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Calcium in PDB 1ydn: Crystal Structure of the Hmg-Coa Lyase From Brucella Melitensis, Northeast Structural Genomics Target LR35.

Enzymatic activity of Crystal Structure of the Hmg-Coa Lyase From Brucella Melitensis, Northeast Structural Genomics Target LR35.

All present enzymatic activity of Crystal Structure of the Hmg-Coa Lyase From Brucella Melitensis, Northeast Structural Genomics Target LR35.:
4.1.3.4;

Protein crystallography data

The structure of Crystal Structure of the Hmg-Coa Lyase From Brucella Melitensis, Northeast Structural Genomics Target LR35., PDB code: 1ydn was solved by F.Forouhar, M.Abashidze, M.Hussain, S.M.Vorobiev, R.Xiao, M.Ciano, T.B.Acton, G.T.Montelione, L.Tong, J.F.Hunt, Northeast Structuralgenomics Consortium (Nesg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.94 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 82.272, 86.399, 87.683, 90.00, 118.70, 90.00
R / Rfree (%) 27.1 / 30.4

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the Hmg-Coa Lyase From Brucella Melitensis, Northeast Structural Genomics Target LR35. (pdb code 1ydn). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of the Hmg-Coa Lyase From Brucella Melitensis, Northeast Structural Genomics Target LR35., PDB code: 1ydn:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 1ydn

Go back to Calcium Binding Sites List in 1ydn
Calcium binding site 1 out of 4 in the Crystal Structure of the Hmg-Coa Lyase From Brucella Melitensis, Northeast Structural Genomics Target LR35.


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 the Hmg-Coa Lyase From Brucella Melitensis, Northeast Structural Genomics Target LR35. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca601

b:24.9
occ:1.00
 NE2 A:HIS207 2.6 26.8 1.0
NE2 A:HIS205 2.6 13.1 1.0
OD1 A:ASN247 2.8 30.7 1.0
OD1 A:ASP14 2.8 36.2 1.0
O A:HOH752 3.1 47.8 1.0
ND2 A:ASN247 3.2 26.8 1.0
OD2 A:ASP14 3.2 32.3 1.0
CG A:ASP14 3.3 33.7 1.0
CG A:ASN247 3.3 29.9 1.0
CE1 A:HIS207 3.4 26.5 1.0
CD2 A:HIS205 3.4 18.3 1.0
CD2 A:HIS207 3.5 25.0 1.0
CE1 A:HIS205 3.7 16.9 1.0
O A:HOH666 4.3 24.5 1.0
ND1 A:HIS207 4.5 27.0 1.0
CB A:ASP14 4.6 33.7 1.0
CG A:HIS207 4.6 23.7 1.0
CG A:HIS205 4.6 17.9 1.0
CB A:ASN247 4.7 28.0 1.0
ND1 A:HIS205 4.8 15.8 1.0
ND2 A:ASN18 4.8 41.1 1.0

Calcium binding site 2 out of 4 in 1ydn

Go back to Calcium Binding Sites List in 1ydn
Calcium binding site 2 out of 4 in the Crystal Structure of the Hmg-Coa Lyase From Brucella Melitensis, Northeast Structural Genomics Target LR35.


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 the Hmg-Coa Lyase From Brucella Melitensis, Northeast Structural Genomics Target LR35. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca602

b:34.5
occ:1.00
 NE2 B:HIS207 2.6 23.6 1.0
NE2 B:HIS205 2.7 19.3 1.0
OD1 B:ASP14 2.7 37.5 1.0
OD1 B:ASN247 2.9 34.1 1.0
O B:HOH661 3.0 54.5 1.0
O B:HOH667 3.0 30.6 1.0
OD2 B:ASP14 3.1 33.7 1.0
CG B:ASP14 3.2 35.8 1.0
ND2 B:ASN247 3.3 32.5 1.0
CE1 B:HIS207 3.4 25.5 1.0
CG B:ASN247 3.4 32.1 1.0
CD2 B:HIS205 3.4 20.1 1.0
CD2 B:HIS207 3.6 24.7 1.0
CE1 B:HIS205 3.7 22.0 1.0
O B:HOH694 4.1 26.4 1.0
ND1 B:HIS207 4.5 27.9 1.0
CB B:ASP14 4.6 34.4 1.0
CG B:HIS207 4.6 26.0 1.0
CG B:HIS205 4.6 21.1 1.0
ND1 B:HIS205 4.7 23.3 1.0
ND2 B:ASN18 4.8 40.0 1.0
CB B:ASN247 4.8 30.8 1.0

Calcium binding site 3 out of 4 in 1ydn

Go back to Calcium Binding Sites List in 1ydn
Calcium binding site 3 out of 4 in the Crystal Structure of the Hmg-Coa Lyase From Brucella Melitensis, Northeast Structural Genomics Target LR35.


