase Mtdl Revealing An Arginine Residue Covalently Mediated Interconversion Between Nucleotide-Based Furanose and Pyranose within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:35.2 occ:1.00 OG A:SER263 2.7 23.5 1.0 O A:VAL226 2.8 26.2 1.0 O A:ASP260 2.8 27.1 1.0 OH A:TYR241 2.9 26.2 1.0 N A:GLY264 3.2 25.4 1.0 CE1 A:TYR241 3.2 24.0 1.0 C A:ASN227 3.3 28.5 1.0 CA A:GLY264 3.3 25.7 1.0 CZ A:TYR241 3.3 27.4 1.0 O A:ASN227 3.5 31.4 1.0 C A:VAL226 3.6 25.9 1.0 N A:SER228 3.7 28.4 1.0 CB A:ASP260 3.7 29.5 1.0 CA A:ASN227 3.7 31.5 1.0 C A:ASP260 3.7 26.7 1.0 CA A:ASP260 3.9 26.1 1.0 C A:SER263 4.0 28.8 1.0 N A:ASN227 4.0 29.6 1.0 CB A:SER263 4.1 27.7 1.0 O A:HOH556 4.1 27.5 1.0 CG1 A:VAL226 4.2 22.9 1.0 CA A:SER228 4.2 27.5 1.0 CB A:SER228 4.3 33.7 1.0 CD1 A:TYR241 4.3 26.3 1.0 CE2 A:TYR241 4.5 24.6 1.0 CA A:SER263 4.6 23.4 1.0 O A:SER263 4.7 29.8 1.0 CB A:VAL226 4.7 31.1 1.0 CG A:ASP260 4.7 30.3 1.0 CA A:VAL226 4.8 29.4 1.0 C A:GLY264 4.8 28.3 1.0 OD2 A:ASP260 4.9 30.2 1.0 O A:HOH554 4.9 28.4 1.0 N A:ILE261 5.0 28.9 1.0

Magnesium binding site 2 out of 11 in the Structural Insight Into A Metal-Dependent Mutase Mtdl Revealing An Arginine Residue Covalently Mediated Interconversion Between Nucleotide-Based Furanose and Pyranose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structural Insight Into A Metal-Dependent Mutase Mtdl Revealing An Arginine Residue Covalently Mediated Interconversion Between Nucleotide-Based Furanose and Pyranose within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:41.9 occ:1.00 O A:GLN128 2.5 52.3 1.0 O A:VAL183 2.5 33.7 1.0 OD1 A:ASP182 2.5 31.4 1.0 O A:VAL126 2.9 37.0 1.0 NE A:ARG184 3.2 37.6 1.0 CD A:ARG184 3.3 31.6 1.0 C A:VAL183 3.6 31.9 1.0 C A:GLN128 3.6 42.4 1.0 C A:VAL126 3.7 38.1 1.0 CG A:ASP182 3.8 33.7 1.0 N A:VAL183 3.9 33.6 1.0 N A:GLN128 4.0 38.3 1.0 C A:CYS127 4.2 43.4 1.0 C A:ASP182 4.2 34.0 1.0 CZ A:ARG184 4.3 39.3 1.0 O A:GLY129 4.3 47.4 1.0 CA A:VAL183 4.3 32.6 1.0 CA A:GLN128 4.3 47.3 1.0 O A:HOH532 4.4 37.7 1.0 N A:CYS127 4.4 37.3 1.0 CA A:CYS127 4.4 37.2 1.0 C A:GLY129 4.4 42.2 1.0 OD2 A:ASP182 4.5 37.1 1.0 CG A:ARG184 4.5 34.4 1.0 CA A:VAL126 4.5 37.3 1.0 O A:VAL125 4.5 41.2 1.0 N A:ARG184 4.5 32.1 1.0 N A:GLY129 4.6 41.4 1.0 CA A:GLY129 4.6 52.0 1.0 CA A:ASP182 4.6 32.1 1.0 CA A:ARG184 4.7 29.1 1.0 O A:ASP182 4.7 36.1 1.0 NH2 A:ARG184 4.8 34.2 1.0 CB A:GLN128 4.8 41.6 1.0 O A:CYS127 4.8 48.9 1.0 CB A:ASP182 4.8 34.4 1.0 CB A:VAL183 4.9 33.9 1.0

