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Magnesium in PDB 3b05: Crystal Structure of Sulfolobus Shibatae Isopentenyl Diphosphate Isomerase in Complex with Reduced Fmn and Ipp at 2.2A Resolution.

Enzymatic activity of Crystal Structure of Sulfolobus Shibatae Isopentenyl Diphosphate Isomerase in Complex with Reduced Fmn and Ipp at 2.2A Resolution.

All present enzymatic activity of Crystal Structure of Sulfolobus Shibatae Isopentenyl Diphosphate Isomerase in Complex with Reduced Fmn and Ipp at 2.2A Resolution.:
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 at 2.2A Resolution., PDB code: 3b05 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) 31.62 / 2.20
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 101.617, 101.617, 333.078, 90.00, 90.00, 90.00
R / Rfree (%) 20 / 24.2

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 at 2.2A Resolution. (pdb code 3b05). 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 at 2.2A Resolution., PDB code: 3b05:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3b05

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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 at 2.2A Resolution.


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 at 2.2A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1001

b:47.1
occ:1.00
 O1A A:IPE701 2.0 40.0 1.0
OE1 A:GLU161 2.1 49.0 1.0
O A:HOH437 2.1 36.1 1.0
O A:HOH371 2.2 36.2 1.0
O2B A:IPE701 2.3 42.6 1.0
CD A:GLU161 3.0 43.8 1.0
OE2 A:GLU161 3.2 44.9 1.0
PA A:IPE701 3.3 45.3 1.0
PB A:IPE701 3.4 42.9 1.0
O3A A:IPE701 3.5 41.4 1.0
NH1 A:ARG98 3.7 35.5 1.0
O1B A:IPE701 3.9 42.6 1.0
OD1 A:ASN157 4.0 29.3 1.0
OE1 A:GLN130 4.3 39.5 1.0
O1 A:IPE701 4.3 46.1 1.0
O2A A:IPE701 4.4 37.6 1.0
CG A:GLU161 4.4 38.1 1.0
NH2 A:ARG7 4.4 46.4 1.0
OE1 A:GLN164 4.5 44.0 1.0
OE2 A:GLU168 4.6 54.8 1.0
NE2 A:GLN164 4.7 39.6 1.0
O3B A:IPE701 4.7 42.0 1.0
NE2 A:HIS155 4.8 29.8 1.0
CG A:ASN157 4.9 27.2 1.0
ND2 A:ASN157 4.9 24.5 1.0
CG A:PRO129 5.0 36.7 1.0

Magnesium binding site 2 out of 4 in 3b05

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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 at 2.2A Resolution.


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 at 2.2A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1001

b:60.3
occ:1.00
 O1A B:IPE701 2.1 42.7 1.0
O2B B:IPE701 2.3 38.0 1.0
OE1 B:GLU161 2.7 49.7 1.0
OE2 B:GLU161 2.8 45.4 1.0
CD B:GLU161 3.1 44.0 1.0
PB B:IPE701 3.2 43.0 1.0
PA B:IPE701 3.3 45.5 1.0
O3A B:IPE701 3.4 43.5 1.0
O1B B:IPE701 3.6 41.2 1.0
OD1 B:ASN157 3.9 28.2 1.0
NH1 B:ARG98 3.9 35.0 1.0
OE1 B:GLN130 4.1 38.2 1.0
O1 B:IPE701 4.3 43.5 1.0
NE2 B:HIS155 4.4 29.7 1.0
O2A B:IPE701 4.4 44.9 1.0
CG B:GLU161 4.5 38.4 1.0
ND2 B:ASN157 4.6 24.2 1.0
O3B B:IPE701 4.6 43.8 1.0
NH2 B:ARG7 4.6 46.0 1.0
CG B:ASN157 4.6 26.9 1.0
OE1 B:GLN164 4.7 43.9 1.0
CG B:PRO129 4.8 37.3 1.0
NE2 B:GLN164 4.9 39.4 1.0
O B:HOH446 4.9 27.5 1.0
OE2 B:GLU168 5.0 54.9 1.0

Magnesium binding site 3 out of 4 in 3b05

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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 at 2.2A Resolution.


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 at 2.2A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1001

b:39.2
occ:1.00
 OE1 C:GLU161 2.0 48.8 1.0
O1A C:IPE701 2.1 33.1 1.0
O2B C:IPE701 2.1 34.3 1.0
O C:HOH482 2.2 35.2 1.0
O C:HOH458 2.2 34.4 1.0
CD C:GLU161 3.0 43.9 1.0
OE2 C:GLU161 3.1 45.0 1.0
PA C:IPE701 3.2 35.1 1.0
PB C:IPE701 3.3 34.3 1.0
O3A C:IPE701 3.5 35.1 1.0
OD1 C:ASN157 3.8 28.6 1.0
O1B C:IPE701 3.9 29.0 1.0
NH1 C:ARG98 3.9 35.5 1.0
O1 C:IPE701 4.3 36.6 1.0
O2A C:IPE701 4.3 41.3 1.0
OE1 C:GLN164 4.3 43.4 1.0
CG C:GLU161 4.3 38.2 1.0
NH2 C:ARG7 4.4 46.2 1.0
OE1 C:GLN130 4.5 37.8 1.0
NE2 C:GLN164 4.5 39.7 1.0
O3B C:IPE701 4.6 33.6 1.0
CG C:ASN157 4.6 28.3 1.0
ND2 C:ASN157 4.7 25.6 1.0
NE2 C:HIS155 4.7 29.7 1.0
CD C:GLN164 4.8 41.6 1.0
OE2 C:GLU168 4.9 54.7 1.0

Magnesium binding site 4 out of 4 in 3b05

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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 at 2.2A Resolution.


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 at 2.2A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1001

b:43.6
occ:1.00
 O1A D:IPE701 1.9 37.1 1.0
O2B D:IPE701 2.0 32.6 1.0
O D:HOH476 2.0 31.2 1.0
O D:HOH481 2.1 35.5 1.0
O D:HOH475 2.1 29.0 1.0
OE1 D:GLU161 2.3 48.9 1.0
PA D:IPE701 3.1 35.4 1.0
PB D:IPE701 3.1 35.1 1.0
O3A D:IPE701 3.2 34.0 1.0
CD D:GLU161 3.3 43.8 1.0
OE2 D:GLU161 3.5 44.5 1.0
NH1 D:ARG98 3.7 35.1 1.0
O1B D:IPE701 3.8 30.7 1.0
OD1 D:ASN157 4.0 28.9 1.0
O2A D:IPE701 4.1 38.4 1.0
O1 D:IPE701 4.2 40.5 1.0
NH2 D:ARG7 4.3 45.9 1.0
OE1 D:GLN130 4.3 39.1 1.0
O3B D:IPE701 4.4 30.9 1.0
OE1 D:GLN164 4.5 43.9 1.0
NE2 D:GLN164 4.6 39.0 1.0
CG D:GLU161 4.6 38.1 1.0
NE2 D:HIS155 4.7 29.5 1.0
OE2 D:GLU168 4.7 54.9 1.0
CG D:ASN157 4.9 27.4 1.0
CZ D:ARG98 4.9 39.7 1.0
CD D:GLN164 5.0 41.5 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: Wed Aug 14 08:48:52 2024

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