Magnesium in PDB 7wux: Crystal Structure of AZIU3/U2 Complexed with (5S,6S)-O7-Sulfo Dadh From Streptomyces Sahachiroi

Protein crystallography data

The structure of Crystal Structure of AZIU3/U2 Complexed with (5S,6S)-O7-Sulfo Dadh From Streptomyces Sahachiroi, PDB code: 7wux was solved by S.Kurosawa, A.Yoshida, T.Tomita, M.Nishiyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.87 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 54.872, 131.756, 157.702, 90, 90, 90
R / Rfree (%) 16.4 / 19.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of AZIU3/U2 Complexed with (5S,6S)-O7-Sulfo Dadh From Streptomyces Sahachiroi (pdb code 7wux). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of AZIU3/U2 Complexed with (5S,6S)-O7-Sulfo Dadh From Streptomyces Sahachiroi, PDB code: 7wux:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 7wux

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Magnesium binding site 1 out of 3 in the Crystal Structure of AZIU3/U2 Complexed with (5S,6S)-O7-Sulfo Dadh From Streptomyces Sahachiroi


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 AZIU3/U2 Complexed with (5S,6S)-O7-Sulfo Dadh From Streptomyces Sahachiroi within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg403

b:16.9
occ:1.00
 O C:HOH585 2.0 15.9 1.0
O C:HOH528 2.0 17.6 1.0
O C:HOH703 2.1 18.1 1.0
O C:HOH708 2.1 20.2 1.0
O C:HOH861 2.1 23.2 1.0
O C:HOH695 2.2 21.9 1.0
HA2 C:GLY66 3.8 13.9 1.0
O C:HIS72 3.9 15.2 1.0
O C:GLY66 4.0 13.8 1.0
HA3 C:GLY66 4.0 13.9 1.0
OD2 C:ASP62 4.0 20.2 1.0
HA C:LEU70 4.1 16.5 1.0
O C:LEU70 4.2 16.3 1.0
CA C:GLY66 4.3 13.9 1.0
O C:HOH748 4.3 41.7 1.0
O C:HOH649 4.3 36.8 1.0
O C:HOH520 4.3 28.6 1.0
O C:PHE74 4.3 17.1 1.0
O C:HOH679 4.3 25.0 1.0
O C:HOH507 4.4 37.4 1.0
C C:GLY66 4.4 13.8 1.0
HA C:PRO73 4.5 16.2 1.0
H C:PHE74 4.5 16.8 1.0
HD11 C:LEU70 4.5 19.0 1.0
O C:ALA69 4.8 15.0 1.0
HB3 C:ASP62 4.8 17.5 1.0
C C:LEU70 4.8 16.2 1.0
CA C:LEU70 4.9 16.5 1.0
HG2 C:GLU75 5.0 23.2 1.0
C C:HIS72 5.0 15.7 1.0

Magnesium binding site 2 out of 3 in 7wux

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Magnesium binding site 2 out of 3 in the Crystal Structure of AZIU3/U2 Complexed with (5S,6S)-O7-Sulfo Dadh From Streptomyces Sahachiroi


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 AZIU3/U2 Complexed with (5S,6S)-O7-Sulfo Dadh From Streptomyces Sahachiroi within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg404

b:39.6
occ:1.00
 O C:HOH724 2.0 22.3 1.0
O C:HOH634 2.2 23.0 1.0
O C:HOH505 2.2 32.4 1.0
O C:HOH836 2.3 34.8 1.0
HD3 C:ARG192 3.4 23.5 1.0
HA C:VAL335 3.9 23.6 1.0
O C:SER336 4.1 29.2 1.0
O C:HOH637 4.1 37.4 1.0
O C:ALA334 4.1 20.6 1.0
O C:VAL335 4.1 25.2 1.0
O C:HOH557 4.1 33.5 1.0
O C:HOH821 4.2 30.6 1.0
CD C:ARG192 4.3 23.5 1.0
C C:VAL335 4.4 24.9 1.0
HD2 C:ARG192 4.5 23.5 1.0
CA C:VAL335 4.6 23.6 1.0
HE C:ARG192 4.7 24.8 1.0
HB3 C:ARG192 4.7 21.0 1.0
NE C:ARG192 4.9 24.9 1.0
C C:ALA334 5.0 21.2 1.0

Magnesium binding site 3 out of 3 in 7wux

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Magnesium binding site 3 out of 3 in the Crystal Structure of AZIU3/U2 Complexed with (5S,6S)-O7-Sulfo Dadh From Streptomyces Sahachiroi


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 AZIU3/U2 Complexed with (5S,6S)-O7-Sulfo Dadh From Streptomyces Sahachiroi within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg402

b:23.5
occ:1.00
 O D:HOH527 2.0 24.4 1.0
O D:HOH558 2.1 23.1 1.0
O D:HOH823 2.1 30.0 1.0
O D:HOH585 2.1 21.1 1.0
O D:HOH666 2.1 24.4 1.0
O D:HOH677 2.1 24.2 1.0
HA2 D:GLY66 3.8 17.4 1.0
O D:HIS72 3.9 20.7 1.0
O D:GLY66 4.1 16.9 1.0
O D:LEU70 4.1 21.4 1.0
OD2 D:ASP62 4.1 24.1 1.0
HA3 D:GLY66 4.1 17.4 1.0
HA D:LEU70 4.1 20.6 1.0
O D:HOH526 4.2 30.9 1.0
O D:HOH744 4.2 27.9 1.0
CA D:GLY66 4.3 17.4 1.0
O D:PHE74 4.3 23.2 1.0
O D:HOH534 4.4 43.6 1.0
HD11 D:LEU70 4.4 22.4 1.0
C D:GLY66 4.5 17.1 1.0
O D:HOH670 4.5 38.8 1.0
HA D:PRO73 4.5 22.7 1.0
H D:PHE74 4.5 23.1 1.0
O D:ALA69 4.7 19.6 1.0
HB3 D:ASP62 4.8 21.8 1.0
C D:LEU70 4.8 20.9 1.0
CA D:LEU70 4.9 20.6 1.0

Reference:

S.Kurosawa, F.Hasebe, H.Okamura, A.Yoshida, K.Matsuda, Y.Sone, T.Tomita, T.Shinada, H.Takikawa, T.Kuzuyama, S.Kosono, M.Nishiyama. Molecular Basis For Enzymatic Aziridine Formation Via Sulfate Elimination. J.Am.Chem.Soc. V. 144 16164 2022.
ISSN: ESSN 1520-5126
PubMed: 35998388
DOI: 10.1021/JACS.2C07243
Page generated: Thu Oct 3 11:22:12 2024

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