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

Enzymatic activity of Crystal Structure of Sulfolobus Shibatae Isopentenyl Diphosphate Isomerase in Complex with Fmn and Dmapp.

All present enzymatic activity of Crystal Structure of Sulfolobus Shibatae Isopentenyl Diphosphate Isomerase in Complex with Fmn and Dmapp.:
5.3.3.2;

Protein crystallography data

The structure of Crystal Structure of Sulfolobus Shibatae Isopentenyl Diphosphate Isomerase in Complex with Fmn and Dmapp., PDB code: 2zrx 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) 45.22 / 3.00
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 101.071, 101.071, 333.430, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 21.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Sulfolobus Shibatae Isopentenyl Diphosphate Isomerase in Complex with Fmn and Dmapp. (pdb code 2zrx). 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 Fmn and Dmapp., PDB code: 2zrx:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 2zrx

Go back to Magnesium Binding Sites List in 2zrx
Magnesium binding site 1 out of 4 in the Crystal Structure of Sulfolobus Shibatae Isopentenyl Diphosphate Isomerase in Complex with 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 Fmn and Dmapp. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg702

b:63.0
occ:1.00
 OE1 A:GLU161 2.0 56.5 1.0
O2A A:DMA701 2.0 63.2 1.0
O1B A:DMA701 2.6 64.1 1.0
CD A:GLU161 2.9 54.0 1.0
OE2 A:GLU161 3.2 55.0 1.0
PA A:DMA701 3.2 63.8 1.0
O3A A:DMA701 3.4 64.2 1.0
PB A:DMA701 3.5 64.9 1.0
ND2 A:ASN157 3.9 38.9 1.0
O2B A:DMA701 3.9 64.5 1.0
O1 A:DMA701 4.2 63.4 1.0
NE2 A:GLN164 4.2 53.2 1.0
CG A:GLU161 4.3 49.5 1.0
O1A A:DMA701 4.4 64.0 1.0
OE1 A:GLN164 4.5 54.2 1.0
OE2 A:GLU168 4.5 64.2 1.0
CG A:PRO129 4.6 49.0 1.0
OE1 A:GLN130 4.7 55.3 1.0
OD1 A:ASN157 4.7 40.2 1.0
CG A:ASN157 4.7 39.4 1.0
NH2 A:ARG7 4.8 66.2 1.0
NE2 A:HIS155 4.8 40.7 1.0
CD A:GLN164 4.8 53.6 1.0
O3B A:DMA701 4.9 64.3 1.0

Magnesium binding site 2 out of 4 in 2zrx

Go back to Magnesium Binding Sites List in 2zrx
Magnesium binding site 2 out of 4 in the Crystal Structure of Sulfolobus Shibatae Isopentenyl Diphosphate Isomerase in Complex with 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 Fmn and Dmapp. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg702

b:60.7
occ:1.00
 OE1 B:GLU161 2.2 56.5 1.0
O2A B:DMA701 2.2 63.3 1.0
O1B B:DMA701 2.2 64.0 1.0
CD B:GLU161 3.1 54.1 1.0
OE2 B:GLU161 3.3 54.9 1.0
PB B:DMA701 3.3 65.0 1.0
PA B:DMA701 3.3 64.1 1.0
O3A B:DMA701 3.4 64.4 1.0
O2B B:DMA701 3.8 64.7 1.0
NE2 B:GLN164 4.0 53.3 1.0
ND2 B:ASN157 4.1 38.9 1.0
O1A B:DMA701 4.4 64.0 1.0
NH2 B:ARG7 4.4 66.1 1.0
OE1 B:GLN164 4.4 54.0 1.0
OE2 B:GLU168 4.4 64.1 1.0
O1 B:DMA701 4.5 63.4 1.0
CG B:GLU161 4.5 49.7 1.0
CD B:GLN164 4.6 53.6 1.0
O3B B:DMA701 4.6 64.2 1.0
OE1 B:GLN130 4.7 55.5 1.0
CG B:PRO129 4.9 49.0 1.0
CZ B:ARG7 4.9 65.8 1.0

Magnesium binding site 3 out of 4 in 2zrx

Go back to Magnesium Binding Sites List in 2zrx
Magnesium binding site 3 out of 4 in the Crystal Structure of Sulfolobus Shibatae Isopentenyl Diphosphate Isomerase in Complex with 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 Fmn and Dmapp. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg702

b:62.6
occ:1.00
 O2A C:DMA701 2.2 63.2 1.0
OE1 C:GLU161 2.2 56.6 1.0
O1B C:DMA701 2.2 64.2 1.0
O3A C:DMA701 3.1 64.3 1.0
PB C:DMA701 3.1 64.9 1.0
PA C:DMA701 3.2 63.9 1.0
CD C:GLU161 3.3 54.0 1.0
O2B C:DMA701 3.4 64.5 1.0
OE2 C:GLU161 3.7 54.8 1.0
ND2 C:ASN157 3.7 39.0 1.0
O1 C:DMA701 4.1 63.5 1.0
O1A C:DMA701 4.4 63.9 1.0
NE2 C:HIS155 4.4 40.7 1.0
OE1 C:GLN130 4.5 55.4 1.0
O3B C:DMA701 4.5 64.1 1.0
CG C:GLU161 4.6 49.6 1.0
NE2 C:GLN164 4.6 53.3 1.0
CG C:PRO129 4.6 49.1 1.0
CG C:ASN157 4.7 39.4 1.0
NH2 C:ARG7 4.7 66.2 1.0
OD1 C:ASN157 4.7 40.1 1.0
OE2 C:GLU168 4.8 64.1 1.0
OE1 C:GLN164 4.8 54.2 1.0

Magnesium binding site 4 out of 4 in 2zrx

Go back to Magnesium Binding Sites List in 2zrx
Magnesium binding site 4 out of 4 in the Crystal Structure of Sulfolobus Shibatae Isopentenyl Diphosphate Isomerase in Complex with 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 Fmn and Dmapp. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg702

b:60.1
occ:1.00
 O2A D:DMA701 2.2 63.1 1.0
OE1 D:GLU161 2.2 56.6 1.0
O1B D:DMA701 2.2 63.9 1.0
CD D:GLU161 3.2 54.0 1.0
PB D:DMA701 3.2 64.8 1.0
PA D:DMA701 3.3 63.6 1.0
O3A D:DMA701 3.3 64.1 1.0
OE2 D:GLU161 3.4 54.7 1.0
O2B D:DMA701 3.6 64.5 1.0
ND2 D:ASN157 4.0 39.0 1.0
O1 D:DMA701 4.3 63.3 1.0
OE1 D:GLN130 4.3 55.5 1.0
O1A D:DMA701 4.4 63.9 1.0
OE2 D:GLU168 4.5 64.1 1.0
CG D:GLU161 4.5 49.5 1.0
CG D:PRO129 4.5 49.0 1.0
NE2 D:GLN164 4.6 53.3 1.0
O3B D:DMA701 4.6 64.2 1.0
NE2 D:HIS155 4.6 40.6 1.0
NH2 D:ARG7 4.7 66.2 1.0
OD1 D:ASN157 4.8 40.2 1.0
CG D:ASN157 4.8 39.5 1.0
OE1 D:GLN164 4.9 54.0 1.0

Reference:

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
Page generated: Sun Aug 10 17:02:32 2025

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