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Calcium in PDB 3cdx: Crystal Structure of Succinylglutamatedesuccinylase/Aspartoacylase From Rhodobacter Sphaeroides

Protein crystallography data

The structure of Crystal Structure of Succinylglutamatedesuccinylase/Aspartoacylase From Rhodobacter Sphaeroides, PDB code: 3cdx was solved by J.B.Bonanno, M.Rutter, K.T.Bain, M.Iizuka, K.Patterson, D.Smith, S.Wasserman, J.M.Sauder, S.K.Burley, S.C.Almo, New York Sgx Researchcenter For Structural Genomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.10
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 152.475, 174.426, 77.406, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 24.4

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Succinylglutamatedesuccinylase/Aspartoacylase From Rhodobacter Sphaeroides (pdb code 3cdx). 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 Succinylglutamatedesuccinylase/Aspartoacylase From Rhodobacter Sphaeroides, PDB code: 3cdx:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 3cdx

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Calcium binding site 1 out of 6 in the Crystal Structure of Succinylglutamatedesuccinylase/Aspartoacylase From Rhodobacter Sphaeroides


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 Succinylglutamatedesuccinylase/Aspartoacylase From Rhodobacter Sphaeroides within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:51.5
occ:1.00
 OE1 A:GLU65 2.3 27.7 1.0
ND1 A:HIS148 2.3 25.6 1.0
ND1 A:HIS62 2.4 23.6 1.0
OE2 A:GLU65 2.4 27.4 1.0
CD A:GLU65 2.6 27.8 1.0
O A:HOH412 2.9 27.4 1.0
CE1 A:HIS62 3.1 21.9 1.0
CE1 A:HIS148 3.2 24.6 1.0
CG A:HIS148 3.3 22.2 1.0
CG A:HIS62 3.5 23.9 1.0
CB A:HIS148 3.6 23.6 1.0
O A:THR149 3.8 24.7 1.0
NH1 A:ARG104 4.0 29.6 1.0
CB A:HIS62 4.0 25.3 1.0
CG A:GLU65 4.1 25.5 1.0
O A:HOH414 4.1 22.7 1.0
NE2 A:HIS62 4.3 21.1 1.0
NE2 A:HIS148 4.3 26.5 1.0
CD2 A:HIS148 4.4 23.6 1.0
O A:HOH477 4.5 44.7 1.0
CA A:HIS148 4.5 23.7 1.0
CD2 A:HIS62 4.6 23.0 1.0
N A:THR149 4.7 23.5 1.0
O A:HOH436 4.7 24.2 1.0
CZ A:ARG104 4.7 27.2 1.0
NH2 A:ARG104 4.8 29.0 1.0
CB A:GLU65 4.9 22.1 1.0
C A:THR149 5.0 24.2 1.0

Calcium binding site 2 out of 6 in 3cdx

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Calcium binding site 2 out of 6 in the Crystal Structure of Succinylglutamatedesuccinylase/Aspartoacylase From Rhodobacter Sphaeroides


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 Succinylglutamatedesuccinylase/Aspartoacylase From Rhodobacter Sphaeroides within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca401

b:40.5
occ:1.00
 OE2 B:GLU65 2.2 24.7 1.0
ND1 B:HIS62 2.3 28.6 1.0
OE1 B:GLU65 2.4 27.9 1.0
ND1 B:HIS148 2.5 26.8 1.0
CD B:GLU65 2.6 26.7 1.0
O B:HOH612 2.6 52.2 1.0
CE1 B:HIS62 3.1 29.4 1.0
CE1 B:HIS148 3.3 27.2 1.0
CG B:HIS62 3.4 27.4 1.0
CG B:HIS148 3.5 27.1 1.0
O B:THR149 3.7 28.2 1.0
CB B:HIS62 3.8 24.8 1.0
NH1 B:ARG104 3.8 26.6 1.0
CB B:HIS148 3.8 24.5 1.0
CG B:GLU65 4.1 24.6 1.0
O B:HOH408 4.3 26.2 1.0
NE2 B:HIS62 4.3 27.7 1.0
O B:HOH420 4.3 22.1 1.0
CD2 B:HIS62 4.4 25.4 1.0
NE2 B:HIS148 4.5 27.4 1.0
O B:HOH409 4.5 43.8 1.0
CZ B:ARG104 4.5 27.1 1.0
CD2 B:HIS148 4.6 30.5 1.0
NH2 B:ARG104 4.6 29.8 1.0
CA B:HIS148 4.8 24.9 1.0
N B:THR149 4.8 25.8 1.0
C B:THR149 4.9 26.8 1.0
CB B:GLU65 5.0 24.1 1.0
CH2 C:TRP37 5.0 33.3 0.5