Magnesium binding site 3 out of 11 in the Structural Insight Into A Metal-Dependent Mutase Mtdl Revealing An Arginine Residue Covalently Mediated Interconversion Between Nucleotide-Based Furanose and Pyranose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structural Insight Into A Metal-Dependent Mutase Mtdl Revealing An Arginine Residue Covalently Mediated Interconversion Between Nucleotide-Based Furanose and Pyranose within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg404 b:75.0 occ:1.00 O2B A:GDP401 2.1 85.1 1.0 OD2 A:ASP111 2.6 72.2 1.0 NE2 A:HIS287 2.8 66.5 1.0 OD2 A:ASP109 3.3 56.6 1.0 OD1 A:ASP111 3.3 62.0 1.0 PB A:GDP401 3.3 96.0 1.0 CG A:ASP111 3.3 68.1 1.0 CE1 A:HIS287 3.4 67.3 1.0 H5' A:GDP401 3.6 78.1 1.0 O3B A:GDP401 3.7 86.5 1.0 CD2 A:HIS287 3.8 61.8 1.0 HOB3 A:GDP401 3.9 103.8 1.0 H5'' A:GDP401 3.9 78.1 1.0 O3A A:GDP401 4.1 83.3 1.0 NE2 A:GLN229 4.1 63.4 1.0 CG A:ASP109 4.2 52.3 1.0 C5' A:GDP401 4.2 65.1 1.0 O1A A:GDP401 4.3 82.8 1.0 ND2 A:ASN290 4.3 84.8 1.0 CB A:ASP109 4.4 49.5 1.0 ND1 A:HIS287 4.5 58.3 1.0 O1B A:GDP401 4.5 87.0 1.0 PA A:GDP401 4.6 87.2 1.0 CG A:HIS287 4.7 58.3 1.0 CD A:GLN229 4.7 55.2 1.0 O5' A:GDP401 4.8 64.8 1.0 CB A:ASP111 4.8 55.9 1.0 OD1 A:ASN290 4.9 84.9 1.0 CG A:ASN290 5.0 86.9 1.0

Magnesium binding site 4 out of 11 in the Structural Insight Into A Metal-Dependent Mutase Mtdl Revealing An Arginine Residue Covalently Mediated Interconversion Between Nucleotide-Based Furanose and Pyranose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structural Insight Into A Metal-Dependent Mutase Mtdl Revealing An Arginine Residue Covalently Mediated Interconversion Between Nucleotide-Based Furanose and Pyranose within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:36.2 occ:1.00 OG B:SER263 2.7 21.8 1.0 O B:TYR241 2.7 26.3 1.0 CB B:SER263 3.3 27.6 1.0 CE2 B:TYR241 3.4 25.2 1.0 CZ B:TYR241 3.4 29.3 1.0 OH B:TYR94 3.4 30.7 1.0 CE2 B:TYR94 3.4 27.9 1.0 CD2 B:TYR241 3.5 25.0 1.0 CE1 B:TYR241 3.6 24.6 1.0 CG B:TYR241 3.6 27.1 1.0 CD1 B:TYR241 3.7 25.8 1.0 CB B:PHE243 3.8 26.6 1.0 CA B:PHE243 3.8 30.5 1.0 C B:TYR241 3.8 29.8 1.0 N B:PHE243 3.8 31.2 1.0 CZ B:TYR94 3.9 29.4 1.0 CD2 B:PHE243 3.9 31.9 1.0 OH B:TYR241 4.1 32.3 1.0 C B:TYR242 4.1 28.8 1.0 O B:HOH575 4.2 28.1 1.0 CB B:SER228 4.3 29.1 1.0 O B:TYR242 4.3 29.9 1.0 CG B:PHE243 4.3 30.5 1.0 CA B:TYR241 4.5 29.2 1.0 CD2 B:TYR94 4.5 30.9 1.0 CB B:TYR241 4.5 27.4 1.0 CA B:SER263 4.7 24.0 1.0 N B:TYR242 4.8 25.6 1.0 CA B:ASP260 4.8 26.4 1.0 CB B:ASP260 4.9 28.7 1.0 CA B:TYR242 4.9 31.2 1.0

