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Chlorine in PDB 4xym: Ca. Korarchaeum Cryptofilum Dinucleotide Forming Acetyl-Coenzyme A Synthetase 1 in Complex with Coenzyme A, Ca-Ampcp and Hgcl+

Protein crystallography data

The structure of Ca. Korarchaeum Cryptofilum Dinucleotide Forming Acetyl-Coenzyme A Synthetase 1 in Complex with Coenzyme A, Ca-Ampcp and Hgcl+, PDB code: 4xym was solved by R.H.-J.Weisse, A.J.Scheidig, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 85.02 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 99.560, 114.416, 127.040, 90.00, 90.00, 90.00
R / Rfree (%) 19.5 / 23.7

Other elements in 4xym:

The structure of Ca. Korarchaeum Cryptofilum Dinucleotide Forming Acetyl-Coenzyme A Synthetase 1 in Complex with Coenzyme A, Ca-Ampcp and Hgcl+ also contains other interesting chemical elements:

Mercury (Hg) 8 atoms
Calcium (Ca) 2 atoms
Sodium (Na) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Ca. Korarchaeum Cryptofilum Dinucleotide Forming Acetyl-Coenzyme A Synthetase 1 in Complex with Coenzyme A, Ca-Ampcp and Hgcl+ (pdb code 4xym). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Ca. Korarchaeum Cryptofilum Dinucleotide Forming Acetyl-Coenzyme A Synthetase 1 in Complex with Coenzyme A, Ca-Ampcp and Hgcl+, PDB code: 4xym:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 4xym

Go back to Chlorine Binding Sites List in 4xym
Chlorine binding site 1 out of 6 in the Ca. Korarchaeum Cryptofilum Dinucleotide Forming Acetyl-Coenzyme A Synthetase 1 in Complex with Coenzyme A, Ca-Ampcp and Hgcl+


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Ca. Korarchaeum Cryptofilum Dinucleotide Forming Acetyl-Coenzyme A Synthetase 1 in Complex with Coenzyme A, Ca-Ampcp and Hgcl+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl501

b:52.9
occ:0.81
HG A:HG502 2.3 55.5 0.8
HB3 A:PRO59 2.7 53.8 1.0
HD3 A:PRO59 3.0 53.5 1.0
HA A:PRO59 3.2 52.7 1.0
O A:ASN46 3.2 41.3 1.0
O A:PRO47 3.3 46.8 1.0
CB A:PRO59 3.4 44.9 1.0
N A:PRO59 3.4 45.2 1.0
CD A:PRO59 3.5 44.6 1.0
CA A:PRO59 3.5 43.9 1.0
C A:PRO47 3.6 44.0 1.0
HA A:THR48 3.6 53.0 1.0
HG3 A:PRO59 3.7 56.0 1.0
CG A:PRO59 3.8 46.7 1.0
N A:THR48 3.8 44.6 1.0
C A:TYR58 3.8 44.0 1.0
O A:ALA49 3.9 49.1 1.0
CA A:THR48 4.0 44.2 1.0
C A:THR48 4.0 49.0 1.0
HA A:TYR58 4.1 48.7 1.0
HA A:PRO47 4.2 51.0 1.0
O A:THR48 4.2 46.9 1.0
HB2 A:PRO59 4.3 53.8 1.0
O A:TYR58 4.3 44.9 1.0
H A:THR48 4.3 53.6 1.0
C A:ASN46 4.3 40.7 1.0
CA A:PRO47 4.4 42.5 1.0
HD2 A:PRO59 4.4 53.5 1.0
N A:ALA49 4.4 48.5 1.0
CA A:TYR58 4.5 40.6 1.0
H A:ALA49 4.6 58.2 1.0
HG2 A:PRO59 4.7 56.0 1.0
C A:ALA49 4.8 47.9 1.0
O A:CYS57 4.8 42.9 1.0
H A:ASN46 4.9 45.1 1.0
N A:PRO47 4.9 43.2 1.0
N A:TYR58 5.0 38.3 1.0

Chlorine binding site 2 out of 6 in 4xym

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Chlorine binding site 2 out of 6 in the Ca. Korarchaeum Cryptofilum Dinucleotide Forming Acetyl-Coenzyme A Synthetase 1 in Complex with Coenzyme A, Ca-Ampcp and Hgcl+


