Magnesium in PDB 7qib: Crystal Structure of Mycobacterium Hassiacum Glucosyl-3- Phosphoglycerate Synthase at pH 8.5 in Complex with Udp

Enzymatic activity of Crystal Structure of Mycobacterium Hassiacum Glucosyl-3- Phosphoglycerate Synthase at pH 8.5 in Complex with Udp

All present enzymatic activity of Crystal Structure of Mycobacterium Hassiacum Glucosyl-3- Phosphoglycerate Synthase at pH 8.5 in Complex with Udp:
2.4.1.266;

Protein crystallography data

The structure of Crystal Structure of Mycobacterium Hassiacum Glucosyl-3- Phosphoglycerate Synthase at pH 8.5 in Complex with Udp, PDB code: 7qib was solved by A.Silva, D.Nunes-Costa, P.J.Barbosa Pereira, S.Macedo-Ribeiro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.80 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 70.045, 89.957, 95.217, 90, 90, 90
R / Rfree (%) 17.4 / 19.6

Other elements in 7qib:

The structure of Crystal Structure of Mycobacterium Hassiacum Glucosyl-3- Phosphoglycerate Synthase at pH 8.5 in Complex with Udp also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Mycobacterium Hassiacum Glucosyl-3- Phosphoglycerate Synthase at pH 8.5 in Complex with Udp (pdb code 7qib). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of Mycobacterium Hassiacum Glucosyl-3- Phosphoglycerate Synthase at pH 8.5 in Complex with Udp, PDB code: 7qib:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 7qib

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Magnesium binding site 1 out of 6 in the Crystal Structure of Mycobacterium Hassiacum Glucosyl-3- Phosphoglycerate Synthase at pH 8.5 in Complex with Udp


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 Mycobacterium Hassiacum Glucosyl-3- Phosphoglycerate Synthase at pH 8.5 in Complex with Udp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:34.9
occ:0.46
 O A:HOH593 2.0 40.2 1.0
OE2 A:GLU51 2.1 28.3 1.0
O A:HOH557 2.1 46.6 1.0
O A:HOH588 2.2 40.2 1.0
O A:HOH595 2.3 38.1 1.0
O A:HOH507 2.3 45.2 1.0
CD A:GLU51 3.0 28.2 1.0
OE1 A:GLU51 3.3 27.9 1.0
O A:HOH521 3.6 51.4 1.0
O A:LEU49 3.7 24.2 1.0
O3B A:UDP405 3.8 59.0 1.0
O2' A:UDP405 4.1 24.5 1.0
O A:HOH525 4.2 46.7 1.0
C2' A:UDP405 4.3 25.2 1.0
CG A:GLU51 4.3 25.1 1.0
O A:ASN50 4.3 27.7 1.0
O3A A:UDP405 4.6 42.4 1.0
O2A A:UDP405 4.7 45.0 1.0
CB A:ASP133 4.7 26.0 1.0
PB A:UDP405 4.8 57.4 1.0
OD2 A:ASP133 4.8 31.2 1.0
C3' A:UDP405 4.8 24.6 1.0
O2B A:UDP405 4.8 54.9 1.0
C A:LEU49 4.9 25.6 1.0

Magnesium binding site 2 out of 6 in 7qib

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Magnesium binding site 2 out of 6 in the Crystal Structure of Mycobacterium Hassiacum Glucosyl-3- Phosphoglycerate Synthase at pH 8.5 in Complex with Udp


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 Mycobacterium Hassiacum Glucosyl-3- Phosphoglycerate Synthase at pH 8.5 in Complex with Udp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:36.5
occ:0.63
 O A:HOH504 2.0 44.8 0.8
O A:HOH529 2.0 43.6 1.0
OD2 A:ASP133 2.1 31.2 1.0
O A:HOH514 2.1 42.3 1.0
O2A A:UDP405 2.3 45.0 1.0
CG A:ASP133 3.2 34.5 1.0
O A:HOH521 3.4 51.4 1.0
PA A:UDP405 3.6 37.5 1.0
OD1 A:ASP133 3.6 27.2 1.0
O A:HOH593 3.9 40.2 1.0
C5' A:UDP405 4.1 27.6 1.0
O1A A:UDP405 4.1 36.3 1.0
O5' A:UDP405 4.2 28.5 1.0
CB A:ASP133 4.5 26.0 1.0
O3B A:UDP405 4.5 59.0 1.0
OD2 A:ASP131 4.6 29.5 1.0
O3A A:UDP405 4.7 42.4 1.0
C3' A:UDP405 5.0 24.6 1.0

Magnesium binding site 3 out of 6 in 7qib

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Magnesium binding site 3 out of 6 in the Crystal Structure of Mycobacterium Hassiacum Glucosyl-3- Phosphoglycerate Synthase at pH 8.5 in Complex with Udp


