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Calcium in PDB 5yzx: Crystal Structure of E.Coli Lysu T146D Mutant

Enzymatic activity of Crystal Structure of E.Coli Lysu T146D Mutant

All present enzymatic activity of Crystal Structure of E.Coli Lysu T146D Mutant:
6.1.1.6;

Protein crystallography data

The structure of Crystal Structure of E.Coli Lysu T146D Mutant, PDB code: 5yzx was solved by P.Fang, M.Guo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.15 / 3.20
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 144.544, 249.855, 179.652, 90.00, 90.00, 90.00
R / Rfree (%) 23.6 / 26.9

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of E.Coli Lysu T146D Mutant (pdb code 5yzx). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the Crystal Structure of E.Coli Lysu T146D Mutant, PDB code: 5yzx:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 5yzx

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Calcium binding site 1 out of 9 in the Crystal Structure of E.Coli Lysu T146D Mutant


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 E.Coli Lysu T146D Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca602

b:56.6
occ:1.00
 OE2 A:GLU264 2.4 0.1 1.0
O1G A:B4P601 2.4 62.9 1.0
O1B A:B4P601 2.6 81.8 1.0
O2A A:B4P601 3.0 73.5 1.0
CD A:GLU264 3.4 98.2 1.0
PG A:B4P601 3.7 57.4 1.0
OE1 A:GLU264 3.9 97.5 1.0
PB A:B4P601 3.9 62.9 1.0
NH1 A:ARG262 4.0 52.0 1.0
O A:SER218 4.2 54.9 1.0
O3B A:B4P601 4.2 45.0 1.0
O3G A:B4P601 4.3 36.9 1.0
PA A:B4P601 4.3 82.9 1.0
NE2 A:HIS270 4.4 49.7 1.0
N7A A:B4P601 4.4 92.8 1.0
CG A:GLU264 4.6 96.1 1.0
O3A A:B4P601 4.6 74.5 1.0
C8A A:B4P601 4.6 0.8 1.0
N7B A:B4P601 4.7 48.2 1.0
O2G A:B4P601 4.8 75.9 1.0
CB A:ALA219 4.9 60.2 1.0
CD2 A:HIS270 4.9 50.7 1.0

Calcium binding site 2 out of 9 in 5yzx

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Calcium binding site 2 out of 9 in the Crystal Structure of E.Coli Lysu T146D Mutant


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 E.Coli Lysu T146D Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca603

b:64.3
occ:1.00
 OE2 A:GLU414 2.3 94.6 1.0
O2G A:B4P601 2.4 75.9 1.0
OE2 A:GLU421 2.5 39.9 1.0
O1D A:B4P601 2.5 45.8 1.0
ND2 A:ASN424 2.7 0.4 1.0
OE1 A:GLU421 3.0 64.9 1.0
CD A:GLU421 3.1 52.0 1.0
CD A:GLU414 3.2 79.1 1.0
PG A:B4P601 3.6 57.4 1.0
PD A:B4P601 3.8 38.5 1.0
CG A:ASN424 3.8 94.8 1.0
CG A:GLU414 3.9 59.8 1.0
O3B A:B4P601 4.1 45.0 1.0
OE1 A:GLU414 4.1 80.8 1.0
O3G A:B4P601 4.1 36.9 1.0
O2D A:B4P601 4.3 28.5 1.0
CA A:CA604 4.3 93.4 1.0
CB A:ASN424 4.4 59.9 1.0
NH2 A:ARG412 4.4 79.7 1.0
CG A:GLU421 4.6 36.7 1.0
NH1 A:ARG412 4.8 83.8 1.0
O1G A:B4P601 4.8 62.9 1.0
OD1 A:ASN424 4.8 0.6 1.0
CZ A:ARG412 4.9 69.3 1.0

Calcium binding site 3 out of 9 in 5yzx

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Calcium binding site 3 out of 9 in the Crystal Structure of E.Coli Lysu T146D Mutant


