Magnesium in PDB 2zrz: Crystal Structure of Sulfolobus Shibatae Isopentenyl Diphosphate Isomerase in Complex with Reduced Fmn and Dmapp

The structure of Crystal Structure of Sulfolobus Shibatae Isopentenyl Diphosphate Isomerase in Complex with Reduced Fmn and Dmapp, PDB code: 2zrz was solved by H.Unno, S.Yamashita, Y.Ikeda, S.Sekiguchi, N.Yoshida, T.Yoshimura, M.Kusunoki, T.Nakayama, T.Nishino, H.Hemmi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.85 / 2.90
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	100.879, 100.879, 334.864, 90.00, 90.00, 90.00
R / Rfree (%)	19.2 / 21.3

The binding sites of Magnesium atom in the Crystal Structure of Sulfolobus Shibatae Isopentenyl Diphosphate Isomerase in Complex with Reduced Fmn and Dmapp (pdb code 2zrz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Sulfolobus Shibatae Isopentenyl Diphosphate Isomerase in Complex with Reduced Fmn and Dmapp, PDB code: 2zrz:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Sulfolobus Shibatae Isopentenyl Diphosphate Isomerase in Complex with Reduced Fmn and Dmapp


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 Sulfolobus Shibatae Isopentenyl Diphosphate Isomerase in Complex with Reduced Fmn and Dmapp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg702 b:47.4 occ:1.00 OE1 A:GLU161 2.4 56.7 1.0 O2A A:DMA701 2.6 61.7 1.0 O2B A:DMA701 2.8 59.2 1.0 O1B A:DMA701 3.2 59.5 1.0 NE2 A:HIS155 3.4 39.7 1.0 ND2 A:ASN157 3.4 37.2 1.0 CG A:PRO129 3.4 47.2 1.0 PB A:DMA701 3.5 60.3 1.0 CD A:GLU161 3.6 54.7 1.0 PA A:DMA701 3.7 62.6 1.0 OD1 A:ASN157 3.8 38.9 1.0 O3A A:DMA701 3.9 61.1 1.0 CG A:ASN157 4.0 37.2 1.0 OE1 A:GLN130 4.1 54.3 1.0 O1 A:DMA701 4.1 62.3 1.0 CD A:PRO129 4.2 46.8 1.0 CE1 A:HIS155 4.3 39.6 1.0 OE2 A:GLU161 4.3 56.8 1.0 CD2 A:HIS155 4.4 38.9 1.0 CG A:GLU161 4.6 49.4 1.0 CA A:GLY127 4.7 44.4 1.0 CB A:PRO129 4.8 47.4 1.0 O3B A:DMA701 4.9 59.6 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Sulfolobus Shibatae Isopentenyl Diphosphate Isomerase in Complex with Reduced Fmn and Dmapp


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 Sulfolobus Shibatae Isopentenyl Diphosphate Isomerase in Complex with Reduced Fmn and Dmapp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg702 b:65.1 occ:1.00 O2A B:DMA701 2.2 67.9 1.0 OE1 B:GLU161 2.2 56.7 1.0 O1B B:DMA701 2.2 67.1 1.0 CD B:GLU161 3.2 54.7 1.0 PB B:DMA701 3.3 67.5 1.0 PA B:DMA701 3.3 69.4 1.0 O3A B:DMA701 3.3 68.8 1.0 OE2 B:GLU161 3.6 56.8 1.0 O2B B:DMA701 3.7 67.2 1.0 ND2 B:ASN157 3.9 37.2 1.0 O1 B:DMA701 4.3 69.2 1.0 NE2 B:GLN164 4.3 57.0 1.0 O1A B:DMA701 4.5 69.6 1.0 NH2 B:ARG7 4.5 64.6 1.0 CG B:PRO129 4.6 47.2 1.0 CG B:GLU161 4.6 49.4 1.0 O3B B:DMA701 4.6 66.9 1.0 NE2 B:HIS155 4.8 39.7 1.0 OE1 B:GLN130 4.8 54.3 1.0 OE1 B:GLN164 4.8 57.6 1.0 OD1 B:ASN157 4.8 38.9 1.0 CG B:ASN157 4.8 37.2 1.0 NH2 B:ARG98 5.0 60.4 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Sulfolobus Shibatae Isopentenyl Diphosphate Isomerase in Complex with Reduced Fmn and Dmapp


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 Sulfolobus Shibatae Isopentenyl Diphosphate Isomerase in Complex with Reduced Fmn and Dmapp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg702 b:62.8 occ:1.00 O2A C:DMA701 2.2 62.9 1.0 OE1 C:GLU161 2.2 56.7 1.0 O1B C:DMA701 2.2 65.4 1.0 PB C:DMA701 3.1 65.7 1.0 O3B C:DMA701 3.2 66.5 1.0 PA C:DMA701 3.3 65.0 1.0 CD C:GLU161 3.4 54.7 1.0 O3A C:DMA701 3.5 65.5 1.0 ND2 C:ASN157 3.5 37.2 1.0 O1 C:DMA701 3.9 65.2 1.0 OE2 C:GLU161 3.9 56.8 1.0 NE2 C:HIS155 4.1 39.7 1.0 CG C:PRO129 4.3 47.2 1.0 OD1 C:ASN157 4.4 38.9 1.0 CG C:ASN157 4.4 37.2 1.0 O2B C:DMA701 4.5 65.7 1.0 OE1 C:GLN130 4.6 54.3 1.0 CG C:GLU161 4.6 49.4 1.0 O1A C:DMA701 4.7 64.9 1.0 CE1 C:HIS155 4.8 39.6 1.0 NE2 C:GLN164 4.9 57.0 1.0 C1 C:DMA701 5.0 64.8 1.0 NH2 C:ARG7 5.0 64.6 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Sulfolobus Shibatae Isopentenyl Diphosphate Isomerase in Complex with Reduced Fmn and Dmapp


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 Sulfolobus Shibatae Isopentenyl Diphosphate Isomerase in Complex with Reduced Fmn and Dmapp within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg702 b:58.0 occ:1.00 O2A D:DMA701 2.2 59.0 1.0 OE1 D:GLU161 2.2 56.7 1.0 O1B D:DMA701 2.2 60.2 1.0 O3A D:DMA701 3.1 59.8 1.0 PB D:DMA701 3.1 60.3 1.0 PA D:DMA701 3.2 59.1 1.0 CD D:GLU161 3.3 54.7 1.0 O2B D:DMA701 3.5 60.8 1.0 OE2 D:GLU161 3.7 56.8 1.0 ND2 D:ASN157 3.8 37.2 1.0 CG D:PRO129 4.1 47.2 1.0 O1 D:DMA701 4.2 58.6 1.0 NE2 D:HIS155 4.3 39.7 1.0 OE1 D:GLN130 4.4 54.3 1.0 O1A D:DMA701 4.4 60.8 1.0 OD1 D:ASN157 4.5 38.9 1.0 O3B D:DMA701 4.6 59.8 1.0 CG D:GLU161 4.6 49.4 1.0 CG D:ASN157 4.6 37.2 1.0 NE2 D:GLN164 4.9 57.0 1.0 NH2 D:ARG7 4.9 64.6 1.0

H.Unno, S.Yamashita, Y.Ikeda, S.Y.Sekiguchi, N.Yoshida, T.Yoshimura, M.Kusunoki, T.Nakayama, T.Nishino, H.Hemmi. New Role of Flavin As A General Acid-Base Catalyst with No Redox Function in Type 2 Isopentenyl-Diphosphate Isomerase. J.Biol.Chem. V. 284 9160 2009.
ISSN: ISSN 0021-9258
PubMed: 19158086
DOI: 10.1074/JBC.M808438200