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Calcium in PDB 3m1r: The Crystal Structure of Formimidoylglutamase From Bacillus Subtilis Subsp. Subtilis Str. 168

Enzymatic activity of The Crystal Structure of Formimidoylglutamase From Bacillus Subtilis Subsp. Subtilis Str. 168

All present enzymatic activity of The Crystal Structure of Formimidoylglutamase From Bacillus Subtilis Subsp. Subtilis Str. 168:
3.5.3.8;

Protein crystallography data

The structure of The Crystal Structure of Formimidoylglutamase From Bacillus Subtilis Subsp. Subtilis Str. 168, PDB code: 3m1r was solved by K.Tan, L.Bigelow, D.Trevino, K.Buck, A.Joachimiak, Midwest Centerfor Structural Genomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.47 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 142.038, 118.980, 123.340, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 23

Other elements in 3m1r:

The structure of The Crystal Structure of Formimidoylglutamase From Bacillus Subtilis Subsp. Subtilis Str. 168 also contains other interesting chemical elements:

Arsenic (As) 4 atoms
Chlorine (Cl) 9 atoms

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Calcium atom in the The Crystal Structure of Formimidoylglutamase From Bacillus Subtilis Subsp. Subtilis Str. 168 (pdb code 3m1r). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 12 binding sites of Calcium where determined in the The Crystal Structure of Formimidoylglutamase From Bacillus Subtilis Subsp. Subtilis Str. 168, PDB code: 3m1r:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 12 in 3m1r

Go back to Calcium Binding Sites List in 3m1r
Calcium binding site 1 out of 12 in the The Crystal Structure of Formimidoylglutamase From Bacillus Subtilis Subsp. Subtilis Str. 168


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Crystal Structure of Formimidoylglutamase From Bacillus Subtilis Subsp. Subtilis Str. 168 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca322

b:36.0
occ:1.00
 OD2 A:ASP242 2.3 34.4 1.0
OD2 A:ASP244 2.3 44.2 1.0
ND1 A:HIS152 2.4 41.9 1.0
OD1 A:ASP150 2.4 36.3 1.0
OD1 A:ASP244 2.5 37.5 1.0
CG A:ASP244 2.8 41.3 1.0
CA A:CA323 3.2 69.4 1.0
CG A:ASP150 3.2 42.0 1.0
CE1 A:HIS152 3.2 44.8 1.0
CG A:ASP242 3.2 31.0 1.0
CL A:CL320 3.3 49.8 1.0
CG A:HIS152 3.4 40.7 1.0
OD2 A:ASP150 3.5 42.9 1.0
CB A:HIS152 3.8 37.0 1.0
OD1 A:ASP242 3.8 39.4 1.0
N A:HIS152 3.9 43.9 1.0
OD1 A:ASP154 4.0 60.8 1.0
OD1 A:ASN127 4.1 82.1 1.0
N A:ALA151 4.2 34.5 1.0
CB A:ASP244 4.3 29.9 1.0
CB A:ASP242 4.3 33.5 1.0
NE2 A:HIS152 4.4 49.4 1.0
CA A:HIS152 4.4 35.9 1.0
CB A:ASP150 4.5 39.0 1.0
CD2 A:HIS152 4.5 49.2 1.0
CA A:ASP150 4.7 38.4 1.0
C A:ALA151 4.8 40.5 1.0
CA A:ALA151 4.9 39.0 1.0
CB A:ALA151 4.9 33.1 1.0
CG A:ASP154 4.9 60.9 1.0
C A:ASP150 4.9 39.2 1.0
O A:HIS152 4.9 43.4 1.0

Calcium binding site 2 out of 12 in 3m1r

Go back to Calcium Binding Sites List in 3m1r
Calcium binding site 2 out of 12 in the The Crystal Structure of Formimidoylglutamase From Bacillus Subtilis Subsp. Subtilis Str. 168


