Magnesium in PDB 4f86: Structure Analysis of Geranyl Diphosphate Methyltransferase in Complex with Gpp and Sinefungin

The structure of Structure Analysis of Geranyl Diphosphate Methyltransferase in Complex with Gpp and Sinefungin, PDB code: 4f86 was solved by O.Ariyawutthiphan, T.Ose, A.Minami, Y.G.Gao, M.Yao, H.Oikawa, I.Tanaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.51 / 3.00
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	78.937, 87.731, 160.222, 100.01, 96.65, 90.89
R / Rfree (%)	27.9 / 29.8

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

Binding sites:

The binding sites of Magnesium atom in the Structure Analysis of Geranyl Diphosphate Methyltransferase in Complex with Gpp and Sinefungin (pdb code 4f86). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the Structure Analysis of Geranyl Diphosphate Methyltransferase in Complex with Gpp and Sinefungin, PDB code: 4f86:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in the Structure Analysis of Geranyl Diphosphate Methyltransferase in Complex with Gpp and Sinefungin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure Analysis of Geranyl Diphosphate Methyltransferase in Complex with Gpp and Sinefungin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:17.9 occ:1.00 O2A A:GPP502 2.7 45.5 1.0 OD1 A:ASN45 2.8 40.7 1.0 O2B A:GPP502 2.8 41.8 1.0 O A:HIS58 3.2 46.1 1.0 OE2 A:GLU89 3.3 47.0 1.0 OE1 A:GLU89 3.3 50.1 1.0 CD A:GLU89 3.6 48.3 1.0 O A:VAL44 3.7 44.3 1.0 CG A:ASN45 4.0 39.9 1.0 OH A:TYR264 4.0 45.6 1.0 PA A:GPP502 4.0 43.1 1.0 NH1 A:ARG268 4.2 41.3 1.0 PB A:GPP502 4.3 40.1 1.0 C A:HIS58 4.4 45.0 1.0 N A:HIS58 4.5 47.4 1.0 CE1 A:TYR59 4.5 40.5 1.0 O1A A:GPP502 4.5 44.3 1.0 CD1 A:TYR59 4.6 40.4 1.0 C A:VAL44 4.6 44.2 1.0 O3A A:GPP502 4.7 41.3 1.0 O1B A:GPP502 4.7 40.2 1.0 CA A:ASN45 4.7 41.8 1.0 CA A:HIS57 4.8 48.1 1.0 ND2 A:ASN45 4.8 39.8 1.0 CB A:ASN45 4.8 39.4 1.0 O A:HIS56 4.9 47.1 1.0 CG A:GLU89 4.9 47.5 1.0 CG2 A:VAL44 4.9 43.5 1.0 C A:HIS57 4.9 48.3 1.0

Magnesium binding site 2 out of 12 in the Structure Analysis of Geranyl Diphosphate Methyltransferase in Complex with Gpp and Sinefungin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure Analysis of Geranyl Diphosphate Methyltransferase in Complex with Gpp and Sinefungin within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg503 b:10.0 occ:1.00 O2B B:GPP502 2.6 55.7 1.0 OD1 B:ASN45 2.7 53.7 1.0 O B:HIS58 3.1 45.2 1.0 O1A B:GPP502 3.1 61.0 1.0 OE2 B:GLU89 3.4 46.2 1.0 OE1 B:GLU89 3.5 48.6 1.0 CD B:GLU89 3.7 47.2 1.0 PA B:GPP502 3.8 59.8 1.0 PB B:GPP502 3.9 55.6 1.0 CG B:ASN45 3.9 52.5 1.0 O3A B:GPP502 3.9 57.9 1.0 O2A B:GPP502 4.0 60.4 1.0 OH B:TYR264 4.0 45.0 1.0 O B:VAL44 4.0 45.6 1.0 NH1 B:ARG268 4.1 41.7 1.0 C B:HIS58 4.3 43.6 1.0 N B:HIS58 4.3 43.4 1.0 O1B B:GPP502 4.5 57.0 1.0 CE1 B:TYR59 4.6 38.0 1.0 CD1 B:TYR59 4.6 39.2 1.0 ND2 B:ASN45 4.6 53.5 1.0 CA B:ASN45 4.8 48.2 1.0 CA B:HIS58 4.9 43.3 1.0 C B:HIS57 4.9 43.9 1.0 CA B:HIS57 4.9 45.1 1.0 C B:VAL44 4.9 45.7 1.0 CB B:ASN45 4.9 50.5 1.0 O B:HIS56 4.9 45.5 1.0 CG B:GLU89 5.0 47.2 1.0