Magnesium binding site 5 out of 11 in the Structural Insight Into A Metal-Dependent Mutase Mtdl Revealing An Arginine Residue Covalently Mediated Interconversion Between Nucleotide-Based Furanose and Pyranose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structural Insight Into A Metal-Dependent Mutase Mtdl Revealing An Arginine Residue Covalently Mediated Interconversion Between Nucleotide-Based Furanose and Pyranose within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg403 b:36.7 occ:1.00 O B:GLN128 2.1 51.3 1.0 OD1 B:ASP182 2.4 32.6 1.0 O B:VAL183 2.6 31.5 1.0 C B:GLN128 3.3 40.9 1.0 CA B:GLY129 3.5 33.1 1.0 C B:VAL183 3.5 27.2 1.0 N B:VAL183 3.6 31.3 1.0 CD B:ARG184 3.6 27.3 1.0 CG B:ASP182 3.6 36.5 1.0 C B:GLY129 3.7 31.9 1.0 NE B:ARG184 3.7 32.7 1.0 O B:GLY129 3.7 35.4 1.0 O B:VAL126 3.8 38.6 1.0 N B:GLY129 3.9 32.7 1.0 C B:ASP182 3.9 33.8 1.0 O B:HOH604 4.0 36.1 1.0 CA B:VAL183 4.1 27.6 1.0 CA B:ASP182 4.2 28.9 1.0 C B:VAL126 4.3 40.2 1.0 OD2 B:ASP182 4.5 37.2 1.0 N B:PRO130 4.5 31.6 1.0 N B:GLN128 4.5 40.6 1.0 CA B:GLN128 4.5 39.4 1.0 CG B:ARG184 4.5 32.1 1.0 CB B:ASP182 4.6 32.9 1.0 O B:ASP182 4.6 32.6 1.0 N B:ARG184 4.6 29.0 1.0 CB B:VAL183 4.6 33.6 1.0 C B:CYS127 4.7 45.1 1.0 CZ B:ARG184 4.8 36.7 1.0 O B:VAL125 4.8 35.9 1.0 N B:CYS127 4.9 39.7 1.0 CA B:VAL126 4.9 28.1 1.0 CA B:ARG184 4.9 28.4 1.0

Magnesium binding site 6 out of 11 in the Structural Insight Into A Metal-Dependent Mutase Mtdl Revealing An Arginine Residue Covalently Mediated Interconversion Between Nucleotide-Based Furanose and Pyranose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structural Insight Into A Metal-Dependent Mutase Mtdl Revealing An Arginine Residue Covalently Mediated Interconversion Between Nucleotide-Based Furanose and Pyranose within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg404 b:80.7 occ:1.00 O1B B:GDP401 2.0 81.5 1.0 OD2 B:ASP111 2.3 64.0 1.0 O1A B:GDP401 2.9 81.6 1.0 NE2 B:HIS287 3.0 64.0 1.0 CG B:ASP111 3.1 61.4 1.0 PB B:GDP401 3.1 96.6 1.0 OD1 B:ASP111 3.4 60.7 1.0 O3B B:GDP401 3.5 80.3 1.0 H5'' B:GDP401 3.6 79.5 1.0 O3A B:GDP401 3.6 81.6 1.0 PA B:GDP401 3.7 84.0 1.0 CE1 B:HIS287 3.9 67.2 1.0 CD2 B:HIS287 4.0 55.4 1.0 CB B:ASP111 4.2 50.9 1.0 C5' B:GDP401 4.3 66.3 1.0 HOB3 B:GDP401 4.3 96.4 1.0 H5' B:GDP401 4.3 79.5 1.0 O2B B:GDP401 4.4 75.1 1.0 O5' B:GDP401 4.5 71.4 1.0 H3' B:GDP401 4.7 71.3 1.0