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Crystal Structure of Formimidoylglutamase From Bacillus Subtilis Subsp. Subtilis Str. 168 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca323

b:69.4
occ:1.00
 OD2 A:ASP150 2.3 42.9 1.0
OD1 A:ASN127 2.3 82.1 1.0
OD2 A:ASP242 2.4 34.4 1.0
OD2 A:ASP154 2.6 62.2 1.0
ND2 A:ASN127 2.7 72.3 1.0
CG A:ASN127 2.8 71.1 1.0
OD1 A:ASP154 3.0 60.8 1.0
CG A:ASP154 3.0 60.9 1.0
CG A:ASP150 3.2 42.0 1.0
CA A:CA322 3.2 36.0 1.0
CG A:ASP242 3.3 31.0 1.0
CB A:ASP242 3.5 33.5 1.0
OD1 A:ASP150 3.5 36.3 1.0
CL A:CL320 3.7 49.8 1.0
CB A:ASN127 4.3 62.1 1.0
CB A:ASP154 4.3 54.3 1.0
CB A:ASP150 4.4 39.0 1.0
OD1 A:ASP242 4.4 39.4 1.0
OD2 A:ASP244 4.8 44.2 1.0
CG2 A:VAL286 4.9 31.8 1.0
O A:HIS152 4.9 43.4 1.0
NE2 A:GLN148 4.9 47.3 1.0
CG A:GLU287 4.9 40.4 1.0
CA A:ASP242 5.0 28.9 1.0

Calcium binding site 3 out of 12 in 3m1r

Go back to Calcium Binding Sites List in 3m1r
Calcium binding site 3 out of 12 in the The Crystal Structure of Formimidoylglutamase From Bacillus Subtilis Subsp. Subtilis Str. 168


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The Crystal Structure of Formimidoylglutamase From Bacillus Subtilis Subsp. Subtilis Str. 168 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca322

b:39.9
occ:1.00
 OD2 B:ASP242 2.3 36.6 1.0
OD1 B:ASP150 2.4 34.6 1.0
ND1 B:HIS152 2.4 45.5 1.0
OD1 B:ASP244 2.4 38.5 1.0
OD2 B:ASP244 2.5 39.6 1.0
CG B:ASP244 2.8 40.5 1.0
CA B:CA323 3.0 59.3 1.0
CL B:CL320 3.1 36.0 1.0
CE1 B:HIS152 3.2 50.0 1.0
CG B:ASP242 3.3 36.1 1.0
CG B:ASP150 3.4 38.9 1.0
CG B:HIS152 3.5 49.4 1.0
OD2 B:ASP150 3.8 40.0 1.0
OD1 B:ASP242 3.9 35.2 1.0
CB B:HIS152 3.9 48.7 1.0
N B:HIS152 4.0 36.0 1.0
N B:ALA151 4.2 31.5 1.0
CB B:ASP244 4.3 36.8 1.0
NE2 B:HIS152 4.4 51.3 1.0
CB B:ASP242 4.4 31.6 1.0
CA B:HIS152 4.5 47.0 1.0
CD2 B:HIS152 4.5 50.5 1.0
CB B:ASP150 4.7 36.3 1.0
CB B:ALA151 4.8 32.8 1.0
CA B:ASP150 4.8 34.6 1.0
C B:ALA151 4.8 38.6 1.0
CA B:ALA151 4.8 33.8 1.0
O B:HOH352 4.9 38.6 1.0
OD1 B:ASP154 4.9 57.3 1.0
C B:ASP150 5.0 40.8 1.0

Calcium binding site 4 out of 12 in 3m1r

Go back to Calcium Binding Sites List in 3m1r
Calcium binding site 4 out of 12 in the The Crystal Structure of Formimidoylglutamase From Bacillus Subtilis Subsp. Subtilis Str. 168


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of The Crystal Structure of Formimidoylglutamase From Bacillus Subtilis Subsp. Subtilis Str. 168 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca323

b:59.3
occ:1.00
 OD2 B:ASP242 2.4 36.6 1.0
OD2 B:ASP154 2.4 61.0 1.0
OD1 B:ASN127 2.5 47.3 1.0
OD2 B:ASP150 2.5 40.0 1.0
CA B:CA322 3.0 39.9 1.0
CL B:CL320 3.0 36.0 1.0
OD1 B:ASP150 3.1 34.6 1.0
CG B:ASP154 3.1 54.2 1.0
CG B:ASP150 3.1 38.9 1.0
OD1 B:ASP154 3.3 57.3 1.0
CG B:ASN127 3.3 42.5 1.0
CG B:ASP242 3.4 36.1 1.0
CB B:ASP242 3.8 31.6 1.0
CB B:ASN127 3.9 37.9 1.0
ND2 B:ASN127 4.4 39.8 1.0
CB B:ASP154 4.4 40.4 1.0
OD1 B:ASP242 4.5 35.2 1.0
CB B:ASP150 4.6 36.3 1.0
OD2 B:ASP244 4.7 39.6 1.0
ND1 B:HIS152 4.7 45.5 1.0
CB B:HIS152 4.8 48.7 1.0
O B:ASN165 4.8 37.7 1.0
OD1 B:ASP244 4.8 38.5 1.0
O B:HIS152 4.9 48.7 1.0
CG B:GLU287 4.9 44.2 1.0

