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Magnesium in PDB 3e4d: Structural and Kinetic Study of An S-Formylglutathione Hydrolase From Agrobacterium Tumefaciens

Protein crystallography data

The structure of Structural and Kinetic Study of An S-Formylglutathione Hydrolase From Agrobacterium Tumefaciens, PDB code: 3e4d was solved by K.E.Van Straaten, C.F.Gonzalez, R.B.Valladares, X.Xu, A.V.Savchenko, D.A.R.Sanders, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 2.01
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 68.433, 68.949, 95.648, 92.41, 99.79, 98.47
R / Rfree (%) 18.1 / 21.9

Other elements in 3e4d:

The structure of Structural and Kinetic Study of An S-Formylglutathione Hydrolase From Agrobacterium Tumefaciens also contains other interesting chemical elements:

Chlorine (Cl) 12 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structural and Kinetic Study of An S-Formylglutathione Hydrolase From Agrobacterium Tumefaciens (pdb code 3e4d). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Structural and Kinetic Study of An S-Formylglutathione Hydrolase From Agrobacterium Tumefaciens, PDB code: 3e4d:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 3e4d

Go back to Magnesium Binding Sites List in 3e4d
Magnesium binding site 1 out of 6 in the Structural and Kinetic Study of An S-Formylglutathione Hydrolase From Agrobacterium Tumefaciens


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structural and Kinetic Study of An S-Formylglutathione Hydrolase From Agrobacterium Tumefaciens within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg278

b:27.7
occ:1.00
 O A:MSE97 2.1 22.2 1.0
O A:HOH368 2.2 28.0 1.0
O A:ASN94 2.2 29.4 1.0
O A:GLU91 2.3 32.0 1.0
OD1 A:ASP90 3.2 24.5 1.0
C A:ASN94 3.3 29.5 1.0
C A:MSE97 3.3 22.1 1.0
C A:GLU91 3.4 32.5 1.0
N A:GLU91 4.1 30.8 1.0
N A:TRP95 4.1 28.0 1.0
N A:MSE97 4.1 23.3 1.0
CG A:ASP90 4.1 27.0 1.0
CA A:TRP95 4.1 27.2 1.0
CA A:GLU91 4.1 32.5 1.0
N A:ASN94 4.1 32.0 1.0
CA A:MSE97 4.2 22.9 1.0
CA A:ASN94 4.2 30.6 1.0
N A:GLY98 4.3 21.3 1.0
CB A:GLU91 4.3 32.1 1.0
O A:LYS99 4.3 18.7 1.0
CA A:GLY98 4.4 21.1 1.0
OD2 A:ASP90 4.4 26.4 1.0
N A:LEU92 4.4 33.5 1.0
N A:LYS99 4.4 19.9 1.0
C A:TRP95 4.5 26.5 1.0
CB A:ASN94 4.6 30.7 1.0
C A:LEU92 4.6 34.5 1.0
CA A:LEU92 4.7 34.2 1.0
CB A:MSE97 4.7 23.2 1.0
C A:GLY98 4.7 20.5 1.0
O A:LEU92 4.8 35.0 1.0
O A:TRP95 4.8 26.8 1.0
N A:GLN96 4.9 25.4 1.0
O A:HOH374 4.9 21.4 1.0

Magnesium binding site 2 out of 6 in 3e4d

Go back to Magnesium Binding Sites List in 3e4d
Magnesium binding site 2 out of 6 in the Structural and Kinetic Study of An S-Formylglutathione Hydrolase From Agrobacterium Tumefaciens


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structural and Kinetic Study of An S-Formylglutathione Hydrolase From Agrobacterium Tumefaciens within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg278

b:27.2
occ:1.00
 O B:HOH292 2.0 21.7 1.0
O B:MSE97 2.2 20.5 1.0
O B:ASN94 2.3 20.8 1.0
O B:GLU91 2.4 23.1 1.0
OD1 B:ASP90 2.5 21.7 1.0
C B:ASN94 3.4 21.6 1.0
C B:GLU91 3.4 23.4 1.0
C B:MSE97 3.4 20.0 1.0
CG B:ASP90 3.5 23.2 1.0
O B:HOH350 3.6 27.7 1.0
OD2 B:ASP90 3.8 23.3 1.0
N B:GLU91 3.9 23.9 1.0
O B:LYS99 4.0 19.1 1.0
O B:LEU92 4.0 23.9 1.0
N B:LYS99 4.1 18.5 1.0
CA B:GLU91 4.1 24.1 1.0
N B:ASN94 4.2 22.1 1.0
CA B:ASN94 4.2 21.8 1.0
N B:TRP95 4.2 22.0 1.0
N B:MSE97 4.3 21.0 1.0
C B:LEU92 4.3 23.1 1.0
CB B:GLU91 4.3 24.1 1.0
N B:GLY98 4.3 19.6 1.0
CA B:MSE97 4.3 20.6 1.0
N B:LEU92 4.4 23.3 1.0
CA B:TRP95 4.4 22.4 1.0
CA B:GLY98 4.4 18.7 1.0
C B:GLY98 4.5 18.9 1.0
CA B:LEU92 4.6 23.3 1.0
CB B:ASN94 4.6 21.8 1.0
C B:TRP95 4.8 22.1 1.0
CA B:LYS99 4.8 18.6 1.0
C B:LYS99 4.9 18.3 1.0
CB B:ASP90 4.9 24.0 1.0
CB B:MSE97 4.9 20.4 1.0
N B:THR93 5.0 22.6 1.0
C B:ASP90 5.0 24.2 1.0
CB B:LYS99 5.0 18.1 1.0

