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Magnesium in PDB 3wry: Crystal Structure of Heliase Complex 2

Enzymatic activity of Crystal Structure of Heliase Complex 2

All present enzymatic activity of Crystal Structure of Heliase Complex 2:
3.6.4.13;

Protein crystallography data

The structure of Crystal Structure of Heliase Complex 2, PDB code: 3wry was solved by H.Matsumura, E.Katoh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.75 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.981, 133.550, 195.786, 90.00, 90.00, 90.00
R / Rfree (%) 20.2 / 24.8

Other elements in 3wry:

The structure of Crystal Structure of Heliase Complex 2 also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Heliase Complex 2 (pdb code 3wry). 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 Heliase Complex 2, PDB code: 3wry:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3wry

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Magnesium binding site 1 out of 4 in the Crystal Structure of Heliase Complex 2


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 Heliase Complex 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:26.1
occ:1.00
 O A:GLY86 2.2 31.8 1.0
O A:HOH762 2.2 27.4 1.0
O C:ASN978 2.3 25.2 1.0
O A:MET85 2.4 32.3 1.0
O C:TYR981 2.5 34.6 1.0
O C:GLY983 2.8 31.2 1.0
C A:MET85 3.2 32.7 1.0
C A:GLY86 3.2 31.3 1.0
C C:ASN978 3.4 25.4 1.0
C C:GLY983 3.7 30.4 1.0
C C:TYR981 3.7 32.9 1.0
N A:GLY86 3.8 30.5 1.0
CA A:GLY86 3.9 29.4 1.0
CA C:ASN978 4.0 25.2 1.0
N C:GLY983 4.0 32.5 1.0
CA A:MET85 4.1 33.1 1.0
N A:THR87 4.2 29.2 1.0
OD1 C:ASN978 4.4 26.7 1.0
CB C:ASN978 4.4 24.1 1.0
O A:THR84 4.5 30.6 1.0
C C:GLU982 4.5 32.8 1.0
CA C:GLY983 4.5 30.1 1.0
N C:HIS984 4.5 30.2 1.0
CA A:THR87 4.5 30.2 1.0
N C:GLN979 4.6 24.3 1.0
N C:TYR981 4.6 30.6 1.0
CA C:GLU982 4.6 33.7 1.0
CA C:HIS984 4.6 28.9 1.0
N C:GLU982 4.6 33.0 1.0
CA C:TYR981 4.6 31.8 1.0
CG C:ASN978 4.9 28.1 1.0
CA C:GLN979 4.9 26.9 1.0

Magnesium binding site 2 out of 4 in 3wry

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Magnesium binding site 2 out of 4 in the Crystal Structure of Heliase Complex 2


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 Heliase Complex 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1202

b:24.9
occ:1.00
 O2G C:AGS1201 2.0 25.4 1.0
O C:HOH1360 2.1 20.4 1.0
O C:HOH1393 2.1 21.8 1.0
O2B C:AGS1201 2.1 23.1 1.0
O C:HOH1517 2.1 16.2 1.0
OG1 C:THR840 2.1 27.7 1.0
CB C:THR840 3.2 27.9 1.0
PG C:AGS1201 3.4 24.8 1.0
PB C:AGS1201 3.4 26.8 1.0
O3B C:AGS1201 3.8 28.4 1.0
N C:THR840 3.9 26.6 1.0
OD2 C:ASP906 3.9 30.7 1.0
O C:HOH1319 3.9 25.7 1.0
O2A C:AGS1201 4.0 29.9 1.0
O3G C:AGS1201 4.0 28.2 1.0
CA C:THR840 4.2 26.2 1.0
O C:HOH1340 4.2 30.0 1.0
OD1 C:ASP906 4.2 32.7 1.0
CA C:GLY1044 4.2 28.5 1.0
O3A C:AGS1201 4.3 28.7 1.0
CG2 C:THR840 4.3 26.4 1.0
OE1 C:GLU907 4.4 32.8 1.0
CE C:LYS839 4.5 26.2 1.0
CG C:ASP906 4.5 30.7 1.0
CB C:LYS839 4.5 26.0 1.0
O1B C:AGS1201 4.5 28.9 1.0
PA C:AGS1201 4.5 27.3 1.0
O C:GLY1044 4.6 27.6 1.0
O1A C:AGS1201 4.7 25.3 1.0
S1G C:AGS1201 4.8 25.1 1.0
C C:LYS839 4.9 26.5 1.0
NH1 C:ARG868 5.0 25.3 1.0
C C:GLY1044 5.0 27.1 1.0
CE C:MET864 5.0 35.5 1.0
NZ C:LYS839 5.0 29.1 1.0

Magnesium binding site 3 out of 4 in 3wry

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Magnesium binding site 3 out of 4 in the Crystal Structure of Heliase Complex 2


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 Heliase Complex 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1202

b:33.7
occ:1.00
 OG1 D:THR840 2.1 31.1 1.0
O2G D:AGS1201 2.1 28.1 1.0
O D:HOH1349 2.1 23.4 1.0
O D:HOH1477 2.1 26.1 1.0
O D:HOH1449 2.1 24.4 1.0
O2B D:AGS1201 2.2 30.7 1.0
CB D:THR840 3.1 32.3 1.0
PB D:AGS1201 3.4 28.9 1.0
PG D:AGS1201 3.4 30.7 1.0
O3A D:AGS1201 3.9 38.3 1.0
N D:THR840 3.9 30.1 1.0
O3B D:AGS1201 3.9 33.7 1.0
O D:HOH1337 3.9 26.6 1.0
OD2 D:ASP906 3.9 30.9 1.0
O3G D:AGS1201 4.0 29.8 1.0
CA D:GLY1044 4.0 33.1 1.0
CA D:THR840 4.1 31.3 1.0
O D:HOH1303 4.2 23.9 1.0
CG2 D:THR840 4.2 32.8 1.0
OE2 D:GLU907 4.2 28.6 1.0
OD1 D:ASP906 4.2 30.5 1.0
O1A D:AGS1201 4.3 37.3 1.0
CE D:MET864 4.5 46.4 1.0
O D:GLY1044 4.5 33.0 1.0
CG D:ASP906 4.5 31.4 1.0
O1B D:AGS1201 4.7 34.1 1.0
CE D:LYS839 4.7 30.0 1.0
PA D:AGS1201 4.7 34.7 1.0
CB D:LYS839 4.7 29.1 1.0
C D:GLY1044 4.8 34.0 1.0
S1G D:AGS1201 4.9 31.2 1.0
NZ D:LYS839 4.9 29.2 1.0
C D:LYS839 5.0 29.9 1.0

Magnesium binding site 4 out of 4 in 3wry

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Magnesium binding site 4 out of 4 in the Crystal Structure of Heliase Complex 2


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 Heliase Complex 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1203

b:40.6
occ:1.00
 O D:TYR981 2.3 31.0 1.0
O D:ASN978 2.3 26.9 1.0
O B:HOH719 2.4 42.7 1.0
O B:GLY86 2.6 41.7 1.0
O B:MET85 2.7 46.6 1.0
O D:GLY983 2.8 39.2 1.0
C B:MET85 3.4 48.7 1.0
C D:ASN978 3.4 26.3 1.0
C D:TYR981 3.5 31.0 1.0
C B:GLY86 3.5 40.8 1.0
C D:GLY983 3.8 37.4 1.0
CA D:ASN978 3.9 26.8 1.0
N D:GLY983 3.9 35.6 1.0
N B:GLY86 4.1 44.9 1.0
CA B:MET85 4.2 52.7 1.0
CA B:GLY86 4.2 42.5 1.0
N D:TYR981 4.3 30.2 1.0
C D:GLU982 4.4 35.8 1.0
CA D:TYR981 4.4 30.9 1.0
OD1 D:ASN978 4.4 28.4 1.0
N D:GLU982 4.4 33.1 1.0
CB D:ASN978 4.4 25.3 1.0
N B:THR87 4.5 37.7 1.0
CA D:GLY983 4.5 36.0 1.0
CA D:GLU982 4.5 35.1 1.0
N D:GLN979 4.6 27.9 1.0
N D:HIS984 4.7 37.1 1.0
CA B:THR87 4.7 36.5 1.0
CA D:HIS984 4.8 36.2 1.0
CG D:ASN978 4.8 26.8 1.0
CB D:TYR981 4.9 26.8 1.0
C D:GLN979 5.0 29.3 1.0
O D:LEU977 5.0 25.4 1.0
O B:THR84 5.0 55.8 1.0
CA D:GLN979 5.0 28.9 1.0

Reference:

K.Ishibashi, Y.Kezuka, C.Kobayashi, M.Kato, T.Inoue, T.Nonaka, M.Ishikawa, H.Matsumura, E.Katoh. Structural Basis For the Recognition-Evasion Arms Race Between Tomato Mosaic Virus and the Resistance Gene Tm-1 Proc.Natl.Acad.Sci.Usa 2014.
ISSN: ESSN 1091-6490
DOI: 10.1073/PNAS.1407888111
Page generated: Mon Aug 11 05:01:30 2025

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