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Magnesium in PDB 4e6m: Crystal Structure of Putative Dehydratase Protein From Salmonella Enterica Subsp. Enterica Serovar Typhimurium (Salmonella Typhimurium)

Protein crystallography data

The structure of Crystal Structure of Putative Dehydratase Protein From Salmonella Enterica Subsp. Enterica Serovar Typhimurium (Salmonella Typhimurium), PDB code: 4e6m 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) 19.96 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 113.128, 87.137, 200.586, 90.00, 91.39, 90.00
R / Rfree (%) 17.3 / 20.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Putative Dehydratase Protein From Salmonella Enterica Subsp. Enterica Serovar Typhimurium (Salmonella Typhimurium) (pdb code 4e6m). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of Putative Dehydratase Protein From Salmonella Enterica Subsp. Enterica Serovar Typhimurium (Salmonella Typhimurium), PDB code: 4e6m:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 4e6m

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Magnesium binding site 1 out of 8 in the Crystal Structure of Putative Dehydratase Protein From Salmonella Enterica Subsp. Enterica Serovar Typhimurium (Salmonella Typhimurium)


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 Dehydratase Protein From Salmonella Enterica Subsp. Enterica Serovar Typhimurium (Salmonella Typhimurium) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:31.6
occ:1.00
 O A:HOH772 1.9 34.1 1.0
OE2 A:GLU248 2.0 27.1 1.0
OE2 A:GLU274 2.1 31.6 1.0
O A:HOH773 2.2 28.6 1.0
OE1 A:GLU222 2.2 28.7 1.0
O A:HOH754 2.4 40.5 1.0
CD A:GLU274 3.1 32.7 1.0
CD A:GLU222 3.1 27.2 1.0
CD A:GLU248 3.1 23.1 1.0
OE2 A:GLU222 3.3 25.3 1.0
OE1 A:GLU274 3.3 35.6 1.0
OE1 A:GLU248 3.9 22.2 1.0
NZ A:LYS168 4.0 20.6 1.0
CG A:GLU248 4.1 21.4 1.0
OE1 A:GLU249 4.1 24.4 1.0
O A:HOH615 4.1 29.1 1.0
NE2 A:GLN134 4.2 29.1 1.0
CD2 A:HIS324 4.2 28.0 1.0
O A:HOH622 4.3 22.0 1.0
O A:HOH774 4.3 39.3 1.0
CG A:GLU274 4.4 27.4 1.0
CD2 A:HIS224 4.5 24.0 1.0
NE2 A:HIS324 4.5 29.1 1.0
CG A:GLU222 4.5 24.0 1.0
NE2 A:HIS224 4.5 26.2 1.0
CE A:LYS168 4.7 20.3 1.0
CG A:GLU249 4.8 21.4 1.0
O A:HOH775 4.8 47.1 1.0
CD A:GLU249 4.9 24.6 1.0

Magnesium binding site 2 out of 8 in 4e6m

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Magnesium binding site 2 out of 8 in the Crystal Structure of Putative Dehydratase Protein From Salmonella Enterica Subsp. Enterica Serovar Typhimurium (Salmonella Typhimurium)


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 Dehydratase Protein From Salmonella Enterica Subsp. Enterica Serovar Typhimurium (Salmonella Typhimurium) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg700

b:27.9
occ:1.00
 OE2 B:GLU274 2.1 30.7 1.0
O B:HOH883 2.1 33.0 1.0
OE2 B:GLU248 2.2 25.7 1.0
O B:HOH972 2.2 27.9 1.0
O B:HOH944 2.2 40.0 1.0
OE1 B:GLU222 2.3 29.4 1.0
CD B:GLU274 3.0 30.5 1.0
CD B:GLU222 3.1 27.8 1.0
OE2 B:GLU222 3.2 27.0 1.0
CD B:GLU248 3.2 22.9 1.0
OE1 B:GLU274 3.3 31.6 1.0
NZ B:LYS168 3.9 21.9 1.0
OE1 B:GLU249 4.0 23.2 1.0
CG B:GLU248 4.1 20.6 1.0
OE1 B:GLU248 4.1 23.4 1.0
O B:HOH827 4.1 23.7 1.0
O B:HOH812 4.2 26.1 1.0
NE2 B:GLN134 4.2 25.4 1.0
CD2 B:HIS324 4.2 29.5 1.0
O B:HOH975 4.3 40.3 1.0
CG B:GLU274 4.4 27.0 1.0
NE2 B:HIS324 4.5 30.4 1.0
CD2 B:HIS224 4.5 25.7 1.0
CG B:GLU222 4.5 23.8 1.0
NE2 B:HIS224 4.6 25.9 1.0
CG B:GLU249 4.7 19.9 1.0
CD B:GLU249 4.8 22.8 1.0
O B:HOH965 4.8 45.3 1.0
CE B:LYS168 4.9 20.7 1.0

