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Magnesium in PDB 3ozm: Crystal Structure of Enolase Superfamily Member From Bordetella Bronchiseptica Complexed with Mg, M-Xylarate and L-Lyxarate

Protein crystallography data

The structure of Crystal Structure of Enolase Superfamily Member From Bordetella Bronchiseptica Complexed with Mg, M-Xylarate and L-Lyxarate, PDB code: 3ozm was solved by A.A.Fedorov, E.V.Fedorov, D.Wichelecki, 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) 39.00 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 91.175, 134.335, 146.754, 90.00, 97.03, 90.00
R / Rfree (%) 19.1 / 22.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Enolase Superfamily Member From Bordetella Bronchiseptica Complexed with Mg, M-Xylarate and L-Lyxarate (pdb code 3ozm). 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 Enolase Superfamily Member From Bordetella Bronchiseptica Complexed with Mg, M-Xylarate and L-Lyxarate, PDB code: 3ozm:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 3ozm

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Magnesium binding site 1 out of 8 in the Crystal Structure of Enolase Superfamily Member From Bordetella Bronchiseptica Complexed with Mg, M-Xylarate and L-Lyxarate


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 Enolase Superfamily Member From Bordetella Bronchiseptica Complexed with Mg, M-Xylarate and L-Lyxarate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg390

b:21.1
occ:1.00
 O A:HOH2283 2.1 19.0 1.0
OE2 A:GLU254 2.2 18.0 1.0
OE2 A:GLU227 2.2 15.5 1.0
OAK A:DXL391 2.2 18.8 1.0
OD2 A:ASP201 2.2 16.3 1.0
OAC A:DXL391 2.2 18.9 1.0
CAJ A:DXL391 3.0 22.4 1.0
CD A:GLU254 3.1 20.8 1.0
CAI A:DXL391 3.1 19.0 1.0
CG A:ASP201 3.1 17.6 1.0
CD A:GLU227 3.2 15.0 1.0
OE1 A:GLU254 3.3 19.9 1.0
OD1 A:ASP201 3.4 17.6 1.0
CG A:GLU227 3.8 14.9 1.0
NZ A:LYS171 3.9 15.7 1.0
NZ A:LYS173 3.9 29.1 1.0
OE1 A:GLU227 4.0 13.9 1.0
O A:HOH412 4.1 15.4 1.0
ND2 A:ASN203 4.2 17.8 1.0
O A:HOH417 4.2 16.4 1.0
OAD A:DXL391 4.2 24.4 1.0
OE1 A:GLU228 4.4 17.3 1.0
CAH A:DXL391 4.4 22.6 1.0
CG A:GLU254 4.4 14.9 1.0
CD2 A:HIS304 4.4 18.4 1.0
CB A:ASP201 4.5 13.8 1.0
OAL A:DXL391 4.5 34.5 1.0
CE A:LYS171 4.6 15.0 1.0
CG A:ASN203 4.8 15.5 1.0
CD A:GLU228 4.9 18.2 1.0
OD1 A:ASN203 5.0 18.8 1.0
CB A:GLU254 5.0 14.4 1.0

Magnesium binding site 2 out of 8 in 3ozm

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Magnesium binding site 2 out of 8 in the Crystal Structure of Enolase Superfamily Member From Bordetella Bronchiseptica Complexed with Mg, M-Xylarate and L-Lyxarate


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 Enolase Superfamily Member From Bordetella Bronchiseptica Complexed with Mg, M-Xylarate and L-Lyxarate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg390

b:19.1
occ:1.00
 OE2 B:GLU227 2.1 17.5 1.0
O B:HOH2286 2.1 19.0 1.0
OE2 B:GLU254 2.2 17.9 1.0
OD2 B:ASP201 2.2 16.6 1.0
OAK B:DXL391 2.3 17.3 1.0
OAC B:DXL391 2.3 20.1 1.0
CAJ B:DXL391 3.0 22.2 1.0
CD B:GLU227 3.1 13.3 1.0
CD B:GLU254 3.1 20.5 1.0
CG B:ASP201 3.1 17.9 1.0
CAI B:DXL391 3.1 20.4 1.0
OE1 B:GLU254 3.4 23.7 1.0
OD1 B:ASP201 3.4 17.4 1.0
CG B:GLU227 3.7 13.6 1.0
NZ B:LYS171 3.8 14.4 1.0
OE1 B:GLU227 3.9 17.8 1.0
NZ B:LYS173 3.9 31.8 1.0
O B:HOH537 4.0 20.3 1.0
O B:HOH394 4.1 16.5 1.0
ND2 B:ASN203 4.2 19.1 1.0
OAD B:DXL391 4.2 22.0 1.0
CAH B:DXL391 4.4 30.4 1.0
OE1 B:GLU228 4.4 20.7 1.0
CB B:ASP201 4.4 15.8 1.0
CG B:GLU254 4.5 18.6 1.0
CD2 B:HIS304 4.6 21.6 1.0
OAL B:DXL391 4.6 31.6 1.0
CE B:LYS171 4.7 17.2 1.0
CG B:ASN203 4.9 20.7 1.0
CD B:GLU228 4.9 21.9 1.0
CG B:GLU228 4.9 17.5 1.0
OD1 B:ASN203 5.0 21.4 1.0