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 Mycobacterium Hassiacum Glucosyl-3- Phosphoglycerate Synthase at pH 8.5 in Complex with Udp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:27.4
occ:0.52
 NE2 A:HIS323 2.0 41.0 1.0
O A:HOH629 2.0 41.9 1.0
O A:HOH540 2.1 30.0 1.0
O A:HOH651 2.1 41.7 1.0
O A:HOH592 2.1 26.1 1.0
O A:HOH726 2.2 40.2 1.0
CE1 A:HIS323 3.0 39.4 1.0
CD2 A:HIS323 3.0 40.1 1.0
O A:HOH528 3.8 33.8 1.0
ND1 A:HIS323 4.1 37.5 1.0
CG A:HIS323 4.1 38.0 1.0
O A:LEU237 4.4 20.1 1.0
O A:HOH704 4.4 37.4 1.0
O A:HOH723 4.4 40.0 1.0
OD2 A:ASP240 4.5 29.3 1.0
O A:HOH692 4.6 46.3 1.0
CB A:ASP240 4.7 23.2 1.0

Magnesium binding site 4 out of 6 in 7qib

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Magnesium binding site 4 out of 6 in the Crystal Structure of Mycobacterium Hassiacum Glucosyl-3- Phosphoglycerate Synthase at pH 8.5 in Complex with Udp


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 Mycobacterium Hassiacum Glucosyl-3- Phosphoglycerate Synthase at pH 8.5 in Complex with Udp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:55.2
occ:1.00
 O A:HOH732 2.1 45.4 1.0
O A:HOH555 2.2 48.8 1.0
O A:HOH509 2.2 41.6 1.0
O A:HOH716 2.2 52.7 1.0
O A:HOH527 3.5 53.3 1.0
O A:HOH532 3.9 33.9 1.0
OE2 A:GLU85 4.1 41.4 1.0
O A:SER80 4.2 33.1 1.0
O A:HOH621 4.4 43.6 1.0
OE1 A:GLU85 4.5 38.9 1.0
CD A:GLU85 4.7 35.8 1.0
CA A:GLY79 5.0 31.2 1.0
OD2 A:ASP77 5.0 30.4 1.0

Magnesium binding site 5 out of 6 in 7qib

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Magnesium binding site 5 out of 6 in the Crystal Structure of Mycobacterium Hassiacum Glucosyl-3- Phosphoglycerate Synthase at pH 8.5 in Complex with Udp


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 Mycobacterium Hassiacum Glucosyl-3- Phosphoglycerate Synthase at pH 8.5 in Complex with Udp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg401

b:31.0
occ:0.52
 O B:HOH527 1.9 39.3 1.0
OE2 B:GLU51 2.0 38.9 1.0
O B:HOH520 2.1 47.8 1.0
O B:HOH643 2.2 43.9 1.0
O B:HOH628 2.2 42.2 1.0
O B:HOH631 2.2 42.5 1.0
CD B:GLU51 2.9 32.7 1.0
OE1 B:GLU51 3.3 36.0 1.0
O2B B:UDP403 3.6 54.6 1.0
O B:LEU49 3.8 34.3 1.0
O2' B:UDP403 4.0 27.2 1.0
O B:HOH526 4.0 49.1 1.0
O B:HOH669 4.1 42.7 1.0
CG B:GLU51 4.2 32.8 1.0
C2' B:UDP403 4.2 27.8 1.0
CB B:ASP133 4.4 31.0 1.0
OD2 B:ASP133 4.5 38.6 1.0
O B:ASN50 4.5 37.4 1.0
O2A B:UDP403 4.6 45.6 1.0
O3A B:UDP403 4.7 42.7 1.0
C3' B:UDP403 4.7 23.6 1.0
PB B:UDP403 4.8 61.4 1.0
CG B:ASP133 5.0 40.0 1.0

Magnesium binding site 6 out of 6 in 7qib

Go back to Magnesium Binding Sites List in 7qib
Magnesium binding site 6 out of 6 in the Crystal Structure of Mycobacterium Hassiacum Glucosyl-3- Phosphoglycerate Synthase at pH 8.5 in Complex with Udp


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 Mycobacterium Hassiacum Glucosyl-3- Phosphoglycerate Synthase at pH 8.5 in Complex with Udp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:42.3
occ:1.00
 O B:HOH503 2.0 44.4 1.0
OD2 B:ASP133 2.1 38.6 1.0
O2A B:UDP403 2.2 45.6 1.0
O B:HOH550 2.2 39.0 1.0
O B:HOH533 2.2 52.9 1.0
O B:HOH639 2.3 49.1 1.0
CG B:ASP133 3.2 40.0 1.0
PA B:UDP403 3.5 41.4 1.0
OD1 B:ASP133 3.6 35.4 1.0
O B:HOH527 3.9 39.3 1.0
O1A B:UDP403 4.0 47.2 1.0
O B:HOH696 4.0 54.2 1.0
O B:HOH669 4.0 42.7 1.0
O5' B:UDP403 4.2 32.2 1.0
C5' B:UDP403 4.2 29.4 1.0
CB B:ASP133 4.5 31.0 1.0
O2B B:UDP403 4.5 54.6 1.0
O3A B:UDP403 4.6 42.7 1.0
OD2 B:ASP131 4.8 36.6 1.0

Reference:

A.Silva, D.Nunes-Costa, P.J.Barbosa Pereira, S.Macedo-Ribeiro. Crystal Structure of Mycobacterium Hassiacum Glucosyl-3-Phosphoglycerate Synthase at pH 8.5 in Complex with Udp To Be Published.
Page generated: Thu Apr 6 19:41:38 2023

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