Magnesium binding site 3 out of 12 in the Structure Analysis of Geranyl Diphosphate Methyltransferase in Complex with Gpp and Sinefungin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure Analysis of Geranyl Diphosphate Methyltransferase in Complex with Gpp and Sinefungin within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg503 b:58.8 occ:1.00 O2B C:GPP502 2.7 56.2 1.0 O2A C:GPP502 2.8 57.9 1.0 OD1 C:ASN45 2.8 48.6 1.0 OE2 C:GLU89 2.8 49.4 1.0 O C:HIS58 3.1 59.1 1.0 OE1 C:GLU89 3.2 50.6 1.0 CD C:GLU89 3.3 49.9 1.0 OH C:TYR264 3.5 47.5 1.0 NH1 C:ARG268 3.9 43.1 1.0 O C:VAL44 3.9 59.4 1.0 CG C:ASN45 4.0 50.7 1.0 PA C:GPP502 4.2 57.1 1.0 PB C:GPP502 4.2 56.3 1.0 C C:HIS58 4.3 58.6 1.0 CD1 C:TYR59 4.3 60.7 1.0 CE1 C:TYR59 4.4 60.5 1.0 CG C:GLU89 4.6 48.8 1.0 N C:HIS58 4.7 60.2 1.0 O3A C:GPP502 4.7 56.6 1.0 C C:VAL44 4.8 59.5 1.0 CZ C:TYR264 4.8 48.1 1.0 O C:HIS56 4.8 63.4 1.0 O3B C:GPP502 4.8 56.3 1.0 CA C:ASN45 4.8 56.5 1.0 ND2 C:ASN45 4.9 50.0 1.0 CB C:ASN45 4.9 53.3 1.0 CG2 C:VAL44 4.9 57.2 1.0 CZ C:ARG268 4.9 41.1 1.0 O1 C:GPP502 4.9 57.1 1.0 CD2 C:LEU48 5.0 56.6 1.0

Magnesium binding site 4 out of 12 in the Structure Analysis of Geranyl Diphosphate Methyltransferase in Complex with Gpp and Sinefungin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure Analysis of Geranyl Diphosphate Methyltransferase in Complex with Gpp and Sinefungin within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg503 b:31.7 occ:1.00 OD1 D:ASN45 2.6 58.2 1.0 O2A D:GPP502 2.6 35.8 1.0 O D:HIS58 2.9 41.6 1.0 OE2 D:GLU89 2.9 50.1 1.0 O2B D:GPP502 2.9 43.1 1.0 OE1 D:GLU89 3.0 50.1 1.0 CD D:GLU89 3.1 50.1 1.0 OH D:TYR264 3.7 44.8 1.0 CG D:ASN45 3.8 58.3 1.0 C D:HIS58 4.0 40.3 1.0 N D:HIS58 4.1 40.5 1.0 PA D:GPP502 4.1 38.2 1.0 O D:HIS56 4.2 47.5 1.0 O D:VAL44 4.2 61.0 1.0 NH1 D:ARG268 4.2 45.2 1.0 CG D:GLU89 4.4 48.6 1.0 PB D:GPP502 4.4 43.2 1.0 CD1 D:TYR59 4.5 36.6 1.0 CE1 D:TYR59 4.5 37.1 1.0 CA D:HIS58 4.7 39.9 1.0 CA D:HIS57 4.7 41.5 1.0 CB D:ASN45 4.7 57.4 1.0 C D:HIS57 4.7 40.3 1.0 ND2 D:ASN45 4.8 58.9 1.0 O3A D:GPP502 4.8 41.5 1.0 CA D:ASN45 4.8 57.6 1.0 O1 D:GPP502 4.8 37.9 1.0 C D:HIS56 4.9 46.9 1.0 CG2 D:VAL44 4.9 59.1 1.0 CZ D:TYR264 4.9 46.3 1.0 O1B D:GPP502 5.0 41.7 1.0 C D:VAL44 5.0 60.1 1.0

