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Chlorine in PDB 2dfd: Crystal Structure of Human Malate Dehydrogenase Type 2

Enzymatic activity of Crystal Structure of Human Malate Dehydrogenase Type 2

All present enzymatic activity of Crystal Structure of Human Malate Dehydrogenase Type 2:
1.1.1.37;

Protein crystallography data

The structure of Crystal Structure of Human Malate Dehydrogenase Type 2, PDB code: 2dfd was solved by E.Ugochukwu, N.Shafqat, A.Rojkova, M.Sundstrom, C.Arrowsmith, J.Weigelt, A.Edwards, F.Von Delft, U.Oppermann, Structural Genomics Consortium(Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 6.01 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.943, 152.526, 154.827, 90.00, 90.00, 90.00
R / Rfree (%) 15.6 / 19.4

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Human Malate Dehydrogenase Type 2 (pdb code 2dfd). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 7 binding sites of Chlorine where determined in the Crystal Structure of Human Malate Dehydrogenase Type 2, PDB code: 2dfd:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in 2dfd

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Chlorine binding site 1 out of 7 in the Crystal Structure of Human Malate Dehydrogenase Type 2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Human Malate Dehydrogenase Type 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl3203

b:36.3
occ:1.00
 NH1 A:ARG92 3.1 37.7 1.0
O A:HOH3343 3.1 33.5 1.0
O A:HOH3398 3.2 41.5 1.0
N A:ARG92 3.2 32.4 1.0
CG A:ARG92 3.5 33.0 1.0
CB A:ARG92 3.7 33.2 1.0
CD A:ARG92 3.9 35.1 1.0
CA A:ARG92 4.0 32.9 1.0
CB A:ALA183 4.1 34.9 1.0
CA A:THR91 4.1 32.2 1.0
C A:THR91 4.1 31.9 1.0
CZ A:ARG92 4.2 37.3 1.0
CB A:THR91 4.2 33.3 1.0
NH1 A:ARG86 4.4 31.7 1.0
NE A:ARG92 4.5 35.7 1.0
O A:HOH3351 4.5 34.3 1.0
CA A:ALA183 4.6 35.8 1.0
N A:GLY184 4.6 35.1 1.0
CZ A:ARG86 4.7 32.4 1.0
O A:HOH3393 4.8 43.4 1.0
N A:ASP93 4.9 33.5 1.0
NH2 A:ARG86 5.0 33.4 1.0
C A:ALA183 5.0 35.8 1.0

Chlorine binding site 2 out of 7 in 2dfd

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Chlorine binding site 2 out of 7 in the Crystal Structure of Human Malate Dehydrogenase Type 2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Human Malate Dehydrogenase Type 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl3205

b:86.3
occ:1.00
 ND2 A:ASN146 3.1 34.2 1.0
O A:HOH3399 3.6 52.5 1.0
O A:HOH3363 3.7 30.1 1.0
O A:PRO145 3.9 30.6 1.0
O A:LYS261 3.9 29.7 1.0
CB A:PRO145 3.9 30.1 1.0
C A:PRO145 4.0 30.1 1.0
CG A:PRO145 4.2 31.9 1.0
CD1 A:ILE281 4.3 30.7 1.0
CG A:ASN146 4.3 33.7 1.0
N A:ASN146 4.3 29.7 1.0
CB A:LYS261 4.6 30.9 1.0
CA A:ASN146 4.6 30.1 1.0
CA A:PRO145 4.6 30.4 1.0
O A:HOH3465 4.7 52.0 1.0
C A:LYS261 4.7 31.1 1.0
CG A:LYS261 4.8 31.5 1.0

Chlorine binding site 3 out of 7 in 2dfd

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Chlorine binding site 3 out of 7 in the Crystal Structure of Human Malate Dehydrogenase Type 2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Human Malate Dehydrogenase Type 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl3206

b:76.5
occ:1.00
 O B:HOH3533 2.6 56.8 1.0
O B:VAL198 3.1 36.2 1.0
N B:PHE200 3.5 35.6 1.0
O B:PHE200 4.1 34.4 1.0
O B:HOH3520 4.1 54.6 1.0
CA B:ASP199 4.1 36.5 1.0
CG2 B:ILE191 4.2 32.1 1.0
C B:VAL198 4.2 35.6 1.0
CB B:PHE200 4.3 35.3 1.0
C B:ASP199 4.3 36.3 1.0
CD2 B:PHE200 4.3 35.6 1.0
CA B:PHE200 4.4 35.4 1.0
CD2 B:LEU205 4.6 31.9 1.0
N B:ASP199 4.6 35.8 1.0
C B:PHE200 4.7 34.8 1.0
OD1 B:ASP199 4.8 41.6 1.0
CG B:PHE200 4.8 34.8 1.0
CB B:ILE191 4.8 31.9 1.0
O B:ILE191 4.9 29.6 1.0
O B:HOH3524 4.9 44.4 1.0
C B:ILE191 5.0 30.8 1.0

