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Magnesium in PDB 5wi5: 2.0 Angstrom Resolution Crystal Structure of Udp-N-Acetylglucosamine 1-Carboxyvinyltransferase From Streptococcus Pneumoniae in Complex with Uridine-Diphosphate-2(N-Acetylglucosaminyl) Butyric Acid, (2R)- 2-(Phosphonooxy)Propanoic Acid and Magnesium.

Enzymatic activity of 2.0 Angstrom Resolution Crystal Structure of Udp-N-Acetylglucosamine 1-Carboxyvinyltransferase From Streptococcus Pneumoniae in Complex with Uridine-Diphosphate-2(N-Acetylglucosaminyl) Butyric Acid, (2R)- 2-(Phosphonooxy)Propanoic Acid and Magnesium.

All present enzymatic activity of 2.0 Angstrom Resolution Crystal Structure of Udp-N-Acetylglucosamine 1-Carboxyvinyltransferase From Streptococcus Pneumoniae in Complex with Uridine-Diphosphate-2(N-Acetylglucosaminyl) Butyric Acid, (2R)- 2-(Phosphonooxy)Propanoic Acid and Magnesium.:
2.5.1.7;

Protein crystallography data

The structure of 2.0 Angstrom Resolution Crystal Structure of Udp-N-Acetylglucosamine 1-Carboxyvinyltransferase From Streptococcus Pneumoniae in Complex with Uridine-Diphosphate-2(N-Acetylglucosaminyl) Butyric Acid, (2R)- 2-(Phosphonooxy)Propanoic Acid and Magnesium., PDB code: 5wi5 was solved by G.Minasov, L.Shuvalova, I.Dubrovska, O.Kiryukhina, S.Grimshaw, K.Kwon, W.F.Anderson, Center For Structural Genomics Of Infectious Diseases(Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.29 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 84.243, 80.130, 126.511, 90.00, 95.76, 90.00
R / Rfree (%) 22.2 / 26.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the 2.0 Angstrom Resolution Crystal Structure of Udp-N-Acetylglucosamine 1-Carboxyvinyltransferase From Streptococcus Pneumoniae in Complex with Uridine-Diphosphate-2(N-Acetylglucosaminyl) Butyric Acid, (2R)- 2-(Phosphonooxy)Propanoic Acid and Magnesium. (pdb code 5wi5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the 2.0 Angstrom Resolution Crystal Structure of Udp-N-Acetylglucosamine 1-Carboxyvinyltransferase From Streptococcus Pneumoniae in Complex with Uridine-Diphosphate-2(N-Acetylglucosaminyl) Butyric Acid, (2R)- 2-(Phosphonooxy)Propanoic Acid and Magnesium., PDB code: 5wi5:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5wi5

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Magnesium binding site 1 out of 4 in the 2.0 Angstrom Resolution Crystal Structure of Udp-N-Acetylglucosamine 1-Carboxyvinyltransferase From Streptococcus Pneumoniae in Complex with Uridine-Diphosphate-2(N-Acetylglucosaminyl) Butyric Acid, (2R)- 2-(Phosphonooxy)Propanoic Acid and Magnesium.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of 2.0 Angstrom Resolution Crystal Structure of Udp-N-Acetylglucosamine 1-Carboxyvinyltransferase From Streptococcus Pneumoniae in Complex with Uridine-Diphosphate-2(N-Acetylglucosaminyl) Butyric Acid, (2R)- 2-(Phosphonooxy)Propanoic Acid and Magnesium. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:31.5
occ:1.00
 O A:HOH780 2.0 25.5 1.0
O A:HOH736 2.0 23.5 1.0
O2' A:0V5501 2.1 32.2 1.0
O A:HOH881 2.1 32.6 1.0
O A:HOH827 2.2 25.0 1.0
O3P A:0V5501 2.2 28.3 1.0
C1 A:0V5501 3.1 30.8 1.0
P A:0V5501 3.4 25.9 1.0
O2P A:0V5501 3.6 25.9 1.0
O1 A:0V5501 3.9 31.2 1.0
O2 A:0V5501 3.9 26.4 1.0
C2 A:0V5501 4.0 29.8 1.0
NH1 A:ARG401 4.0 28.6 1.0
O A:LYS94 4.1 26.3 1.0
O A:HOH673 4.3 42.0 1.0
C3 A:0V5501 4.4 31.8 1.0
O A:SER93 4.5 28.1 1.0
C A:LYS94 4.5 26.6 1.0
O1P A:0V5501 4.6 26.4 1.0
O A:HOH738 4.6 42.0 1.0
O A:HOH691 4.6 25.5 1.0
CA A:LYS94 4.9 30.0 1.0
CZ A:ARG401 5.0 28.7 1.0