Calcium binding site 5 out of 12 in 3m1r

Go back to Calcium Binding Sites List in 3m1r
Calcium binding site 5 out of 12 in the The Crystal Structure of Formimidoylglutamase From Bacillus Subtilis Subsp. Subtilis Str. 168


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of The Crystal Structure of Formimidoylglutamase From Bacillus Subtilis Subsp. Subtilis Str. 168 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca323

b:33.5
occ:1.00
 OD2 C:ASP242 2.3 36.3 1.0
OD1 C:ASP150 2.3 29.9 1.0
ND1 C:HIS152 2.4 36.3 1.0
OD2 C:ASP244 2.4 39.5 1.0
OD1 C:ASP244 2.4 32.3 1.0
CG C:ASP244 2.7 36.5 1.0
CA C:CA324 2.8 62.1 1.0
CL C:CL321 3.1 42.5 1.0
CE1 C:HIS152 3.2 40.3 1.0
CG C:ASP150 3.3 33.8 1.0
CG C:ASP242 3.3 28.9 1.0
CG C:HIS152 3.5 42.6 1.0
OD2 C:ASP150 3.5 29.1 1.0
OD1 C:ASP242 3.8 29.3 1.0
CB C:HIS152 3.8 37.0 1.0
N C:HIS152 4.0 26.8 1.0
N C:ALA151 4.2 24.6 1.0
CB C:ASP244 4.3 21.3 1.0
NE2 C:HIS152 4.4 51.0 1.0
CB C:ASP242 4.4 26.0 1.0
OD1 C:ASP154 4.4 39.0 1.0
CD2 C:HIS152 4.5 48.3 1.0
CA C:HIS152 4.5 34.7 1.0
CB C:ASP150 4.6 30.9 1.0
CB C:ALA151 4.7 27.0 1.0
CA C:ALA151 4.8 22.2 1.0
CA C:ASP150 4.8 26.8 1.0
OD1 C:ASN127 4.8 60.0 1.0
C C:ALA151 4.8 33.0 1.0
OD2 C:ASP154 4.8 52.2 1.0
C C:ASP150 4.9 27.3 1.0
CG C:ASP154 5.0 45.6 1.0
O C:HIS152 5.0 30.4 1.0

Calcium binding site 6 out of 12 in 3m1r

Go back to Calcium Binding Sites List in 3m1r
Calcium binding site 6 out of 12 in the The Crystal Structure of Formimidoylglutamase From Bacillus Subtilis Subsp. Subtilis Str. 168


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of The Crystal Structure of Formimidoylglutamase From Bacillus Subtilis Subsp. Subtilis Str. 168 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca324

b:62.1
occ:1.00
 OD1 C:ASN127 2.3 60.0 1.0
OD2 C:ASP242 2.3 36.3 1.0
OD2 C:ASP154 2.4 52.2 1.0
OD2 C:ASP150 2.5 29.1 1.0
CA C:CA323 2.8 33.5 1.0
CL C:CL321 3.0 42.5 1.0
CG C:ASP154 3.1 45.6 1.0
CG C:ASN127 3.1 56.5 1.0
OD1 C:ASP154 3.2 39.0 1.0
CG C:ASP150 3.3 33.8 1.0
OD1 C:ASP150 3.4 29.9 1.0
CG C:ASP242 3.4 28.9 1.0
CB C:ASN127 3.5 51.0 1.0
CB C:ASP242 3.9 26.0 1.0
ND2 C:ASN127 4.2 44.3 1.0
CB C:ASP154 4.4 31.3 1.0
OD1 C:ASP242 4.4 29.3 1.0
OD2 C:ASP244 4.5 39.5 1.0
ND1 C:HIS152 4.6 36.3 1.0
CB C:ASP150 4.7 30.9 1.0
CG C:GLU287 4.8 40.3 1.0
OD1 C:ASP244 4.8 32.3 1.0
O C:ASN165 4.8 49.7 1.0
CB C:HIS152 4.9 37.0 1.0
CA C:ASN127 5.0 44.3 1.0