Magnesium binding site 3 out of 8 in 3ozm

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Magnesium binding site 3 out of 8 in the Crystal Structure of Enolase Superfamily Member From Bordetella Bronchiseptica Complexed with Mg, M-Xylarate and L-Lyxarate


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 Enolase Superfamily Member From Bordetella Bronchiseptica Complexed with Mg, M-Xylarate and L-Lyxarate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg390

b:20.2
occ:1.00
 OE2 C:GLU254 2.1 20.0 1.0
O C:HOH2285 2.2 20.5 1.0
OE2 C:GLU227 2.2 16.9 1.0
OD2 C:ASP201 2.2 16.3 1.0
OAK C:DXL391 2.2 20.9 1.0
OAC C:DXL391 2.3 17.3 1.0
CD C:GLU254 3.0 19.2 1.0
CAJ C:DXL391 3.0 21.3 1.0
CD C:GLU227 3.1 18.5 1.0
CG C:ASP201 3.1 16.7 1.0
CAI C:DXL391 3.1 21.0 1.0
OE1 C:GLU254 3.3 20.0 1.0
OD1 C:ASP201 3.4 17.5 1.0
CG C:GLU227 3.7 16.0 1.0
NZ C:LYS171 3.9 15.1 1.0
NZ C:LYS173 3.9 32.7 1.0
OE1 C:GLU227 4.0 15.8 1.0
O C:HOH422 4.0 17.4 1.0
O C:HOH407 4.1 15.5 1.0
OAD C:DXL391 4.2 20.2 1.0
ND2 C:ASN203 4.3 21.9 1.0
CG C:GLU254 4.3 15.5 1.0
OE1 C:GLU228 4.4 18.9 1.0
CAH C:DXL391 4.4 27.3 1.0
CB C:ASP201 4.5 16.0 1.0
CD2 C:HIS304 4.5 16.5 1.0
OAL C:DXL391 4.6 35.4 1.0
CE C:LYS171 4.6 18.2 1.0
CD C:GLU228 4.8 19.2 1.0
CG C:ASN203 4.9 17.0 1.0
CG C:GLU228 4.9 14.3 1.0
CB C:GLU254 5.0 15.5 1.0

Magnesium binding site 4 out of 8 in 3ozm

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Magnesium binding site 4 out of 8 in the Crystal Structure of Enolase Superfamily Member From Bordetella Bronchiseptica Complexed with Mg, M-Xylarate and L-Lyxarate


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 Enolase Superfamily Member From Bordetella Bronchiseptica Complexed with Mg, M-Xylarate and L-Lyxarate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg390

b:16.7
occ:1.00
 OE2 D:GLU254 2.1 16.4 1.0
OAK D:LY9391 2.2 16.6 1.0
OE2 D:GLU227 2.2 15.9 1.0
O D:HOH2281 2.2 16.7 1.0
OAC D:LY9391 2.2 15.9 1.0
OD2 D:ASP201 2.2 15.9 1.0
CAJ D:LY9391 3.0 19.3 1.0
CD D:GLU254 3.0 16.9 1.0
CAI D:LY9391 3.1 16.9 1.0
CD D:GLU227 3.1 16.4 1.0
CG D:ASP201 3.2 19.0 1.0
OE1 D:GLU254 3.3 21.1 1.0
OD1 D:ASP201 3.5 16.8 1.0
CG D:GLU227 3.8 13.4 1.0
O D:HOH422 3.9 16.9 1.0
NZ D:LYS171 3.9 15.7 1.0
OE1 D:GLU227 4.0 16.1 1.0
O D:HOH394 4.1 15.7 1.0
OAL D:LY9391 4.1 38.6 1.0
ND2 D:ASN203 4.2 24.0 1.0
OAD D:LY9391 4.2 18.0 1.0
CAH D:LY9391 4.2 24.6 1.0
OE1 D:GLU228 4.3 19.8 1.0
CG D:GLU254 4.4 17.1 1.0
CB D:ASP201 4.5 15.7 1.0
CD2 D:HIS304 4.6 15.5 1.0
CE D:LYS171 4.8 16.1 1.0
CD D:GLU228 4.9 19.9 1.0
CB D:GLU254 5.0 16.9 1.0

