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Chlorine in PDB 3m1u: Crystal Structure of A Putative Gamma-D-Glutamyl-L-Diamino Acid Endopeptidase (DVU_0896) From Desulfovibrio Vulgaris Hildenborough at 1.75 A Resolution

Protein crystallography data

The structure of Crystal Structure of A Putative Gamma-D-Glutamyl-L-Diamino Acid Endopeptidase (DVU_0896) From Desulfovibrio Vulgaris Hildenborough at 1.75 A Resolution, PDB code: 3m1u was solved by Joint Center For Structural Genomics (Jcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.59 / 1.75
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 59.337, 54.465, 122.982, 90.00, 94.06, 90.00
R / Rfree (%) 13.9 / 17.3

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of A Putative Gamma-D-Glutamyl-L-Diamino Acid Endopeptidase (DVU_0896) From Desulfovibrio Vulgaris Hildenborough at 1.75 A Resolution (pdb code 3m1u). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 10 binding sites of Chlorine where determined in the Crystal Structure of A Putative Gamma-D-Glutamyl-L-Diamino Acid Endopeptidase (DVU_0896) From Desulfovibrio Vulgaris Hildenborough at 1.75 A Resolution, PDB code: 3m1u:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 10 in 3m1u

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Chlorine binding site 1 out of 10 in the Crystal Structure of A Putative Gamma-D-Glutamyl-L-Diamino Acid Endopeptidase (DVU_0896) From Desulfovibrio Vulgaris Hildenborough at 1.75 A Resolution


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 A Putative Gamma-D-Glutamyl-L-Diamino Acid Endopeptidase (DVU_0896) From Desulfovibrio Vulgaris Hildenborough at 1.75 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl17

b:29.4
occ:1.00
N A:ASP68 3.2 18.4 1.0
O A:HOH931 3.5 39.1 1.0
CA A:ASP68 3.7 19.1 1.0
CB A:ASP68 3.7 22.7 1.0
N A:ARG69 3.7 17.0 1.0
C A:ASP68 3.8 20.0 1.0
N A:ALA67 3.8 11.8 1.0
C A:GLY66 3.8 16.6 1.0
CA A:GLY66 4.1 17.1 1.0
C A:ALA67 4.3 19.0 1.0
O A:HOH597 4.3 18.2 1.0
O A:GLY66 4.3 13.1 1.0
OD2 A:ASP68 4.5 39.2 1.0
CG A:ASP68 4.5 27.5 1.0
O A:ASP68 4.5 21.6 1.0
CA A:ARG69 4.5 17.0 1.0
CA A:ALA67 4.5 15.8 1.0
CB A:ARG69 4.6 17.9 1.0

Chlorine binding site 2 out of 10 in 3m1u

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Chlorine binding site 2 out of 10 in the Crystal Structure of A Putative Gamma-D-Glutamyl-L-Diamino Acid Endopeptidase (DVU_0896) From Desulfovibrio Vulgaris Hildenborough at 1.75 A Resolution


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 A Putative Gamma-D-Glutamyl-L-Diamino Acid Endopeptidase (DVU_0896) From Desulfovibrio Vulgaris Hildenborough at 1.75 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl18

b:30.6
occ:1.00
O A:HOH470 3.1 13.6 1.0
NH2 A:ARG87 3.1 29.1 1.0
NE1 A:TRP347 3.2 16.4 1.0
NH1 A:ARG87 3.5 31.9 1.0
CA A:PRO349 3.7 14.6 1.0
CB A:PRO349 3.7 15.4 1.0
CZ A:ARG87 3.7 35.8 1.0
CE2 A:TRP347 3.9 10.8 1.0
O A:ALA209 3.9 18.4 1.0
CZ2 A:TRP347 3.9 15.4 1.0
CA A:PHE210 3.9 12.7 1.0
CB A:PHE210 4.0 15.1 1.0
CD1 A:TRP347 4.4 15.7 1.0
N A:PRO349 4.5 14.0 1.0
C A:ALA209 4.6 17.2 1.0
N A:PHE210 4.7 13.6 1.0
N A:ARG350 4.8 15.7 1.0
C A:PRO349 4.8 15.3 1.0
O A:PHE210 4.8 14.3 1.0
CG A:PRO349 4.9 14.1 1.0
O A:HOH832 4.9 43.5 1.0
C A:PHE210 4.9 16.5 1.0
NE A:ARG87 4.9 28.2 1.0
O A:LEU348 4.9 15.1 1.0