Magnesium binding site 3 out of 6 in 3e4d

Go back to Magnesium Binding Sites List in 3e4d
Magnesium binding site 3 out of 6 in the Structural and Kinetic Study of An S-Formylglutathione Hydrolase From Agrobacterium Tumefaciens


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structural and Kinetic Study of An S-Formylglutathione Hydrolase From Agrobacterium Tumefaciens within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg278

b:25.7
occ:1.00
 O C:ASN94 2.2 28.1 1.0
O C:MSE97 2.2 25.4 1.0
O C:GLU91 2.2 32.1 1.0
O C:HOH405 2.4 31.9 1.0
OD1 C:ASP90 2.8 29.9 1.0
C C:ASN94 3.3 28.8 1.0
C C:GLU91 3.3 31.9 1.0
C C:MSE97 3.4 25.3 1.0
CG C:ASP90 3.6 31.4 1.0
OD2 C:ASP90 3.8 32.4 1.0
N C:GLU91 3.8 31.9 1.0
CA C:GLU91 3.9 32.2 1.0
N C:ASN94 4.1 30.5 1.0
CB C:GLU91 4.1 32.3 1.0
CA C:ASN94 4.1 29.6 1.0
N C:TRP95 4.1 28.2 1.0
N C:MSE97 4.2 25.8 1.0
N C:LYS99 4.2 23.6 1.0
O C:LYS99 4.2 23.0 1.0
CA C:TRP95 4.3 28.4 1.0
N C:LEU92 4.3 32.0 1.0
CA C:MSE97 4.3 25.5 1.0
N C:GLY98 4.4 24.9 1.0
O C:HOH407 4.5 32.8 1.0
CB C:ASN94 4.5 29.9 1.0
CA C:GLY98 4.5 24.1 1.0
CA C:LEU92 4.6 31.9 1.0
C C:LEU92 4.6 31.8 1.0
C C:TRP95 4.7 27.9 1.0
C C:GLY98 4.7 23.9 1.0
CB C:MSE97 4.7 25.6 1.0
O C:LEU92 4.8 32.5 1.0
C C:ASP90 4.9 31.8 1.0
CB C:ASP90 5.0 31.4 1.0
N C:GLN96 5.0 27.4 1.0
N C:THR93 5.0 31.7 1.0

Magnesium binding site 4 out of 6 in 3e4d

Go back to Magnesium Binding Sites List in 3e4d
Magnesium binding site 4 out of 6 in the Structural and Kinetic Study of An S-Formylglutathione Hydrolase From Agrobacterium Tumefaciens


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structural and Kinetic Study of An S-Formylglutathione Hydrolase From Agrobacterium Tumefaciens within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg278

b:41.0
occ:1.00
 O E:MSE97 2.1 26.8 1.0
O E:ASN94 2.2 31.8 1.0
O E:HOH358 2.5 27.7 1.0
O E:GLU91 2.5 32.9 1.0
OD1 E:ASP90 3.2 29.7 1.0
C E:ASN94 3.3 32.3 1.0
C E:MSE97 3.3 26.4 1.0
C E:GLU91 3.5 33.0 1.0
CG E:ASP90 4.0 30.4 1.0
N E:GLU91 4.0 31.3 1.0
N E:MSE97 4.1 27.7 1.0
O E:LYS99 4.1 23.7 1.0
OD2 E:ASP90 4.2 30.5 1.0
N E:TRP95 4.2 31.9 1.0
N E:ASN94 4.2 33.9 1.0
CA E:GLU91 4.2 32.6 1.0
CA E:ASN94 4.2 33.0 1.0
CA E:MSE97 4.2 27.3 1.0
CB E:GLU91 4.2 32.3 1.0
CA E:TRP95 4.2 31.4 1.0
N E:LYS99 4.3 23.5 1.0
N E:GLY98 4.3 25.4 1.0
CA E:GLY98 4.4 24.7 1.0
CB E:ASN94 4.5 32.7 1.0
C E:TRP95 4.5 30.8 1.0
O E:HOH386 4.5 34.9 1.0
N E:LEU92 4.6 33.9 1.0
C E:GLY98 4.6 24.1 1.0
CB E:MSE97 4.7 27.5 1.0
C E:LEU92 4.7 34.9 1.0
O E:HOH322 4.8 22.8 1.0
CA E:LEU92 4.8 34.6 1.0
O E:LEU92 4.8 35.1 1.0
N E:GLN96 4.9 30.0 1.0
O E:TRP95 4.9 31.2 1.0

