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Chlorine in PDB 2j5r: 2.25 A Resolution Structure of the Wild Type Malate Dehydrogenase From Haloarcula Marismortui After Second Radiation Burn (Radiation Damage Series)

Enzymatic activity of 2.25 A Resolution Structure of the Wild Type Malate Dehydrogenase From Haloarcula Marismortui After Second Radiation Burn (Radiation Damage Series)

All present enzymatic activity of 2.25 A Resolution Structure of the Wild Type Malate Dehydrogenase From Haloarcula Marismortui After Second Radiation Burn (Radiation Damage Series):
1.1.1.37;

Protein crystallography data

The structure of 2.25 A Resolution Structure of the Wild Type Malate Dehydrogenase From Haloarcula Marismortui After Second Radiation Burn (Radiation Damage Series), PDB code: 2j5r was solved by E.Fioravanti, F.M.D.Vellieux, P.Amara, D.Madern, M.Weik, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.25
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 127.377, 114.574, 124.529, 90.00, 93.34, 90.00
R / Rfree (%) 22 / 27.1

Chlorine Binding Sites:

The binding sites of Chlorine atom in the 2.25 A Resolution Structure of the Wild Type Malate Dehydrogenase From Haloarcula Marismortui After Second Radiation Burn (Radiation Damage Series) (pdb code 2j5r). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the 2.25 A Resolution Structure of the Wild Type Malate Dehydrogenase From Haloarcula Marismortui After Second Radiation Burn (Radiation Damage Series), PDB code: 2j5r:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 2j5r

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Chlorine binding site 1 out of 8 in the 2.25 A Resolution Structure of the Wild Type Malate Dehydrogenase From Haloarcula Marismortui After Second Radiation Burn (Radiation Damage Series)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of 2.25 A Resolution Structure of the Wild Type Malate Dehydrogenase From Haloarcula Marismortui After Second Radiation Burn (Radiation Damage Series) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1331

b:17.8
occ:1.00
 NZ A:LYS205 2.9 27.6 1.0
N A:ASP306 3.1 22.9 1.0
N D:ASP211 3.2 15.4 1.0
O D:HOH2176 3.3 44.8 1.0
CA D:THR210B 3.6 13.0 1.0
CB A:ASP306 3.6 27.8 1.0
CB D:THR210B 3.7 14.4 1.0
CE A:LYS205 3.9 22.8 1.0
CA A:ASP306 3.9 24.6 1.0
C D:THR210B 3.9 13.1 1.0
CA A:TRP305 4.0 23.7 1.0
C A:TRP305 4.0 25.0 1.0
CA D:ASP211 4.2 19.2 1.0
O A:ASP306 4.3 24.9 1.0
CG2 D:THR210B 4.3 8.3 1.0
O D:ASP211 4.4 18.6 1.0
CB D:ASP211 4.4 21.8 1.0
CB A:TRP305 4.4 22.4 1.0
C D:ASP211 4.5 20.7 1.0
C A:ASP306 4.5 25.4 1.0
O D:GLY210A 4.9 12.3 1.0
OD2 D:ASP211 4.9 21.1 1.0
N D:THR210B 4.9 14.8 1.0
OG1 D:THR210B 4.9 13.5 1.0
CG D:ASP211 4.9 25.2 1.0

Chlorine binding site 2 out of 8 in 2j5r

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Chlorine binding site 2 out of 8 in the 2.25 A Resolution Structure of the Wild Type Malate Dehydrogenase From Haloarcula Marismortui After Second Radiation Burn (Radiation Damage Series)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of 2.25 A Resolution Structure of the Wild Type Malate Dehydrogenase From Haloarcula Marismortui After Second Radiation Burn (Radiation Damage Series) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1332

b:26.8
occ:1.00
 O A:HOH2072 2.9 36.1 1.0
NZ D:LYS205 3.0 29.0 1.0
N A:ASP211 3.1 22.6 1.0
N D:ASP306 3.3 24.7 1.0
CA A:THR210B 3.4 22.2 1.0
O A:HOH2185 3.4 37.6 1.0
CB A:THR210B 3.5 24.3 1.0
CE D:LYS205 3.7 26.4 1.0
C A:THR210B 3.7 22.2 1.0
CB D:ASP306 3.8 26.3 1.0
CA D:ASP306 4.1 25.4 1.0
CG2 A:THR210B 4.1 21.0 1.0
O A:HOH2073 4.2 19.0 1.0
CA A:ASP211 4.2 24.2 1.0
CA D:TRP305 4.2 21.7 1.0
O D:ASP306 4.3 29.1 1.0
C D:TRP305 4.3 24.7 1.0
CB A:ASP211 4.4 25.1 1.0
C A:ASP211 4.5 23.2 1.0
C D:ASP306 4.6 27.0 1.0
O A:ASP211 4.7 23.0 1.0
OD2 A:ASP211 4.7 23.5 1.0
CB D:TRP305 4.7 20.1 1.0
N A:THR210B 4.7 19.7 1.0
OG1 A:THR210B 4.7 21.2 1.0
O A:GLY210A 4.8 21.5 1.0
CG A:ASP211 4.8 26.7 1.0
O A:THR210B 4.9 23.7 1.0

Chlorine binding site 3 out of 8 in 2j5r

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Chlorine binding site 3 out of 8 in the 2.25 A Resolution Structure of the Wild Type Malate Dehydrogenase From Haloarcula Marismortui After Second Radiation Burn (Radiation Damage Series)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of 2.25 A Resolution Structure of the Wild Type Malate Dehydrogenase From Haloarcula Marismortui After Second Radiation Burn (Radiation Damage Series) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1333

b:43.3
occ:1.00
 O B:HOH2036 2.5 37.9 1.0
ND1 A:HIS256 2.7 22.6 1.0
OD2 B:ASP73 2.8 31.4 1.0
NH2 A:ARG166 3.0 17.6 1.0
CG A:HIS256 3.3 21.0 1.0
CG B:ASP73 3.4 28.7 1.0
OD1 B:ASP73 3.4 28.7 1.0
CE1 A:HIS256 3.5 20.2 1.0
CB A:HIS256 3.6 15.0 1.0
NH2 A:ARG252 3.6 24.8 1.0
CZ A:ARG252 3.6 21.2 1.0
O B:HOH2033 3.6 22.1 1.0
CB B:TYR72 3.8 11.1 1.0
NH1 A:ARG252 4.0 19.9 1.0
NE A:ARG252 4.0 15.5 1.0
CZ A:ARG166 4.1 16.1 1.0
CD2 A:HIS256 4.2 22.4 1.0
NE2 A:HIS256 4.3 27.3 1.0
NE A:ARG166 4.3 9.5 1.0
CG A:ARG252 4.4 16.1 1.0
O A:HOH2214 4.4 43.7 1.0
O A:ARG252 4.6 11.8 1.0
CG B:TYR72 4.6 14.6 1.0
C B:TYR72 4.6 12.5 1.0
CB B:ASP73 4.7 20.4 1.0
CA A:HIS256 4.7 15.7 1.0
CD A:ARG252 4.8 15.5 1.0
O B:TYR72 4.8 15.3 1.0
N B:ASP73 4.8 15.2 1.0
CA B:TYR72 4.9 13.7 1.0

Chlorine binding site 4 out of 8 in 2j5r

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Chlorine binding site 4 out of 8 in the 2.25 A Resolution Structure of the Wild Type Malate Dehydrogenase From Haloarcula Marismortui After Second Radiation Burn (Radiation Damage Series)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of 2.25 A Resolution Structure of the Wild Type Malate Dehydrogenase From Haloarcula Marismortui After Second Radiation Burn (Radiation Damage Series) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1331

b:22.4
occ:1.00
 N B:ASP306 3.1 21.9 1.0
N C:ASP211 3.2 19.9 1.0
NZ B:LYS205 3.2 33.4 1.0
O C:HOH2178 3.5 22.3 1.0
CA C:THR210B 3.6 16.4 1.0
CB C:THR210B 3.6 20.3 1.0
CE B:LYS205 3.6 27.9 1.0
O C:HOH2179 3.7 34.2 1.0
CB B:ASP306 3.7 22.4 1.0
C C:THR210B 3.9 19.0 1.0
CA B:ASP306 3.9 20.8 1.0
CA B:TRP305 4.0 18.4 1.0
O B:ASP306 4.0 22.1 1.0
C B:TRP305 4.0 21.1 1.0
CA C:ASP211 4.2 20.2 1.0
CG2 C:THR210B 4.2 12.9 1.0
CB B:TRP305 4.3 13.7 1.0
C B:ASP306 4.4 23.1 1.0
CB C:ASP211 4.4 19.8 1.0
O C:ASP211 4.5 19.6 1.0
C C:ASP211 4.5 21.8 1.0
OD2 C:ASP211 4.8 25.0 1.0
CG C:ASP211 4.8 21.6 1.0
O C:GLY210A 4.8 12.4 1.0
OG1 C:THR210B 4.8 19.6 1.0
N C:THR210B 4.9 14.9 1.0
CG B:TRP305 4.9 19.4 1.0

