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Magnesium in PDB 4y1p: Crystal Structure of 3-Isopropylmalate Dehydrogenase (SACI_0600) From Sulfolobus Acidocaldarius Complex with 3-Isopropylmalate and MG2+

Enzymatic activity of Crystal Structure of 3-Isopropylmalate Dehydrogenase (SACI_0600) From Sulfolobus Acidocaldarius Complex with 3-Isopropylmalate and MG2+

All present enzymatic activity of Crystal Structure of 3-Isopropylmalate Dehydrogenase (SACI_0600) From Sulfolobus Acidocaldarius Complex with 3-Isopropylmalate and MG2+:
1.1.1.85;

Protein crystallography data

The structure of Crystal Structure of 3-Isopropylmalate Dehydrogenase (SACI_0600) From Sulfolobus Acidocaldarius Complex with 3-Isopropylmalate and MG2+, PDB code: 4y1p was solved by K.Takahashi, T.Tomita, T.Kuzuyama, M.Nishiyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.51 / 2.20
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 89.024, 136.719, 112.519, 90.00, 90.00, 90.00
R / Rfree (%) 19 / 25

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of 3-Isopropylmalate Dehydrogenase (SACI_0600) From Sulfolobus Acidocaldarius Complex with 3-Isopropylmalate and MG2+ (pdb code 4y1p). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of 3-Isopropylmalate Dehydrogenase (SACI_0600) From Sulfolobus Acidocaldarius Complex with 3-Isopropylmalate and MG2+, PDB code: 4y1p:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 4y1p

Go back to Magnesium Binding Sites List in 4y1p
Magnesium binding site 1 out of 2 in the Crystal Structure of 3-Isopropylmalate Dehydrogenase (SACI_0600) From Sulfolobus Acidocaldarius Complex with 3-Isopropylmalate and MG2+


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 3-Isopropylmalate Dehydrogenase (SACI_0600) From Sulfolobus Acidocaldarius Complex with 3-Isopropylmalate and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:21.3
occ:1.00
 OD1 A:ASP225 2.0 19.9 1.0
O A:HOH522 2.1 19.5 1.0
O A:HOH501 2.1 11.2 1.0
O1 A:IPM402 2.1 18.9 1.0
O3 A:IPM402 2.1 21.8 1.0
C1 A:IPM402 3.0 21.3 1.0
C2 A:IPM402 3.0 20.8 1.0
CG A:ASP225 3.1 18.1 1.0
OD2 A:ASP225 3.6 18.2 1.0
OD1 A:ASP229 3.7 28.5 1.0
NH2 A:ARG96 3.9 22.6 1.0
O A:ASP225 4.0 18.1 1.0
C4 A:IPM402 4.1 22.2 1.0
O2 A:IPM402 4.2 20.9 1.0
O A:HOH520 4.2 30.8 1.0
C3 A:IPM402 4.2 20.8 1.0
O4 A:IPM402 4.3 24.6 1.0
CB A:ASP225 4.3 17.6 1.0
CG A:ASP229 4.4 25.2 1.0
O5 A:IPM402 4.5 21.8 1.0
O A:HOH505 4.5 34.5 1.0
CA A:ASP225 4.5 16.6 1.0
C A:ASP225 4.6 16.9 1.0
OD2 A:ASP229 4.6 28.5 1.0
O A:VAL256 4.8 19.9 1.0
NH1 A:ARG117 4.8 17.1 1.0

Magnesium binding site 2 out of 2 in 4y1p

Go back to Magnesium Binding Sites List in 4y1p
Magnesium binding site 2 out of 2 in the Crystal Structure of 3-Isopropylmalate Dehydrogenase (SACI_0600) From Sulfolobus Acidocaldarius Complex with 3-Isopropylmalate and MG2+


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 3-Isopropylmalate Dehydrogenase (SACI_0600) From Sulfolobus Acidocaldarius Complex with 3-Isopropylmalate and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg401

b:19.0
occ:1.00
 OD1 B:ASP225 2.0 19.3 1.0
O B:HOH503 2.0 12.0 1.0
O2 B:IPM402 2.1 24.0 1.0
O1 B:IPM402 2.2 25.1 1.0
C1 B:IPM402 2.9 25.3 1.0
C2 B:IPM402 3.1 25.9 1.0
CG B:ASP225 3.2 18.6 1.0
OD2 B:ASP225 3.8 18.4 1.0
OD1 B:ASP229 4.0 26.3 1.0
C4 B:IPM402 4.1 28.8 1.0
NH1 B:ARG96 4.1 26.8 1.0
O3 B:IPM402 4.1 23.4 1.0
O B:ASP225 4.1 15.9 1.0
O B:HOH511 4.2 24.8 1.0
C3 B:IPM402 4.2 27.5 1.0
O4 B:IPM402 4.3 27.4 1.0
O5 B:IPM402 4.3 31.2 1.0
CB B:ASP225 4.4 17.3 1.0
CG B:ASP229 4.5 25.9 1.0
CA B:ASP225 4.5 16.5 1.0
OD2 B:ASP229 4.6 31.5 1.0
NH1 B:ARG117 4.6 19.1 1.0
O B:HOH510 4.7 22.9 1.0
C B:ASP225 4.7 17.0 1.0

Reference:

K.Takahashi, F.Nakanishi, T.Tomita, N.Akiyama, K.Lassak, S.V.Albers, T.Kuzuyama, M.Nishiyama. Characterization of Two Beta-Decarboxylating Dehydrogenases From Sulfolobus Acidocaldarius Extremophiles V. 20 843 2016.
ISSN: ESSN 1433-4909
PubMed: 27590116
DOI: 10.1007/S00792-016-0872-4
Page generated: Tue Aug 20 16:09:35 2024

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