Calcium binding site 3 out of 6 in 3cdx

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Calcium binding site 3 out of 6 in the Crystal Structure of Succinylglutamatedesuccinylase/Aspartoacylase From Rhodobacter Sphaeroides


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 Succinylglutamatedesuccinylase/Aspartoacylase From Rhodobacter Sphaeroides within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca401

b:45.8
occ:1.00
 OE2 C:GLU65 2.3 24.2 1.0
OE1 C:GLU65 2.3 28.7 1.0
ND1 C:HIS148 2.4 29.7 1.0
ND1 C:HIS62 2.5 28.5 1.0
O C:HOH411 2.5 29.9 1.0
CD C:GLU65 2.6 26.3 1.0
CE1 C:HIS62 3.3 30.4 1.0
CE1 C:HIS148 3.3 33.7 1.0
CG C:HIS148 3.4 27.8 1.0
O C:THR149 3.6 23.5 1.0
CG C:HIS62 3.6 27.1 1.0
CB C:HIS148 3.7 24.4 1.0
NH1 C:ARG104 3.9 27.7 1.0
CB C:HIS62 4.0 24.6 1.0
CG C:GLU65 4.1 22.8 1.0
O C:HOH611 4.2 44.5 1.0
O C:HOH562 4.3 29.2 1.0
O C:HOH565 4.5 27.1 1.0
NE2 C:HIS148 4.5 33.8 1.0
NE2 C:HIS62 4.5 29.3 1.0
CD2 C:HIS148 4.5 30.4 1.0
NH2 C:ARG104 4.6 32.4 1.0
CZ C:ARG104 4.6 31.1 1.0
CD2 C:HIS62 4.6 26.7 1.0
CH2 D:TRP37 4.7 33.0 0.5
N C:THR149 4.7 24.0 1.0
CA C:HIS148 4.7 24.6 1.0
C C:THR149 4.8 23.6 1.0
CZ2 D:TRP37 4.8 33.0 0.5
CB C:GLU65 5.0 21.5 1.0

Calcium binding site 4 out of 6 in 3cdx

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Calcium binding site 4 out of 6 in the Crystal Structure of Succinylglutamatedesuccinylase/Aspartoacylase From Rhodobacter Sphaeroides


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 Succinylglutamatedesuccinylase/Aspartoacylase From Rhodobacter Sphaeroides within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca401

b:65.9
occ:1.00
 OE2 D:GLU65 2.2 37.2 1.0
OE1 D:GLU65 2.5 40.5 1.0
ND1 D:HIS148 2.6 38.5 1.0
O D:HOH532 2.6 51.0 1.0
CD D:GLU65 2.7 37.9 1.0
ND1 D:HIS62 2.7 38.7 1.0
CE1 D:HIS62 3.4 39.0 1.0
CG D:HIS148 3.5 39.1 1.0
O D:THR149 3.5 40.2 1.0
CE1 D:HIS148 3.5 37.3 1.0
CB D:HIS148 3.7 36.7 1.0
NH1 D:ARG104 3.8 37.1 1.0
CG D:HIS62 3.9 36.4 1.0
CG D:GLU65 4.2 34.5 1.0
CB D:HIS62 4.3 34.8 1.0
O D:HOH445 4.4 29.7 1.0
O D:HOH447 4.5 47.8 1.0
CZ D:ARG104 4.5 38.7 1.0
CA D:HIS148 4.6 38.2 1.0
CD2 D:HIS148 4.6 38.1 1.0
NE2 D:HIS148 4.6 39.2 1.0
NH2 D:ARG104 4.6 37.8 1.0
N D:THR149 4.6 38.5 1.0
O D:HOH531 4.6 37.7 1.0
NE2 D:HIS62 4.7 39.5 1.0
CZ2 B:TRP37 4.7 39.0 0.5
C D:THR149 4.7 39.2 1.0
CH2 B:TRP37 4.7 39.3 0.5
OE2 D:GLU213 4.9 43.1 1.0
CD2 D:HIS62 4.9 38.1 1.0