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Ca. Korarchaeum Cryptofilum Dinucleotide Forming Acetyl-Coenzyme A Synthetase 1 in Complex with Coenzyme A, Ca-Ampcp and Hgcl+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl503

b:31.5
occ:0.31
H A:VAL61 2.2 42.8 1.0
HG A:HG504 2.4 50.7 0.3
HG23 A:VAL61 2.6 48.7 1.0
HA A:LYS60 3.0 47.5 1.0
HG13 A:VAL83 3.0 43.3 1.0
N A:VAL61 3.1 35.6 1.0
OD2 A:ASP86 3.1 44.1 1.0
O A:HOH751 3.1 47.8 1.0
HG21 A:ILE45 3.2 42.0 1.0
HB3 A:ASP86 3.2 48.2 1.0
HB A:VAL61 3.4 44.3 1.0
CG2 A:VAL61 3.4 40.6 1.0
HB3 A:LYS60 3.6 54.2 1.0
CA A:LYS60 3.7 39.6 1.0
HG21 A:VAL61 3.7 48.7 1.0
CB A:VAL61 3.8 36.9 1.0
HB2 A:LYS60 3.8 54.2 1.0
CG A:ASP86 3.8 43.7 1.0
HA A:VAL83 3.9 50.4 1.0
HG11 A:VAL16 3.9 41.0 1.0
C A:LYS60 3.9 43.3 1.0
CB A:LYS60 3.9 45.2 1.0
CB A:ASP86 4.0 40.2 1.0
CG1 A:VAL83 4.0 36.1 1.0
HG21 A:VAL16 4.0 43.3 1.0
CA A:VAL61 4.0 37.5 1.0
HG22 A:VAL83 4.0 50.4 1.0
HG13 A:VAL16 4.0 41.0 1.0
CG2 A:ILE45 4.1 35.0 1.0
HG22 A:VAL16 4.1 43.3 1.0
HG22 A:VAL61 4.2 48.7 1.0
HB2 A:ASP86 4.3 48.2 1.0
HG12 A:VAL83 4.4 43.3 1.0
CG1 A:VAL16 4.4 34.1 1.0
HG22 A:ILE45 4.4 42.0 1.0
HG11 A:VAL83 4.4 43.3 1.0
O A:VAL83 4.5 39.9 1.0
HG23 A:ILE45 4.5 42.0 1.0
H A:SER62 4.5 51.3 1.0
CG2 A:VAL16 4.5 36.1 1.0
HA A:VAL61 4.6 45.0 1.0
HG13 A:ILE45 4.6 43.8 1.0
CA A:VAL83 4.6 42.0 1.0
CB A:VAL83 4.7 37.7 1.0
SG A:CYS87 4.7 35.6 1.0
H A:CYS87 4.8 49.9 1.0
CG2 A:VAL83 4.8 42.0 1.0
O A:PRO59 4.8 42.9 1.0
OD1 A:ASP86 4.9 43.6 1.0
H62A A:COA508 4.9 48.3 1.0
N1A A:COA508 4.9 33.4 1.0
HD12 A:ILE45 5.0 41.1 1.0
N A:LYS60 5.0 43.2 1.0

Chlorine binding site 3 out of 6 in 4xym

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Chlorine binding site 3 out of 6 in the Ca. Korarchaeum Cryptofilum Dinucleotide Forming Acetyl-Coenzyme A Synthetase 1 in Complex with Coenzyme A, Ca-Ampcp and Hgcl+


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Ca. Korarchaeum Cryptofilum Dinucleotide Forming Acetyl-Coenzyme A Synthetase 1 in Complex with Coenzyme A, Ca-Ampcp and Hgcl+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl506