Chlorine binding site 3 out of 10 in 3m1u

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Chlorine binding site 3 out of 10 in the Crystal Structure of A Putative Gamma-D-Glutamyl-L-Diamino Acid Endopeptidase (DVU_0896) From Desulfovibrio Vulgaris Hildenborough at 1.75 A Resolution


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 A Putative Gamma-D-Glutamyl-L-Diamino Acid Endopeptidase (DVU_0896) From Desulfovibrio Vulgaris Hildenborough at 1.75 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl21

b:25.4
occ:1.00
N A:GLY173 3.1 21.6 1.0
O A:HOH584 3.1 22.9 1.0
NE1 A:TRP411 3.3 13.8 1.0
O A:HOH779 3.3 44.4 1.0
CA A:GLY173 3.8 22.1 1.0
CG A:ARG423 3.8 17.5 1.0
CB A:ARG423 4.0 14.9 1.0
C A:ALA172 4.1 23.3 1.0
CE2 A:TRP411 4.1 14.7 1.0
CA A:ALA172 4.2 26.2 1.0
CZ2 A:TRP411 4.3 13.8 1.0
CD1 A:TRP411 4.3 14.2 1.0
CE2 A:PHE178 4.3 14.9 1.0
O A:HOH747 4.5 28.5 1.0
C A:GLY173 4.9 21.8 1.0
CB A:ALA172 4.9 26.7 1.0
CD2 A:PHE178 5.0 13.2 1.0

Chlorine binding site 4 out of 10 in 3m1u

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Chlorine binding site 4 out of 10 in the Crystal Structure of A Putative Gamma-D-Glutamyl-L-Diamino Acid Endopeptidase (DVU_0896) From Desulfovibrio Vulgaris Hildenborough at 1.75 A Resolution


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 A Putative Gamma-D-Glutamyl-L-Diamino Acid Endopeptidase (DVU_0896) From Desulfovibrio Vulgaris Hildenborough at 1.75 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl23

b:23.7
occ:0.50
CL A:CL23 0.0 23.7 0.5
CL A:CL23 2.0 26.1 0.5
N A:ARG414 3.0 17.5 1.0
NH1 A:ARG452 3.1 26.1 1.0
O3 A:GOL8 3.2 35.0 1.0
CG A:ARG414 3.5 27.0 1.0
NH2 A:ARG452 3.6 24.2 1.0
CA A:ILE413 3.6 14.7 1.0
CB A:ARG414 3.7 24.0 1.0
O A:GLY412 3.7 14.6 1.0
C A:ILE413 3.8 16.5 1.0
CZ A:ARG452 3.8 28.3 1.0
CD A:ARG414 3.9 37.5 1.0
CD2 A:LEU449 3.9 20.8 1.0
CA A:ARG414 4.0 20.1 1.0
O A:HOH668 4.2 35.8 1.0
NE A:ARG414 4.3 39.0 1.0
C3 A:GOL8 4.4 35.5 1.0
CG2 A:ILE413 4.5 14.6 1.0
C A:GLY412 4.5 15.6 1.0
N A:ILE413 4.6 13.8 1.0
O A:HOH799 4.6 30.6 1.0
CB A:ILE413 4.6 14.9 1.0
CD1 A:ILE413 4.7 19.1 1.0
O A:ILE413 5.0 14.5 1.0
CG A:LEU449 5.0 15.8 1.0

Chlorine binding site 5 out of 10 in 3m1u

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Chlorine binding site 5 out of 10 in the Crystal Structure of A Putative Gamma-D-Glutamyl-L-Diamino Acid Endopeptidase (DVU_0896) From Desulfovibrio Vulgaris Hildenborough at 1.75 A Resolution


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 A Putative Gamma-D-Glutamyl-L-Diamino Acid Endopeptidase (DVU_0896) From Desulfovibrio Vulgaris Hildenborough at 1.75 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl23

b:26.1
occ:0.50
CL A:CL23 0.0 26.1 0.5
CL A:CL23 2.0 23.7 0.5
O A:HOH668 3.0 35.8 1.0
O A:HOH531 3.4 17.0 1.0
NH1 A:ARG452 3.6 26.1 1.0
CG2 A:ILE413 3.8 14.6 1.0
CD2 A:LEU449 3.9 20.8 1.0
N A:ARG414 3.9 17.5 1.0
CD1 A:ILE413 4.0 19.1 1.0
CA A:ILE413 4.1 14.7 1.0
N A:LEU449 4.2 15.8 1.0
CG A:LEU449 4.3 15.8 1.0
C A:GLY448 4.4 18.6 1.0
CB A:ILE413 4.4 14.9 1.0
CA A:GLY448 4.4 17.9 1.0
O A:HOH837 4.4 28.3 1.0
C A:ILE413 4.5 16.5 1.0
CZ A:ARG452 4.6 28.3 1.0
O A:HOH612 4.6 21.5 1.0
NH2 A:ARG452 4.8 24.2 1.0
CG1 A:ILE413 4.8 15.0 1.0
CB A:ARG414 4.8 24.0 1.0
CA A:LEU449 4.8 14.5 1.0
ND2 A:ASN443 4.9 25.1 1.0
O3 A:GOL8 4.9 35.0 1.0
CA A:ARG414 4.9 20.1 1.0
O A:GLY448 5.0 15.8 1.0

