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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy