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Chlorine in PDB 4x04: Crystal Structure of A Trap Periplasmic Solute Binding Protein From Citrobacter Koseri (CKO_04899, Target Efi-510094) with Bound D- Glucuronate

Protein crystallography data

The structure of Crystal Structure of A Trap Periplasmic Solute Binding Protein From Citrobacter Koseri (CKO_04899, Target Efi-510094) with Bound D- Glucuronate, PDB code: 4x04 was solved by U.Yadava, M.W.Vetting, N.F.Al Obaidi, R.Toro, L.L.Morisco, J.Benach, S.R.Wasserman, J.D.Attonito, A.Scott Glenn, S.Chamala, S.Chowdhury, J.Lafleur, J.Love, R.D.Seidel, K.L.Whalen, J.A.Gerlt, S.C.Almo, Enzymefunction Initiative (Efi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.73 / 2.50
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 175.000, 175.000, 125.640, 90.00, 90.00, 90.00
R / Rfree (%) 15.4 / 20.5

Other elements in 4x04:

The structure of Crystal Structure of A Trap Periplasmic Solute Binding Protein From Citrobacter Koseri (CKO_04899, Target Efi-510094) with Bound D- Glucuronate also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of A Trap Periplasmic Solute Binding Protein From Citrobacter Koseri (CKO_04899, Target Efi-510094) with Bound D- Glucuronate (pdb code 4x04). 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 A Trap Periplasmic Solute Binding Protein From Citrobacter Koseri (CKO_04899, Target Efi-510094) with Bound D- Glucuronate, PDB code: 4x04:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 4x04

Go back to Chlorine Binding Sites List in 4x04
Chlorine binding site 1 out of 6 in the Crystal Structure of A Trap Periplasmic Solute Binding Protein From Citrobacter Koseri (CKO_04899, Target Efi-510094) with Bound D- Glucuronate


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 Trap Periplasmic Solute Binding Protein From Citrobacter Koseri (CKO_04899, Target Efi-510094) with Bound D- Glucuronate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:11.1
occ:1.00
 O A:HOH580 3.1 6.1 1.0
N A:VAL196 3.3 7.1 1.0
N A:GLU74 3.3 11.8 1.0
O A:HOH640 3.5 10.8 1.0
CB A:GLU74 3.6 5.5 1.0
CG A:GLU74 3.7 7.1 1.0
CB A:VAL196 3.8 10.1 1.0
O A:HOH546 3.8 10.5 1.0
CB A:ASP73 3.8 7.5 1.0
CA A:GLY195 3.9 3.3 1.0
CG1 A:VAL196 3.9 8.8 1.0
O6B A:BDP401 4.0 3.9 1.0
NH2 A:ARG173 4.0 6.0 1.0
CA A:GLU74 4.1 10.5 1.0
C A:GLY195 4.1 3.3 1.0
CA A:VAL196 4.1 8.6 1.0
C A:ASP73 4.3 12.2 1.0
O4 A:BDP401 4.3 16.4 1.0
CA A:ASP73 4.3 8.3 1.0
CG A:ASP73 4.4 11.9 1.0
OD1 A:ASP73 4.5 10.0 1.0
CD A:GLU74 4.6 13.4 1.0
OE1 A:GLU74 4.7 13.2 1.0
O A:MSE194 4.8 9.2 1.0
N A:LYS75 4.8 8.4 1.0
O A:HOH632 5.0 19.0 1.0
C A:GLU74 5.0 14.8 1.0
N A:GLY195 5.0 3.3 1.0

Chlorine binding site 2 out of 6 in 4x04

Go back to Chlorine Binding Sites List in 4x04
Chlorine binding site 2 out of 6 in the Crystal Structure of A Trap Periplasmic Solute Binding Protein From Citrobacter Koseri (CKO_04899, Target Efi-510094) with Bound D- Glucuronate


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 Trap Periplasmic Solute Binding Protein From Citrobacter Koseri (CKO_04899, Target Efi-510094) with Bound D- Glucuronate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl403