Magnesium binding site 7 out of 11 in the Structural Insight Into A Metal-Dependent Mutase Mtdl Revealing An Arginine Residue Covalently Mediated Interconversion Between Nucleotide-Based Furanose and Pyranose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structural Insight Into A Metal-Dependent Mutase Mtdl Revealing An Arginine Residue Covalently Mediated Interconversion Between Nucleotide-Based Furanose and Pyranose within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg402 b:35.1 occ:1.00 O C:VAL226 2.6 24.1 1.0 OG C:SER263 3.0 25.3 1.0 O C:ASP260 3.0 26.4 1.0 OH C:TYR241 3.1 28.2 1.0 C C:ASN227 3.2 28.4 1.0 O C:ASN227 3.2 28.1 1.0 CE1 C:TYR241 3.2 23.8 1.0 N C:GLY264 3.2 25.4 1.0 CA C:GLY264 3.3 23.0 1.0 C C:VAL226 3.4 31.2 1.0 CZ C:TYR241 3.5 23.0 1.0 CA C:ASN227 3.6 28.4 1.0 N C:SER228 3.6 25.1 1.0 CB C:ASP260 3.7 28.7 1.0 N C:ASN227 3.8 30.3 1.0 C C:ASP260 3.9 25.4 1.0 CG1 C:VAL226 3.9 21.1 1.0 CA C:ASP260 4.0 29.6 1.0 C C:SER263 4.1 26.9 1.0 CA C:SER228 4.2 27.1 1.0 O C:HOH542 4.2 19.4 1.0 CB C:SER228 4.3 27.8 1.0 CB C:SER263 4.3 23.9 1.0 CD1 C:TYR241 4.3 20.9 1.0 CB C:VAL226 4.4 25.6 1.0 CA C:VAL226 4.5 28.6 1.0 OD2 C:ASP260 4.6 29.7 1.0 CG C:ASP260 4.7 31.9 1.0 CA C:SER263 4.8 22.7 1.0 CE2 C:TYR241 4.8 21.6 1.0 C C:GLY264 4.8 24.2 1.0 O C:SER263 4.8 23.7 1.0 O C:HOH538 4.9 25.5 1.0 OG C:SER228 4.9 31.8 1.0

Magnesium binding site 8 out of 11 in the Structural Insight Into A Metal-Dependent Mutase Mtdl Revealing An Arginine Residue Covalently Mediated Interconversion Between Nucleotide-Based Furanose and Pyranose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structural Insight Into A Metal-Dependent Mutase Mtdl Revealing An Arginine Residue Covalently Mediated Interconversion Between Nucleotide-Based Furanose and Pyranose within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg403 b:73.3 occ:1.00 OD2 C:ASP111 2.1 63.0 1.0 O2B C:GDP401 2.2 83.7 1.0 O2A C:GDP401 2.6 76.9 1.0 CG C:ASP111 2.8 51.1 1.0 OD1 C:ASP111 3.0 50.2 1.0 ND2 C:ASN290 3.1 79.2 1.0 PB C:GDP401 3.4 91.3 1.0 H5'' C:GDP401 3.5 68.6 1.0 NE2 C:HIS287 3.6 64.0 1.0 PA C:GDP401 3.7 80.8 1.0 O3A C:GDP401 4.0 76.1 1.0 CB C:ASP111 4.1 41.8 1.0 O1B C:GDP401 4.1 74.3 1.0 OD2 C:ASP109 4.1 59.5 1.0 C5' C:GDP401 4.2 57.2 1.0 H5' C:GDP401 4.3 68.6 1.0 CG C:ASN290 4.3 82.4 1.0 CE1 C:HIS287 4.4 64.7 1.0 O5' C:GDP401 4.4 62.3 1.0 CD2 C:HIS287 4.5 57.6 1.0 O3B C:GDP401 4.8 76.5 1.0 HOB3 C:GDP401 4.8 91.9 1.0 H3' C:GDP401 4.9 57.1 1.0 CB C:ASN290 5.0 82.5 1.0

