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Chlorine in PDB 2vjk: Formyl-Coa Transferase with Aspartyl-Coa Thioester Intermediate Derived From Oxalyl-Coa

Enzymatic activity of Formyl-Coa Transferase with Aspartyl-Coa Thioester Intermediate Derived From Oxalyl-Coa

All present enzymatic activity of Formyl-Coa Transferase with Aspartyl-Coa Thioester Intermediate Derived From Oxalyl-Coa:
2.8.3.16;

Protein crystallography data

The structure of Formyl-Coa Transferase with Aspartyl-Coa Thioester Intermediate Derived From Oxalyl-Coa, PDB code: 2vjk was solved by C.L.Berthold, C.G.Toyota, N.G.J.Richards, Y.Lindqvist, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.97
Space group I 4
Cell size a, b, c (Å), α, β, γ (°) 151.906, 151.906, 99.504, 90.00, 90.00, 90.00
R / Rfree (%) 17.3 / 21.4

Other elements in 2vjk:

The structure of Formyl-Coa Transferase with Aspartyl-Coa Thioester Intermediate Derived From Oxalyl-Coa also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Formyl-Coa Transferase with Aspartyl-Coa Thioester Intermediate Derived From Oxalyl-Coa (pdb code 2vjk). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Formyl-Coa Transferase with Aspartyl-Coa Thioester Intermediate Derived From Oxalyl-Coa, PDB code: 2vjk:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 2vjk

Go back to Chlorine Binding Sites List in 2vjk
Chlorine binding site 1 out of 3 in the Formyl-Coa Transferase with Aspartyl-Coa Thioester Intermediate Derived From Oxalyl-Coa


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Formyl-Coa Transferase with Aspartyl-Coa Thioester Intermediate Derived From Oxalyl-Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1430

b:24.6
occ:1.00
OG A:SER170 2.9 18.4 1.0
CB A:ALA166 3.2 18.5 1.0
O B:HOH2203 3.3 13.4 1.0
O A:HOH2013 3.3 35.2 1.0
N A:SER170 3.4 18.3 1.0
CB A:SER170 3.5 18.3 1.0
CZ A:PHE63 3.6 19.2 1.0
CB A:GLN17 3.7 23.4 1.0
CB A:ASP169 3.7 22.6 1.0
CE2 A:PHE63 3.7 21.1 1.0
CG2 B:ILE210 3.8 17.9 1.0
CG A:GLN17 3.9 27.1 1.0
CA A:SER170 3.9 17.4 1.0
OE1 A:GLN17 4.1 35.2 1.0
CD A:GLN17 4.4 29.2 1.0
C A:ASP169 4.4 18.7 1.0
CA A:ASP169 4.6 21.1 1.0
OE2 A:GLU140 4.7 21.5 1.0
CA A:ALA166 4.7 18.4 1.0
CA A:GLN17 4.8 21.8 1.0
CE1 A:PHE63 4.9 19.5 1.0
CG A:ASP169 4.9 26.7 1.0
C A:GLN17 5.0 20.0 1.0

Chlorine binding site 2 out of 3 in 2vjk

Go back to Chlorine Binding Sites List in 2vjk
Chlorine binding site 2 out of 3 in the Formyl-Coa Transferase with Aspartyl-Coa Thioester Intermediate Derived From Oxalyl-Coa


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Formyl-Coa Transferase with Aspartyl-Coa Thioester Intermediate Derived From Oxalyl-Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1432

b:27.0
occ:1.00
O A:HOH2263 3.0 46.0 1.0
N A:GLN262 3.0 17.3 1.0
O A:HOH2261 3.2 18.7 1.0
CB B:TYR139 3.5 25.0 1.0
C6P B:COA1169 3.5 32.9 1.0
CA A:GLY261 3.5 17.1 1.0
N4P B:COA1169 3.5 29.9 1.0
C A:GLY261 3.8 16.1 1.0
CG B:TYR139 3.8 26.3 1.0
CD2 B:TYR139 3.8 26.7 1.0
CB A:GLN262 3.9 18.9 1.0
CG2 A:THR283 3.9 18.1 1.0
C5P B:COA1169 4.0 31.2 1.0
CA A:GLN262 4.0 17.3 1.0
CG A:GLN262 4.2 22.5 1.0
OG1 A:THR283 4.4 18.9 1.0
O A:GLN262 4.4 14.4 1.0
O A:HOH2256 4.6 10.9 1.0
C3P B:COA1169 4.6 27.7 1.0
C A:GLN262 4.7 15.7 1.0
CB A:THR283 4.7 17.1 1.0
C7P B:COA1169 4.8 34.2 1.0
C2P B:COA1169 4.8 26.4 1.0
CA B:TYR139 4.8 23.2 1.0
CD1 B:TYR139 4.9 26.5 1.0
CE2 B:TYR139 4.9 26.8 1.0
N A:GLY261 4.9 17.0 1.0
O A:GLY261 5.0 14.7 1.0

Chlorine binding site 3 out of 3 in 2vjk

Go back to Chlorine Binding Sites List in 2vjk
Chlorine binding site 3 out of 3 in the Formyl-Coa Transferase with Aspartyl-Coa Thioester Intermediate Derived From Oxalyl-Coa


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Formyl-Coa Transferase with Aspartyl-Coa Thioester Intermediate Derived From Oxalyl-Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1430

b:22.3
occ:1.00
N B:ALA18 3.0 14.7 1.0
O B:HOH2188 3.1 19.3 1.0
O B:HOH2106 3.2 21.9 1.0
N B:GLN17 3.2 15.8 1.0
CG B:ASP169 3.7 19.9 1.0
CA B:GLN17 3.7 15.2 1.0
CB B:ALA18 3.8 14.2 1.0
S1P B:COA1169 3.8 23.9 1.0
C3P B:COA1169 3.8 27.7 1.0
OD1 B:ASP169 3.8 19.5 1.0
C2P B:COA1169 3.8 26.4 1.0
CB B:GLN17 3.8 15.8 1.0
C B:GLN17 3.9 14.9 1.0
CB B:VAL16 4.0 17.7 1.0
CA B:ALA18 4.0 15.2 1.0
ND2 B:ASN96 4.1 21.3 1.0
CG1 B:VAL16 4.1 18.0 1.0
CB B:ASP169 4.2 18.3 1.0
CE B:MET200 4.2 22.5 1.0
O B:HIS15 4.3 16.1 1.0
C B:VAL16 4.4 16.1 1.0
O5P B:COA1169 4.5 32.3 1.0
CA B:VAL16 4.7 17.0 1.0
N4P B:COA1169 4.8 29.9 1.0
CA B:ASP169 4.9 17.4 1.0
N B:GLY19 4.9 15.4 1.0

Reference:

C.L.Berthold, C.G.Toyota, N.G.J.Richards, Y.Lindqvist. Reinvestigation of the Catalytic Mechanism of Formyl-Coa Transferase, A Class III Coa- Transferase. J.Biol.Chem. V. 283 6519 2008.
ISSN: ISSN 0021-9258
PubMed: 18162462
DOI: 10.1074/JBC.M709353200
Page generated: Sat Jul 20 11:57:22 2024

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