Chlorine binding site 6 out of 10 in 3m1u

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Chlorine binding site 6 out of 10 in the Crystal Structure of A Putative Gamma-D-Glutamyl-L-Diamino Acid Endopeptidase (DVU_0896) From Desulfovibrio Vulgaris Hildenborough at 1.75 A Resolution


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 A Putative Gamma-D-Glutamyl-L-Diamino Acid Endopeptidase (DVU_0896) From Desulfovibrio Vulgaris Hildenborough at 1.75 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl16

b:29.0
occ:1.00
O B:HOH817 3.2 31.0 1.0
O B:HOH810 3.2 28.4 1.0
O B:HOH733 3.2 28.2 1.0
O B:HOH485 3.2 14.1 1.0
NE1 B:TRP347 3.2 17.8 1.0
O B:ALA209 3.7 17.6 1.0
CA B:PRO349 3.7 16.6 1.0
CB B:PRO349 3.8 15.8 1.0
CZ2 B:TRP347 3.8 15.7 1.0
CE2 B:TRP347 3.9 14.0 1.0
CA B:PHE210 3.9 13.8 1.0
CB B:PHE210 3.9 15.8 1.0
CD1 B:TRP347 4.4 19.3 1.0
C B:ALA209 4.4 16.1 1.0
O B:HOH700 4.5 38.1 1.0
N B:PRO349 4.5 14.8 1.0
N B:PHE210 4.6 13.5 1.0
N B:ARG350 4.8 15.6 1.0
O B:PHE210 4.8 16.6 1.0
C B:PRO349 4.8 15.7 1.0
C B:PHE210 4.8 16.2 1.0

Chlorine binding site 7 out of 10 in 3m1u

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Chlorine binding site 7 out of 10 in the Crystal Structure of A Putative Gamma-D-Glutamyl-L-Diamino Acid Endopeptidase (DVU_0896) From Desulfovibrio Vulgaris Hildenborough at 1.75 A Resolution


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 A Putative Gamma-D-Glutamyl-L-Diamino Acid Endopeptidase (DVU_0896) From Desulfovibrio Vulgaris Hildenborough at 1.75 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl19

b:26.1
occ:1.00
NZ B:LYS64 3.1 17.1 1.0
N B:GLU401 3.2 16.4 1.0
O B:HOH673 3.4 23.7 1.0
CA B:HIS400 3.7 13.8 1.0
ND1 B:HIS400 3.8 15.7 1.0
CD B:LYS64 4.0 22.2 1.0
C B:HIS400 4.0 15.9 1.0
O B:LEU399 4.0 15.0 1.0
CE B:LYS64 4.1 20.8 1.0
CA B:GLU401 4.2 17.7 1.0
CG B:GLU401 4.3 22.2 1.0
CG B:HIS400 4.3 14.3 1.0
CE1 B:HIS400 4.4 19.3 1.0
CB B:HIS400 4.6 16.2 1.0
N B:HIS400 4.6 13.7 1.0
C B:LEU399 4.7 13.9 1.0
CB B:GLU401 4.9 18.3 1.0

Chlorine binding site 8 out of 10 in 3m1u

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Chlorine binding site 8 out of 10 in the Crystal Structure of A Putative Gamma-D-Glutamyl-L-Diamino Acid Endopeptidase (DVU_0896) From Desulfovibrio Vulgaris Hildenborough at 1.75 A Resolution


