Atomistry » Magnesium » PDB 2zjp-2zvj » 2zry
Atomistry »
  Magnesium »
    PDB 2zjp-2zvj »
      2zry »

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

Go back to Magnesium Binding Sites List in 2zry
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

Go back to Magnesium Binding Sites List in 2zry
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

Go back to Magnesium Binding Sites List in 2zry
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

Go back to Magnesium Binding Sites List in 2zry
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

Last articles

Mg in 8FV4
Mg in 8FZK
Mg in 8FZV
Mg in 8FVW
Mg in 8FWP
Mg in 8FVE
Mg in 8FVD
Mg in 8FW5
Mg in 8FVR
Mg in 8FVS
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy