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Magnesium in PDB 3dfy: Crystal Structure of Apo Dipeptide Epimerase From Thermotoga Maritima

Protein crystallography data

The structure of Crystal Structure of Apo Dipeptide Epimerase From Thermotoga Maritima, PDB code: 3dfy was solved by A.A.Fedorov, E.V.Fedorov, H.J.Imker, J.A.Gerlt, S.C.Almo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 104.808, 165.142, 209.641, 90.00, 96.06, 90.00
R / Rfree (%) 24.6 / 27.7

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of Apo Dipeptide Epimerase From Thermotoga Maritima (pdb code 3dfy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 16 binding sites of Magnesium where determined in the Crystal Structure of Apo Dipeptide Epimerase From Thermotoga Maritima, PDB code: 3dfy:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 16 in 3dfy

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Magnesium binding site 1 out of 16 in the Crystal Structure of Apo Dipeptide Epimerase From Thermotoga Maritima


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 Apo Dipeptide Epimerase From Thermotoga Maritima within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:26.7
occ:1.00
 OD1 A:ASP241 2.0 18.0 1.0
OE2 A:GLU216 2.0 28.0 1.0
O A:HOH404 2.0 40.1 1.0
O A:HOH403 2.1 20.4 1.0
O A:HOH402 2.1 26.2 1.0
OD2 A:ASP188 2.4 21.2 1.0
CG A:ASP241 3.0 21.7 1.0
CD A:GLU216 3.1 25.3 1.0
CG A:ASP188 3.2 21.7 1.0
OD1 A:ASP188 3.4 20.6 1.0
CB A:ASP241 3.5 17.8 1.0
ND2 A:ASN190 3.8 30.3 1.0
OE1 A:GLU242 3.8 23.3 1.0
CG A:GLU216 3.9 26.6 1.0
OE1 A:GLU216 4.0 26.0 1.0
NZ A:LYS159 4.1 37.0 1.0
OD2 A:ASP241 4.1 21.4 1.0
ND2 A:ASN263 4.2 21.7 1.0
NZ A:LYS161 4.3 37.8 1.0
NZ A:LYS265 4.4 24.8 1.0
CD A:GLU242 4.4 25.4 1.0
OE2 A:GLU242 4.5 29.5 1.0
O A:HOH408 4.5 22.4 1.0
CB A:ASP188 4.6 20.9 1.0
CG A:ASN190 4.6 29.7 1.0
CE A:LYS265 4.6 22.3 1.0
O A:HOH418 4.8 28.4 1.0
OD1 A:ASN190 4.9 31.2 1.0
CB A:GLU216 4.9 24.4 1.0
CE A:LYS159 5.0 36.2 1.0

Magnesium binding site 2 out of 16 in 3dfy

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Magnesium binding site 2 out of 16 in the Crystal Structure of Apo Dipeptide Epimerase From Thermotoga Maritima


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 Apo Dipeptide Epimerase From Thermotoga Maritima within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg401

b:27.2
occ:1.00
 OE2 B:GLU216 1.9 27.9 1.0
OD2 B:ASP241 2.0 24.0 1.0
O B:HOH404 2.0 31.7 1.0
O B:HOH403 2.1 21.4 1.0
OD2 B:ASP188 2.1 24.2 1.0
O B:HOH402 2.1 31.1 1.0
CD B:GLU216 3.0 26.4 1.0
CG B:ASP241 3.1 25.7 1.0
CG B:ASP188 3.1 24.4 1.0
OD1 B:ASP188 3.5 25.1 1.0
CB B:ASP241 3.6 23.2 1.0
CG B:GLU216 3.8 27.6 1.0
OE1 B:GLU216 3.9 27.2 1.0
OE2 B:GLU242 4.0 37.0 1.0
ND2 B:ASN190 4.0 38.4 1.0
NZ B:LYS159 4.1 43.6 1.0
OD1 B:ASP241 4.1 25.3 1.0
OE1 B:GLU242 4.2 29.9 1.0
NZ B:LYS265 4.2 23.6 1.0
ND2 B:ASN263 4.2 23.9 1.0
CB B:ASP188 4.4 24.6 1.0
CD B:GLU242 4.5 30.8 1.0
O B:HOH434 4.5 27.2 1.0
CE B:LYS265 4.6 22.8 1.0
CG B:ASN190 4.8 39.1 1.0
CB B:GLU216 4.9 26.2 1.0
CE B:LYS159 4.9 41.9 1.0

Magnesium binding site 3 out of 16 in 3dfy

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Magnesium binding site 3 out of 16 in the Crystal Structure of Apo Dipeptide Epimerase From Thermotoga Maritima


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 Apo Dipeptide Epimerase From Thermotoga Maritima within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg401

b:24.9
occ:1.00
 OD2 C:ASP241 1.9 24.5 1.0
O C:HOH404 2.0 37.3 1.0
OE2 C:GLU216 2.0 25.1 1.0
O C:HOH403 2.1 20.7 1.0
O C:HOH402 2.1 22.2 1.0
OD2 C:ASP188 2.2 23.9 1.0
CG C:ASP241 3.0 24.6 1.0
CD C:GLU216 3.1 27.0 1.0
CG C:ASP188 3.2 23.7 1.0
OD1 C:ASP188 3.4 20.9 1.0
CB C:ASP241 3.6 20.4 1.0
CG C:GLU216 3.8 27.7 1.0
ND2 C:ASN190 3.9 36.3 1.0
OE1 C:GLU216 3.9 26.6 1.0
OE2 C:GLU242 4.0 31.7 1.0
OD1 C:ASP241 4.0 24.0 1.0
OE1 C:GLU242 4.0 24.4 1.0
NZ C:LYS159 4.1 39.0 1.0
NZ C:LYS161 4.2 39.9 1.0
ND2 C:ASN263 4.2 27.2 1.0
NZ C:LYS265 4.4 24.5 1.0
CD C:GLU242 4.4 27.2 1.0
CB C:ASP188 4.5 22.4 1.0
CG C:ASN190 4.6 36.5 1.0
CE C:LYS265 4.6 24.2 1.0
O C:HOH411 4.7 24.5 1.0
OD1 C:ASN190 4.8 38.2 1.0
CE C:LYS159 4.9 38.8 1.0
CB C:GLU216 4.9 28.3 1.0

Magnesium binding site 4 out of 16 in 3dfy

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Magnesium binding site 4 out of 16 in the Crystal Structure of Apo Dipeptide Epimerase From Thermotoga Maritima


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 Apo Dipeptide Epimerase From Thermotoga Maritima within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg401

b:28.5
occ:1.00
 OD2 D:ASP241 1.9 24.2 1.0
OE2 D:GLU216 2.0 31.6 1.0
O D:HOH404 2.0 35.3 1.0
O D:HOH403 2.1 20.9 1.0
O D:HOH402 2.1 37.1 1.0
OD2 D:ASP188 2.2 26.4 1.0
CG D:ASP241 3.1 24.7 1.0
CG D:ASP188 3.1 28.7 1.0
CD D:GLU216 3.1 33.0 1.0
OD1 D:ASP188 3.4 23.7 1.0
CB D:ASP241 3.6 21.6 1.0
OE2 D:GLU242 3.8 34.4 1.0
ND2 D:ASN190 3.9 38.4 1.0
CG D:GLU216 3.9 32.1 1.0
OE1 D:GLU216 4.0 33.8 1.0
OE1 D:GLU242 4.0 30.1 1.0
NZ D:LYS265 4.0 28.0 1.0
OD1 D:ASP241 4.1 23.9 1.0
ND2 D:ASN263 4.2 27.5 1.0
CD D:GLU242 4.3 31.1 1.0
CB D:ASP188 4.5 25.8 1.0
CE D:LYS265 4.6 28.0 1.0
O D:HOH432 4.6 28.1 1.0
CG D:ASN190 4.8 38.9 1.0
CB D:GLU216 4.9 28.6 1.0

Magnesium binding site 5 out of 16 in 3dfy

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Magnesium binding site 5 out of 16 in the Crystal Structure of Apo Dipeptide Epimerase From Thermotoga Maritima


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 Apo Dipeptide Epimerase From Thermotoga Maritima within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg401

b:29.9
occ:1.00
 OE2 E:GLU216 1.9 33.3 1.0
OD2 E:ASP241 2.0 23.9 1.0
O E:HOH404 2.0 30.2 1.0
O E:HOH403 2.1 21.2 1.0
O E:HOH402 2.1 26.9 1.0
OD2 E:ASP188 2.2 26.0 1.0
CG E:ASP241 3.1 24.9 1.0
CD E:GLU216 3.1 31.5 1.0
CG E:ASP188 3.2 25.4 1.0
OD1 E:ASP188 3.5 23.9 1.0
CB E:ASP241 3.6 21.5 1.0
OE2 E:GLU242 3.8 34.0 1.0
OE1 E:GLU216 3.9 31.0 1.0
CG E:GLU216 3.9 29.9 1.0
OE1 E:GLU242 4.0 27.4 1.0
NZ E:LYS265 4.1 24.9 1.0
OD1 E:ASP241 4.1 22.1 1.0
ND2 E:ASN263 4.2 23.3 1.0
ND2 E:ASN190 4.2 42.5 1.0
CD E:GLU242 4.3 30.8 1.0
CB E:ASP188 4.5 25.5 1.0
O E:HOH413 4.6 21.9 1.0
CE E:LYS265 4.6 23.5 1.0
CG E:ASN190 4.9 40.5 1.0
CB E:GLU216 4.9 28.8 1.0

Magnesium binding site 6 out of 16 in 3dfy

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Magnesium binding site 6 out of 16 in the Crystal Structure of Apo Dipeptide Epimerase From Thermotoga Maritima


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 Apo Dipeptide Epimerase From Thermotoga Maritima within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg401

b:29.8
occ:1.00
 OE2 F:GLU216 1.9 29.3 1.0
OD2 F:ASP241 2.0 26.2 1.0
O F:HOH404 2.0 30.7 1.0
O F:HOH403 2.1 22.4 1.0
O F:HOH402 2.1 24.8 1.0
OD2 F:ASP188 2.2 24.5 1.0
CD F:GLU216 3.0 30.3 1.0
CG F:ASP188 3.1 25.6 1.0
CG F:ASP241 3.1 24.8 1.0
OD1 F:ASP188 3.4 25.1 1.0
CB F:ASP241 3.7 22.8 1.0
CG F:GLU216 3.8 31.4 1.0
OE1 F:GLU216 3.9 30.0 1.0
OE2 F:GLU242 3.9 35.8 1.0
ND2 F:ASN190 4.0 36.2 1.0
ND2 F:ASN263 4.0 22.8 1.0
OE1 F:GLU242 4.0 31.2 1.0
OD1 F:ASP241 4.2 23.0 1.0
NZ F:LYS265 4.3 30.9 1.0
CD F:GLU242 4.4 31.2 1.0
CB F:ASP188 4.5 26.2 1.0
CE F:LYS265 4.7 29.9 1.0
CG F:ASN190 4.7 36.9 1.0
O F:HOH421 4.7 29.1 1.0
CB F:GLU216 4.9 27.9 1.0

Magnesium binding site 7 out of 16 in 3dfy

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Magnesium binding site 7 out of 16 in the Crystal Structure of Apo Dipeptide Epimerase From Thermotoga Maritima


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 Apo Dipeptide Epimerase From Thermotoga Maritima within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg401

b:26.1
occ:1.00
 OE2 G:GLU216 1.9 28.9 1.0
O G:HOH404 2.0 24.6 1.0
O G:HOH403 2.1 18.8 1.0
OD2 G:ASP241 2.1 25.4 1.0
O G:HOH402 2.1 28.8 1.0
OD2 G:ASP188 2.2 22.4 1.0
CD G:GLU216 2.9 28.7 1.0
CG G:ASP188 3.1 25.8 1.0
CG G:ASP241 3.2 23.4 1.0
OD1 G:ASP188 3.4 23.7 1.0
CB G:ASP241 3.7 23.7 1.0
OE1 G:GLU216 3.8 29.3 1.0
CG G:GLU216 3.8 29.2 1.0
OE1 G:GLU242 3.9 30.9 1.0
OE2 G:GLU242 3.9 35.7 1.0
ND2 G:ASN190 4.0 39.1 1.0
ND2 G:ASN263 4.2 21.3 1.0
OD1 G:ASP241 4.3 19.8 1.0
NZ G:LYS265 4.3 24.5 1.0
CD G:GLU242 4.4 30.0 1.0
CB G:ASP188 4.5 25.9 1.0
O G:HOH411 4.6 28.9 1.0
CE G:LYS265 4.7 23.8 1.0
CG G:ASN190 4.7 38.7 1.0
CB G:GLU216 4.9 26.6 1.0
OD1 G:ASN190 4.9 42.9 1.0

Magnesium binding site 8 out of 16 in 3dfy

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Magnesium binding site 8 out of 16 in the Crystal Structure of Apo Dipeptide Epimerase From Thermotoga Maritima


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 Apo Dipeptide Epimerase From Thermotoga Maritima within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg401

b:25.5
occ:1.00
 OE2 H:GLU216 1.9 28.6 1.0
O H:HOH404 2.0 27.7 1.0
OD2 H:ASP241 2.0 22.3 1.0
O H:HOH403 2.1 23.4 1.0
O H:HOH402 2.1 28.9 1.0
OD2 H:ASP188 2.2 20.7 1.0
CD H:GLU216 3.0 29.0 1.0
CG H:ASP188 3.1 24.2 1.0
CG H:ASP241 3.1 25.2 1.0
OD1 H:ASP188 3.4 22.6 1.0
CB H:ASP241 3.6 21.6 1.0
OE1 H:GLU216 3.8 29.3 1.0
OE2 H:GLU242 3.8 32.9 1.0
CG H:GLU216 3.8 28.5 1.0
OE1 H:GLU242 4.1 22.9 1.0
NZ H:LYS265 4.1 24.4 1.0
ND2 H:ASN190 4.1 38.1 1.0
ND2 H:ASN263 4.1 26.5 1.0
OD1 H:ASP241 4.2 23.8 1.0
CD H:GLU242 4.4 27.1 1.0
CB H:ASP188 4.5 23.3 1.0
CE H:LYS265 4.6 26.0 1.0
O H:HOH407 4.7 26.0 1.0
CB H:GLU216 4.9 27.6 1.0
CG H:ASN190 4.9 38.6 1.0