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 E.Coli Lysu T146D Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca604

b:93.4
occ:1.00
 O1A A:B4P601 2.8 80.4 1.0
OE1 A:GLU414 3.2 80.8 1.0
OE2 A:GLU414 3.4 94.6 1.0
OD1 A:ASP376 3.5 58.3 1.0
OE1 A:GLU421 3.6 64.9 1.0
CD A:GLU414 3.7 79.1 1.0
OD2 A:ASP376 4.0 54.3 1.0
PA A:B4P601 4.1 82.9 1.0
CG A:ASP376 4.1 61.6 1.0
O3A A:B4P601 4.2 74.5 1.0
CA A:CA603 4.3 64.3 1.0
O2G A:B4P601 4.5 75.9 1.0
OE1 A:GLU380 4.7 95.0 1.0
CD A:GLU421 4.7 52.0 1.0
C5E A:B4P601 4.8 0.4 1.0
O5E A:B4P601 4.9 0.5 1.0

Calcium binding site 4 out of 9 in 5yzx

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Calcium binding site 4 out of 9 in the Crystal Structure of E.Coli Lysu T146D Mutant


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 E.Coli Lysu T146D Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca602

b:88.5
occ:1.00
 O1G B:B4P601 2.3 84.9 1.0
OE2 B:GLU264 2.5 0.2 1.0
O1B B:B4P601 2.7 86.5 1.0
O2A B:B4P601 3.1 72.8 1.0
CD B:GLU264 3.6 0.8 1.0
PG B:B4P601 3.6 93.2 1.0
PB B:B4P601 3.9 76.5 1.0
O3B B:B4P601 4.0 84.4 1.0
CE1 B:HIS270 4.2 74.2 1.0
OE1 B:GLU264 4.4 0.9 1.0
PA B:B4P601 4.4 96.4 1.0
O2G B:B4P601 4.4 98.8 1.0
O B:SER218 4.4 82.6 1.0
CG B:GLU264 4.5 0.6 1.0
NH1 B:ARG262 4.5 56.6 1.0
O3A B:B4P601 4.6 95.7 1.0
O3G B:B4P601 4.7 86.9 1.0
C8A B:B4P601 4.9 0.9 1.0
C5E B:B4P601 4.9 0.5 1.0
ND1 B:HIS270 4.9 72.9 1.0
N7A B:B4P601 5.0 0.2 1.0

Calcium binding site 5 out of 9 in 5yzx

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Calcium binding site 5 out of 9 in the Crystal Structure of E.Coli Lysu T146D Mutant


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 E.Coli Lysu T146D Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca603

b:0.4
occ:1.00
 OE2 B:GLU414 2.3 77.4 1.0
O1D B:B4P601 2.3 72.2 1.0
O2G B:B4P601 2.4 98.8 1.0
OE1 B:GLU421 2.5 84.1 1.0
OE2 B:GLU421 2.8 35.1 1.0
CD B:GLU421 3.0 56.9 1.0
CD B:GLU414 3.2 61.6 1.0
PG B:B4P601 3.5 93.2 1.0
PD B:B4P601 3.6 69.5 1.0
OE1 B:GLU414 3.7 57.5 1.0
O3B B:B4P601 3.8 84.4 1.0
O1A B:B4P601 3.8 0.6 1.0
ND2 B:ASN424 3.9 0.6 1.0
O3G B:B4P601 4.0 86.9 1.0
O3A B:B4P601 4.0 95.7 1.0
O5F B:B4P601 4.2 38.8 1.0
CG B:GLU414 4.4 40.4 1.0
CG B:GLU421 4.5 43.4 1.0
PA B:B4P601 4.5 96.4 1.0
PB B:B4P601 4.6 76.5 1.0
CA B:CA604 4.7 86.1 1.0
O2D B:B4P601 4.8 67.7 1.0
O1G B:B4P601 4.8 84.9 1.0

Calcium binding site 6 out of 9 in 5yzx

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Calcium binding site 6 out of 9 in the Crystal Structure of E.Coli Lysu T146D Mutant