Magnesium binding site 5 out of 12 in the Structure Analysis of Geranyl Diphosphate Methyltransferase in Complex with Gpp and Sinefungin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure Analysis of Geranyl Diphosphate Methyltransferase in Complex with Gpp and Sinefungin within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg503 b:45.9 occ:1.00 O2A E:GPP502 2.6 53.9 1.0 OD1 E:ASN45 2.7 67.3 1.0 O2B E:GPP502 2.8 50.5 1.0 OE2 E:GLU89 3.1 46.1 1.0 O E:HIS58 3.1 42.1 1.0 OE1 E:GLU89 3.1 46.8 1.0 CD E:GLU89 3.3 46.2 1.0 OH E:TYR264 3.8 48.3 1.0 PA E:GPP502 3.9 55.4 1.0 CG E:ASN45 3.9 66.5 1.0 O E:VAL44 4.1 66.7 1.0 NH1 E:ARG268 4.2 43.8 1.0 C E:HIS58 4.2 40.2 1.0 O1 E:GPP502 4.2 57.2 1.0 N E:HIS58 4.3 41.9 1.0 O E:HIS56 4.3 49.0 1.0 PB E:GPP502 4.3 51.7 1.0 CD1 E:TYR59 4.6 41.1 1.0 CE1 E:TYR59 4.6 42.5 1.0 O3A E:GPP502 4.6 53.5 1.0 CA E:HIS57 4.6 46.0 1.0 CG E:GLU89 4.6 45.7 1.0 C E:HIS57 4.7 43.9 1.0 ND2 E:ASN45 4.7 67.0 1.0 CA E:HIS58 4.9 40.4 1.0 CA E:ASN45 4.9 64.8 1.0 C E:HIS56 4.9 49.0 1.0 CB E:ASN45 5.0 65.2 1.0

Magnesium binding site 6 out of 12 in the Structure Analysis of Geranyl Diphosphate Methyltransferase in Complex with Gpp and Sinefungin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure Analysis of Geranyl Diphosphate Methyltransferase in Complex with Gpp and Sinefungin within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg503 b:36.8 occ:1.00 OD1 F:ASN45 2.6 48.9 1.0 O2B F:GPP502 2.9 61.5 1.0 O F:HIS58 3.0 61.8 1.0 O2A F:GPP502 3.1 60.6 1.0 O1B F:GPP502 3.2 61.3 1.0 OE1 F:GLU89 3.4 53.5 1.0 OE2 F:GLU89 3.4 49.4 1.0 CD F:GLU89 3.7 51.2 1.0 PB F:GPP502 3.7 61.1 1.0 CG F:ASN45 3.8 50.9 1.0 OH F:TYR264 4.0 50.5 1.0 NH1 F:ARG268 4.2 44.5 1.0 O F:VAL44 4.2 58.4 1.0 C F:HIS58 4.2 62.2 1.0 O3A F:GPP502 4.3 60.4 1.0 PA F:GPP502 4.3 60.7 1.0 O F:HIS56 4.3 65.9 1.0 N F:HIS58 4.4 64.7 1.0 CE1 F:TYR59 4.5 63.4 1.0 CD1 F:TYR59 4.5 63.1 1.0 C F:HIS57 4.6 65.5 1.0 CA F:ASN45 4.6 54.7 1.0 CA F:HIS57 4.6 66.4 1.0 CB F:ASN45 4.7 52.3 1.0 ND2 F:ASN45 4.8 50.4 1.0 C F:VAL44 4.9 57.8 1.0 CA F:HIS58 4.9 63.0 1.0 CG F:GLU89 4.9 49.8 1.0 O3B F:GPP502 5.0 59.2 1.0

