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Magnesium in PDB 2ox4: Crystal Structure of Putative Dehydratase From Zymomonas Mobilis ZM4

Enzymatic activity of Crystal Structure of Putative Dehydratase From Zymomonas Mobilis ZM4

All present enzymatic activity of Crystal Structure of Putative Dehydratase From Zymomonas Mobilis ZM4:
5.1.2.2;

Protein crystallography data

The structure of Crystal Structure of Putative Dehydratase From Zymomonas Mobilis ZM4, PDB code: 2ox4 was solved by Y.Patskovsky, R.Toro, J.M.Sauder, J.C.Freeman, K.Bain, T.Gheyi, S.R.Wasserman, D.Smith, J.Gerlt, S.K.Burley, S.C.Almo, New York Sgxresearch Center For Structural Genomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.80
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 190.178, 190.409, 85.922, 90.00, 90.00, 90.00
R / Rfree (%) 14.4 / 18.6

Other elements in 2ox4:

The structure of Crystal Structure of Putative Dehydratase From Zymomonas Mobilis ZM4 also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Putative Dehydratase From Zymomonas Mobilis ZM4 (pdb code 2ox4). 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 From Zymomonas Mobilis ZM4, PDB code: 2ox4:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 2ox4

Go back to Magnesium Binding Sites List in 2ox4
Magnesium binding site 1 out of 8 in the Crystal Structure of Putative Dehydratase From Zymomonas Mobilis ZM4


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 From Zymomonas Mobilis ZM4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:10.7
occ:1.00
 OE1 A:GLU265 2.1 22.1 1.0
OE2 A:GLU239 2.1 26.2 1.0
O A:HOH3470 2.1 21.9 1.0
O A:HOH3575 2.2 24.6 1.0
OE1 A:GLU213 2.2 55.7 0.5
O A:HOH3504 2.4 24.9 1.0
OE1 A:GLU213 2.4 9.7 0.5
CD A:GLU265 3.0 21.9 1.0
CD A:GLU213 3.3 12.9 0.5
CD A:GLU239 3.3 14.3 1.0
OE2 A:GLU265 3.3 18.7 1.0
CD A:GLU213 3.4 48.1 0.5
OE2 A:GLU213 3.4 7.2 0.5
CG A:GLU213 3.9 36.9 0.5
NZ A:LYS164 4.0 13.2 1.0
O A:HOH3492 4.0 18.6 1.0
OE1 A:GLU239 4.1 13.8 1.0
OE1 A:GLU240 4.1 20.8 1.0
CG A:GLU239 4.2 12.8 1.0
CD2 A:HIS315 4.3 13.3 1.0
O A:HOH3456 4.3 14.5 1.0
CD2 A:HIS215 4.3 22.9 1.0
CG A:GLU265 4.4 12.0 1.0
NE2 A:HIS315 4.4 21.4 1.0
NE2 A:GLN130 4.4 28.5 1.0
O A:HOH3785 4.4 31.1 1.0
OE2 A:GLU213 4.4 37.0 0.5
NE2 A:HIS215 4.4 37.4 1.0
O A:HOH3744 4.4 41.5 1.0
CG A:GLU213 4.7 2.0 0.5
CG A:GLU240 4.7 15.2 1.0
CE A:LYS164 4.8 14.1 1.0
CD A:GLU240 4.8 20.9 1.0
O A:HOH3709 4.9 35.8 1.0

Magnesium binding site 2 out of 8 in 2ox4

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Magnesium binding site 2 out of 8 in the Crystal Structure of Putative Dehydratase From Zymomonas Mobilis ZM4