Magnesium binding site 3 out of 8 in 4e6m

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Magnesium binding site 3 out of 8 in the Crystal Structure of Putative Dehydratase Protein From Salmonella Enterica Subsp. Enterica Serovar Typhimurium (Salmonella Typhimurium)


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 Dehydratase Protein From Salmonella Enterica Subsp. Enterica Serovar Typhimurium (Salmonella Typhimurium) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg501

b:29.2
occ:1.00
 OE2 C:GLU274 2.0 33.2 1.0
OE1 C:GLU222 2.0 27.2 1.0
OE2 C:GLU248 2.1 32.3 1.0
O C:HOH724 2.2 34.8 1.0
O C:HOH745 2.3 29.9 1.0
O C:HOH722 2.3 37.3 1.0
CD C:GLU222 2.9 26.5 1.0
CD C:GLU274 3.0 35.0 1.0
CD C:GLU248 3.1 27.3 1.0
OE2 C:GLU222 3.2 26.6 1.0
OE1 C:GLU274 3.5 36.0 1.0
CG C:GLU248 3.9 23.0 1.0
NZ C:LYS168 3.9 25.8 1.0
OE1 C:GLU248 4.0 26.1 1.0
OE1 C:GLU249 4.0 26.0 1.0
NE2 C:GLN134 4.1 27.1 1.0
O C:HOH607 4.2 30.7 1.0
CD2 C:HIS224 4.3 27.8 1.0
O C:HOH747 4.3 38.6 1.0
O C:HOH620 4.3 29.1 1.0
CG C:GLU222 4.3 23.8 1.0
CG C:GLU274 4.3 30.4 1.0
CD2 C:HIS324 4.4 29.3 1.0
NE2 C:HIS224 4.4 27.1 1.0
NE2 C:HIS324 4.6 30.1 1.0
CE C:LYS168 4.6 25.4 1.0
CG C:GLU249 4.8 23.6 1.0
CD C:GLU249 4.9 26.8 1.0

Magnesium binding site 4 out of 8 in 4e6m

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Magnesium binding site 4 out of 8 in the Crystal Structure of Putative Dehydratase Protein From Salmonella Enterica Subsp. Enterica Serovar Typhimurium (Salmonella Typhimurium)


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 Dehydratase Protein From Salmonella Enterica Subsp. Enterica Serovar Typhimurium (Salmonella Typhimurium) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg501

b:29.1
occ:1.00
 OE2 D:GLU248 2.0 30.2 1.0
OE2 D:GLU274 2.0 31.6 1.0
O D:HOH696 2.0 32.0 1.0
O D:HOH772 2.1 31.5 1.0
OE1 D:GLU222 2.1 28.3 1.0
O D:HOH752 2.2 35.4 1.0
CD D:GLU274 2.9 31.8 1.0
CD D:GLU222 3.0 28.2 1.0
CD D:GLU248 3.1 27.4 1.0
OE2 D:GLU222 3.2 28.6 1.0
OE1 D:GLU274 3.2 33.1 1.0
NZ D:LYS168 3.9 25.0 1.0
OE1 D:GLU248 4.0 26.7 1.0
CG D:GLU248 4.0 24.3 1.0
O D:HOH681 4.1 26.9 1.0
O D:HOH793 4.1 32.1 1.0
OE1 D:GLU249 4.1 26.6 1.0
NE2 D:GLN134 4.2 28.2 1.0
CG D:GLU274 4.3 28.8 1.0
CD2 D:HIS324 4.3 27.3 1.0
O D:HOH664 4.3 24.9 1.0
CG D:GLU222 4.4 24.1 1.0
NE2 D:HIS324 4.4 29.6 1.0
CD2 D:HIS224 4.4 27.4 1.0
NE2 D:HIS224 4.5 28.8 1.0
CE D:LYS168 4.6 23.2 1.0
CG D:GLU249 4.9 23.2 1.0
CD D:GLU249 5.0 25.5 1.0

