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Magnesium in PDB 3b06: Crystal Structure of Sulfolobus Shibatae Isopentenyl Diphosphate Isomerase in Complex with Reduced Fmn and Dmapp.

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

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

Protein crystallography data

The structure of Crystal Structure of Sulfolobus Shibatae Isopentenyl Diphosphate Isomerase in Complex with Reduced Fmn and Dmapp., PDB code: 3b06 was solved by H.Unno, T.Nagai, H.Hemmi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.39 / 2.29
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 100.842, 100.842, 334.499, 90.00, 90.00, 90.00
R / Rfree (%) 20.4 / 23.9

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 Dmapp. (pdb code 3b06). 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: 3b06:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3b06

Go back to Magnesium Binding Sites List in 3b06
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:Mg1001

b:73.7
occ:1.00
 O1A A:DMA701 2.0 55.0 1.0
OE1 A:GLU161 2.2 62.3 1.0
O3B A:DMA701 2.4 53.0 1.0
PA A:DMA701 3.1 58.2 1.0
O3A A:DMA701 3.2 55.6 1.0
CD A:GLU161 3.3 59.6 1.0
PB A:DMA701 3.3 56.5 1.0
OE2 A:GLU161 3.5 64.2 1.0
OD1 A:ASN157 3.8 45.3 1.0
O2B A:DMA701 3.9 54.8 1.0
NH1 A:ARG98 4.0 59.8 1.0
O2A A:DMA701 4.1 60.7 1.0
O1 A:DMA701 4.2 57.5 1.0
OE1 A:GLU168 4.3 79.1 1.0
OE1 A:GLN130 4.4 59.2 1.0
NH2 A:ARG7 4.5 62.9 1.0
NE2 A:HIS155 4.6 40.0 1.0
CG A:ASN157 4.6 39.4 1.0
ND2 A:ASN157 4.6 34.9 1.0
OE1 A:GLN164 4.7 62.3 1.0
CG A:GLU161 4.7 51.8 1.0
O1B A:DMA701 4.7 55.3 1.0
CG A:PRO129 4.9 49.0 1.0

Magnesium binding site 2 out of 4 in 3b06

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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 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:Mg1001

b:71.0
occ:1.00
 O1A B:DMA701 2.0 62.6 1.0
O3B B:DMA701 2.3 54.4 1.0
OE1 B:GLU161 2.4 62.6 1.0
PA B:DMA701 3.2 57.5 1.0
PB B:DMA701 3.3 59.5 1.0
O3A B:DMA701 3.3 58.8 1.0
CD B:GLU161 3.4 59.6 1.0
OE2 B:GLU161 3.7 63.6 1.0
O2B B:DMA701 3.7 57.0 1.0
NH1 B:ARG98 3.8 59.8 1.0
OD1 B:ASN157 4.0 44.9 1.0
OE1 B:GLN130 4.1 59.4 1.0
OE1 B:GLU168 4.2 79.0 1.0
O2A B:DMA701 4.2 59.8 1.0
O1 B:DMA701 4.4 59.3 1.0
NH2 B:ARG7 4.4 63.9 1.0
NE2 B:HIS155 4.6 40.5 1.0
O1B B:DMA701 4.6 57.2 1.0
CG B:PRO129 4.8 49.6 1.0
OE1 B:GLN164 4.8 62.0 1.0
CG B:GLU161 4.8 52.0 1.0
CG B:ASN157 4.8 39.3 1.0
ND2 B:ASN157 4.8 34.8 1.0
NE2 B:GLN164 4.9 61.9 1.0
O B:HOH410 4.9 48.4 1.0

Magnesium binding site 3 out of 4 in 3b06

Go back to Magnesium Binding Sites List in 3b06
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:Mg1001

b:66.6
occ:1.00
 OE1 C:GLU161 2.2 62.3 1.0
O1A C:DMA701 2.2 53.1 1.0
O3B C:DMA701 2.3 52.1 1.0
PB C:DMA701 3.2 50.9 1.0
CD C:GLU161 3.3 59.6 1.0
PA C:DMA701 3.4 54.9 1.0
O3A C:DMA701 3.4 53.3 1.0
O2B C:DMA701 3.7 51.3 1.0
OD1 C:ASN157 3.7 44.3 1.0
OE2 C:GLU161 3.8 63.3 1.0
OE1 C:GLN130 4.0 59.4 1.0
NH1 C:ARG98 4.1 60.0 1.0
O1 C:DMA701 4.3 59.7 1.0
OE1 C:GLU168 4.3 78.9 1.0
NE2 C:HIS155 4.3 40.0 1.0
ND2 C:ASN157 4.4 35.8 1.0
CG C:PRO129 4.5 49.5 1.0
CG C:ASN157 4.5 39.7 1.0
O2A C:DMA701 4.5 53.5 1.0
CG C:GLU161 4.6 51.8 1.0
O1B C:DMA701 4.7 49.5 1.0
NH2 C:ARG7 4.9 63.6 1.0
O C:HOH416 4.9 38.9 1.0
CD C:PRO129 4.9 48.9 1.0
CB C:PRO129 5.0 48.9 1.0

Magnesium binding site 4 out of 4 in 3b06

Go back to Magnesium Binding Sites List in 3b06
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:Mg1001

b:62.3
occ:1.00
 O1A D:DMA701 2.0 55.6 1.0
O3B D:DMA701 2.0 52.4 1.0
OE1 D:GLU161 2.3 62.4 1.0
PA D:DMA701 3.1 51.3 1.0
PB D:DMA701 3.2 52.3 1.0
CD D:GLU161 3.3 59.5 1.0
O3A D:DMA701 3.4 49.0 1.0
OE2 D:GLU161 3.4 63.3 1.0
NH1 D:ARG98 3.7 59.9 1.0
O2B D:DMA701 4.0 45.8 1.0
OD1 D:ASN157 4.0 45.1 1.0
O2A D:DMA701 4.0 56.3 1.0
OE1 D:GLU168 4.1 79.0 1.0
OE1 D:GLN130 4.3 59.5 1.0
O1 D:DMA701 4.3 54.9 1.0
NH2 D:ARG7 4.3 61.5 1.0
O1B D:DMA701 4.5 52.8 1.0
OE1 D:GLN164 4.6 62.2 1.0
CG D:GLU161 4.7 52.0 1.0
NE2 D:GLN164 4.8 61.8 1.0
CG D:ASN157 4.9 39.2 1.0
ND2 D:ASN157 4.9 34.6 1.0
NE2 D:HIS155 4.9 40.6 1.0
CZ D:ARG98 5.0 59.6 1.0
CG D:PRO129 5.0 48.9 1.0

Reference:

T.Nagai, H.Unno, M.W.Janczak, T.Yoshimura, C.D.Poulter, H.Hemmi. Covalent Modification of Reduced Flavin Mononucleotide in Type-2 Isopentenyl Diphosphate Isomerase By Active-Site-Directed Inhibitors. Proc.Natl.Acad.Sci.Usa V. 108 20461 2011.
ISSN: ISSN 0027-8424
PubMed: 22158896
DOI: 10.1073/PNAS.1115749108
Page generated: Sun Aug 10 17:36:44 2025

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