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Calcium in PDB 8vw0: Crystal Structure of Apo Udp-N-Acetylmuramoylalanine--D-Glutamate Ligase (Murd) From E. Coli (Amp Bound)

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

All present enzymatic activity of Crystal Structure of Apo Udp-N-Acetylmuramoylalanine--D-Glutamate Ligase (Murd) From E. Coli (Amp 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 (Amp Bound), PDB code: 8vw0 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) 40.63 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 58.136, 68.824, 100.576, 90, 90, 90
R / Rfree (%) 16.1 / 19.8

Other elements in 8vw0:

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

Magnesium (Mg) 1 atom

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 (Amp Bound) (pdb code 8vw0). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of Apo Udp-N-Acetylmuramoylalanine--D-Glutamate Ligase (Murd) From E. Coli (Amp Bound), PDB code: 8vw0:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 8vw0

Go back to Calcium Binding Sites List in 8vw0
Calcium binding site 1 out of 6 in the Crystal Structure of Apo Udp-N-Acetylmuramoylalanine--D-Glutamate Ligase (Murd) From E. Coli (Amp 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 (Amp Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:60.4
occ:1.00
 N A:THR37 3.5 24.5 1.0
OG1 A:THR37 3.6 31.0 1.0
CG A:ASP36 3.9 26.1 1.0
OD2 A:ASP36 3.9 27.2 1.0
OD1 A:ASP36 3.9 27.2 1.0
CG2 A:THR37 4.0 36.9 1.0
CA A:ASP36 4.0 25.2 1.0
CG2 A:ILE12 4.2 22.4 1.0
CB A:THR37 4.2 33.2 1.0
C A:ASP36 4.2 26.8 1.0
CA A:GLY13 4.4 23.4 1.0
CB A:ASP36 4.5 24.7 1.0
CA A:THR37 4.5 27.2 1.0
N A:GLY13 4.5 23.6 1.0
O A:MET35 5.0 22.7 1.0
CD2 A:LEU58 5.0 26.3 1.0

Calcium binding site 2 out of 6 in 8vw0

Go back to Calcium Binding Sites List in 8vw0
Calcium binding site 2 out of 6 in the Crystal Structure of Apo Udp-N-Acetylmuramoylalanine--D-Glutamate Ligase (Murd) From E. Coli (Amp 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 (Amp Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca504

b:55.8
occ:1.00
 O A:GLN387 3.7 28.2 1.0
C A:THR388 3.8 27.5 1.0
CA A:THR388 3.9 27.9 1.0
C A:GLN387 4.0 26.6 1.0
NE2 A:GLN387 4.1 39.4 1.0
N A:GLU389 4.1 26.6 1.0
CD A:GLN387 4.1 34.3 1.0
CG A:GLN387 4.1 29.5 1.0
N A:THR388 4.2 25.4 1.0
O A:THR388 4.2 25.9 1.0
CB A:GLN387 4.5 31.2 1.0
O A:HOH641 4.6 31.5 1.0
OE1 A:GLN387 4.7 35.4 1.0
CA A:GLU389 4.8 25.8 1.0
CA A:GLN387 4.9 27.0 1.0

Calcium binding site 3 out of 6 in 8vw0

Go back to Calcium Binding Sites List in 8vw0
Calcium binding site 3 out of 6 in the Crystal Structure of Apo Udp-N-Acetylmuramoylalanine--D-Glutamate Ligase (Murd) From E. Coli (Amp 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 (Amp Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca505

b:41.0
occ:1.00
 O A:HOH796 2.7 35.1 1.0
N A:SER416 3.2 28.1 1.0
OG A:SER416 3.2 32.5 1.0
CB A:SER416 3.8 29.0 1.0
CA A:ALA415 3.9 31.4 1.0
N A:PHE423 3.9 27.1 1.0
CB A:ALA415 4.0 29.7 1.0
CB A:PHE423 4.0 29.1 1.0
CA A:SER416 4.0 28.1 1.0
CG2 A:THR322 4.0 32.0 1.0
C A:ALA415 4.0 30.9 1.0
CD2 A:LEU417 4.1 35.9 1.0
CA A:PHE423 4.3 24.8 1.0
CG A:LEU417 4.4 39.3 1.0
C A:ASN422 4.6 30.1 1.0
N A:LEU417 4.6 29.9 1.0
CD2 A:PHE423 4.6 34.5 1.0
C A:SER416 4.7 31.0 1.0
CA A:ASN422 4.7 28.8 1.0
CG A:PHE423 4.8 28.4 1.0
CB A:THR322 4.9 30.5 1.0
NH2 A:ARG426 4.9 29.1 1.0

