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Chlorine in PDB 2wjp: Crystal Structure of Murd Ligase in Complex with D-Glu Containing Rhodanine Inhibitor

Enzymatic activity of Crystal Structure of Murd Ligase in Complex with D-Glu Containing Rhodanine Inhibitor

All present enzymatic activity of Crystal Structure of Murd Ligase in Complex with D-Glu Containing Rhodanine Inhibitor:
6.3.2.9;

Protein crystallography data

The structure of Crystal Structure of Murd Ligase in Complex with D-Glu Containing Rhodanine Inhibitor, PDB code: 2wjp was solved by T.Tomasic, N.Zidar, R.Sink, A.Kovac, V.Rupnik, S.Turk, C.Contreras-Martel, A.Dessen, D.Blanot, M.Muller-Premru, S.Gobec, A.Zega, L.Peterlin-Masic, D.Kikelj, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.63 / 1.60
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 65.917, 65.917, 136.063, 90.00, 90.00, 90.00
R / Rfree (%) 16.6 / 18.9

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Murd Ligase in Complex with D-Glu Containing Rhodanine Inhibitor (pdb code 2wjp). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Crystal Structure of Murd Ligase in Complex with D-Glu Containing Rhodanine Inhibitor, PDB code: 2wjp:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 2wjp

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Chlorine binding site 1 out of 6 in the Crystal Structure of Murd Ligase in Complex with D-Glu Containing Rhodanine Inhibitor


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 Murd Ligase in Complex with D-Glu Containing Rhodanine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1453

b:44.5
occ:1.00
 O A:HOH2395 3.1 49.7 1.0
ND1 A:HIS309 3.2 29.8 1.0
N A:ASN310 3.6 21.0 1.0
CA A:HIS309 3.8 22.0 1.0
CE1 A:HIS309 3.9 29.6 1.0
CG A:HIS309 4.0 27.3 1.0
C A:HIS309 4.2 18.9 1.0
CB A:HIS309 4.3 20.4 1.0
O A:HOH2398 4.4 18.9 1.0
O A:GLU308 4.4 24.6 1.0
OD1 A:ASN310 4.6 31.1 1.0
CA A:ASN310 4.6 20.3 1.0
N A:HIS309 4.8 19.6 1.0
NE2 A:HIS309 4.9 35.3 1.0
CD2 A:HIS309 5.0 28.6 1.0

Chlorine binding site 2 out of 6 in 2wjp

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Chlorine binding site 2 out of 6 in the Crystal Structure of Murd Ligase in Complex with D-Glu Containing Rhodanine Inhibitor


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 Murd Ligase in Complex with D-Glu Containing Rhodanine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1454

b:51.2
occ:1.00
 O A:HOH2467 3.3 19.8 1.0
O A:ARG395 3.6 19.2 1.0
C A:ARG395 3.8 18.7 1.0
CA A:LEU396 3.9 17.9 1.0
N A:LEU396 4.0 19.1 1.0
CD1 A:LEU396 4.3 28.7 1.0
O A:HOH2219 4.5 36.8 1.0
CB A:ARG395 4.5 16.5 1.0
CB A:LEU396 4.5 18.2 1.0
O A:HOH2473 4.6 28.0 1.0
O A:HOH2216 4.6 21.8 1.0
CA A:ARG395 4.8 18.3 1.0
O A:HOH2471 4.9 19.5 1.0

Chlorine binding site 3 out of 6 in 2wjp

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Chlorine binding site 3 out of 6 in the Crystal Structure of Murd Ligase in Complex with D-Glu Containing Rhodanine Inhibitor


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 Murd Ligase in Complex with D-Glu Containing Rhodanine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1455

b:28.0
occ:1.00
 N A:TYR3 3.0 19.3 1.0
NE2 A:GLN4 3.2 29.7 1.0
NE A:ARG27 3.4 22.8 0.5
NH2 A:ARG27 3.4 15.9 0.5
N A:GLN4 3.8 21.1 1.0
OD1 A:ASP2 3.8 39.9 1.0
CA A:TYR3 3.8 18.9 1.0
CB A:TYR3 3.8 18.7 1.0
CZ A:ARG27 3.9 16.8 0.5
CG A:GLN4 3.9 28.8 1.0
C A:ASP2 4.0 26.5 1.0
CD2 A:TYR3 4.0 19.4 1.0
CG A:ARG27 4.0 25.0 0.5
CD A:GLN4 4.1 31.6 1.0
C A:TYR3 4.1 18.9 1.0
CA A:ASP2 4.1 31.3 1.0
CB A:ARG27 4.2 21.6 0.5
CB A:ARG27 4.3 22.4 0.5
O A:ALA1 4.4 27.9 1.0
CG A:TYR3 4.4 17.9 1.0
CD A:ARG27 4.5 22.8 0.5
O A:ARG27 4.5 24.5 1.0
CD A:ARG27 4.5 26.6 0.5
CA A:GLN4 4.7 23.6 1.0
CG A:ASP2 4.8 41.2 1.0
CG A:ARG27 4.8 19.1 0.5
CB A:GLN4 4.8 23.0 1.0
CG2 A:VAL29 4.9 19.5 1.0