Magnesium binding site 9 out of 16 in 3dfy

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Magnesium binding site 9 out of 16 in the Crystal Structure of Apo Dipeptide Epimerase From Thermotoga Maritima


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of Apo Dipeptide Epimerase From Thermotoga Maritima within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg401

b:26.7
occ:1.00
 OD2 I:ASP241 2.0 21.1 1.0
OE2 I:GLU216 2.0 26.1 1.0
O I:HOH404 2.0 42.9 1.0
O I:HOH403 2.1 18.7 1.0
O I:HOH402 2.1 23.3 1.0
OD2 I:ASP188 2.4 22.2 1.0
CG I:ASP241 3.0 23.1 1.0
CD I:GLU216 3.1 23.6 1.0
CG I:ASP188 3.2 20.1 1.0
OD1 I:ASP188 3.4 19.5 1.0
CB I:ASP241 3.5 19.8 1.0
ND2 I:ASN190 3.7 29.4 1.0
O I:HOH478 3.8 41.5 1.0
OE1 I:GLU242 3.8 27.4 1.0
CG I:GLU216 3.9 25.7 1.0
OE1 I:GLU216 4.0 24.6 1.0
OD1 I:ASP241 4.1 22.9 1.0
ND2 I:ASN263 4.2 24.3 1.0
NZ I:LYS159 4.2 35.0 1.0
OE2 I:GLU242 4.3 33.2 1.0
NZ I:LYS161 4.3 37.0 1.0
NZ I:LYS265 4.3 25.0 1.0
CD I:GLU242 4.4 29.1 1.0
CB I:ASP188 4.6 20.3 1.0
CG I:ASN190 4.6 29.2 1.0
O I:HOH416 4.7 22.6 1.0
CE I:LYS265 4.7 22.9 1.0
O I:HOH413 4.9 30.9 1.0
CB I:GLU216 4.9 25.4 1.0
OD1 I:ASN190 4.9 31.7 1.0
CE I:LYS159 5.0 36.9 1.0

Magnesium binding site 10 out of 16 in 3dfy

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Magnesium binding site 10 out of 16 in the Crystal Structure of Apo Dipeptide Epimerase From Thermotoga Maritima


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of Apo Dipeptide Epimerase From Thermotoga Maritima within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg401

b:27.3
occ:1.00
 OE2 J:GLU216 1.9 29.6 1.0
OD2 J:ASP241 2.0 22.7 1.0
O J:HOH404 2.0 27.3 1.0
O J:HOH403 2.1 22.0 1.0
O J:HOH402 2.1 31.0 1.0
OD2 J:ASP188 2.2 24.3 1.0
CD J:GLU216 3.0 27.9 1.0
CG J:ASP241 3.1 24.6 1.0
CG J:ASP188 3.2 25.5 1.0
OD1 J:ASP188 3.5 24.6 1.0
CB J:ASP241 3.6 21.2 1.0
OD1 J:ASN190 3.8 37.7 1.0
CG J:GLU216 3.8 28.7 1.0
OE2 J:GLU242 3.9 33.8 1.0
OE1 J:GLU216 3.9 28.1 1.0
OE1 J:GLU242 4.0 27.9 1.0
NZ J:LYS159 4.1 43.3 1.0
OD1 J:ASP241 4.1 24.6 1.0
ND2 J:ASN263 4.1 24.3 1.0
NZ J:LYS265 4.2 22.4 1.0
CD J:GLU242 4.4 29.3 1.0
CB J:ASP188 4.5 24.7 1.0
CG J:ASN190 4.7 36.3 1.0
CE J:LYS265 4.7 21.9 1.0
O J:HOH438 4.7 27.2 1.0
CB J:GLU216 4.9 26.6 1.0
CE J:LYS159 5.0 41.8 1.0

Reference:

C.Kalyanaraman, H.J.Imker, A.A.Fedorov, E.V.Fedorov, M.E.Glasner, P.C.Babbitt, S.C.Almo, J.A.Gerlt, M.P.Jacobson. Discovery of A Dipeptide Epimerase Enzymatic Function Guided By Homology Modeling and Virtual Screening. Structure V. 16 1668 2008.
ISSN: ISSN 0969-2126
PubMed: 19000819
DOI: 10.1016/J.STR.2008.08.015
Page generated: Wed Aug 14 12:30:07 2024

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