b:25.4
occ:1.00
 O A:HOH577 3.0 10.8 1.0
NZ A:LYS303 3.2 6.3 1.0
O A:HOH609 3.3 7.3 1.0
O C:HOH674 3.4 19.0 1.0
CG C:ARG113 3.6 7.0 1.0
CE A:LYS303 3.6 6.2 1.0
CA A:TYR300 3.8 7.7 1.0
CA C:ARG113 3.9 8.9 1.0
CB A:TYR300 3.9 8.2 1.0
N A:TYR300 3.9 7.0 1.0
N C:ARG113 3.9 11.7 1.0
CD1 A:TYR300 4.1 13.3 1.0
O C:VAL111 4.2 15.3 1.0
C C:PHE112 4.2 11.0 1.0
CB C:ARG113 4.3 10.8 1.0
O C:PHE112 4.3 12.3 1.0
O C:HOH632 4.5 8.9 1.0
O A:HOH647 4.5 15.8 1.0
CG A:TYR300 4.5 15.0 1.0
C A:ALA299 4.6 10.0 1.0
O C:HOH717 4.6 12.1 1.0
CB A:ALA299 4.7 8.8 1.0
O C:HOH616 4.8 13.3 1.0
O C:TYR110 4.8 8.4 1.0
C C:VAL111 4.8 9.8 1.0
CD C:ARG113 4.8 9.7 1.0

Chlorine binding site 3 out of 6 in 4x04

Go back to Chlorine Binding Sites List in 4x04
Chlorine binding site 3 out of 6 in the Crystal Structure of A Trap Periplasmic Solute Binding Protein From Citrobacter Koseri (CKO_04899, Target Efi-510094) with Bound D- Glucuronate


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 Trap Periplasmic Solute Binding Protein From Citrobacter Koseri (CKO_04899, Target Efi-510094) with Bound D- Glucuronate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl402

b:16.9
occ:1.00
 O B:HOH623 3.1 14.1 1.0
N B:VAL196 3.1 11.5 1.0
N B:GLU74 3.4 8.0 1.0
O B:HOH635 3.6 25.2 1.0
O B:HOH592 3.6 12.7 1.0
CB B:ASP73 3.7 18.4 1.0
CG B:GLU74 3.7 8.3 1.0
CB B:GLU74 3.7 8.0 1.0
CB B:VAL196 3.8 12.4 1.0
CA B:GLY195 3.8 9.6 1.0
O6B B:BDP401 3.8 13.3 1.0
NH1 B:ARG173 3.9 11.8 1.0
C B:GLY195 4.0 14.6 1.0
CG1 B:VAL196 4.0 14.8 1.0
CA B:VAL196 4.0 11.1 1.0
O4 B:BDP401 4.1 11.0 1.0
CA B:GLU74 4.1 9.5 1.0
CG B:ASP73 4.2 22.1 1.0
C B:ASP73 4.3 12.7 1.0
CA B:ASP73 4.3 12.4 1.0
OD1 B:ASP73 4.4 19.6 1.0
OE1 B:GLU74 4.5 13.1 1.0
CD B:GLU74 4.5 12.1 1.0
O B:MSE194 4.6 15.0 1.0
O B:HOH680 4.6 19.6 1.0
N B:LYS75 4.8 20.5 1.0
N B:GLY195 4.9 11.8 1.0

Chlorine binding site 4 out of 6 in 4x04

Go back to Chlorine Binding Sites List in 4x04
Chlorine binding site 4 out of 6 in the Crystal Structure of A Trap Periplasmic Solute Binding Protein From Citrobacter Koseri (CKO_04899, Target Efi-510094) with Bound D- Glucuronate


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 Trap Periplasmic Solute Binding Protein From Citrobacter Koseri (CKO_04899, Target Efi-510094) with Bound D- Glucuronate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl402

b:9.4
occ:1.00
 N C:VAL196 3.1 10.9 1.0
O C:HOH653 3.2 6.5 1.0
N C:GLU74 3.4 2.4 1.0
O C:HOH698 3.4 17.1 1.0
CG1 C:VAL196 3.7 6.0 1.0
CB C:GLU74 3.7 2.5 1.0
CB C:VAL196 3.7 11.3 1.0
CA C:GLY195 3.8 12.3 1.0
CB C:ASP73 3.8 9.0 1.0
CG C:GLU74 3.8 5.6 1.0
O6B C:BDP401 3.9 11.9 1.0
O C:HOH637 3.9 16.6 1.0
C C:GLY195 3.9 12.4 1.0
NH2 C:ARG173 4.0 9.2 1.0
CA C:VAL196 4.0 6.0 1.0
CA C:GLU74 4.1 5.7 1.0
O4 C:BDP401 4.2 5.0 1.0
C C:ASP73 4.3 13.0 1.0
CA C:ASP73 4.3 10.0 1.0
CG C:ASP73 4.4 13.6 1.0
OD1 C:ASP73 4.5 13.6 1.0
O C:MSE194 4.6 9.8 1.0
O C:HOH721 4.7 16.3 1.0
CD C:GLU74 4.7 10.8 1.0
OE1 C:GLU74 4.8 14.8 1.0
N C:LYS75 4.8 6.6 1.0
N C:GLY195 4.9 6.1 1.0