Chlorine binding site 4 out of 6 in 2wjp

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Chlorine binding site 4 out of 6 in the Crystal Structure of Murd Ligase in Complex with D-Glu Containing Rhodanine Inhibitor


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 Murd Ligase in Complex with D-Glu Containing Rhodanine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1456

b:31.2
occ:1.00
 O A:HOH2149 2.6 16.4 1.0
O A:THR165 2.8 12.7 1.0
OG A:SER167 2.9 19.7 0.8
OG A:SER167 2.9 12.3 0.2
N A:SER167 3.4 11.3 1.0
CB A:SER167 3.5 14.2 0.2
CB A:SER167 3.5 17.1 0.8
CG A:GLU96 3.6 10.8 1.0
C A:THR165 3.6 11.4 1.0
CD A:GLU96 3.6 12.2 1.0
OE1 A:GLU96 3.7 13.3 1.0
C A:THR166 3.8 11.8 1.0
CG1 A:VAL92 3.8 14.5 1.0
CA A:THR166 3.9 9.9 1.0
N A:THR166 4.1 10.6 1.0
CB A:GLU96 4.1 10.1 1.0
CA A:SER167 4.1 13.4 0.2
O A:HOH2146 4.1 17.3 1.0
O A:ILE91 4.1 14.3 1.0
CA A:SER167 4.1 13.8 0.8
OE2 A:GLU96 4.1 14.2 1.0
O A:HOH2243 4.2 18.4 1.0
CB A:VAL92 4.2 11.3 1.0
CA A:VAL92 4.3 10.0 1.0
O A:THR166 4.6 13.6 1.0
CA A:THR165 4.7 10.2 1.0

Chlorine binding site 5 out of 6 in 2wjp

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Chlorine binding site 5 out of 6 in the Crystal Structure of Murd Ligase in Complex with D-Glu Containing Rhodanine Inhibitor


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 Murd Ligase in Complex with D-Glu Containing Rhodanine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1457

b:44.7
occ:1.00
 O A:HOH2127 2.4 38.3 1.0
N A:LEU57 3.0 16.4 1.0
CB A:SER56 3.7 18.9 1.0
CA A:SER56 3.7 16.2 1.0
NE2 A:HIS78 3.8 27.4 1.0
C A:SER56 3.9 17.2 1.0
CB A:LEU57 4.0 14.9 1.0
CA A:LEU57 4.0 15.9 1.0
CE1 A:HIS78 4.1 25.1 1.0
CG A:LEU57 4.2 17.7 1.0
O A:LEU57 4.2 21.2 1.0
C A:LEU57 4.6 16.6 1.0
CG2 A:THR36 4.7 18.2 1.0
OG A:SER56 4.9 19.8 1.0

Chlorine binding site 6 out of 6 in 2wjp

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Chlorine binding site 6 out of 6 in the Crystal Structure of Murd Ligase in Complex with D-Glu Containing Rhodanine Inhibitor


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 Murd Ligase in Complex with D-Glu Containing Rhodanine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1505

b:62.6
occ:1.00
 O A:HOH2437 3.2 25.6 1.0
OD1 A:ASN363 4.0 40.6 1.0
O A:HOH2436 4.1 34.2 1.0
CA A:GLY361 4.6 37.6 1.0
O A:HOH2432 4.7 27.1 1.0
O A:ASN360 4.7 35.4 1.0
CG A:ASN363 4.8 32.7 1.0
CB A:ASN363 4.8 25.0 1.0

Reference:

N.Zidar, T.Tomasic, R.Sink, V.Rupnik, A.Kovac, S.Turk, D.Patin, D.Blanot, C.Contreras Martel, A.Dessen, M.Muller Premru, A.Zega, S.Gobec, L.Peterlin Masic, D.Kikelj. Discovery of Novel 5-Benzylidenerhodanine and 5- Benzylidenethiazolidine-2,4-Dione Inhibitors of Murd Ligase. J.Med.Chem. V. 53 6584 2010.
ISSN: ISSN 0022-2623
PubMed: 20804196
DOI: 10.1021/JM100285G
Page generated: Sat Jul 20 12:58:54 2024

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