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Magnesium in PDB 3b04: Crystal Structure of Sulfolobus Shibatae Isopentenyl Diphosphate Isomerase in Complex with Oipp.

Enzymatic activity of Crystal Structure of Sulfolobus Shibatae Isopentenyl Diphosphate Isomerase in Complex with Oipp.

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

Protein crystallography data

The structure of Crystal Structure of Sulfolobus Shibatae Isopentenyl Diphosphate Isomerase in Complex with Oipp., PDB code: 3b04 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) 48.48 / 2.30
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 101.234, 101.234, 337.420, 90.00, 90.00, 90.00
R / Rfree (%) 18.6 / 22

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Sulfolobus Shibatae Isopentenyl Diphosphate Isomerase in Complex with Oipp. (pdb code 3b04). 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 Oipp., PDB code: 3b04:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3b04

Go back to Magnesium Binding Sites List in 3b04
Magnesium binding site 1 out of 4 in the Crystal Structure of Sulfolobus Shibatae Isopentenyl Diphosphate Isomerase in Complex with Oipp.


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 Oipp. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1002

b:74.2
occ:1.00
 O1A A:OOP669 2.2 71.8 1.0
OE2 A:GLU161 3.6 48.3 1.0
PA A:OOP669 3.6 71.2 1.0
NE2 A:GLN164 3.8 51.9 1.0
O A:HOH474 3.9 51.2 1.0
O1B A:OOP669 4.1 70.2 1.0
OE1 A:GLN164 4.2 49.9 1.0
CG A:GLU161 4.3 39.0 1.0
O2A A:OOP669 4.3 71.2 1.0
CD A:GLU161 4.4 44.8 1.0
NH1 A:ARG98 4.4 66.2 1.0
O3A A:OOP669 4.5 71.5 1.0
CD A:GLN164 4.5 49.7 1.0
NH2 A:ARG7 4.6 74.6 1.0
ND2 A:ASN157 4.6 27.5 1.0
O2B A:OOP669 4.6 63.0 1.0
PB A:OOP669 4.7 68.4 1.0
O11 A:OOP669 4.7 65.4 1.0

Magnesium binding site 2 out of 4 in 3b04

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Magnesium binding site 2 out of 4 in the Crystal Structure of Sulfolobus Shibatae Isopentenyl Diphosphate Isomerase in Complex with Oipp.


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 Oipp. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1002

b:76.2
occ:1.00
 O1A B:OOP669 2.0 69.0 1.0
OE2 B:GLU161 3.3 48.7 1.0
PA B:OOP669 3.5 67.7 1.0
O B:HOH399 3.6 44.7 1.0
CG B:GLU161 3.7 39.0 1.0
ND2 B:ASN157 3.8 27.7 1.0
CD B:GLU161 3.9 45.0 1.0
NE2 B:GLN164 3.9 51.7 1.0
O2B B:OOP669 4.0 62.2 1.0
OE1 B:GLN164 4.1 50.1 1.0
O11 B:OOP669 4.2 66.0 1.0
O2A B:OOP669 4.4 63.3 1.0
CD B:GLN164 4.4 49.5 1.0
O3A B:OOP669 4.5 65.9 1.0
CG B:ASN157 4.8 26.2 1.0
PB B:OOP669 4.8 64.7 1.0
OD1 B:ASN157 4.9 26.3 1.0
C11 B:OOP669 4.9 60.8 1.0
CB B:GLU161 5.0 34.1 1.0

Magnesium binding site 3 out of 4 in 3b04

Go back to Magnesium Binding Sites List in 3b04
Magnesium binding site 3 out of 4 in the Crystal Structure of Sulfolobus Shibatae Isopentenyl Diphosphate Isomerase in Complex with Oipp.


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 Oipp. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1002

b:67.2
occ:1.00
 O1A C:OOP669 2.1 64.0 1.0
O1B C:OOP669 3.3 66.2 1.0
PA C:OOP669 3.4 66.2 1.0
OE2 C:GLU161 3.5 48.4 1.0
ND2 C:ASN157 3.6 27.1 1.0
O2B C:OOP669 3.6 67.3 1.0
O3A C:OOP669 3.8 66.2 1.0
PB C:OOP669 3.8 66.5 1.0
O11 C:OOP669 3.9 62.9 1.0
C11 C:OOP669 4.1 57.6 1.0
CD C:GLU161 4.2 45.2 1.0
OD1 C:ASN157 4.3 27.0 1.0
CG C:ASN157 4.4 26.5 1.0
CG C:GLU161 4.4 39.0 1.0
NE2 C:HIS155 4.6 30.3 1.0
O2A C:OOP669 4.7 66.6 1.0
NH1 C:ARG98 4.8 66.0 1.0

Magnesium binding site 4 out of 4 in 3b04

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Magnesium binding site 4 out of 4 in the Crystal Structure of Sulfolobus Shibatae Isopentenyl Diphosphate Isomerase in Complex with Oipp.


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 Oipp. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1002

b:63.7
occ:1.00
 O D:HOH431 2.8 60.9 1.0
O1A D:OOP669 2.8 69.2 1.0
NE2 D:HIS155 3.0 30.8 1.0
ND2 D:ASN157 3.5 27.4 1.0
O2B D:OOP669 3.6 70.0 1.0
OD1 D:ASN157 3.6 26.3 1.0
O1B D:OOP669 3.8 71.1 1.0
C11 D:OOP669 3.8 61.9 1.0
OE2 D:GLU161 3.9 48.6 1.0
CD2 D:HIS155 3.9 28.6 1.0
CG D:ASN157 3.9 26.7 1.0
PA D:OOP669 3.9 72.0 1.0
O3A D:OOP669 3.9 70.3 1.0
CE1 D:HIS155 4.0 27.3 1.0
PB D:OOP669 4.1 69.9 1.0
OE1 D:GLN130 4.2 56.3 1.0
O11 D:OOP669 4.3 66.3 1.0
CD D:PRO129 4.4 34.7 1.0
CA D:GLY127 4.4 29.2 1.0
CD D:GLU161 4.5 44.6 1.0
CG D:PRO129 4.5 35.9 1.0
O D:HOH471 4.7 47.7 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 17:36:24 2025

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