Magnesium in PDB 8vw1: Crystal Structure of Apo Udp-N-Acetylmuramoylalanine--D-Glutamate Ligase (Murd) From E. Coli (Adp Bound)

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

All present enzymatic activity of Crystal Structure of Apo Udp-N-Acetylmuramoylalanine--D-Glutamate Ligase (Murd) From E. Coli (Adp 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 (Adp Bound), PDB code: 8vw1 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) 40.82 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 58.47, 69.235, 100.468, 90, 90, 90
R / Rfree (%) 16.3 / 19.7

Other elements in 8vw1:

The structure of Crystal Structure of Apo Udp-N-Acetylmuramoylalanine--D-Glutamate Ligase (Murd) From E. Coli (Adp 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 (Adp Bound) (pdb code 8vw1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Apo Udp-N-Acetylmuramoylalanine--D-Glutamate Ligase (Murd) From E. Coli (Adp Bound), PDB code: 8vw1:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 8vw1

Go back to Magnesium Binding Sites List in 8vw1
Magnesium binding site 1 out of 3 in the Crystal Structure of Apo Udp-N-Acetylmuramoylalanine--D-Glutamate Ligase (Murd) From E. Coli (Adp 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 (Adp Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:39.6
occ:1.00
 OE2 A:GLU158 2.1 40.5 1.0
O1B A:ADP501 2.3 21.8 1.0
O A:HOH774 2.4 46.9 1.0
CD A:GLU158 3.1 40.5 1.0
PB A:ADP501 3.3 20.9 1.0
O3B A:ADP501 3.5 22.8 1.0
OE1 A:GLU158 3.5 33.8 1.0
CB A:SER117 3.6 22.1 1.0
OG A:SER117 3.8 30.7 1.0
N A:SER117 4.1 19.2 1.0
O2B A:ADP501 4.1 21.0 1.0
NZ A:LYS320 4.2 35.1 1.0
CG A:GLU158 4.3 33.0 1.0
CA A:SER117 4.4 20.3 1.0
O A:HOH601 4.5 40.5 1.0
CE A:LYS116 4.6 26.0 1.0
O2A A:ADP501 4.6 22.4 1.0
O3A A:ADP501 4.6 23.4 1.0
CB A:LYS116 4.7 19.2 1.0
CB A:ASN139 4.9 42.0 1.0
NZ A:LYS116 4.9 26.1 1.0

Magnesium binding site 2 out of 3 in 8vw1

Go back to Magnesium Binding Sites List in 8vw1
Magnesium binding site 2 out of 3 in the Crystal Structure of Apo Udp-N-Acetylmuramoylalanine--D-Glutamate Ligase (Murd) From E. Coli (Adp 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 (Adp Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:55.0
occ:1.00
 O A:HOH762 2.0 53.0 1.0
O A:HOH793 2.2 59.4 1.0
O A:HOH604 2.4 37.9 1.0
OD1 A:ASP347 4.1 40.8 1.0
O A:HOH721 4.2 48.5 1.0
OD1 A:ASP373 4.4 44.6 1.0
OD2 A:ASP373 4.5 44.8 1.0
OG A:SER350 4.6 60.2 1.0
N A:SER350 4.7 53.5 1.0
N A:LYS349 4.9 38.6 1.0
CG A:ASP373 4.9 39.1 1.0

Magnesium binding site 3 out of 3 in 8vw1

Go back to Magnesium Binding Sites List in 8vw1
Magnesium binding site 3 out of 3 in the Crystal Structure of Apo Udp-N-Acetylmuramoylalanine--D-Glutamate Ligase (Murd) From E. Coli (Adp 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 (Adp Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg504

b:49.5
occ:1.00
 O A:HOH688 2.2 41.0 1.0
O A:HOH820 2.2 43.8 1.0
O A:HOH624 2.3 32.8 1.0
O A:HOH811 2.4 43.1 1.0
O A:ASP214 4.1 26.5 1.0
OD1 A:ASP214 4.5 31.9 1.0
CA A:ASP214 4.7 25.9 1.0
C A:ASP214 4.8 27.0 1.0
CB A:ASP214 4.9 26.1 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 (Adp Bound) To Be Published.
Page generated: Fri Oct 4 22:15:31 2024

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