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Magnesium in PDB 4iym: Crystal Structure of Putative Methylmalonate-Semialdehyde Dehydrogenase From Sinorhizobium Meliloti 1021 Complexed with Nad, Target 011934

Enzymatic activity of Crystal Structure of Putative Methylmalonate-Semialdehyde Dehydrogenase From Sinorhizobium Meliloti 1021 Complexed with Nad, Target 011934

All present enzymatic activity of Crystal Structure of Putative Methylmalonate-Semialdehyde Dehydrogenase From Sinorhizobium Meliloti 1021 Complexed with Nad, Target 011934:
1.2.1.27;

Protein crystallography data

The structure of Crystal Structure of Putative Methylmalonate-Semialdehyde Dehydrogenase From Sinorhizobium Meliloti 1021 Complexed with Nad, Target 011934, PDB code: 4iym was solved by V.N.Malashkevich, R.Bhosle, R.Toro, B.Hillerich, A.Gizzi, S.Garforth, A.Kar, M.K.Chan, J.Lafluer, H.Patel, B.Matikainen, S.Chamala, S.Lim, A.Celikgil, G.Villegas, B.Evans, W.Zenchek, J.Love, A.Fiser, K.Khafizov, R.Seidel, J.B.Bonanno, S.C.Almo, New York Structural Genomics Researchconsortium (Nysgrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.99 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 159.472, 170.910, 170.466, 90.00, 106.33, 90.00
R / Rfree (%) 16.5 / 20.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Putative Methylmalonate-Semialdehyde Dehydrogenase From Sinorhizobium Meliloti 1021 Complexed with Nad, Target 011934 (pdb code 4iym). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of Putative Methylmalonate-Semialdehyde Dehydrogenase From Sinorhizobium Meliloti 1021 Complexed with Nad, Target 011934, PDB code: 4iym:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 4iym

Go back to Magnesium Binding Sites List in 4iym
Magnesium binding site 1 out of 6 in the Crystal Structure of Putative Methylmalonate-Semialdehyde Dehydrogenase From Sinorhizobium Meliloti 1021 Complexed with Nad, Target 011934


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 Putative Methylmalonate-Semialdehyde Dehydrogenase From Sinorhizobium Meliloti 1021 Complexed with Nad, Target 011934 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:47.2
occ:1.00
 O A:HOH792 2.0 39.3 1.0
O A:HOH918 2.1 40.2 1.0
O A:HOH919 2.2 45.1 1.0
OD2 A:ASP261 3.9 33.6 1.0
OD2 A:ASP259 4.2 35.5 1.0
OD1 A:ASP259 4.5 31.1 1.0
CG A:ASP259 4.8 32.0 1.0
O A:HOH903 4.8 30.6 1.0
CB A:ASP261 4.8 27.5 1.0
CG A:ASP261 4.8 30.6 1.0

Magnesium binding site 2 out of 6 in 4iym

Go back to Magnesium Binding Sites List in 4iym
Magnesium binding site 2 out of 6 in the Crystal Structure of Putative Methylmalonate-Semialdehyde Dehydrogenase From Sinorhizobium Meliloti 1021 Complexed with Nad, Target 011934


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 Putative Methylmalonate-Semialdehyde Dehydrogenase From Sinorhizobium Meliloti 1021 Complexed with Nad, Target 011934 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:49.4
occ:1.00
 O A:HOH803 2.1 40.5 1.0
O A:HOH921 2.2 41.6 1.0
O A:HOH922 2.2 40.4 1.0
O A:HOH837 2.5 39.3 1.0
OD2 A:ASP318 3.5 37.6 1.0
O A:HOH915 3.8 43.4 1.0
OD1 A:ASP318 3.8 35.5 1.0
CG A:ASP318 4.1 35.9 1.0
O A:HOH766 4.4 36.0 1.0
O A:SER306 4.5 26.9 1.0

Magnesium binding site 3 out of 6 in 4iym

Go back to Magnesium Binding Sites List in 4iym
Magnesium binding site 3 out of 6 in the Crystal Structure of Putative Methylmalonate-Semialdehyde Dehydrogenase From Sinorhizobium Meliloti 1021 Complexed with Nad, Target 011934