b:19.4
occ:0.48
HG A:HG507 2.3 47.9 0.5
HB3 A:LEU380 2.8 32.0 1.0
HG23 A:VAL414 2.8 32.9 1.0
HB3 A:PRO437 2.9 33.2 1.0
H A:TYR381 2.9 35.8 1.0
HD3 A:PRO437 3.0 35.1 1.0
HD22 A:LEU380 3.1 30.4 1.0
HB1 A:ALA310 3.3 37.4 1.0
O A:GLY412 3.4 27.6 1.0
HA A:LEU380 3.4 28.8 1.0
HA A:PRO437 3.5 30.3 1.0
HA3 A:GLY412 3.5 33.5 1.0
C A:GLY412 3.6 22.4 1.0
N A:TYR381 3.6 29.8 1.0
CB A:LEU380 3.6 26.7 1.0
CB A:PRO437 3.6 27.6 1.0
CD A:PRO437 3.7 29.3 1.0
CG2 A:VAL414 3.7 27.4 1.0
HG3 A:PRO437 3.8 35.6 1.0
HG21 A:VAL414 3.8 32.9 1.0
O A:TYR381 3.8 26.9 1.0
HA A:MET413 3.9 33.6 1.0
CA A:LEU380 3.9 24.0 1.0
N A:PRO437 3.9 25.3 1.0
CD2 A:LEU380 3.9 25.4 1.0
CA A:PRO437 3.9 25.3 1.0
HD23 A:LEU380 3.9 30.4 1.0
CG A:PRO437 3.9 29.7 1.0
HB2 A:ALA310 4.0 37.4 1.0
H A:VAL414 4.0 31.6 1.0
N A:MET413 4.0 27.3 1.0
CB A:ALA310 4.1 31.2 1.0
CA A:GLY412 4.1 28.0 1.0
C A:LEU380 4.1 29.6 1.0
C A:TYR381 4.2 29.0 1.0
O A:HOH691 4.3 34.3 1.0
N A:VAL414 4.3 26.4 1.0
HG22 A:VAL414 4.3 32.9 1.0
CA A:MET413 4.3 28.0 1.0
HB2 A:LEU380 4.3 32.0 1.0
CG A:LEU380 4.3 29.9 1.0
HB A:VAL414 4.4 31.8 1.0
HD13 A:LEU380 4.4 28.3 1.0
HB2 A:PRO437 4.5 33.2 1.0
HB3 A:ALA310 4.5 37.4 1.0
C A:MET413 4.5 28.1 1.0
H A:MET413 4.5 32.8 1.0
CA A:TYR381 4.5 27.0 1.0
HD2 A:PRO437 4.5 35.1 1.0
C A:THR436 4.6 27.8 1.0
CB A:VAL414 4.6 26.5 1.0
HA A:THR436 4.6 31.9 1.0
HD21 A:LEU380 4.7 30.4 1.0
HA2 A:GLY412 4.7 33.5 1.0
H A:GLY412 4.9 27.8 1.0
SG A:CYS382 4.9 33.4 1.0
HG2 A:PRO437 4.9 35.6 1.0
N A:CYS382 4.9 27.9 1.0
CD1 A:LEU380 5.0 23.6 1.0

Chlorine binding site 4 out of 6 in 4xym

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Chlorine binding site 4 out of 6 in the Ca. Korarchaeum Cryptofilum Dinucleotide Forming Acetyl-Coenzyme A Synthetase 1 in Complex with Coenzyme A, Ca-Ampcp and Hgcl+


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Ca. Korarchaeum Cryptofilum Dinucleotide Forming Acetyl-Coenzyme A Synthetase 1 in Complex with Coenzyme A, Ca-Ampcp and Hgcl+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl501

b:47.6
occ:0.78
HG C:HG502 2.2 60.1 0.8
HB3 C:PRO59 3.1 50.1 1.0
HD3 C:PRO59 3.2 53.6 1.0
O C:ASN46 3.4 45.2 1.0
O C:PRO47 3.5 41.8 1.0
O C:ALA49 3.5 40.5 1.0
HA C:THR48 3.6 56.8 1.0
HA C:PRO59 3.6 54.3 1.0
N C:PRO59 3.7 44.4 1.0
C C:PRO47 3.7 48.7 1.0
CD C:PRO59 3.8 44.6 1.0
CB C:PRO59 3.8 41.8 1.0
C C:THR48 3.8 49.1 1.0
N C:THR48 3.9 47.7 1.0
CA C:THR48 3.9 47.3 1.0
CA C:PRO59 3.9 45.2 1.0
HG3 C:PRO59 4.0 56.1 1.0
O C:THR48 4.0 53.5 1.0
C C:TYR58 4.1 45.8 1.0
CG C:PRO59 4.1 46.7 1.0
HA C:TYR58 4.1 51.9 1.0
N C:ALA49 4.2 50.2 1.0
H C:THR48 4.3 57.2 1.0
C C:ALA49 4.4 49.2 1.0
H C:ALA49 4.4 60.3 1.0
HA C:PRO47 4.5 57.6 1.0
C C:ASN46 4.5 45.2 1.0
O C:CYS57 4.5 49.6 1.0
O C:TYR58 4.5 45.9 1.0
CA C:TYR58 4.6 43.3 1.0
CA C:PRO47 4.6 48.0 1.0
HB2 C:PRO59 4.6 50.1 1.0
HD2 C:PRO59 4.6 53.6 1.0
C C:CYS57 4.9 48.3 1.0
HA C:ASP50 4.9 61.7 1.0
SG C:CYS57 4.9 52.8 1.0
H C:ASN46 4.9 45.9 1.0
CA C:ALA49 4.9 48.8 1.0
N C:TYR58 5.0 41.2 1.0