Magnesium binding site 5 out of 8 in 3ozm

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Magnesium binding site 5 out of 8 in the Crystal Structure of Enolase Superfamily Member From Bordetella Bronchiseptica Complexed with Mg, M-Xylarate and L-Lyxarate


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 Enolase Superfamily Member From Bordetella Bronchiseptica Complexed with Mg, M-Xylarate and L-Lyxarate within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg390

b:22.8
occ:1.00
 O E:HOH2287 2.1 22.4 1.0
OE2 E:GLU254 2.1 19.1 1.0
OAK E:DXL391 2.2 17.6 1.0
OD2 E:ASP201 2.2 19.3 1.0
OE2 E:GLU227 2.2 17.6 1.0
OAC E:DXL391 2.3 21.8 1.0
CAJ E:DXL391 3.0 28.8 1.0
CD E:GLU254 3.0 23.0 1.0
CAI E:DXL391 3.1 23.1 1.0
CD E:GLU227 3.1 17.3 1.0
CG E:ASP201 3.1 20.2 1.0
OE1 E:GLU254 3.3 23.5 1.0
OD1 E:ASP201 3.5 20.9 1.0
CG E:GLU227 3.8 16.0 1.0
NZ E:LYS173 3.9 30.2 1.0
NZ E:LYS171 3.9 16.5 1.0
OE1 E:GLU227 3.9 16.3 1.0
O E:HOH438 4.0 19.3 1.0
ND2 E:ASN203 4.1 21.9 1.0
O E:HOH403 4.1 18.7 1.0
OAD E:DXL391 4.2 25.9 1.0
OE1 E:GLU228 4.4 18.7 1.0
CAH E:DXL391 4.4 28.6 1.0
CG E:GLU254 4.4 17.7 1.0
CB E:ASP201 4.5 16.6 1.0
OAL E:DXL391 4.5 34.8 1.0
CD2 E:HIS304 4.5 17.1 1.0
CE E:LYS171 4.7 19.8 1.0
CG E:ASN203 4.8 21.6 1.0
CD E:GLU228 4.8 20.3 1.0
CG E:GLU228 5.0 17.7 1.0
OD1 E:ASN203 5.0 21.5 1.0

Magnesium binding site 6 out of 8 in 3ozm

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Magnesium binding site 6 out of 8 in the Crystal Structure of Enolase Superfamily Member From Bordetella Bronchiseptica Complexed with Mg, M-Xylarate and L-Lyxarate


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 Enolase Superfamily Member From Bordetella Bronchiseptica Complexed with Mg, M-Xylarate and L-Lyxarate within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg390

b:19.2
occ:1.00
 OE2 F:GLU227 2.1 17.0 1.0
OE2 F:GLU254 2.1 15.7 1.0
OAK F:DXL391 2.2 18.2 1.0
OD2 F:ASP201 2.2 16.9 1.0
O F:HOH399 2.2 18.9 1.0
OAC F:DXL391 2.3 20.0 1.0
CAJ F:DXL391 3.0 19.8 1.0
CD F:GLU254 3.0 21.1 1.0
CD F:GLU227 3.1 15.5 1.0
CAI F:DXL391 3.1 24.1 1.0
CG F:ASP201 3.2 16.4 1.0
OE1 F:GLU254 3.3 19.5 1.0
OD1 F:ASP201 3.5 19.6 1.0
CG F:GLU227 3.8 14.6 1.0
NZ F:LYS171 3.9 17.6 1.0
O F:HOH446 3.9 17.7 1.0
OE1 F:GLU227 3.9 14.8 1.0
NZ F:LYS173 4.0 32.5 1.0
O F:HOH395 4.1 15.7 1.0
OAD F:DXL391 4.2 24.5 1.0
ND2 F:ASN203 4.2 20.2 1.0
CG F:GLU254 4.4 15.3 1.0
CAH F:DXL391 4.4 36.1 1.0
CD2 F:HIS304 4.4 16.8 1.0
CB F:ASP201 4.5 14.3 1.0
OE1 F:GLU228 4.5 16.4 1.0
OAL F:DXL391 4.6 36.5 1.0
CE F:LYS171 4.7 16.6 1.0
CG F:ASN203 4.9 22.3 1.0
CB F:GLU254 5.0 15.3 1.0