Calcium binding site 5 out of 6 in 3cdx

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Calcium binding site 5 out of 6 in the Crystal Structure of Succinylglutamatedesuccinylase/Aspartoacylase From Rhodobacter Sphaeroides


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 Succinylglutamatedesuccinylase/Aspartoacylase From Rhodobacter Sphaeroides within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca401

b:52.3
occ:1.00
 OE2 E:GLU65 2.3 34.9 1.0
OE1 E:GLU65 2.3 34.6 1.0
ND1 E:HIS62 2.4 32.5 1.0
ND1 E:HIS148 2.4 36.4 1.0
CD E:GLU65 2.6 36.1 1.0
O E:HOH530 2.8 44.4 1.0
CE1 E:HIS62 3.2 31.8 1.0
CE1 E:HIS148 3.3 35.7 1.0
CG E:HIS148 3.4 35.4 1.0
CG E:HIS62 3.5 32.2 1.0
CB E:HIS148 3.8 32.9 1.0
NH1 E:ARG104 3.8 33.5 1.0
O E:THR149 3.8 34.1 1.0
CB E:HIS62 3.9 31.5 1.0
CG E:GLU65 4.1 31.6 1.0
O E:HOH450 4.2 33.3 1.0
NE2 E:HIS62 4.4 32.8 1.0
NE2 E:HIS148 4.4 33.4 1.0
CZ E:ARG104 4.4 33.8 1.0
NH2 E:ARG104 4.5 35.0 1.0
CD2 E:HIS148 4.5 34.7 1.0
CD2 E:HIS62 4.5 33.6 1.0
O E:HOH534 4.6 31.6 1.0
CA E:HIS148 4.7 33.7 1.0
CH2 F:TRP37 4.7 36.5 0.5
N E:THR149 4.8 34.5 1.0
CZ2 F:TRP37 4.8 36.9 0.5
O E:HOH455 4.9 60.8 1.0
CB E:GLU65 5.0 32.4 1.0

Calcium binding site 6 out of 6 in 3cdx

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Calcium binding site 6 out of 6 in the Crystal Structure of Succinylglutamatedesuccinylase/Aspartoacylase From Rhodobacter Sphaeroides


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 Succinylglutamatedesuccinylase/Aspartoacylase From Rhodobacter Sphaeroides within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca401

b:48.0
occ:1.00
 ND1 F:HIS62 2.2 21.0 1.0
OE2 F:GLU65 2.2 25.0 1.0
OE1 F:GLU65 2.4 28.0 1.0
ND1 F:HIS148 2.4 24.9 1.0
CD F:GLU65 2.6 26.3 1.0
O F:HOH583 2.7 46.6 1.0
CE1 F:HIS62 3.0 21.4 1.0
CE1 F:HIS148 3.3 27.1 1.0
CG F:HIS62 3.3 22.1 1.0
CG F:HIS148 3.5 24.7 1.0
CB F:HIS62 3.8 23.1 1.0
O F:THR149 3.8 26.3 1.0
CB F:HIS148 3.8 22.6 1.0
NH1 F:ARG104 3.9 28.6 1.0
CG F:GLU65 4.1 25.3 1.0
O F:HOH582 4.1 26.3 1.0
NE2 F:HIS62 4.2 21.0 1.0
O F:HOH515 4.3 49.4 1.0
CD2 F:HIS62 4.4 21.0 1.0
NE2 F:HIS148 4.4 25.1 1.0
O F:HOH431 4.5 26.4 1.0
CD2 F:HIS148 4.5 24.7 1.0
CZ F:ARG104 4.5 30.1 1.0
NH2 F:ARG104 4.6 29.6 1.0
CA F:HIS148 4.7 22.7 1.0
N F:THR149 4.8 22.6 1.0
CH2 A:TRP37 4.9 25.1 0.5
CB F:GLU65 4.9 22.8 1.0
C F:THR149 5.0 24.9 1.0

Reference:

J.B.Bonanno, M.Rutter, K.T.Bain, M.Iizuka, K.Patterson, D.Smith, S.Wasserman, J.M.Sauder, S.K.Burley, S.C.Almo. Crystal Structure of Succinylglutamatedesuccinylase/Aspartoacylase From Rhodobacter Sphaeroides. To Be Published.
Page generated: Tue Jul 8 11:20:43 2025

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