Magnesium binding site 7 out of 12 in the Structure Analysis of Geranyl Diphosphate Methyltransferase in Complex with Gpp and Sinefungin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure Analysis of Geranyl Diphosphate Methyltransferase in Complex with Gpp and Sinefungin within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg503 b:38.4 occ:1.00 O2A G:GPP502 2.5 37.7 1.0 OD1 G:ASN45 2.7 48.3 1.0 O2B G:GPP502 2.8 35.8 1.0 O G:HIS58 3.0 45.6 1.0 OE2 G:GLU89 3.1 49.4 1.0 OE1 G:GLU89 3.1 48.2 1.0 CD G:GLU89 3.3 49.0 1.0 OH G:TYR264 3.8 45.0 1.0 CG G:ASN45 3.9 48.5 1.0 PA G:GPP502 3.9 40.0 1.0 C G:HIS58 4.1 44.7 1.0 NH1 G:ARG268 4.2 44.4 1.0 O G:VAL44 4.2 49.2 1.0 PB G:GPP502 4.2 36.6 1.0 N G:HIS58 4.2 45.0 1.0 O G:HIS56 4.4 51.1 1.0 CD1 G:TYR59 4.4 38.5 1.0 CE1 G:TYR59 4.4 37.1 1.0 O3A G:GPP502 4.5 38.6 1.0 CG G:GLU89 4.6 48.4 1.0 O1 G:GPP502 4.6 37.3 1.0 ND2 G:ASN45 4.8 48.1 1.0 CA G:HIS57 4.8 46.4 1.0 C G:HIS57 4.8 45.2 1.0 CA G:HIS58 4.8 45.0 1.0 CA G:ASN45 4.8 48.7 1.0 CB G:ASN45 4.9 48.1 1.0 O3B G:GPP502 4.9 34.1 1.0 O1A G:GPP502 5.0 39.0 1.0

Magnesium binding site 8 out of 12 in the Structure Analysis of Geranyl Diphosphate Methyltransferase in Complex with Gpp and Sinefungin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure Analysis of Geranyl Diphosphate Methyltransferase in Complex with Gpp and Sinefungin within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg503 b:35.9 occ:1.00 O2A H:GPP502 2.7 57.4 1.0 O2B H:GPP502 2.8 61.8 1.0 O H:HIS58 3.0 53.9 1.0 OE2 H:GLU89 3.4 47.6 1.0 OE1 H:GLU89 3.5 50.5 1.0 CD H:GLU89 3.6 49.0 1.0 O1 H:GPP502 3.8 56.0 1.0 PA H:GPP502 3.8 56.5 1.0 OH H:TYR264 3.8 49.8 1.0 PB H:GPP502 3.8 61.6 1.0 O3B H:GPP502 3.9 62.0 1.0 NH1 H:ARG268 4.0 44.9 1.0 C H:HIS58 4.1 54.5 1.0 CE1 H:TYR59 4.1 56.4 1.0 CD1 H:TYR59 4.1 56.5 1.0 N H:HIS58 4.3 55.6 1.0 O3A H:GPP502 4.4 58.9 1.0 O H:HIS56 4.4 55.4 1.0 C H:HIS57 4.5 56.8 1.0 CA H:HIS57 4.7 57.4 1.0 CA H:HIS58 4.8 54.4 1.0 CG H:GLU89 4.8 49.1 1.0