Calcium binding site 7 out of 12 in 3m1r

Go back to Calcium Binding Sites List in 3m1r
Calcium binding site 7 out of 12 in the The Crystal Structure of Formimidoylglutamase From Bacillus Subtilis Subsp. Subtilis Str. 168


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of The Crystal Structure of Formimidoylglutamase From Bacillus Subtilis Subsp. Subtilis Str. 168 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca321

b:38.0
occ:1.00
 ND1 D:HIS152 2.4 45.7 1.0
OD1 D:ASP150 2.4 33.6 1.0
OD1 D:ASP244 2.4 37.1 1.0
OD2 D:ASP244 2.5 40.0 1.0
CA D:CA322 2.5 84.9 1.0
OD2 D:ASP242 2.6 44.3 1.0
CG D:ASP244 2.7 42.4 1.0
CE1 D:HIS152 3.0 39.3 1.0
CG D:ASP242 3.2 33.0 1.0
CG D:ASP150 3.3 32.4 1.0
OD1 D:ASP242 3.5 31.8 1.0
CG D:HIS152 3.5 41.8 1.0
OD2 D:ASP150 3.5 34.2 1.0
CL D:CL320 3.7 53.4 1.0
CB D:HIS152 4.0 33.1 1.0
N D:HIS152 4.1 38.4 1.0
NE2 D:HIS152 4.2 41.1 1.0
OD1 D:ASN127 4.2 52.6 1.0
CB D:ASP244 4.3 32.6 1.0
N D:ALA151 4.3 29.2 1.0
CB D:ASP242 4.3 26.7 1.0
CD2 D:HIS152 4.5 34.6 1.0
CB D:ASP150 4.6 35.5 1.0
OD1 D:ASP154 4.6 43.2 1.0
CA D:HIS152 4.7 36.5 1.0
CA D:ASP150 4.8 35.2 1.0
CB D:ALA151 4.8 31.8 1.0
OD2 D:ASP154 4.9 42.1 1.0
CA D:ALA151 4.9 30.9 1.0
O D:HOH340 4.9 32.1 1.0
C D:ALA151 4.9 37.6 1.0

Calcium binding site 8 out of 12 in 3m1r

Go back to Calcium Binding Sites List in 3m1r
Calcium binding site 8 out of 12 in the The Crystal Structure of Formimidoylglutamase From Bacillus Subtilis Subsp. Subtilis Str. 168


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of The Crystal Structure of Formimidoylglutamase From Bacillus Subtilis Subsp. Subtilis Str. 168 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca322

b:84.9
occ:1.00
 OD1 D:ASN127 2.4 52.6 1.0
OD2 D:ASP154 2.5 42.1 1.0
CA D:CA321 2.5 38.0 1.0
OD2 D:ASP242 2.5 44.3 1.0
OD1 D:ASP154 2.7 43.2 1.0
OD2 D:ASP150 2.7 34.2 1.0
CG D:ASP154 2.8 43.4 1.0
CL D:CL320 2.9 53.4 1.0
OD1 D:ASP150 3.1 33.6 1.0
CG D:ASP150 3.3 32.4 1.0
CG D:ASN127 3.5 58.7 1.0
CG D:ASP242 3.7 33.0 1.0
ND1 D:HIS152 3.9 45.7 1.0
CB D:HIS152 4.2 33.1 1.0
CB D:ASN127 4.2 49.1 1.0
CB D:ASP154 4.3 40.4 1.0
CG D:HIS152 4.4 41.8 1.0
OD2 D:ASP244 4.4 40.0 1.0
O D:HIS152 4.5 38.9 1.0
ND2 D:ASN127 4.5 58.6 1.0
OD1 D:ASP242 4.5 31.8 1.0
CB D:ASP242 4.6 26.7 1.0
OD1 D:ASP244 4.7 37.1 1.0
CB D:ASP150 4.7 35.5 1.0
CE1 D:HIS152 4.9 39.3 1.0
CA D:HIS152 5.0 36.5 1.0
CG D:ASP244 5.0 42.4 1.0
C D:HIS152 5.0 38.6 1.0