Magnesium binding site 9 out of 11 in the Structural Insight Into A Metal-Dependent Mutase Mtdl Revealing An Arginine Residue Covalently Mediated Interconversion Between Nucleotide-Based Furanose and Pyranose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Structural Insight Into A Metal-Dependent Mutase Mtdl Revealing An Arginine Residue Covalently Mediated Interconversion Between Nucleotide-Based Furanose and Pyranose within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg402 b:37.4 occ:1.00 OG D:SER263 2.8 27.9 1.0 O D:VAL226 2.9 31.9 1.0 O D:ASP260 3.0 28.9 1.0 OH D:TYR241 3.0 33.5 1.0 CE1 D:TYR241 3.2 30.6 1.0 C D:ASN227 3.2 40.1 1.0 N D:GLY264 3.2 31.2 1.0 O D:ASN227 3.4 34.0 1.0 CA D:GLY264 3.4 24.1 1.0 CZ D:TYR241 3.4 32.1 1.0 CB D:ASP260 3.4 30.2 1.0 CA D:ASN227 3.5 35.6 1.0 N D:SER228 3.6 33.1 1.0 C D:VAL226 3.6 30.1 1.0 C D:ASP260 3.7 32.4 1.0 CA D:ASP260 3.8 31.9 1.0 N D:ASN227 3.9 35.3 1.0 C D:SER263 4.1 31.0 1.0 CA D:SER228 4.1 33.5 1.0 CB D:SER228 4.1 33.3 1.0 CB D:SER263 4.2 29.2 1.0 CG1 D:VAL226 4.2 25.4 1.0 O D:HOH551 4.3 29.9 1.0 CD1 D:TYR241 4.3 26.6 1.0 CG D:ASP260 4.5 33.4 1.0 CB D:VAL226 4.6 30.2 1.0 OD2 D:ASP260 4.6 34.0 1.0 CA D:SER263 4.6 30.1 1.0 CE2 D:TYR241 4.7 31.2 1.0 CA D:VAL226 4.7 28.9 1.0 OG D:SER228 4.8 36.4 1.0 O D:SER263 4.8 27.5 1.0 C D:GLY264 4.9 26.6 1.0 N D:ILE261 5.0 31.7 1.0 CB D:ASN227 5.0 34.4 1.0

Magnesium binding site 10 out of 11 in the Structural Insight Into A Metal-Dependent Mutase Mtdl Revealing An Arginine Residue Covalently Mediated Interconversion Between Nucleotide-Based Furanose and Pyranose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Structural Insight Into A Metal-Dependent Mutase Mtdl Revealing An Arginine Residue Covalently Mediated Interconversion Between Nucleotide-Based Furanose and Pyranose within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg403 b:47.5 occ:1.00 OD1 D:ASP182 2.3 33.9 1.0 N D:GLY129 2.7 40.1 1.0 O D:VAL183 3.0 35.4 1.0 O D:VAL126 3.1 45.9 1.0 CA D:GLY129 3.1 38.6 1.0 CG D:ASP182 3.6 35.7 1.0 NE D:ARG184 3.6 38.6 1.0 C D:GLY129 3.7 37.9 1.0 N D:GLN128 3.7 42.0 1.0 O D:GLY129 3.8 39.1 1.0 C D:VAL126 3.8 43.9 1.0 C D:GLN128 3.8 41.8 1.0 CD D:ARG184 3.8 30.0 1.0 N D:VAL183 3.9 32.1 1.0 C D:VAL183 4.0 32.5 1.0 C D:CYS127 4.1 44.7 1.0 OD2 D:ASP182 4.2 43.3 1.0 CA D:GLN128 4.2 48.5 1.0 CA D:CYS127 4.2 48.5 1.0 C D:ASP182 4.3 34.0 1.0 O D:HOH597 4.3 40.0 1.0 N D:CYS127 4.4 46.4 1.0 CA D:ASP182 4.5 34.9 1.0 CZ D:ARG184 4.5 34.1 1.0 CA D:VAL183 4.5 31.0 1.0 N D:PRO130 4.6 39.6 1.0 CB D:ASP182 4.6 34.6 1.0 CA D:VAL126 4.7 39.9 1.0 CB D:GLN128 4.7 43.3 1.0 O D:CYS127 4.8 51.8 1.0 NH2 D:ARG184 4.8 29.5 1.0 O D:GLN128 4.9 44.2 1.0 CG D:ARG184 4.9 29.5 1.0 O D:ASP182 4.9 30.3 1.0 N D:ARG184 4.9 30.0 1.0 O D:VAL125 4.9 42.5 1.0

C.B.Chi, R.Xu, Q.Q.Chen, X.H.Zhang, X.M.Shi, H.W.Jin, F.Yin, H.L.Jia, L.R.Zhang, D.H.Yang, J.H.Ju, Q.L.Li, M.Ma. Structural Insight Into A Metal-Dependent Mutase Revealing An Arginine Residue-Covalently Mediated Interconversion Between Nucleotide-Based Pyranose and Furanose. Acs Catalysis V. 13 1597 2023.
ISSN: ESSN 2155-5435
DOI: 10.1021/ACSCATAL.2C04907