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 From Zymomonas Mobilis ZM4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:9.1
occ:1.00
 OE1 B:GLU265 2.1 17.2 1.0
O B:HOH3509 2.1 20.2 1.0
OE2 B:GLU239 2.2 17.3 1.0
O B:HOH3766 2.2 24.3 1.0
OE1 B:GLU213 2.2 48.7 0.5
OE1 B:GLU213 2.4 12.0 0.5
O B:HOH3594 2.4 28.0 1.0
CD B:GLU265 3.0 15.6 1.0
CD B:GLU213 3.2 5.3 0.5
CD B:GLU239 3.3 16.6 1.0
OE2 B:GLU265 3.3 18.1 1.0
OE2 B:GLU213 3.3 3.0 0.5
CD B:GLU213 3.4 37.2 0.5
CG B:GLU213 3.9 30.1 0.5
NZ B:LYS164 4.0 12.8 1.0
O B:HOH3452 4.1 15.7 1.0
OE1 B:GLU240 4.1 17.1 1.0
OE1 B:GLU239 4.1 13.5 1.0
CG B:GLU239 4.2 9.3 1.0
O B:HOH3466 4.3 14.9 1.0
CD2 B:HIS215 4.3 15.6 1.0
O B:HOH3529 4.3 26.8 1.0
CD2 B:HIS315 4.3 12.9 1.0
CG B:GLU265 4.4 15.7 1.0
OE2 B:GLU213 4.4 23.9 0.5
NE2 B:GLN130 4.4 20.7 1.0
NE2 B:HIS215 4.4 29.7 1.0
O B:HOH3793 4.6 47.1 1.0
NE2 B:HIS315 4.6 16.6 1.0
CG B:GLU213 4.6 2.5 0.5
CG B:GLU240 4.8 11.9 1.0
CE B:LYS164 4.8 10.1 1.0
CD B:GLU240 4.8 14.5 1.0
O B:HOH3704 4.9 36.0 1.0

Magnesium binding site 3 out of 8 in 2ox4

Go back to Magnesium Binding Sites List in 2ox4
Magnesium binding site 3 out of 8 in the Crystal Structure of Putative Dehydratase From Zymomonas Mobilis ZM4


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 From Zymomonas Mobilis ZM4 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg402

b:8.2
occ:1.00
 OE2 C:GLU239 2.1 18.9 1.0
O C:HOH3576 2.1 25.0 1.0
OE1 C:GLU265 2.1 21.7 1.0
O C:HOH3447 2.2 21.0 1.0
OE1 C:GLU213 2.2 20.5 1.0
O C:HOH3506 2.4 27.1 1.0
CD C:GLU265 3.1 19.3 1.0
CD C:GLU213 3.2 25.8 1.0
CD C:GLU239 3.2 17.4 1.0
OE2 C:GLU213 3.4 16.5 1.0
OE2 C:GLU265 3.4 20.8 1.0
NZ C:LYS164 3.9 15.8 1.0
OE1 C:GLU239 4.0 14.5 1.0
O C:HOH3467 4.0 16.1 1.0
CG C:GLU239 4.1 12.8 1.0
OE1 C:GLU240 4.2 20.2 1.0
NE2 C:GLN130 4.2 22.0 1.0
O C:HOH3438 4.3 12.5 1.0
O C:HOH3776 4.3 29.1 1.0
CD2 C:HIS315 4.4 13.8 1.0
CD2 C:HIS215 4.4 23.8 1.0
O C:HOH3641 4.4 36.7 1.0
CG C:GLU265 4.4 12.6 1.0
NE2 C:HIS215 4.5 24.6 1.0
CG C:GLU213 4.6 13.6 1.0
NE2 C:HIS315 4.6 14.8 1.0
CE C:LYS164 4.7 15.6 1.0
CG C:GLU240 4.8 14.9 1.0
CD C:GLU240 4.9 17.0 1.0

Magnesium binding site 4 out of 8 in 2ox4

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Magnesium binding site 4 out of 8 in the Crystal Structure of Putative Dehydratase From Zymomonas Mobilis ZM4


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 From Zymomonas Mobilis ZM4 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg402

b:8.2
occ:1.00
 O D:HOH3564 2.0 22.2 1.0
OE1 D:GLU265 2.1 22.3 1.0
OE2 D:GLU239 2.2 21.2 1.0
O D:HOH3519 2.2 20.2 1.0
O D:HOH3550 2.2 30.7 1.0
OE1 D:GLU213 2.3 23.9 1.0
CD D:GLU265 3.1 24.5 1.0
CD D:GLU213 3.2 27.1 1.0
CD D:GLU239 3.3 17.4 1.0
OE2 D:GLU213 3.4 18.0 1.0
OE2 D:GLU265 3.5 19.3 1.0
NZ D:LYS164 3.9 12.1 1.0
OE1 D:GLU239 4.1 17.7 1.0
O D:HOH3530 4.1 19.5 1.0
CG D:GLU239 4.1 13.5 1.0
OE1 D:GLU240 4.2 16.9 1.0
NE2 D:GLN130 4.2 19.7 1.0
O D:HOH3709 4.2 27.3 1.0
CD2 D:HIS215 4.3 19.2 1.0
CD2 D:HIS315 4.3 13.9 1.0
NE2 D:HIS215 4.3 26.4 1.0
O D:HOH3441 4.3 13.5 1.0
CG D:GLU265 4.4 13.2 1.0
NE2 D:HIS315 4.5 17.1 1.0
O D:HOH3616 4.5 29.2 1.0
CG D:GLU213 4.6 16.1 1.0
CE D:LYS164 4.7 12.1 1.0
CG D:GLU240 4.9 11.5 1.0
CD D:GLU240 4.9 17.2 1.0

Magnesium binding site 5 out of 8 in 2ox4

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Magnesium binding site 5 out of 8 in the Crystal Structure of Putative Dehydratase From Zymomonas Mobilis ZM4


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 From Zymomonas Mobilis ZM4 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg402

b:6.9
occ:1.00
 OE2 E:GLU239 2.1 18.0 1.0
OE1 E:GLU265 2.1 16.0 1.0
O E:HOH3534 2.1 21.8 1.0
OE2 E:GLU213 2.2 41.8 0.5
O E:HOH3574 2.2 26.5 1.0
O E:HOH3453 2.2 17.8 1.0
OE1 E:GLU213 2.3 8.1 0.5
CD E:GLU265 3.1 17.3 1.0
CD E:GLU213 3.2 7.2 0.5
CD E:GLU239 3.2 14.9 1.0
CD E:GLU213 3.3 38.9 0.5
OE2 E:GLU213 3.4 4.7 0.5
OE2 E:GLU265 3.4 16.1 1.0
CG E:GLU213 3.8 32.6 0.5
NZ E:LYS164 3.9 8.8 1.0
OE1 E:GLU239 4.0 10.9 1.0
O E:HOH3505 4.1 16.1 1.0
CG E:GLU239 4.2 8.5 1.0
O E:HOH3801 4.2 26.6 1.0
OE1 E:GLU240 4.2 18.7 1.0
O E:HOH3429 4.2 12.0 1.0
NE2 E:GLN130 4.3 19.8 1.0
CD2 E:HIS215 4.3 16.9 1.0
CD2 E:HIS315 4.4 16.7 1.0
OE1 E:GLU213 4.4 32.9 0.5
CG E:GLU265 4.4 16.1 1.0
NE2 E:HIS215 4.4 23.0 1.0
CG E:GLU213 4.6 2.0 0.5
NE2 E:HIS315 4.6 17.0 1.0
O E:HOH3758 4.6 46.2 1.0
CE E:LYS164 4.7 9.3 1.0
CG E:GLU240 4.8 14.6 1.0
CD E:GLU240 4.9 13.4 1.0

Magnesium binding site 6 out of 8 in 2ox4

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Magnesium binding site 6 out of 8 in the Crystal Structure of Putative Dehydratase From Zymomonas Mobilis ZM4


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 From Zymomonas Mobilis ZM4 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg402

b:8.2
occ:1.00
 OE2 F:GLU239 2.1 18.1 1.0
OE1 F:GLU265 2.1 17.1 1.0
O F:HOH3486 2.2 19.3 1.0
O F:HOH3536 2.2 25.3 1.0
O F:HOH3534 2.2 28.9 1.0
OE1 F:GLU213 2.3 23.5 1.0
CD F:GLU265 3.1 18.6 1.0
CD F:GLU239 3.2 15.4 1.0
CD F:GLU213 3.2 24.1 1.0
OE2 F:GLU213 3.3 17.7 1.0
OE2 F:GLU265 3.4 20.5 1.0
NZ F:LYS164 4.0 13.0 1.0
OE1 F:GLU239 4.0 14.3 1.0
OE1 F:GLU240 4.1 18.7 1.0
O F:HOH3489 4.1 17.1 1.0
CG F:GLU239 4.1 15.0 1.0
O F:HOH3753 4.3 32.6 1.0
CD2 F:HIS215 4.3 19.5 1.0
CD2 F:HIS315 4.3 15.7 1.0
NE2 F:GLN130 4.3 21.7 1.0
O F:HOH3503 4.4 15.3 1.0
CG F:GLU265 4.4 16.3 1.0
NE2 F:HIS215 4.4 27.4 1.0
NE2 F:HIS315 4.5 19.3 1.0
CG F:GLU213 4.6 13.0 1.0
O F:HOH3801 4.7 41.1 1.0
CG F:GLU240 4.8 12.6 1.0
CE F:LYS164 4.8 13.9 1.0
CD F:GLU240 4.8 11.3 1.0

