Calcium 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:

Magnesium (Mg) 3 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 (Adp Bound) (pdb code 8vw1). 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 (Adp Bound), PDB code: 8vw1:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 8vw1

Go back to Calcium Binding Sites List in 8vw1
Calcium 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 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 (Adp Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca505

b:59.5
occ:1.00
 OG1 A:THR37 3.5 33.3 1.0
N A:THR37 3.5 26.2 1.0
CG A:ASP36 3.9 27.4 1.0
OD1 A:ASP36 3.9 30.5 1.0
OD2 A:ASP36 4.0 30.7 1.0
CG2 A:THR37 4.0 35.9 1.0
CA A:ASP36 4.0 24.7 1.0
CG2 A:ILE12 4.1 26.1 1.0
CB A:THR37 4.2 34.7 1.0
C A:ASP36 4.3 27.1 1.0
CA A:GLY13 4.4 25.5 1.0
N A:GLY13 4.5 25.7 1.0
CA A:THR37 4.5 26.7 1.0
CB A:ASP36 4.5 25.9 1.0
O A:MET35 4.9 27.1 1.0
CD2 A:LEU58 5.0 26.2 1.0

Calcium binding site 2 out of 3 in 8vw1

Go back to Calcium Binding Sites List in 8vw1
Calcium 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 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 (Adp Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca506

b:60.3
occ:1.00
 O A:GLN387 3.7 33.0 1.0
C A:THR388 4.0 29.3 1.0
CA A:THR388 4.0 31.6 1.0
C A:GLN387 4.1 30.5 1.0
NE2 A:GLN387 4.1 39.7 1.0
N A:GLU389 4.2 28.9 1.0
CD A:GLN387 4.2 37.9 1.0
CG A:GLN387 4.2 37.2 1.0
N A:THR388 4.3 31.5 1.0
O A:HOH809 4.4 47.1 1.0
O A:THR388 4.4 30.5 1.0
CB A:GLN387 4.6 37.3 1.0
O A:HOH662 4.7 32.6 1.0
OE1 A:GLN387 4.8 42.2 1.0
CA A:GLU389 4.9 29.3 1.0

Calcium binding site 3 out of 3 in 8vw1

Go back to Calcium Binding Sites List in 8vw1
Calcium 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 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 (Adp Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca507

b:40.8
occ:1.00
 O A:HOH789 2.7 33.2 1.0
N A:SER416 3.2 26.6 1.0
OG A:SER416 3.2 31.6 1.0
CB A:SER416 3.8 28.4 1.0
CA A:ALA415 3.9 27.1 1.0
N A:PHE423 3.9 25.8 1.0
CB A:PHE423 4.0 25.9 1.0
CA A:SER416 4.0 23.6 1.0
C A:ALA415 4.0 27.8 1.0
CB A:ALA415 4.0 28.1 1.0
CG2 A:THR322 4.1 28.9 1.0
CD2 A:LEU417 4.3 35.3 1.0
CA A:PHE423 4.4 25.0 1.0
CG A:LEU417 4.4 36.1 1.0
N A:LEU417 4.6 30.0 1.0
C A:ASN422 4.6 27.7 1.0
CD2 A:PHE423 4.6 30.0 1.0
C A:SER416 4.7 26.5 1.0
CA A:ASN422 4.7 27.3 1.0
CG A:PHE423 4.8 28.6 1.0
NH2 A:ARG426 4.9 27.0 1.0
CB A:THR322 4.9 28.9 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 Jul 19 12:33:53 2024

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