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Crystal Structure of A Putative Gamma-D-Glutamyl-L-Diamino Acid Endopeptidase (DVU_0896) From Desulfovibrio Vulgaris Hildenborough at 1.75 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl20

b:27.1
occ:1.00
N B:GLY437 3.0 14.8 1.0
O B:HOH800 3.1 27.2 1.0
N B:LEU449 3.3 17.9 1.0
CA B:GLY448 3.3 20.6 1.0
O B:HOH815 3.4 27.1 1.0
CA B:GLY437 3.6 19.9 1.0
ND2 B:ASN443 3.6 27.0 1.0
N B:PRO436 3.7 15.2 1.0
C B:ARG435 3.8 17.2 1.0
CD B:PRO436 3.8 15.7 1.0
CA B:ARG435 3.8 14.2 1.0
C B:GLY448 3.8 19.7 1.0
CG B:LEU449 3.9 15.3 1.0
C B:GLY437 4.1 21.8 1.0
CG B:PRO436 4.2 18.9 1.0
CD1 B:ILE413 4.2 21.9 1.0
C B:PRO436 4.2 18.3 1.0
O B:ARG435 4.4 17.1 1.0
N B:LEU438 4.4 22.0 1.0
CA B:LEU449 4.4 16.2 1.0
CB B:LEU449 4.4 14.0 1.0
CB B:ARG435 4.4 15.0 1.0
CA B:PRO436 4.5 17.7 1.0
CD2 B:LEU449 4.5 21.0 1.0
N B:GLY448 4.6 19.1 1.0
CG B:ASN443 4.7 26.8 1.0
O B:THR434 4.8 16.3 1.0
O B:GLY437 4.8 22.0 1.0
CD1 B:LEU449 4.9 16.8 1.0
OD1 B:ASN443 4.9 26.9 1.0
CB B:PRO436 4.9 17.7 1.0
N B:ARG435 5.0 15.2 1.0
CG B:ARG435 5.0 16.3 1.0

Chlorine binding site 9 out of 10 in 3m1u

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Chlorine binding site 9 out of 10 in the Crystal Structure of A Putative Gamma-D-Glutamyl-L-Diamino Acid Endopeptidase (DVU_0896) From Desulfovibrio Vulgaris Hildenborough at 1.75 A Resolution


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Crystal Structure of A Putative Gamma-D-Glutamyl-L-Diamino Acid Endopeptidase (DVU_0896) From Desulfovibrio Vulgaris Hildenborough at 1.75 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl22

b:31.1
occ:1.00
N B:GLY173 3.1 21.8 1.0
O B:HOH660 3.2 23.4 1.0
NE1 B:TRP411 3.3 15.3 1.0
CG B:ARG423 3.7 20.6 1.0
CA B:GLY173 3.8 22.7 1.0
CB B:ARG423 3.9 16.4 1.0
CE2 B:TRP411 4.0 15.8 1.0
CZ2 B:TRP411 4.1 15.7 1.0
C B:ALA172 4.1 23.1 1.0
CA B:ALA172 4.3 24.1 1.0
CD1 B:TRP411 4.3 13.2 1.0
CE2 B:PHE178 4.6 19.4 1.0
O B:HOH577 4.7 33.0 1.0
O B:HOH882 4.7 30.4 1.0
CB B:ALA172 4.7 25.6 1.0
CG2 B:VAL425 4.8 12.2 1.0
C B:GLY173 4.8 19.4 1.0
CD B:ARG423 5.0 21.4 1.0

Chlorine binding site 10 out of 10 in 3m1u

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Chlorine binding site 10 out of 10 in the Crystal Structure of A Putative Gamma-D-Glutamyl-L-Diamino Acid Endopeptidase (DVU_0896) From Desulfovibrio Vulgaris Hildenborough at 1.75 A Resolution


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Crystal Structure of A Putative Gamma-D-Glutamyl-L-Diamino Acid Endopeptidase (DVU_0896) From Desulfovibrio Vulgaris Hildenborough at 1.75 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl24

b:29.9
occ:0.50
N B:ASP68 3.1 18.9 1.0
C B:GLY66 3.6 18.6 1.0
N B:ALA67 3.6 17.1 1.0
CB B:ASP68 3.6 23.3 1.0
CA B:ASP68 3.6 21.3 1.0
N B:ARG69 3.7 19.1 1.0
C B:ASP68 3.7 20.2 1.0
CA B:GLY66 3.9 16.6 1.0
O B:GLY66 4.0 20.8 1.0
C B:ALA67 4.2 19.1 1.0
O B:HOH596 4.3 18.1 1.0
CA B:ALA67 4.4 18.6 1.0
CG B:ASP68 4.5 27.8 1.0
O B:ASP68 4.5 24.8 1.0
CA B:ARG69 4.5 20.6 1.0
OD2 B:ASP68 4.6 39.5 1.0
CB B:ARG69 4.7 21.4 1.0

Reference:

Joint Center For Structural Genomics (Jcsg), Joint Center For Structural Genomics (Jcsg). N/A N/A.
Page generated: Fri Jul 11 07:43:23 2025

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