Magnesium binding site 5 out of 6 in 3e4d

Go back to Magnesium Binding Sites List in 3e4d
Magnesium binding site 5 out of 6 in the Structural and Kinetic Study of An S-Formylglutathione Hydrolase From Agrobacterium Tumefaciens


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structural and Kinetic Study of An S-Formylglutathione Hydrolase From Agrobacterium Tumefaciens within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg278

b:43.4
occ:1.00
 O D:ASN94 2.1 44.6 1.0
O D:MSE97 2.2 39.4 1.0
O D:GLU91 2.3 48.7 1.0
O D:HOH352 2.4 35.6 1.0
OD1 D:ASP90 2.7 45.3 1.0
C D:GLU91 3.3 48.5 1.0
C D:ASN94 3.3 44.9 1.0
C D:MSE97 3.4 39.4 1.0
CG D:ASP90 3.6 45.8 1.0
N D:GLU91 3.8 47.7 1.0
OD2 D:ASP90 3.9 45.2 1.0
CA D:GLU91 4.0 48.4 1.0
O D:HOH353 4.0 42.3 1.0
O D:LYS99 4.1 33.2 1.0
N D:LYS99 4.1 35.0 1.0
CB D:GLU91 4.1 48.5 1.0
N D:TRP95 4.2 44.2 1.0
CA D:ASN94 4.2 45.3 1.0
N D:ASN94 4.3 46.2 1.0
CA D:GLY98 4.3 36.9 1.0
N D:GLY98 4.3 38.2 1.0
N D:LEU92 4.3 48.7 1.0
CA D:TRP95 4.3 43.4 1.0
N D:MSE97 4.3 40.7 1.0
CA D:MSE97 4.4 40.2 1.0
C D:GLY98 4.5 35.9 1.0
O D:LEU92 4.5 48.4 1.0
CB D:ASN94 4.6 45.2 1.0
C D:LEU92 4.6 48.4 1.0
CA D:LEU92 4.6 48.8 1.0
C D:TRP95 4.7 43.0 1.0
C D:ASP90 4.8 47.1 1.0
O D:HOH319 4.9 37.7 1.0
CA D:LYS99 4.9 34.2 1.0
CB D:MSE97 4.9 41.0 1.0
C D:LYS99 4.9 33.7 1.0
CB D:ASP90 5.0 46.4 1.0

Magnesium binding site 6 out of 6 in 3e4d

Go back to Magnesium Binding Sites List in 3e4d
Magnesium binding site 6 out of 6 in the Structural and Kinetic Study of An S-Formylglutathione Hydrolase From Agrobacterium Tumefaciens


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structural and Kinetic Study of An S-Formylglutathione Hydrolase From Agrobacterium Tumefaciens within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg278

b:35.6
occ:1.00
 O F:MSE97 2.2 31.8 1.0
O F:ASN94 2.3 33.6 1.0
O F:GLU91 2.5 34.6 1.0
OD1 F:ASP90 2.8 31.8 1.0
O F:HOH343 3.3 56.2 1.0
C F:ASN94 3.4 33.9 1.0
C F:MSE97 3.4 31.5 1.0
C F:GLU91 3.5 35.0 1.0
CG F:ASP90 3.7 33.7 1.0
O F:LYS99 3.9 29.8 1.0
N F:GLU91 3.9 35.2 1.0
OD2 F:ASP90 4.0 31.7 1.0
N F:LYS99 4.1 30.1 1.0
CA F:GLU91 4.1 35.4 1.0
CA F:TRP95 4.2 33.3 1.0
N F:TRP95 4.2 33.7 1.0
CB F:GLU91 4.2 35.1 1.0
N F:MSE97 4.3 32.4 1.0
N F:GLY98 4.3 30.9 1.0
CA F:ASN94 4.3 34.1 1.0
N F:ASN94 4.3 34.1 1.0
CA F:GLY98 4.3 30.5 1.0
CA F:MSE97 4.4 32.3 1.0
C F:GLY98 4.4 30.2 1.0
O F:LEU92 4.5 35.5 1.0
N F:LEU92 4.5 34.9 1.0
C F:LEU92 4.6 35.1 1.0
C F:TRP95 4.6 32.9 1.0
CB F:ASN94 4.7 34.2 1.0
CA F:LEU92 4.7 35.0 1.0
C F:LYS99 4.8 29.9 1.0
CA F:LYS99 4.9 30.0 1.0
CB F:MSE97 4.9 32.9 1.0
N F:GLN96 5.0 32.8 1.0

Reference:

K.E.Van Straaten, C.F.Gonzalez, R.B.Valladares, X.Xu, A.V.Savchenko, D.A.Sanders. The Structure of A Putative S-Formylglutathione Hydrolase From Agrobacterium Tumefaciens Protein Sci. V. 18 2196 2009.
ISSN: ISSN 0961-8368
PubMed: 19653299
DOI: 10.1002/PRO.216
Page generated: Mon Dec 14 08:05:41 2020

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