Magnesium binding site 9 out of 12 in the Structure Analysis of Geranyl Diphosphate Methyltransferase in Complex with Gpp and Sinefungin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Structure Analysis of Geranyl Diphosphate Methyltransferase in Complex with Gpp and Sinefungin within 5.0Å range: probe atom residue distance (Å) B Occ I:Mg503 b:43.0 occ:1.00 O2B I:GPP502 2.7 46.1 1.0 O2A I:GPP502 2.7 49.7 1.0 OD1 I:ASN45 2.8 36.5 1.0 O I:HIS58 3.0 41.4 1.0 OE1 I:GLU89 3.1 47.6 1.0 OE2 I:GLU89 3.2 47.5 1.0 CD I:GLU89 3.3 48.1 1.0 C I:HIS58 3.9 40.8 1.0 OH I:TYR264 3.9 43.6 1.0 N I:HIS58 4.0 44.0 1.0 CG I:ASN45 4.0 37.5 1.0 PA I:GPP502 4.0 49.3 1.0 PB I:GPP502 4.2 45.9 1.0 CD1 I:TYR59 4.2 39.3 1.0 NH1 I:ARG268 4.3 42.5 1.0 CE1 I:TYR59 4.3 38.6 1.0 C I:HIS57 4.4 45.6 1.0 CA I:HIS57 4.5 46.3 1.0 O3A I:GPP502 4.5 47.5 1.0 CA I:HIS58 4.5 41.4 1.0 O I:HIS56 4.5 49.4 1.0 CG I:GLU89 4.5 47.6 1.0 O1A I:GPP502 4.7 50.6 1.0 N I:TYR59 4.8 39.6 1.0 ND2 I:ASN45 4.8 34.6 1.0 CA I:TYR59 4.9 38.8 1.0 O3B I:GPP502 4.9 44.1 1.0 C I:HIS56 5.0 49.0 1.0 N I:HIS57 5.0 48.1 1.0 CB I:ASN45 5.0 39.7 1.0

Magnesium binding site 10 out of 12 in the Structure Analysis of Geranyl Diphosphate Methyltransferase in Complex with Gpp and Sinefungin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Structure Analysis of Geranyl Diphosphate Methyltransferase in Complex with Gpp and Sinefungin within 5.0Å range: probe atom residue distance (Å) B Occ J:Mg503 b:21.3 occ:1.00 O2A J:GPP502 2.6 45.3 1.0 O2B J:GPP502 2.7 46.0 1.0 OD1 J:ASN45 2.7 50.8 1.0 O J:HIS58 3.3 36.0 1.0 OE1 J:GLU89 3.3 51.6 1.0 OE2 J:GLU89 3.4 50.5 1.0 CD J:GLU89 3.6 50.8 1.0 PA J:GPP502 3.9 46.7 1.0 CG J:ASN45 4.0 49.7 1.0 O J:HIS56 4.1 47.2 1.0 PB J:GPP502 4.1 47.7 1.0 OH J:TYR264 4.2 47.3 1.0 N J:HIS58 4.2 42.2 1.0 O J:VAL44 4.3 48.0 1.0 NH1 J:ARG268 4.4 43.4 1.0 C J:HIS58 4.4 36.6 1.0 O3A J:GPP502 4.4 46.5 1.0 CA J:HIS57 4.5 45.5 1.0 O1A J:GPP502 4.6 48.3 1.0 C J:HIS57 4.6 44.0 1.0 O3B J:GPP502 4.6 47.8 1.0 ND2 J:ASN45 4.8 51.3 1.0 CA J:ASN45 4.8 46.9 1.0 C J:HIS56 4.8 48.0 1.0 CG1 J:VAL44 4.9 45.5 1.0 CB J:ASN45 4.9 48.1 1.0 CA J:HIS58 4.9 38.3 1.0 C J:VAL44 4.9 47.1 1.0 CG J:GLU89 4.9 49.4 1.0 CE1 J:TYR59 5.0 29.0 1.0

O.Ariyawutthiphan, T.Ose, A.Minami, S.Sinde, M.Tsuda, Y.-G.Gao, M.Yao, H.Oikawa, I.Tanaka. Structure Analysis of Geranyl Pyrophosphate Methyltransferase and the Proposed Reaction Mechanism of Sam-Dependent C-Methylation Acta Crystallogr.,Sect.D V. 68 1558 2012.
ISSN: ISSN 0907-4449
PubMed: 23090405
DOI: 10.1107/S0907444912038486