Magnesium binding site 2 out of 4 in 5wi5

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Magnesium binding site 2 out of 4 in the 2.0 Angstrom Resolution Crystal Structure of Udp-N-Acetylglucosamine 1-Carboxyvinyltransferase From Streptococcus Pneumoniae in Complex with Uridine-Diphosphate-2(N-Acetylglucosaminyl) Butyric Acid, (2R)- 2-(Phosphonooxy)Propanoic Acid and Magnesium.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of 2.0 Angstrom Resolution Crystal Structure of Udp-N-Acetylglucosamine 1-Carboxyvinyltransferase From Streptococcus Pneumoniae in Complex with Uridine-Diphosphate-2(N-Acetylglucosaminyl) Butyric Acid, (2R)- 2-(Phosphonooxy)Propanoic Acid and Magnesium. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:35.3
occ:1.00
 O B:HOH642 2.0 34.8 1.0
O3P B:0V5501 2.1 28.6 1.0
O B:HOH645 2.1 31.7 1.0
O B:HOH739 2.1 34.3 1.0
O1 B:0V5501 2.2 31.6 1.0
O B:HOH750 2.3 30.8 1.0
C1 B:0V5501 3.2 41.8 1.0
P B:0V5501 3.3 31.6 1.0
O1P B:0V5501 3.7 28.6 1.0
NH1 B:ARG401 3.9 37.7 1.0
O B:LYS94 3.9 25.0 1.0
O2' B:0V5501 3.9 47.8 1.0
C2 B:0V5501 4.0 34.2 1.0
O2 B:0V5501 4.0 32.3 1.0
C3 B:0V5501 4.3 31.6 1.0
C B:LYS94 4.4 31.1 1.0
O B:SER93 4.4 28.9 1.0
O2P B:0V5501 4.5 32.6 1.0
O B:HOH647 4.5 34.1 1.0
CA B:LYS94 4.8 35.9 1.0
CZ B:ARG401 4.9 39.6 1.0

Magnesium binding site 3 out of 4 in 5wi5

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Magnesium binding site 3 out of 4 in the 2.0 Angstrom Resolution Crystal Structure of Udp-N-Acetylglucosamine 1-Carboxyvinyltransferase From Streptococcus Pneumoniae in Complex with Uridine-Diphosphate-2(N-Acetylglucosaminyl) Butyric Acid, (2R)- 2-(Phosphonooxy)Propanoic Acid and Magnesium.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of 2.0 Angstrom Resolution Crystal Structure of Udp-N-Acetylglucosamine 1-Carboxyvinyltransferase From Streptococcus Pneumoniae in Complex with Uridine-Diphosphate-2(N-Acetylglucosaminyl) Butyric Acid, (2R)- 2-(Phosphonooxy)Propanoic Acid and Magnesium. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:60.0
occ:1.00
 O C:HOH625 1.8 45.8 1.0
O C:HOH606 1.9 49.3 1.0
O1P C:0V5501 2.0 43.8 1.0
O2' C:0V5501 2.8 64.1 1.0
NH1 C:ARG401 3.3 61.6 1.0
P C:0V5501 3.3 57.2 1.0
C1 C:0V5501 3.6 57.6 1.0
O2P C:0V5501 3.6 54.0 1.0
O C:LYS94 3.6 53.0 1.0
O1 C:0V5501 4.2 51.0 1.0
C C:LYS94 4.2 53.8 1.0
O2 C:0V5501 4.2 55.0 1.0
CZ C:ARG401 4.3 61.1 1.0
C2 C:0V5501 4.4 54.2 1.0
O3P C:0V5501 4.4 37.9 1.0
O C:SER93 4.6 66.3 1.0
C3 C:0V5501 4.6 48.3 1.0
CA C:LYS94 4.6 62.3 1.0
NH2 C:ARG401 4.7 58.0 1.0
O C:HOH605 4.9 45.7 1.0

Magnesium binding site 4 out of 4 in 5wi5

Go back to Magnesium Binding Sites List in 5wi5
Magnesium binding site 4 out of 4 in the 2.0 Angstrom Resolution Crystal Structure of Udp-N-Acetylglucosamine 1-Carboxyvinyltransferase From Streptococcus Pneumoniae in Complex with Uridine-Diphosphate-2(N-Acetylglucosaminyl) Butyric Acid, (2R)- 2-(Phosphonooxy)Propanoic Acid and Magnesium.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of 2.0 Angstrom Resolution Crystal Structure of Udp-N-Acetylglucosamine 1-Carboxyvinyltransferase From Streptococcus Pneumoniae in Complex with Uridine-Diphosphate-2(N-Acetylglucosaminyl) Butyric Acid, (2R)- 2-(Phosphonooxy)Propanoic Acid and Magnesium. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg502

b:59.8
occ:1.00
 O D:HOH667 1.6 44.9 1.0
O3P D:0V5501 1.8 56.5 1.0
O D:HOH618 2.0 60.9 1.0
O D:HOH624 2.1 54.9 1.0
O1 D:0V5501 2.6 56.1 1.0
P D:0V5501 3.0 55.1 1.0
O2P D:0V5501 3.2 48.4 1.0
C1 D:0V5501 3.4 53.6 1.0
NH1 D:ARG401 3.7 57.4 1.0
O2 D:0V5501 3.9 50.4 1.0
O D:LYS94 4.0 74.5 1.0
C2 D:0V5501 4.1 57.8 1.0
O1P D:0V5501 4.1 36.5 1.0
O2' D:0V5501 4.2 46.2 1.0
C3 D:0V5501 4.4 58.7 1.0
C D:LYS94 4.4 68.0 1.0
O D:SER93 4.5 69.6 1.0
O D:HOH607 4.6 44.9 1.0
CZ D:ARG401 4.8 61.7 1.0
CA D:LYS94 4.8 67.6 1.0
O D:HOH675 4.8 44.2 1.0

Reference:

G.Minasov, L.Shuvalova, I.Dubrovska, O.Kiryukhina, S.Grimshaw, K.Kwon, W.F.Anderson. 2.0 Angstrom Resolution Crystal Structure of Udp-N-Acetylglucosamine 1-Carboxyvinyltransferase From Streptococcus Pneumoniae in Complex with Uridine-Diphosphate-2(N-Acetylglucosaminyl) Butyric Acid, (2R)-2-(Phosphonooxy)Propanoic Acid and Magnesium. To Be Published.
Page generated: Mon Sep 30 06:36:04 2024

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