Magnesium binding site 5 out of 8 in 4e6m

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Magnesium binding site 5 out of 8 in the Crystal Structure of Putative Dehydratase Protein From Salmonella Enterica Subsp. Enterica Serovar Typhimurium (Salmonella Typhimurium)


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 Dehydratase Protein From Salmonella Enterica Subsp. Enterica Serovar Typhimurium (Salmonella Typhimurium) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg501

b:30.1
occ:1.00
 O E:HOH739 2.0 35.2 1.0
OE2 E:GLU274 2.0 31.1 1.0
OE2 E:GLU248 2.1 30.6 1.0
OE1 E:GLU222 2.2 29.5 1.0
O E:HOH757 2.3 26.2 1.0
O E:HOH690 2.4 34.1 1.0
CD E:GLU274 3.0 31.0 1.0
CD E:GLU222 3.1 27.7 1.0
CD E:GLU248 3.2 25.9 1.0
OE2 E:GLU222 3.3 26.7 1.0
OE1 E:GLU274 3.3 32.7 1.0
OE1 E:GLU249 4.0 24.9 1.0
NZ E:LYS168 4.0 23.1 1.0
OE1 E:GLU248 4.0 24.4 1.0
CG E:GLU248 4.1 21.1 1.0
O E:HOH664 4.1 27.4 1.0
NE2 E:GLN134 4.1 27.5 1.0
O E:HOH632 4.2 24.7 1.0
CG E:GLU274 4.3 27.2 1.0
CD2 E:HIS324 4.4 29.2 1.0
O E:HOH833 4.4 40.8 1.0
CD2 E:HIS224 4.4 25.7 1.0
CG E:GLU222 4.5 24.2 1.0
NE2 E:HIS324 4.6 28.6 1.0
NE2 E:HIS224 4.6 27.4 1.0
CE E:LYS168 4.8 23.5 1.0
CD E:GLU249 4.9 24.4 1.0
CG E:GLU249 4.9 22.6 1.0

Magnesium binding site 6 out of 8 in 4e6m

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Magnesium binding site 6 out of 8 in the Crystal Structure of Putative Dehydratase Protein From Salmonella Enterica Subsp. Enterica Serovar Typhimurium (Salmonella Typhimurium)


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 Dehydratase Protein From Salmonella Enterica Subsp. Enterica Serovar Typhimurium (Salmonella Typhimurium) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg700

b:29.5
occ:1.00
 OE2 F:GLU274 2.0 30.3 1.0
O F:HOH901 2.1 34.4 1.0
OE2 F:GLU248 2.1 26.7 1.0
O F:HOH956 2.2 36.6 1.0
O F:HOH832 2.2 29.4 1.0
OE1 F:GLU222 2.3 28.9 1.0
CD F:GLU274 3.0 31.1 1.0
CD F:GLU222 3.2 28.0 1.0
CD F:GLU248 3.2 24.7 1.0
OE1 F:GLU274 3.3 35.2 1.0
OE2 F:GLU222 3.4 26.7 1.0
OE1 F:GLU249 4.0 25.7 1.0
OE1 F:GLU248 4.0 26.2 1.0
O F:HOH917 4.0 34.0 1.0
CG F:GLU248 4.1 20.8 1.0
NZ F:LYS168 4.1 21.1 1.0
O F:HOH833 4.2 26.6 1.0
NE2 F:GLN134 4.2 28.8 1.0
O F:HOH1053 4.2 39.4 1.0
CG F:GLU274 4.3 27.5 1.0
CD2 F:HIS324 4.4 29.7 1.0
CD2 F:HIS224 4.5 25.4 1.0
CG F:GLU222 4.6 25.5 1.0
NE2 F:HIS224 4.6 27.2 1.0
NE2 F:HIS324 4.6 28.4 1.0
CE F:LYS168 4.7 21.5 1.0
CG F:GLU249 4.8 23.4 1.0
CD F:GLU249 4.8 25.0 1.0

