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Magnesium in PDB 2zry: Crystal Structure of Sulfolobus Shibatae Isopentenyl Diphosphate Isomerase in Complex with Reduced Fmn and Ipp.

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

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

Protein crystallography data

The structure of Crystal Structure of Sulfolobus Shibatae Isopentenyl Diphosphate Isomerase in Complex with Reduced Fmn and Ipp., PDB code: 2zry 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) 49.63 / 2.64
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 100.359, 100.359, 334.607, 90.00, 90.00, 90.00
R / Rfree (%) 18.3 / 22.3

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 4 in 2zry

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


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 Ipp. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg702

b:67.8
occ:1.00
 O1A A:IPE701 2.1 53.7 1.0
O2B A:IPE701 2.2 53.9 1.0
OE1 A:GLU161 2.3 53.8 1.0
O A:HOH782 2.6 44.4 1.0
O3A A:IPE701 3.0 53.6 1.0
PB A:IPE701 3.0 52.8 1.0
PA A:IPE701 3.1 53.4 1.0
O1B A:IPE701 3.4 52.2 1.0
CD A:GLU161 3.5 51.9 1.0
OD1 A:ASN157 3.6 34.6 1.0
OE2 A:GLU161 3.9 54.5 1.0
O1 A:IPE701 4.1 55.0 1.0
NE2 A:HIS155 4.1 35.9 1.0
OE1 A:GLN130 4.3 51.0 1.0
NH1 A:ARG98 4.3 57.0 1.0
O2A A:IPE701 4.3 53.4 1.0
CG A:PRO129 4.4 43.2 1.0
O3B A:IPE701 4.5 50.6 1.0
CG A:ASN157 4.5 33.6 1.0
ND2 A:ASN157 4.5 32.0 1.0
CG A:GLU161 4.7 46.1 1.0
C1 A:IPE701 4.8 55.2 1.0
NH2 A:ARG7 4.8 59.9 1.0
CE1 A:HIS155 4.9 35.4 1.0
OE2 A:GLU168 4.9 62.2 1.0
CD A:PRO129 5.0 42.8 1.0

Magnesium binding site 2 out of 4 in 2zry

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


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 Ipp. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg702

b:56.5
occ:1.00
 O1A B:IPE701 2.2 53.7 1.0
OE1 B:GLU161 2.2 53.9 1.0
O2B B:IPE701 2.2 54.0 1.0
PB B:IPE701 3.2 52.8 1.0
O3A B:IPE701 3.2 53.8 1.0
PA B:IPE701 3.2 53.8 1.0
CD B:GLU161 3.3 52.0 1.0
O1B B:IPE701 3.6 52.2 1.0
OE2 B:GLU161 3.6 54.3 1.0
OD1 B:ASN157 3.8 34.7 1.0
NH1 B:ARG98 4.0 57.0 1.0
O1 B:IPE701 4.3 55.2 1.0
NH2 B:ARG7 4.4 59.9 1.0
O2A B:IPE701 4.4 53.5 1.0
OE1 B:GLN130 4.5 51.2 1.0
O3B B:IPE701 4.6 50.5 1.0
NE2 B:GLN164 4.6 52.7 1.0
CG B:GLU161 4.6 46.2 1.0
OE2 B:GLU168 4.7 62.0 1.0
CG B:PRO129 4.7 43.3 1.0
NE2 B:HIS155 4.7 36.4 1.0
CG B:ASN157 4.7 33.7 1.0
OE1 B:GLN164 4.8 53.4 1.0
ND2 B:ASN157 4.8 32.0 1.0
C1 B:IPE701 5.0 55.2 1.0

Magnesium binding site 3 out of 4 in 2zry

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


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 Ipp. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg702

b:55.9
occ:1.00
 O1A C:IPE701 2.2 53.4 1.0
O2B C:IPE701 2.2 54.0 1.0
OE1 C:GLU161 2.2 53.9 1.0
O3A C:IPE701 3.1 53.6 1.0
PB C:IPE701 3.1 52.5 1.0
PA C:IPE701 3.1 53.5 1.0
CD C:GLU161 3.4 51.9 1.0
O1B C:IPE701 3.4 52.1 1.0
OD1 C:ASN157 3.6 34.9 1.0
OE2 C:GLU161 3.8 54.2 1.0
O1 C:IPE701 4.1 55.2 1.0
NE2 C:HIS155 4.3 36.0 1.0
O2A C:IPE701 4.4 53.4 1.0
NH1 C:ARG98 4.4 57.1 1.0
OE1 C:GLN130 4.4 51.1 1.0
O3B C:IPE701 4.5 50.4 1.0
CG C:ASN157 4.5 33.8 1.0
CG C:PRO129 4.5 43.4 1.0
ND2 C:ASN157 4.6 32.0 1.0
NH2 C:ARG7 4.6 59.9 1.0
CG C:GLU161 4.7 46.1 1.0
C1 C:IPE701 4.8 55.2 1.0
O C:HOH784 4.8 34.6 1.0
OE2 C:GLU168 4.9 62.0 1.0
NE2 C:GLN164 5.0 52.7 1.0

Magnesium binding site 4 out of 4 in 2zry

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


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 Ipp. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg702

b:52.5
occ:1.00
 O1A D:IPE701 2.1 53.6 1.0
O2B D:IPE701 2.2 54.1 1.0
OE1 D:GLU161 2.2 54.0 1.0
O D:HOH773 2.3 52.0 1.0
PB D:IPE701 3.1 52.9 1.0
O3A D:IPE701 3.1 53.5 1.0
PA D:IPE701 3.2 53.3 1.0
CD D:GLU161 3.2 51.9 1.0
O1B D:IPE701 3.5 52.3 1.0
OE2 D:GLU161 3.6 54.0 1.0
OD1 D:ASN157 3.8 34.9 1.0
NH1 D:ARG98 4.0 56.9 1.0
O1 D:IPE701 4.2 55.3 1.0
O2A D:IPE701 4.3 53.4 1.0
OE1 D:GLN130 4.4 51.1 1.0
NH2 D:ARG7 4.5 60.0 1.0
O3B D:IPE701 4.5 50.4 1.0
CG D:GLU161 4.6 46.1 1.0
NE2 D:HIS155 4.6 36.1 1.0
CG D:PRO129 4.6 43.3 1.0
OE2 D:GLU168 4.7 62.2 1.0
CG D:ASN157 4.7 33.9 1.0
ND2 D:ASN157 4.7 31.9 1.0
NE2 D:GLN164 4.8 52.7 1.0
OE1 D:GLN164 4.9 53.5 1.0
C1 D:IPE701 5.0 55.2 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: Wed Aug 14 07:58:47 2024

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