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Calcium in PDB 9o8n: Crystal Structure of 2,3,4,5-Tetrahydropyridine-2,6-Dicarboxylate N- Succinyltransferase (Dapd) From Bordetella Pertussis

Enzymatic activity of Crystal Structure of 2,3,4,5-Tetrahydropyridine-2,6-Dicarboxylate N- Succinyltransferase (Dapd) From Bordetella Pertussis

All present enzymatic activity of Crystal Structure of 2,3,4,5-Tetrahydropyridine-2,6-Dicarboxylate N- Succinyltransferase (Dapd) From Bordetella Pertussis:
2.3.1.117;

Protein crystallography data

The structure of Crystal Structure of 2,3,4,5-Tetrahydropyridine-2,6-Dicarboxylate N- Succinyltransferase (Dapd) From Bordetella Pertussis, PDB code: 9o8n was solved by Seattle Structural Genomics Center For Infectious Disease, Seattlestructural 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) 48.85 / 1.59
Space group P 63
Cell size a, b, c (Å), α, β, γ (°) 97.696, 97.696, 78.288, 90, 90, 120
R / Rfree (%) 15.8 / 18

Other elements in 9o8n:

The structure of Crystal Structure of 2,3,4,5-Tetrahydropyridine-2,6-Dicarboxylate N- Succinyltransferase (Dapd) From Bordetella Pertussis also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of 2,3,4,5-Tetrahydropyridine-2,6-Dicarboxylate N- Succinyltransferase (Dapd) From Bordetella Pertussis (pdb code 9o8n). 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 2,3,4,5-Tetrahydropyridine-2,6-Dicarboxylate N- Succinyltransferase (Dapd) From Bordetella Pertussis, PDB code: 9o8n:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 9o8n

Go back to Calcium Binding Sites List in 9o8n
Calcium binding site 1 out of 3 in the Crystal Structure of 2,3,4,5-Tetrahydropyridine-2,6-Dicarboxylate N- Succinyltransferase (Dapd) From Bordetella Pertussis


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 2,3,4,5-Tetrahydropyridine-2,6-Dicarboxylate N- Succinyltransferase (Dapd) From Bordetella Pertussis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:53.5
occ:1.00
 CE A:MET76 3.0 37.2 1.0
N A:THR89 3.2 18.7 1.0
O A:HOH628 3.4 49.7 1.0
OG1 A:THR89 3.5 23.2 1.0
CA A:PRO88 3.6 17.7 1.0
CB A:ALA92 3.7 35.2 1.0
C A:PRO88 3.9 18.9 1.0
CB A:PRO88 3.9 23.2 1.0
CA A:THR89 4.2 18.6 1.0
CB A:THR89 4.2 21.5 1.0
CG2 A:THR89 4.4 21.8 1.0
O A:THR89 4.4 19.7 1.0
SD A:MET76 4.7 42.2 1.0
C A:THR89 4.8 18.2 1.0
N A:PRO88 4.9 17.9 1.0

Calcium binding site 2 out of 3 in 9o8n

Go back to Calcium Binding Sites List in 9o8n
Calcium binding site 2 out of 3 in the Crystal Structure of 2,3,4,5-Tetrahydropyridine-2,6-Dicarboxylate N- Succinyltransferase (Dapd) From Bordetella Pertussis


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 2,3,4,5-Tetrahydropyridine-2,6-Dicarboxylate N- Succinyltransferase (Dapd) From Bordetella Pertussis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca302

b:26.3
occ:1.00
 OG A:SER25 3.0 20.9 1.0
O A:HOH567 3.1 43.5 1.0
CB A:SER25 3.5 23.0 1.0
CG2 A:VAL28 3.6 22.6 1.0
N A:SER25 4.0 22.1 1.0
CD2 A:LEU19 4.0 30.8 1.0
CA A:SER25 4.4 23.3 1.0
CB A:VAL28 4.4 19.0 1.0
ND2 A:ASN15 4.4 26.5 1.0
O A:HOH566 4.4 40.2 1.0

Calcium binding site 3 out of 3 in 9o8n

Go back to Calcium Binding Sites List in 9o8n
Calcium binding site 3 out of 3 in the Crystal Structure of 2,3,4,5-Tetrahydropyridine-2,6-Dicarboxylate N- Succinyltransferase (Dapd) From Bordetella Pertussis


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 2,3,4,5-Tetrahydropyridine-2,6-Dicarboxylate N- Succinyltransferase (Dapd) From Bordetella Pertussis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:46.2
occ:1.00
 N A:GLY95 3.1 33.3 1.0
N A:ALA98 3.2 28.2 1.0
CA A:GLY95 3.5 36.5 1.0
O A:HOH552 3.5 37.8 1.0
CB A:ALA98 3.6 28.4 1.0
C A:GLY95 3.6 37.6 1.0
CB A:ALA97 3.7 36.2 1.0
O A:GLY95 3.8 35.6 1.0
N A:ALA97 3.8 27.6 1.0
CA A:ALA98 4.0 27.4 1.0
CA A:ALA97 4.1 30.8 1.0
C A:ALA97 4.1 31.0 1.0
C A:TYR94 4.3 35.6 1.0
N A:GLU96 4.3 29.6 1.0
CA A:TYR94 4.7 32.0 1.0
C A:GLU96 4.7 28.1 1.0
O A:GLY93 5.0 40.2 1.0

Reference:

A.R.Ung, S.Lovell, A.Cooper, K.P.Battaile. Crystal Structure of 2,3,4,5-Tetrahydropyridine-2,6-Dicarboxylate N-Succinyltransferase (Dapd) From Bordetella Pertussis To Be Published.
Page generated: Thu Jul 10 10:25:15 2025

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