Calcium binding site 9 out of 12 in 3m1r

Go back to Calcium Binding Sites List in 3m1r
Calcium binding site 9 out of 12 in the The Crystal Structure of Formimidoylglutamase From Bacillus Subtilis Subsp. Subtilis Str. 168


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of The Crystal Structure of Formimidoylglutamase From Bacillus Subtilis Subsp. Subtilis Str. 168 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca322

b:34.2
occ:1.00
 OD2 E:ASP244 2.3 33.0 1.0
OD2 E:ASP242 2.4 34.3 1.0
ND1 E:HIS152 2.4 30.3 1.0
OD1 E:ASP150 2.4 32.7 1.0
OD1 E:ASP244 2.4 33.4 1.0
CG E:ASP244 2.7 38.9 1.0
CA E:CA323 2.7 61.7 1.0
CL E:CL321 3.2 34.5 1.0
CG E:ASP150 3.2 32.2 1.0
CE1 E:HIS152 3.2 34.7 1.0
CG E:ASP242 3.3 30.6 1.0
OD2 E:ASP150 3.4 30.8 1.0
CG E:HIS152 3.4 35.2 1.0
OD1 E:ASP242 3.7 40.2 1.0
CB E:HIS152 3.8 35.6 1.0
N E:HIS152 4.0 27.5 1.0
N E:ALA151 4.1 29.3 1.0
CB E:ASP244 4.2 20.4 1.0
CB E:ASP242 4.3 24.7 1.0
NE2 E:HIS152 4.4 41.8 1.0
CA E:HIS152 4.5 30.9 1.0
CD2 E:HIS152 4.5 35.9 1.0
OD1 E:ASN127 4.6 31.4 1.0
CB E:ASP150 4.6 30.2 1.0
CB E:ALA151 4.8 27.4 1.0
CA E:ALA151 4.8 31.5 1.0
C E:ALA151 4.8 32.1 1.0
CA E:ASP150 4.8 36.2 1.0
OD1 E:ASP154 4.8 37.1 1.0
OD2 E:ASP154 4.9 39.6 1.0
C E:ASP150 5.0 36.5 1.0
C1 E:PEG324 5.0 46.2 1.0
O E:HOH368 5.0 56.8 1.0

Calcium binding site 10 out of 12 in 3m1r

Go back to Calcium Binding Sites List in 3m1r
Calcium binding site 10 out of 12 in the The Crystal Structure of Formimidoylglutamase From Bacillus Subtilis Subsp. Subtilis Str. 168


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of The Crystal Structure of Formimidoylglutamase From Bacillus Subtilis Subsp. Subtilis Str. 168 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca323

b:61.7
occ:1.00
 OD2 E:ASP154 2.3 39.6 1.0
OD1 E:ASN127 2.3 31.4 1.0
OD2 E:ASP150 2.4 30.8 1.0
OD2 E:ASP242 2.4 34.3 1.0
CA E:CA322 2.7 34.2 1.0
CL E:CL321 2.7 34.5 1.0
CG E:ASP154 3.0 42.4 1.0
OD1 E:ASP154 3.1 37.1 1.0
CG E:ASN127 3.2 39.0 1.0
CG E:ASP150 3.3 32.2 1.0
OD1 E:ASP150 3.4 32.7 1.0
CG E:ASP242 3.6 30.6 1.0
CB E:ASN127 3.8 35.8 1.0
CB E:ASP242 4.2 24.7 1.0
ND2 E:ASN127 4.3 33.7 1.0
CB E:ASP154 4.4 33.3 1.0
ND1 E:HIS152 4.4 30.3 1.0
OD2 E:ASP244 4.4 33.0 1.0
CB E:HIS152 4.5 35.6 1.0
OD1 E:ASP242 4.6 40.2 1.0
CB E:ASP150 4.7 30.2 1.0
O E:HIS152 4.8 30.1 1.0
O E:ASN165 4.8 27.7 1.0
CG E:HIS152 4.9 35.2 1.0
CG E:GLU287 4.9 36.5 1.0
OD1 E:ASP244 4.9 33.4 1.0

Reference:

K.Tan, L.Bigelow, K.Buck, A.Joachimiak. The Crystal Structure of Formimidoylglutamase From Bacillus Subtilis Subsp. Subtilis Str. 168 To Be Published.
Page generated: Sat Jul 13 13:26:16 2024

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