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Calcium 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:

Magnesium (Mg) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total 3 binding sites of Calcium 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 Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 8vw2

Go back to Calcium Binding Sites List in 8vw2
Calcium binding site 1 out of 3 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 Calcium with other atoms in the Ca 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:Ca501

b:64.0
occ:1.00
 OG1 A:THR37 3.5 36.6 1.0
N A:THR37 3.7 33.6 1.0
OD1 A:ASP36 3.7 35.8 1.0
CG A:ASP36 3.9 36.4 1.0
OD2 A:ASP36 4.1 32.1 1.0
CA A:ASP36 4.1 31.8 1.0
CG2 A:THR37 4.3 33.9 1.0
CG2 A:ILE12 4.3 27.0 1.0
CA A:GLY13 4.3 30.0 1.0
CB A:THR37 4.4 34.6 1.0
C A:ASP36 4.4 35.4 1.0
N A:GLY13 4.5 26.6 1.0
CB A:ASP36 4.6 31.4 1.0
CA A:THR37 4.6 31.2 1.0

Calcium binding site 2 out of 3 in 8vw2

Go back to Calcium Binding Sites List in 8vw2
Calcium binding site 2 out of 3 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 Calcium with other atoms in the Ca 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:Ca502

b:70.8
occ:1.00
 O A:GLN387 3.6 33.6 1.0
CA A:THR388 4.1 37.7 1.0
C A:THR388 4.1 34.8 1.0
C A:GLN387 4.1 41.9 1.0
NE2 A:GLN387 4.1 40.2 1.0
N A:GLU389 4.3 35.4 1.0
CD A:GLN387 4.3 41.2 1.0
CG A:GLN387 4.3 39.7 1.0
N A:THR388 4.4 34.8 1.0
O A:THR388 4.5 35.1 1.0
CB A:GLN387 4.7 37.4 1.0
O A:HOH666 4.8 40.1 1.0
OE1 A:GLN387 4.9 42.8 1.0

Calcium binding site 3 out of 3 in 8vw2

Go back to Calcium Binding Sites List in 8vw2
Calcium binding site 3 out of 3 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 Calcium with other atoms in the Ca 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:Ca503

b:47.4
occ:1.00
 O A:HOH730 2.7 36.2 1.0
OG A:SER416 3.1 36.8 1.0
N A:SER416 3.2 35.3 1.0
CA A:ALA415 3.9 32.8 1.0
N A:PHE423 3.9 29.4 1.0
CB A:SER416 3.9 36.0 1.0
CB A:PHE423 4.0 28.4 1.0
CG2 A:THR322 4.0 35.5 1.0
CB A:ALA415 4.0 32.5 1.0
C A:ALA415 4.0 30.8 1.0
CA A:SER416 4.1 33.3 1.0
CA A:PHE423 4.3 28.2 1.0
CG A:LEU417 4.4 37.8 1.0
CD2 A:LEU417 4.5 37.8 1.0
C A:ASN422 4.6 33.3 1.0
CD2 A:PHE423 4.6 33.8 1.0
N A:LEU417 4.6 32.8 1.0
CA A:ASN422 4.8 32.0 1.0
CG A:PHE423 4.8 30.3 1.0
C A:SER416 4.8 33.8 1.0
NH2 A:ARG426 4.9 28.8 1.0
CB A:THR322 4.9 38.5 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 Jul 19 12:33:55 2024

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