Chlorine binding site 5 out of 8 in 2j5r

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Chlorine binding site 5 out of 8 in the 2.25 A Resolution Structure of the Wild Type Malate Dehydrogenase From Haloarcula Marismortui After Second Radiation Burn (Radiation Damage Series)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of 2.25 A Resolution Structure of the Wild Type Malate Dehydrogenase From Haloarcula Marismortui After Second Radiation Burn (Radiation Damage Series) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1332

b:78.1
occ:1.00
 NH2 B:ARG166 2.7 14.6 1.0
OD2 A:ASP73 2.8 23.9 1.0
O A:HOH2047 2.8 31.6 1.0
OD1 A:ASP73 3.2 24.9 1.0
CB A:TYR72 3.3 12.7 1.0
CG A:ASP73 3.3 25.7 1.0
ND1 B:HIS256 3.4 13.7 1.0
O A:HOH2043 3.4 6.3 1.0
CG B:HIS256 3.5 16.2 1.0
CB B:HIS256 3.7 14.0 1.0
CZ B:ARG252 3.7 15.2 1.0
NH2 B:ARG252 3.8 20.5 1.0
NE B:ARG252 3.8 15.5 1.0
CZ B:ARG166 3.9 13.2 1.0
CE1 B:HIS256 4.0 16.9 1.0
CG B:ARG252 4.0 12.7 1.0
CD2 B:HIS256 4.1 17.9 1.0
CG A:TYR72 4.1 12.1 1.0
NH1 B:ARG252 4.2 17.9 1.0
C A:TYR72 4.3 18.5 1.0
CA A:TYR72 4.3 15.3 1.0
NE2 B:HIS256 4.3 19.4 1.0
NE B:ARG166 4.3 14.0 1.0
CD B:ARG252 4.5 12.3 1.0
O A:TYR72 4.5 20.4 1.0
N A:ASP73 4.7 20.0 1.0
CB A:ASP73 4.7 21.7 1.0
N A:TYR72 4.8 15.6 1.0
O B:ARG252 4.8 16.1 1.0
CD2 A:TYR72 4.8 8.6 1.0
CD1 A:TYR72 4.8 11.8 1.0
CA B:HIS256 4.8 14.0 1.0
NH1 B:ARG166 5.0 14.8 1.0

Chlorine binding site 6 out of 8 in 2j5r

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Chlorine binding site 6 out of 8 in the 2.25 A Resolution Structure of the Wild Type Malate Dehydrogenase From Haloarcula Marismortui After Second Radiation Burn (Radiation Damage Series)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of 2.25 A Resolution Structure of the Wild Type Malate Dehydrogenase From Haloarcula Marismortui After Second Radiation Burn (Radiation Damage Series) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl1331

b:13.8
occ:1.00
 NZ C:LYS205 3.1 19.8 1.0
N C:ASP306 3.2 20.5 1.0
N B:ASP211 3.4 16.6 1.0
CA B:THR210B 3.6 14.5 1.0
CB B:THR210B 3.6 15.7 1.0
CE C:LYS205 3.7 23.0 1.0
CB C:ASP306 3.7 29.8 1.0
CA C:TRP305 4.0 20.4 1.0
CA C:ASP306 4.0 22.0 1.0
C B:THR210B 4.0 13.5 1.0
C C:TRP305 4.1 23.8 1.0
CG2 B:THR210B 4.1 11.8 1.0
O C:ASP306 4.2 21.1 1.0
CB C:TRP305 4.4 19.1 1.0
O B:ASP211 4.4 21.9 1.0
CA B:ASP211 4.4 20.2 1.0
O B:HOH2150 4.5 48.4 1.0
C C:ASP306 4.5 21.4 1.0
C B:ASP211 4.6 20.0 1.0
CB B:ASP211 4.6 23.0 1.0
O B:GLY210A 4.8 19.9 1.0
OD2 B:ASP211 4.8 30.4 1.0
OG1 B:THR210B 4.9 16.4 1.0
N B:THR210B 4.9 15.1 1.0
CG C:TRP305 5.0 17.8 1.0
CG B:ASP211 5.0 27.4 1.0