Magnesium binding site 7 out of 8 in 4e6m

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Magnesium binding site 7 out of 8 in the Crystal Structure of Putative Dehydratase Protein From Salmonella Enterica Subsp. Enterica Serovar Typhimurium (Salmonella Typhimurium)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Putative Dehydratase Protein From Salmonella Enterica Subsp. Enterica Serovar Typhimurium (Salmonella Typhimurium) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg501

b:27.8
occ:1.00
 OE2 G:GLU248 2.0 28.8 1.0
OE2 G:GLU274 2.0 29.8 1.0
O G:HOH728 2.1 35.0 1.0
OE1 G:GLU222 2.2 26.9 1.0
O G:HOH693 2.2 35.7 1.0
O G:HOH636 2.2 30.3 1.0
CD G:GLU274 3.0 30.5 1.0
CD G:GLU222 3.1 25.6 1.0
CD G:GLU248 3.1 25.9 1.0
OE1 G:GLU274 3.4 32.9 1.0
OE2 G:GLU222 3.4 26.9 1.0
OE1 G:GLU248 3.9 26.0 1.0
NZ G:LYS168 3.9 23.9 1.0
O G:HOH629 4.0 28.3 1.0
CG G:GLU248 4.1 22.0 1.0
NE2 G:GLN134 4.1 29.3 1.0
OE1 G:GLU249 4.2 26.3 1.0
CG G:GLU274 4.3 26.3 1.0
CD2 G:HIS324 4.4 27.4 1.0
O G:HOH617 4.4 24.3 1.0
O G:HOH766 4.4 35.0 1.0
CG G:GLU222 4.5 23.1 1.0
CE G:LYS168 4.5 22.3 1.0
CD2 G:HIS224 4.5 24.4 1.0
NE2 G:HIS324 4.6 27.9 1.0
NE2 G:HIS224 4.6 24.4 1.0
CG G:GLU249 4.9 22.5 1.0
CD G:GLU249 5.0 25.4 1.0

Magnesium binding site 8 out of 8 in 4e6m

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Magnesium binding site 8 out of 8 in the Crystal Structure of Putative Dehydratase Protein From Salmonella Enterica Subsp. Enterica Serovar Typhimurium (Salmonella Typhimurium)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Putative Dehydratase Protein From Salmonella Enterica Subsp. Enterica Serovar Typhimurium (Salmonella Typhimurium) within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg502

b:28.6
occ:1.00
 OE2 H:GLU248 2.0 31.0 1.0
OE2 H:GLU274 2.1 31.0 1.0
O H:HOH729 2.1 32.4 1.0
OE1 H:GLU222 2.3 27.4 1.0
O H:HOH759 2.3 29.3 1.0
O H:HOH664 2.4 33.9 1.0
CD H:GLU274 3.1 30.9 1.0
CD H:GLU248 3.1 25.7 1.0
CD H:GLU222 3.1 26.4 1.0
OE2 H:GLU222 3.3 25.4 1.0
OE1 H:GLU274 3.5 33.2 1.0
O H:HOH671 3.9 30.6 1.0
NZ H:LYS168 3.9 24.5 1.0
OE1 H:GLU248 3.9 25.5 1.0
CG H:GLU248 4.0 21.3 1.0
OE1 H:GLU249 4.0 27.3 1.0
NE2 H:GLN134 4.2 26.2 1.0
O H:HOH648 4.3 24.1 1.0
CD2 H:HIS324 4.3 28.8 1.0
CG H:GLU274 4.4 26.7 1.0
O H:HOH823 4.4 39.8 1.0
CD2 H:HIS224 4.5 26.1 1.0
CG H:GLU222 4.5 23.7 1.0
NE2 H:HIS324 4.6 30.1 1.0
NE2 H:HIS224 4.7 27.6 1.0
CE H:LYS168 4.8 23.4 1.0
CD H:GLU249 4.9 25.2 1.0
CG H:GLU249 4.9 22.7 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 Dehydratase Protein From Salmonella Enterica Subsp. Enterica Serovar Typhimurium (Salmonella Typhimurium) To Be Published.
Page generated: Mon Aug 11 11:57:10 2025

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