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 E.Coli Lysu T146D Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca604

b:86.1
occ:1.00
 O1A B:B4P601 2.4 0.6 1.0
OD2 B:ASP376 2.9 54.3 1.0
PA B:B4P601 3.8 96.4 1.0
CG B:ASP376 3.9 56.8 1.0
OD1 B:ASP376 4.1 48.6 1.0
CG2 B:THR372 4.1 30.8 1.0
O2A B:B4P601 4.3 72.8 1.0
O5E B:B4P601 4.5 0.8 1.0
CA B:CA603 4.7 0.4 1.0
O2G B:B4P601 4.7 98.8 1.0
OE2 B:GLU373 4.9 61.6 1.0
O3A B:B4P601 5.0 95.7 1.0

Calcium binding site 7 out of 9 in 5yzx

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Calcium binding site 7 out of 9 in the Crystal Structure of E.Coli Lysu T146D Mutant


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of E.Coli Lysu T146D Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca602

b:78.9
occ:1.00
 O1A C:B4P601 2.7 86.9 1.0
OD2 C:ASP376 3.3 62.5 1.0
OD1 C:ASP376 3.8 66.6 1.0
CG C:ASP376 3.9 66.3 1.0
PA C:B4P601 4.1 88.8 1.0
CG2 C:THR372 4.2 33.7 1.0
CA C:CA604 4.2 81.5 1.0
OE1 C:GLU414 4.2 48.4 1.0
OE2 C:GLU414 4.4 76.7 1.0
O2G C:B4P601 4.5 83.2 1.0
O2A C:B4P601 4.6 75.9 1.0
CD C:GLU414 4.8 59.3 1.0

Calcium binding site 8 out of 9 in 5yzx

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Calcium binding site 8 out of 9 in the Crystal Structure of E.Coli Lysu T146D Mutant


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of E.Coli Lysu T146D Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca603

b:65.7
occ:1.00
 O1G C:B4P601 2.3 75.5 1.0
OE2 C:GLU264 2.8 98.4 1.0
O1B C:B4P601 3.4 71.4 1.0
CD C:GLU264 3.6 87.5 1.0
OE1 C:GLU264 3.6 0.3 1.0
O2A C:B4P601 3.8 75.9 1.0
PG C:B4P601 3.8 68.8 1.0
O C:SER218 3.9 62.7 1.0
NH1 C:ARG262 4.0 43.7 1.0
O2G C:B4P601 4.5 83.2 1.0
CB C:ALA219 4.6 45.8 1.0
PB C:B4P601 4.6 64.6 1.0
O3G C:B4P601 4.6 54.6 1.0
O3B C:B4P601 4.7 53.1 1.0
CD C:ARG262 4.9 31.7 1.0

Calcium binding site 9 out of 9 in 5yzx

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Calcium binding site 9 out of 9 in the Crystal Structure of E.Coli Lysu T146D Mutant


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of E.Coli Lysu T146D Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca604

b:81.5
occ:1.00
 OE2 C:GLU414 2.2 76.7 1.0
O1D C:B4P601 2.2 69.8 1.0
O2G C:B4P601 2.5 83.2 1.0
OE2 C:GLU421 2.6 53.0 1.0
OE1 C:GLU421 2.6 65.2 1.0
CD C:GLU421 2.9 56.3 1.0
CD C:GLU414 3.2 59.3 1.0
PG C:B4P601 3.4 68.8 1.0
PD C:B4P601 3.5 47.1 1.0
O3B C:B4P601 3.6 53.1 1.0
OE1 C:GLU414 3.7 48.4 1.0
O3G C:B4P601 3.8 54.6 1.0
CA C:CA602 4.2 78.9 1.0
CG C:GLU414 4.3 47.9 1.0
CG C:GLU421 4.5 43.8 1.0
O2D C:B4P601 4.5 56.2 1.0
O5F C:B4P601 4.5 40.3 1.0
O1A C:B4P601 4.6 86.9 1.0
O1G C:B4P601 4.8 75.5 1.0
O3F C:B4P601 4.8 51.5 1.0
CB C:ASN424 5.0 48.7 1.0

Reference:

L.Zheng, H.Ali, J.Wang, M.Guo, P.Fang. A Proposed Role For Msc to Reserve the Canonical Function in High Eukaryotes Prior to Stimuli To Be Published.
Page generated: Mon Jul 15 15:37:40 2024

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