Chlorine binding site 7 out of 8 in 2j5r

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Chlorine binding site 7 out of 8 in the 2.25 A Resolution Structure of the Wild Type Malate Dehydrogenase From Haloarcula Marismortui After Second Radiation Burn (Radiation Damage Series)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of 2.25 A Resolution Structure of the Wild Type Malate Dehydrogenase From Haloarcula Marismortui After Second Radiation Burn (Radiation Damage Series) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl1332

b:36.1
occ:1.00
 O D:HOH2056 2.5 25.5 1.0
OD2 D:ASP73 2.7 28.5 1.0
NH2 C:ARG166 3.0 6.0 1.0
ND1 C:HIS256 3.2 15.3 1.0
CG C:HIS256 3.3 18.8 1.0
CG D:ASP73 3.4 24.8 1.0
OD1 D:ASP73 3.5 25.4 1.0
NH2 C:ARG252 3.5 20.3 1.0
CB C:HIS256 3.5 13.7 1.0
CZ C:ARG252 3.7 17.6 1.0
CE1 C:HIS256 3.7 15.6 1.0
CB D:TYR72 3.8 15.2 1.0
O D:HOH2051 3.9 17.4 1.0
CD2 C:HIS256 3.9 18.9 1.0
NE C:ARG252 3.9 16.2 1.0
CZ C:ARG166 4.1 12.8 1.0
NE2 C:HIS256 4.1 18.7 1.0
NH1 C:ARG252 4.3 23.8 1.0
CA C:HIS256 4.5 13.0 1.0
CG C:ARG252 4.5 11.1 1.0
O D:HOH2053 4.5 35.2 1.0
NE C:ARG166 4.5 12.5 1.0
O D:HOH2030 4.6 18.6 1.0
O C:ARG252 4.6 6.6 1.0
CG D:TYR72 4.6 16.0 1.0
C D:TYR72 4.6 16.5 1.0
O D:TYR72 4.7 18.3 1.0
CD C:ARG252 4.8 17.7 1.0
CA D:TYR72 4.8 16.6 1.0
O C:HOH2205 4.9 31.1 1.0
CB D:ASP73 4.9 17.4 1.0

Chlorine binding site 8 out of 8 in 2j5r

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Chlorine binding site 8 out of 8 in the 2.25 A Resolution Structure of the Wild Type Malate Dehydrogenase From Haloarcula Marismortui After Second Radiation Burn (Radiation Damage Series)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of 2.25 A Resolution Structure of the Wild Type Malate Dehydrogenase From Haloarcula Marismortui After Second Radiation Burn (Radiation Damage Series) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl1331

b:52.2
occ:1.00
 OD2 C:ASP73 2.7 31.5 1.0
NH2 D:ARG166 2.8 20.2 1.0
ND1 D:HIS256 3.1 12.4 1.0
O C:HOH2049 3.1 31.1 1.0
CG D:HIS256 3.1 11.2 1.0
CB D:HIS256 3.2 12.7 1.0
O C:HOH2046 3.6 20.2 1.0
CG C:ASP73 3.7 30.6 1.0
CZ D:ARG252 3.7 23.3 1.0
CB C:TYR72 3.8 20.1 1.0
CE1 D:HIS256 3.9 11.5 1.0
NE D:ARG252 3.9 17.5 1.0
CD2 D:HIS256 3.9 12.3 1.0
CZ D:ARG166 3.9 21.4 1.0
NH2 D:ARG252 3.9 28.2 1.0
CG D:ARG252 3.9 16.7 1.0
OD1 C:ASP73 3.9 32.5 1.0
NH1 D:ARG252 4.0 27.2 1.0
NE D:ARG166 4.2 21.0 1.0
O D:ARG252 4.2 14.5 1.0
CA D:HIS256 4.2 15.9 1.0
NE2 D:HIS256 4.3 15.3 1.0
CD D:ARG252 4.4 17.6 1.0
CG C:TYR72 4.5 19.0 1.0
C D:ARG252 4.7 15.3 1.0
N D:HIS256 4.8 15.8 1.0
O D:HOH2203 4.8 50.5 1.0
O D:HOH2095 4.9 42.8 1.0
CA C:TYR72 4.9 21.9 1.0
C C:TYR72 4.9 22.8 1.0

Reference:

E.Fioravanti, F.M.D.Vellieux, P.Amara, D.Madern, M.Weik. Specific Radiation Damage to Acidic Residues and Its Relation to Their Chemical and Structural Environment. J.Synchrotron Radiat. V. 14 84 2007.
ISSN: ISSN 0909-0495
PubMed: 17211074
DOI: 10.1107/S0909049506038623
Page generated: Thu Jul 10 23:01:27 2025

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