Chlorine binding site 5 out of 6 in 4xym

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Chlorine binding site 5 out of 6 in the Ca. Korarchaeum Cryptofilum Dinucleotide Forming Acetyl-Coenzyme A Synthetase 1 in Complex with Coenzyme A, Ca-Ampcp and Hgcl+


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Ca. Korarchaeum Cryptofilum Dinucleotide Forming Acetyl-Coenzyme A Synthetase 1 in Complex with Coenzyme A, Ca-Ampcp and Hgcl+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl503

b:31.5
occ:0.33
H C:VAL61 2.4 48.7 1.0
HG C:HG504 2.5 51.8 0.3
HG23 C:VAL61 2.7 48.0 1.0
HG13 C:VAL83 2.9 47.0 1.0
O C:HOH603 2.9 38.2 1.0
HA C:LYS60 3.0 53.1 1.0
HG21 C:ILE45 3.1 42.2 1.0
OD2 C:ASP86 3.2 48.5 1.0
N C:VAL61 3.2 40.6 1.0
HB3 C:ASP86 3.3 48.2 1.0
HB C:VAL61 3.6 51.2 1.0
CG2 C:VAL61 3.6 40.0 1.0
HA C:VAL83 3.7 45.5 1.0
HG22 C:VAL83 3.8 51.5 1.0
CA C:LYS60 3.8 44.2 1.0
HB3 C:LYS60 3.8 57.0 1.0
CG1 C:VAL83 3.9 39.2 1.0
HG11 C:VAL16 3.9 45.6 1.0
CG C:ASP86 3.9 44.9 1.0
HG21 C:VAL61 3.9 48.0 1.0
CB C:VAL61 4.0 42.7 1.0
HG21 C:VAL16 4.0 46.0 1.0
C C:LYS60 4.0 44.7 1.0
CB C:ASP86 4.0 40.2 1.0
CG2 C:ILE45 4.0 35.2 1.0
HG13 C:VAL16 4.0 45.6 1.0
HG22 C:VAL16 4.1 46.0 1.0
CA C:VAL61 4.2 46.0 1.0
HG22 C:ILE45 4.3 42.2 1.0
CB C:LYS60 4.3 47.5 1.0
HG12 C:VAL83 4.3 47.0 1.0
HG11 C:VAL83 4.3 47.0 1.0
HG22 C:VAL61 4.3 48.0 1.0
HB2 C:ASP86 4.4 48.2 1.0
HG23 C:ILE45 4.4 42.2 1.0
CG1 C:VAL16 4.4 38.0 1.0
HG2 C:LYS60 4.5 59.2 1.0
CG2 C:VAL16 4.5 38.3 1.0
CA C:VAL83 4.5 37.9 1.0
CB C:VAL83 4.5 40.5 1.0
CG2 C:VAL83 4.5 42.9 1.0
HG13 C:ILE45 4.6 42.9 1.0
O C:VAL83 4.6 38.4 1.0
H C:SER62 4.6 54.0 1.0
O C:PRO59 4.7 46.0 1.0
N1A C:COA508 4.7 39.2 1.0
HA C:VAL61 4.7 55.3 1.0
H62A C:COA508 4.8 46.6 1.0
SG C:CYS87 4.8 41.6 1.0
H C:CYS87 4.8 44.4 1.0
OD1 C:ASP86 4.9 50.2 1.0
HG21 C:VAL83 4.9 51.5 1.0
CG C:LYS60 4.9 49.4 1.0
H2A C:COA508 4.9 49.4 1.0
N C:LYS60 5.0 42.9 1.0
HD12 C:ILE45 5.0 50.3 1.0