Chlorine binding site 5 out of 6 in 4x04

Go back to Chlorine Binding Sites List in 4x04
Chlorine binding site 5 out of 6 in the Crystal Structure of A Trap Periplasmic Solute Binding Protein From Citrobacter Koseri (CKO_04899, Target Efi-510094) with Bound D- Glucuronate


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 Trap Periplasmic Solute Binding Protein From Citrobacter Koseri (CKO_04899, Target Efi-510094) with Bound D- Glucuronate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl403

b:24.4
occ:1.00
 O C:HOH612 3.1 13.9 1.0
O A:HOH564 3.1 11.4 1.0
NZ C:LYS303 3.2 4.3 1.0
O A:HOH686 3.2 18.2 1.0
CE C:LYS303 3.5 4.2 1.0
CA C:TYR300 3.7 11.2 1.0
CB C:TYR300 3.8 10.2 1.0
N C:TYR300 3.8 8.1 1.0
CG A:ARG113 3.8 11.7 1.0
O A:VAL111 4.0 19.5 1.0
CA A:ARG113 4.0 13.6 1.0
N A:ARG113 4.1 12.4 1.0
CD2 C:TYR300 4.1 15.1 1.0
O C:HOH644 4.2 19.5 1.0
C A:PHE112 4.3 9.4 1.0
O A:PHE112 4.4 11.4 1.0
C C:ALA299 4.4 12.6 1.0
CG C:TYR300 4.4 18.4 1.0
O A:HOH706 4.4 17.2 1.0
CB A:ARG113 4.5 10.9 1.0
CB C:ALA299 4.6 14.8 1.0
O A:TYR110 4.7 11.3 1.0
C A:VAL111 4.7 17.3 1.0
O A:HOH648 4.8 20.0 1.0
O A:HOH539 4.9 14.7 1.0
CD C:LYS303 4.9 12.9 1.0
O C:ALA299 4.9 17.2 1.0

Chlorine binding site 6 out of 6 in 4x04

Go back to Chlorine Binding Sites List in 4x04
Chlorine binding site 6 out of 6 in the Crystal Structure of A Trap Periplasmic Solute Binding Protein From Citrobacter Koseri (CKO_04899, Target Efi-510094) with Bound D- Glucuronate


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 Trap Periplasmic Solute Binding Protein From Citrobacter Koseri (CKO_04899, Target Efi-510094) with Bound D- Glucuronate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl402

b:11.9
occ:1.00
 O D:HOH593 3.0 8.3 1.0
N D:VAL196 3.2 15.9 1.0
N D:GLU74 3.3 6.2 1.0
O D:HOH661 3.4 17.9 1.0
CB D:GLU74 3.6 8.3 1.0
CG D:GLU74 3.7 11.5 1.0
O D:HOH574 3.7 12.2 1.0
CB D:VAL196 3.8 6.0 1.0
O6A D:BDP401 3.8 8.1 1.0
CA D:GLY195 3.8 10.5 1.0
NH2 D:ARG173 3.9 9.1 1.0
CB D:ASP73 3.9 9.1 1.0
C D:GLY195 3.9 13.0 1.0
CG1 D:VAL196 4.0 6.0 1.0
CA D:VAL196 4.0 8.9 1.0
CA D:GLU74 4.0 6.6 1.0
C D:ASP73 4.3 10.6 1.0
O4 D:BDP401 4.3 6.7 1.0
OD1 D:ASP73 4.3 9.4 1.0
CA D:ASP73 4.4 12.1 1.0
CG D:ASP73 4.4 11.7 1.0
O D:HOH635 4.6 18.2 1.0
CD D:GLU74 4.6 11.9 1.0
O D:MSE194 4.7 7.2 1.0
OE1 D:GLU74 4.8 15.2 1.0
N D:LYS75 4.8 5.0 1.0
C D:GLU74 4.9 9.7 1.0
O D:HOH686 5.0 26.5 1.0
N D:GLY195 5.0 6.2 1.0

Reference:

U.Yadava, M.W.Vetting, N.F.Al Obaidi, R.Toro, L.L.Morisco, J.Benach, S.R.Wasserman, J.D.Attonito, A.Scott Glenn, S.Chamala, S.Chowdhury, J.Lafleur, J.Love, R.D.Seidel, K.L.Whalen, J.A.Gerlt, S.C.Almo, Enzyme Function Initiative (Efi). Crystal Structure of A Trap Periplasmic Solute Binding Protein From Citrobacter Koseri (CKO_04899, Target Efi-510094) with Bound D-Glucuronate To Be Published.
Page generated: Fri Jul 26 03:10:15 2024

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