Chlorine binding site 4 out of 7 in 2dfd

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Chlorine binding site 4 out of 7 in the Crystal Structure of Human Malate Dehydrogenase Type 2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Human Malate Dehydrogenase Type 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl3201

b:28.7
occ:1.00
 O C:HOH3553 3.1 29.9 1.0
NH1 C:ARG92 3.2 32.3 1.0
N C:ARG92 3.2 30.8 1.0
O C:HOH3740 3.3 45.0 1.0
O C:HOH3623 3.5 37.5 1.0
CG C:ARG92 3.6 30.3 1.0
CB C:ARG92 3.8 31.1 1.0
CB C:ALA183 4.0 33.1 1.0
CD C:ARG92 4.0 29.5 1.0
CA C:THR91 4.1 31.9 1.0
CA C:ARG92 4.1 31.1 1.0
CB C:THR91 4.1 32.6 1.0
C C:THR91 4.1 32.3 1.0
CZ C:ARG92 4.3 33.8 1.0
NH1 C:ARG86 4.3 31.8 1.0
CA C:ALA183 4.3 33.7 1.0
O C:HOH3550 4.4 23.6 1.0
N C:GLY184 4.4 33.9 1.0
NE C:ARG92 4.6 32.3 1.0
O C:HOH3584 4.6 32.2 1.0
CZ C:ARG86 4.6 29.1 1.0
C C:ALA183 4.7 34.0 1.0
CG2 C:THR91 4.8 32.2 1.0
NH2 C:ARG86 4.9 32.1 1.0
N C:ASP93 4.9 31.1 1.0

Chlorine binding site 5 out of 7 in 2dfd

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Chlorine binding site 5 out of 7 in the Crystal Structure of Human Malate Dehydrogenase Type 2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Human Malate Dehydrogenase Type 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl3204

b:69.4
occ:1.00
 CG C:GLN263 3.6 41.2 1.0
N C:GLN263 3.7 34.6 1.0
C C:SER262 3.7 33.7 1.0
NZ C:LYS261 3.8 34.1 1.0
CB C:GLN263 3.9 36.9 1.0
CA C:SER262 4.0 32.8 1.0
N C:SER262 4.1 31.2 1.0
CG C:LYS261 4.1 32.7 1.0
O C:SER262 4.2 33.8 1.0
CE C:LYS261 4.3 38.1 1.0
O C:HOH3731 4.3 43.5 1.0
CD C:GLN263 4.4 42.4 1.0
C C:LYS261 4.4 32.5 1.0
CA C:GLN263 4.4 37.2 1.0
O C:LYS261 4.5 31.7 1.0
OE1 C:GLN263 4.7 51.7 1.0
CD C:LYS261 4.8 35.4 1.0
O C:HOH3657 4.9 38.7 1.0

Chlorine binding site 6 out of 7 in 2dfd

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Chlorine binding site 6 out of 7 in the Crystal Structure of Human Malate Dehydrogenase Type 2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of Human Malate Dehydrogenase Type 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl3202

b:38.3
occ:1.00
 O D:HOH3318 2.9 35.7 1.0
NH1 D:ARG92 3.2 38.0 1.0
N D:ARG92 3.3 33.5 1.0
O D:HOH3403 3.4 48.8 1.0
CG D:ARG92 3.7 32.9 1.0
CB D:ARG92 3.8 32.0 1.0
CD D:ARG92 3.9 34.8 1.0
CA D:THR91 4.0 33.6 1.0
CB D:ALA183 4.1 36.8 1.0
CB D:THR91 4.1 33.5 1.0
C D:THR91 4.1 32.6 1.0
CA D:ARG92 4.1 33.0 1.0
CZ D:ARG92 4.2 36.1 1.0
NH2 D:ARG86 4.3 32.4 1.0
CA D:ALA183 4.5 35.9 1.0
NE D:ARG92 4.5 37.1 1.0
O D:HOH3402 4.6 33.2 1.0
N D:GLY184 4.6 36.5 1.0
CZ D:ARG86 4.7 33.3 1.0
C D:ALA183 4.9 36.0 1.0
CG2 D:THR91 4.9 34.2 1.0
N D:ASP93 5.0 34.3 1.0

Chlorine binding site 7 out of 7 in 2dfd

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Chlorine binding site 7 out of 7 in the Crystal Structure of Human Malate Dehydrogenase Type 2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of Human Malate Dehydrogenase Type 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl3207

b:77.7
occ:1.00
 O D:HOH3416 2.5 53.9 1.0
O D:VAL198 3.5 35.9 1.0
N D:PHE200 3.7 35.3 1.0
CA D:ASP199 4.0 37.5 1.0
O D:PHE200 4.1 34.6 1.0
CD2 D:LEU205 4.3 33.7 1.0
C D:ASP199 4.4 36.4 1.0
OD1 D:ASP199 4.5 49.0 1.0
C D:VAL198 4.5 36.5 1.0
CD1 D:LEU205 4.7 33.5 1.0
CG2 D:ILE191 4.7 32.5 1.0
CA D:PHE200 4.7 34.5 1.0
N D:ASP199 4.8 36.8 1.0
CB D:PHE200 4.8 34.0 1.0
CD2 D:PHE200 4.8 32.2 1.0
C D:PHE200 4.9 34.3 1.0
O D:HOH3223 5.0 30.5 1.0
CB D:ASP199 5.0 39.0 1.0

Reference:

E.Ugochukwu, N.Shafqat, A.Rojkova, M.Sundstrom, C.Arrowsmith, J.Weigelt, A.Edwards, F.Von Delft, U.Oppermann. Crystal Structure of Human Malate Dehydrogenase Type 2 To Be Published.
Page generated: Thu Jul 10 21:50:37 2025

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