Magnesium binding site 7 out of 8 in 3ozm

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Magnesium binding site 7 out of 8 in the Crystal Structure of Enolase Superfamily Member From Bordetella Bronchiseptica Complexed with Mg, M-Xylarate and L-Lyxarate


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 Enolase Superfamily Member From Bordetella Bronchiseptica Complexed with Mg, M-Xylarate and L-Lyxarate within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg390

b:19.8
occ:1.00
 OE2 G:GLU254 2.2 18.3 1.0
OD2 G:ASP201 2.2 19.2 1.0
OE2 G:GLU227 2.2 16.5 1.0
O G:HOH2284 2.2 21.3 1.0
OAK G:DXL391 2.2 19.6 1.0
OAC G:DXL391 2.3 21.5 1.0
CAJ G:DXL391 3.0 20.3 1.0
CD G:GLU254 3.1 22.8 1.0
CAI G:DXL391 3.1 24.5 1.0
CD G:GLU227 3.1 19.7 1.0
CG G:ASP201 3.1 20.7 1.0
OE1 G:GLU254 3.4 20.1 1.0
OD1 G:ASP201 3.5 19.8 1.0
CG G:GLU227 3.8 18.0 1.0
NZ G:LYS171 3.9 17.8 1.0
NZ G:LYS173 3.9 36.6 1.0
OE1 G:GLU227 4.0 18.1 1.0
O G:HOH415 4.0 18.9 1.0
O G:HOH407 4.1 17.2 1.0
ND2 G:ASN203 4.2 21.9 1.0
OAD G:DXL391 4.2 23.2 1.0
CG G:GLU254 4.4 15.3 1.0
CAH G:DXL391 4.4 34.0 1.0
CB G:ASP201 4.5 16.6 1.0
OE1 G:GLU228 4.5 19.1 1.0
CD2 G:HIS304 4.5 16.6 1.0
OAL G:DXL391 4.6 39.3 1.0
CE G:LYS171 4.7 18.0 1.0
CG G:ASN203 4.9 20.8 1.0
CD G:GLU228 5.0 19.8 1.0

Magnesium binding site 8 out of 8 in 3ozm

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Magnesium binding site 8 out of 8 in the Crystal Structure of Enolase Superfamily Member From Bordetella Bronchiseptica Complexed with Mg, M-Xylarate and L-Lyxarate


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 Enolase Superfamily Member From Bordetella Bronchiseptica Complexed with Mg, M-Xylarate and L-Lyxarate within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg390

b:20.1
occ:1.00
 OE2 H:GLU254 2.1 19.5 1.0
OE2 H:GLU227 2.1 17.4 1.0
O H:HOH2282 2.2 19.9 1.0
OAK H:LY9391 2.2 18.5 1.0
OD2 H:ASP201 2.2 20.1 1.0
OAC H:LY9391 2.3 21.2 1.0
CAJ H:LY9391 3.0 21.9 1.0
CD H:GLU254 3.0 23.1 1.0
CD H:GLU227 3.1 17.1 1.0
CG H:ASP201 3.1 19.3 1.0
CAI H:LY9391 3.1 24.6 1.0
OE1 H:GLU254 3.3 23.5 1.0
OD1 H:ASP201 3.4 23.0 1.0
CG H:GLU227 3.8 16.3 1.0
NZ H:LYS171 3.9 19.2 1.0
O H:HOH425 3.9 20.5 1.0
OE1 H:GLU227 4.0 18.6 1.0
O H:HOH396 4.0 18.4 1.0
OAL H:LY9391 4.1 34.9 1.0
OAD H:LY9391 4.2 21.8 1.0
ND2 H:ASN203 4.2 29.2 1.0
CAH H:LY9391 4.3 31.3 1.0
CG H:GLU254 4.4 21.0 1.0
OE1 H:GLU228 4.4 25.1 1.0
CB H:ASP201 4.5 17.4 1.0
CD2 H:HIS304 4.5 22.6 1.0
CE H:LYS171 4.7 18.6 1.0
CD H:GLU228 4.9 25.0 1.0
CG H:GLU228 4.9 19.0 1.0

Reference:

A.A.Fedorov, E.V.Fedorov, D.Wichelecki, J.A.Gerlt, S.C.Almo. Crystal Structure of Enolase Superfamily Member From Bordetella Bronchiseptica Complexed with Mg, M-Xylarate and L-Lyxarate To Be Published.
Page generated: Mon Dec 14 08:38:20 2020

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