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 the Hmg-Coa Lyase From Brucella Melitensis, Northeast Structural Genomics Target LR35. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca603

b:22.6
occ:1.00
 NE2 C:HIS207 2.6 22.4 1.0
NE2 C:HIS205 2.6 19.1 1.0
OD1 C:ASP14 2.7 35.1 1.0
OD1 C:ASN247 2.9 31.3 1.0
OD2 C:ASP14 3.1 34.1 1.0
CG C:ASP14 3.2 32.3 1.0
ND2 C:ASN247 3.3 30.6 1.0
CG C:ASN247 3.4 29.5 1.0
CD2 C:HIS205 3.4 19.8 1.0
CE1 C:HIS207 3.4 23.8 1.0
CD2 C:HIS207 3.6 24.2 1.0
CE1 C:HIS205 3.7 21.8 1.0
O C:HOH734 3.8 34.8 1.0
CB C:ASP14 4.6 31.4 1.0
ND1 C:HIS207 4.6 25.0 1.0
CG C:HIS205 4.6 20.4 1.0
CG C:HIS207 4.7 25.2 1.0
ND1 C:HIS205 4.7 22.5 1.0
ND2 C:ASN18 4.8 38.8 1.0
CB C:ASN247 4.8 28.7 1.0
O C:HOH656 4.8 35.1 1.0

Calcium binding site 4 out of 4 in 1ydn

Go back to Calcium Binding Sites List in 1ydn
Calcium binding site 4 out of 4 in the Crystal Structure of the Hmg-Coa Lyase From Brucella Melitensis, Northeast Structural Genomics Target LR35.


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 the Hmg-Coa Lyase From Brucella Melitensis, Northeast Structural Genomics Target LR35. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca604

b:28.2
occ:1.00
 NE2 D:HIS207 2.6 27.9 1.0
NE2 D:HIS205 2.7 16.7 1.0
OD1 D:ASP14 2.8 36.3 1.0
OD1 D:ASN247 3.0 36.4 1.0
OD2 D:ASP14 3.1 32.5 1.0
CG D:ASP14 3.2 34.1 1.0
ND2 D:ASN247 3.3 31.9 1.0
CE1 D:HIS207 3.4 28.0 1.0
CG D:ASN247 3.4 32.7 1.0
CD2 D:HIS205 3.5 19.7 1.0
CD2 D:HIS207 3.6 26.4 1.0
CE1 D:HIS205 3.8 18.6 1.0
ND1 D:HIS207 4.5 28.2 1.0
CB D:ASP14 4.6 33.8 1.0
CG D:HIS207 4.6 27.6 1.0
ND2 D:ASN18 4.7 40.1 1.0
CG D:HIS205 4.7 19.0 1.0
CB D:ASN247 4.8 30.6 1.0
ND1 D:HIS205 4.8 18.9 1.0
O D:HOH627 5.0 26.8 1.0

Reference:

F.Forouhar, M.Hussain, R.Farid, J.Benach, M.Abashidze, W.C.Edstrom, S.M.Vorobiev, R.Xiao, T.B.Acton, Z.Fu, J.J.Kim, H.M.Miziorko, G.T.Montelione, J.F.Hunt. Crystal Structures of Two Bacterial 3-Hydroxy-3-Methylglutaryl-Coa Lyases Suggest A Common Catalytic Mechanism Among A Family of Tim Barrel Metalloenzymes Cleaving Carbon-Carbon Bonds. J.Biol.Chem. V. 281 7533 2006.
ISSN: ISSN 0021-9258
PubMed: 16330546
DOI: 10.1074/JBC.M507996200
Page generated: Tue Jul 8 03:50:16 2025

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