Magnesium binding site 7 out of 8 in 2ox4

Go back to Magnesium Binding Sites List in 2ox4
Magnesium binding site 7 out of 8 in the Crystal Structure of Putative Dehydratase From Zymomonas Mobilis ZM4


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 From Zymomonas Mobilis ZM4 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg502

b:8.9
occ:1.00
 OE1 G:GLU265 2.1 17.8 1.0
O G:HOH3525 2.1 21.5 1.0
OE2 G:GLU239 2.1 19.7 1.0
OE2 G:GLU213 2.2 41.9 0.3
O G:HOH3539 2.2 19.8 1.0
OE1 G:GLU213 2.3 16.0 0.7
O G:HOH3586 2.3 25.6 1.0
CD G:GLU265 3.0 21.8 1.0
CD G:GLU213 3.2 15.2 0.7
CD G:GLU239 3.2 14.8 1.0
CD G:GLU213 3.3 27.1 0.3
OE2 G:GLU265 3.3 17.8 1.0
OE2 G:GLU213 3.4 9.4 0.7
CG G:GLU213 3.9 23.3 0.3
NZ G:LYS164 3.9 10.1 1.0
OE1 G:GLU239 4.0 14.2 1.0
O G:HOH3491 4.1 15.7 1.0
OE1 G:GLU240 4.1 18.2 1.0
CG G:GLU239 4.1 11.3 1.0
O G:HOH3436 4.3 13.8 1.0
O G:HOH3800 4.3 39.7 1.0
CG G:GLU265 4.3 15.1 1.0
OE1 G:GLU213 4.4 21.7 0.3
CD2 G:HIS315 4.4 15.0 1.0
CD2 G:HIS215 4.4 19.0 1.0
NE2 G:GLN130 4.4 21.2 1.0
NE2 G:HIS215 4.5 22.3 1.0
O G:HOH3689 4.6 38.0 1.0
CG G:GLU213 4.6 3.3 0.7
NE2 G:HIS315 4.6 17.4 1.0
CG G:GLU240 4.8 11.3 1.0
CE G:LYS164 4.8 8.3 1.0
CD G:GLU240 4.8 14.5 1.0

Magnesium binding site 8 out of 8 in 2ox4

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Magnesium binding site 8 out of 8 in the Crystal Structure of Putative Dehydratase From Zymomonas Mobilis ZM4


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 From Zymomonas Mobilis ZM4 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg402

b:8.0
occ:1.00
 OE2 H:GLU239 2.1 20.6 1.0
O H:HOH3494 2.1 19.6 1.0
O H:HOH3520 2.1 23.2 1.0
OE1 H:GLU265 2.1 22.1 1.0
O H:HOH3593 2.2 31.2 1.0
OE1 H:GLU213 2.3 16.4 1.0
CD H:GLU265 3.1 20.3 1.0
CD H:GLU213 3.2 25.3 1.0
CD H:GLU239 3.2 11.6 1.0
OE2 H:GLU213 3.3 18.3 1.0
OE2 H:GLU265 3.4 20.3 1.0
OE1 H:GLU239 4.0 13.0 1.0
NZ H:LYS164 4.0 11.2 1.0
OE1 H:GLU240 4.1 18.2 1.0
CG H:GLU239 4.1 14.4 1.0
O H:HOH3489 4.1 16.9 1.0
O H:HOH3797 4.2 28.8 1.0
NE2 H:GLN130 4.2 22.7 1.0
CD2 H:HIS215 4.3 20.0 1.0
O H:HOH3447 4.3 13.7 1.0
CD2 H:HIS315 4.3 18.5 1.0
NE2 H:HIS215 4.4 23.5 1.0
CG H:GLU265 4.4 16.2 1.0
O H:HOH3610 4.5 36.3 1.0
NE2 H:HIS315 4.5 20.8 1.0
CG H:GLU213 4.6 14.8 1.0
CE H:LYS164 4.7 10.1 1.0
CG H:GLU240 4.8 14.1 1.0
CD H:GLU240 4.8 16.7 1.0

Reference:

Y.Patskovsky, R.Toro, J.M.Sauder, J.C.Freeman, K.Bain, T.Gheyi, S.R.Wasserman, D.Smith, J.Gerlt, S.K.Burley, S.C.Almo. Crystal Structure of Putative Dehydratase From Zymomonas Mobilis ZM4 To Be Published.
Page generated: Wed Aug 14 01:59:19 2024

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