Chlorine binding site 6 out of 6 in 4xym

Go back to Chlorine Binding Sites List in 4xym
Chlorine binding site 6 out of 6 in the Ca. Korarchaeum Cryptofilum Dinucleotide Forming Acetyl-Coenzyme A Synthetase 1 in Complex with Coenzyme A, Ca-Ampcp and Hgcl+


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Ca. Korarchaeum Cryptofilum Dinucleotide Forming Acetyl-Coenzyme A Synthetase 1 in Complex with Coenzyme A, Ca-Ampcp and Hgcl+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl506

b:19.4
occ:0.39
HG C:HG507 2.4 44.3 0.4
HG23 C:VAL414 2.7 34.5 1.0
HD3 C:PRO437 2.9 26.9 1.0
H C:TYR381 2.9 34.4 1.0
HB3 C:LEU380 3.0 35.5 1.0
HB3 C:PRO437 3.0 26.1 1.0
HD22 C:LEU380 3.3 31.1 1.0
O C:GLY412 3.4 30.0 1.0
C C:GLY412 3.5 30.3 1.0
HA3 C:GLY412 3.5 29.7 1.0
HB1 C:ALA310 3.6 41.1 1.0
CG2 C:VAL414 3.6 28.8 1.0
HA C:LEU380 3.6 32.8 1.0
HA C:PRO437 3.6 35.3 1.0
N C:TYR381 3.6 28.6 1.0
CD C:PRO437 3.6 22.4 1.0
HG21 C:VAL414 3.7 34.5 1.0
O C:TYR381 3.7 24.9 1.0
CB C:PRO437 3.7 21.8 1.0
H C:VAL414 3.7 29.2 1.0
HA C:MET413 3.7 35.8 1.0
HG3 C:PRO437 3.8 30.6 1.0
CB C:LEU380 3.8 29.6 1.0
N C:PRO437 3.8 24.8 1.0
N C:MET413 3.9 28.7 1.0
CA C:PRO437 4.0 29.4 1.0
CG C:PRO437 4.0 25.5 1.0
CA C:GLY412 4.0 24.7 1.0
N C:VAL414 4.0 24.3 1.0
HD23 C:LEU380 4.0 31.1 1.0
CD2 C:LEU380 4.1 25.9 1.0
CA C:LEU380 4.1 27.3 1.0
HG C:CYS382 4.1 42.9 1.0
HB2 C:ALA310 4.1 41.1 1.0
CA C:MET413 4.1 29.8 1.0
HG22 C:VAL414 4.1 34.5 1.0
C C:TYR381 4.1 26.4 1.0
HB C:VAL414 4.2 36.7 1.0
C C:LEU380 4.2 31.5 1.0
CB C:ALA310 4.3 34.2 1.0
C C:MET413 4.3 27.2 1.0
O C:HOH640 4.3 30.8 1.0
H C:MET413 4.3 34.4 1.0
CB C:VAL414 4.4 30.6 1.0
HD2 C:PRO437 4.5 26.9 1.0
C C:THR436 4.5 27.3 1.0
HA C:THR436 4.5 27.8 1.0
CA C:TYR381 4.5 30.8 1.0
CG C:LEU380 4.5 28.9 1.0
HB2 C:LEU380 4.5 35.5 1.0
HB2 C:PRO437 4.6 26.1 1.0
HA2 C:GLY412 4.6 29.7 1.0
HD13 C:LEU380 4.6 34.5 1.0
HB3 C:ALA310 4.7 41.1 1.0
N C:CYS382 4.8 23.2 1.0
CA C:VAL414 4.9 24.3 1.0
HD21 C:LEU380 4.9 31.1 1.0
H C:GLY412 4.9 30.4 1.0
SG C:CYS382 4.9 35.7 1.0
HG2 C:PRO437 4.9 30.6 1.0
HA C:CYS382 5.0 29.6 1.0

Reference:

R.H.Weie, A.Faust, M.Schmidt, P.Schonheit, A.J.Scheidig. Structure of Ndp-Forming Acetyl-Coa Synthetase ACD1 Reveals A Large Rearrangement For Phosphoryl Transfer. Proc.Natl.Acad.Sci.Usa V. 113 E519 2016.
ISSN: ESSN 1091-6490
PubMed: 26787904
DOI: 10.1073/PNAS.1518614113
Page generated: Sat Dec 12 11:21:53 2020

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