Magnesium in PDB 8vw2: Crystal Structure of Apo Udp-N-Acetylmuramoylalanine--D-Glutamate Ligase (Murd) From E. Coli (Atp Bound)

Enzymatic activity of Crystal Structure of Apo Udp-N-Acetylmuramoylalanine--D-Glutamate Ligase (Murd) From E. Coli (Atp Bound)

All present enzymatic activity of Crystal Structure of Apo Udp-N-Acetylmuramoylalanine--D-Glutamate Ligase (Murd) From E. Coli (Atp Bound):
6.3.2.9;

Protein crystallography data

The structure of Crystal Structure of Apo Udp-N-Acetylmuramoylalanine--D-Glutamate Ligase (Murd) From E. Coli (Atp Bound), PDB code: 8vw2 was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.85 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 58.456, 69.944, 100.534, 90, 90, 90
R / Rfree (%) 17 / 22.5

Other elements in 8vw2:

The structure of Crystal Structure of Apo Udp-N-Acetylmuramoylalanine--D-Glutamate Ligase (Murd) From E. Coli (Atp Bound) also contains other interesting chemical elements:

Calcium (Ca) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Apo Udp-N-Acetylmuramoylalanine--D-Glutamate Ligase (Murd) From E. Coli (Atp Bound) (pdb code 8vw2). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Apo Udp-N-Acetylmuramoylalanine--D-Glutamate Ligase (Murd) From E. Coli (Atp Bound), PDB code: 8vw2:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 8vw2

Go back to Magnesium Binding Sites List in 8vw2
Magnesium binding site 1 out of 4 in the Crystal Structure of Apo Udp-N-Acetylmuramoylalanine--D-Glutamate Ligase (Murd) From E. Coli (Atp Bound)


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 Udp-N-Acetylmuramoylalanine--D-Glutamate Ligase (Murd) From E. Coli (Atp Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg505

b:30.6
occ:1.00
 O1G A:ATP504 2.0 26.2 1.0
O2B A:ATP504 2.0 24.5 1.0
O A:HOH683 2.2 31.6 1.0
OE2 A:GLU158 2.2 32.5 1.0
O A:HOH713 2.3 33.8 1.0
OG A:SER117 2.3 29.4 1.0
PG A:ATP504 3.1 33.5 1.0
O3B A:ATP504 3.2 32.2 1.0
PB A:ATP504 3.2 23.7 1.0
CD A:GLU158 3.2 40.1 1.0
CB A:SER117 3.4 25.4 1.0
OE1 A:GLU158 3.5 39.1 1.0
O2G A:ATP504 3.9 33.6 1.0
N A:SER117 4.0 26.9 1.0
O1B A:ATP504 4.1 24.6 1.0
O1A A:ATP504 4.2 34.1 1.0
CA A:SER117 4.2 29.2 1.0
O3A A:ATP504 4.2 31.0 1.0
O3G A:ATP504 4.3 31.5 1.0
CG A:GLU158 4.6 31.0 1.0
CE A:LYS116 4.6 22.7 1.0
CB A:LYS116 4.7 24.7 1.0
PA A:ATP504 4.7 31.3 1.0
NH2 A:ARG303 4.9 42.3 1.0
NZ A:LYS116 4.9 25.9 1.0
C A:LYS116 5.0 23.6 1.0

Magnesium binding site 2 out of 4 in 8vw2

Go back to Magnesium Binding Sites List in 8vw2
Magnesium binding site 2 out of 4 in the Crystal Structure of Apo Udp-N-Acetylmuramoylalanine--D-Glutamate Ligase (Murd) From E. Coli (Atp Bound)


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 Udp-N-Acetylmuramoylalanine--D-Glutamate Ligase (Murd) From E. Coli (Atp Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg506

b:56.1
occ:1.00
 O A:HOH736 2.2 44.6 1.0
O A:HOH743 2.5 45.9 1.0
O A:HOH607 2.5 33.5 1.0
O A:ASP214 3.8 30.9 1.0
CA A:ASP214 4.4 26.1 1.0
C A:ASP214 4.4 29.1 1.0
OD1 A:ASP214 4.5 35.1 1.0
CB A:ASP214 4.6 29.1 1.0
CG A:ASP214 5.0 34.8 1.0

Magnesium binding site 3 out of 4 in 8vw2

Go back to Magnesium Binding Sites List in 8vw2
Magnesium binding site 3 out of 4 in the Crystal Structure of Apo Udp-N-Acetylmuramoylalanine--D-Glutamate Ligase (Murd) From E. Coli (Atp Bound)


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 Udp-N-Acetylmuramoylalanine--D-Glutamate Ligase (Murd) From E. Coli (Atp Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg507

b:46.6
occ:1.00
 O A:HOH688 2.2 37.1 1.0
O3G A:ATP504 2.2 31.5 1.0
O A:HOH601 2.5 32.9 1.0
O A:HOH742 2.6 47.8 1.0
PG A:ATP504 3.6 33.5 1.0
NZ A:LYS116 3.9 25.9 1.0
O A:HOH620 4.0 38.8 1.0
O2G A:ATP504 4.0 33.6 1.0
O1G A:ATP504 4.4 26.2 1.0
OQ1 A:KCX199 4.4 34.9 1.0
OQ2 A:KCX199 4.4 35.4 1.0
O A:SER113 4.5 24.3 1.0
O3B A:ATP504 4.6 32.2 1.0
CE A:LYS116 4.8 22.7 1.0
CX A:KCX199 4.8 31.4 1.0

Magnesium binding site 4 out of 4 in 8vw2

Go back to Magnesium Binding Sites List in 8vw2
Magnesium binding site 4 out of 4 in the Crystal Structure of Apo Udp-N-Acetylmuramoylalanine--D-Glutamate Ligase (Murd) From E. Coli (Atp Bound)


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 Udp-N-Acetylmuramoylalanine--D-Glutamate Ligase (Murd) From E. Coli (Atp Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg508

b:60.2
occ:1.00
 O A:HOH734 2.2 43.2 1.0
O A:HOH704 3.2 49.4 1.0
O A:HOH703 3.8 47.8 1.0
O A:HOH624 3.9 39.9 1.0
O A:HOH684 4.0 46.1 1.0
CZ2 A:TRP62 4.8 33.8 1.0
NE1 A:TRP62 4.9 32.5 1.0

Reference:

S.Seibold, S.Lovell, L.Liu, K.P.Battaile. Crystal Structure of Apo Udp-N-Acetylmuramoylalanine--D-Glutamate Ligase (Murd) From E. Coli (Atp Bound) To Be Published.
Page generated: Fri Oct 4 22:15:39 2024

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