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 Putative Methylmalonate-Semialdehyde Dehydrogenase From Sinorhizobium Meliloti 1021 Complexed with Nad, Target 011934 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg502

b:41.1
occ:1.00
 O F:HOH894 2.1 42.2 1.0
O F:HOH792 2.2 47.0 1.0
OD1 F:ASP318 4.2 31.4 1.0
OD2 F:ASP318 4.8 32.8 1.0
CG F:ASP318 4.9 31.4 1.0

Magnesium binding site 4 out of 6 in 4iym

Go back to Magnesium Binding Sites List in 4iym
Magnesium binding site 4 out of 6 in the Crystal Structure of Putative Methylmalonate-Semialdehyde Dehydrogenase From Sinorhizobium Meliloti 1021 Complexed with Nad, Target 011934


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 Putative Methylmalonate-Semialdehyde Dehydrogenase From Sinorhizobium Meliloti 1021 Complexed with Nad, Target 011934 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg502

b:58.0
occ:1.00
 O C:HOH797 1.9 55.2 1.0
O G:HOH869 2.6 51.5 1.0
OD1 G:ASP318 4.1 35.4 1.0
OD2 G:ASP318 4.4 33.9 1.0
OD2 C:ASP318 4.5 36.1 1.0
CG G:ASP318 4.6 33.3 1.0
OD1 C:ASP318 4.7 35.9 1.0
O C:HOH848 4.8 35.4 1.0

Magnesium binding site 5 out of 6 in 4iym

Go back to Magnesium Binding Sites List in 4iym
Magnesium binding site 5 out of 6 in the Crystal Structure of Putative Methylmalonate-Semialdehyde Dehydrogenase From Sinorhizobium Meliloti 1021 Complexed with Nad, Target 011934


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Putative Methylmalonate-Semialdehyde Dehydrogenase From Sinorhizobium Meliloti 1021 Complexed with Nad, Target 011934 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg502

b:54.8
occ:1.00
 O I:HOH750 1.9 48.4 1.0
O I:HOH867 2.4 42.4 1.0
O I:HOH866 2.6 51.0 1.0
OD1 I:ASP318 4.2 30.0 1.0
OD2 I:ASP318 4.3 28.3 1.0
CG I:ASP318 4.7 28.2 1.0
O I:SER306 5.0 29.5 1.0

Magnesium binding site 6 out of 6 in 4iym

Go back to Magnesium Binding Sites List in 4iym
Magnesium binding site 6 out of 6 in the Crystal Structure of Putative Methylmalonate-Semialdehyde Dehydrogenase From Sinorhizobium Meliloti 1021 Complexed with Nad, Target 011934


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Putative Methylmalonate-Semialdehyde Dehydrogenase From Sinorhizobium Meliloti 1021 Complexed with Nad, Target 011934 within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Mg502

b:49.6
occ:1.00
 O K:HOH917 2.0 43.3 1.0
O K:HOH813 2.0 46.2 1.0
O O:HOH902 3.6 49.1 1.0
O O:HOH916 4.0 36.6 1.0
O O:HOH915 4.1 35.9 1.0
OD2 O:ASP318 4.3 26.9 1.0
OD1 O:ASP318 4.5 28.0 1.0
OD1 K:ASP318 4.7 26.4 1.0
OD2 K:ASP318 4.8 24.0 1.0
CG O:ASP318 4.8 26.0 1.0

Reference:

V.N.Malashkevich, R.Bhosle, R.Toro, B.Hillerich, A.Gizzi, S.Garforth, A.Kar, M.K.Chan, J.Lafluer, H.Patel, B.Matikainen, S.Chamala, S.Lim, A.Celikgil, G.Villegas, B.Evans, W.Zenchek, J.Love, A.Fiser, K.Khafizov, R.Seidel, J.B.Bonanno, S.C.Almo. Crystal Structure of Putative Methylmalonate-Semialdehyde Dehydrogenase From Sinorhizobium Meliloti 1021 Complexed with Nad, Target 011934 To Be Published.
Page generated: Mon Aug 11 14:29:09 2025

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