Calcium binding site 4 out of 6 in 8vw0

Go back to Calcium Binding Sites List in 8vw0
Calcium binding site 4 out of 6 in the Crystal Structure of Apo Udp-N-Acetylmuramoylalanine--D-Glutamate Ligase (Murd) From E. Coli (Amp Bound)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Apo Udp-N-Acetylmuramoylalanine--D-Glutamate Ligase (Murd) From E. Coli (Amp Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca506

b:38.5
occ:1.00
 N A:GLY15 3.2 25.0 1.0
O A:HOH674 3.2 29.8 1.0
N A:GLY18 3.3 23.3 1.0
O A:HOH822 3.3 39.7 1.0
CA A:GLY15 3.5 27.4 1.0
C A:GLY13 3.7 25.7 1.0
OG A:SER72 3.7 36.7 1.0
CA A:GLY13 3.8 23.4 1.0
C A:GLY15 3.8 24.8 1.0
CB A:SER72 3.8 35.8 1.0
N A:LEU14 3.9 22.4 1.0
CB A:THR17 3.9 26.4 1.0
O A:GLY15 3.9 22.2 1.0
CA A:GLY18 3.9 23.3 1.0
O A:GLY13 4.0 27.1 1.0
N A:THR17 4.1 22.7 1.0
C A:THR17 4.2 23.7 1.0
C A:LEU14 4.3 29.9 1.0
CA A:THR17 4.3 22.2 1.0
N A:LEU16 4.6 22.2 1.0
CA A:LEU14 4.6 23.0 1.0
OG1 A:THR17 4.7 27.5 1.0
CG2 A:THR17 4.8 32.1 1.0
O A:ILE12 4.8 23.2 1.0
CA A:SER72 4.9 28.9 1.0

Calcium binding site 5 out of 6 in 8vw0

Go back to Calcium Binding Sites List in 8vw0
Calcium binding site 5 out of 6 in the Crystal Structure of Apo Udp-N-Acetylmuramoylalanine--D-Glutamate Ligase (Murd) From E. Coli (Amp Bound)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Apo Udp-N-Acetylmuramoylalanine--D-Glutamate Ligase (Murd) From E. Coli (Amp Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca507

b:68.9
occ:1.00
 O A:HOH863 2.2 48.1 1.0
O A:HOH604 2.4 29.9 1.0
OD1 A:ASP373 3.9 40.7 1.0
OD2 A:ASP373 4.3 47.5 1.0
OD1 A:ASP347 4.4 42.5 1.0
CG A:ASP373 4.6 38.7 1.0
OG A:SER350 4.7 69.7 1.0
N A:SER350 4.8 63.0 1.0
CG A:ARG372 4.9 31.5 1.0

Calcium binding site 6 out of 6 in 8vw0

Go back to Calcium Binding Sites List in 8vw0
Calcium binding site 6 out of 6 in the Crystal Structure of Apo Udp-N-Acetylmuramoylalanine--D-Glutamate Ligase (Murd) From E. Coli (Amp Bound)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Apo Udp-N-Acetylmuramoylalanine--D-Glutamate Ligase (Murd) From E. Coli (Amp Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca508

b:68.0
occ:1.00
 O A:HOH827 3.3 42.4 1.0
O A:GLN387 3.3 28.2 1.0
N A:GLN387 4.0 35.2 1.0
CB A:GLU386 4.2 35.2 1.0
C A:GLN387 4.3 26.6 1.0
CD2 A:LEU397 4.4 42.6 1.0
CG A:GLU386 4.5 40.4 1.0
CA A:GLU386 4.7 33.0 1.0
CA A:GLN387 4.8 27.0 1.0
C A:GLU386 4.8 28.8 1.0
CG2 A:THR388 4.9 27.1 1.0
OE2 A:GLU386 5.0 44.2 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 (Amp Bound) To Be Published.
Page generated: Thu Jul 10 08:03:42 2025

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