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Sodium in PDB 4kaf: Crystal Structure of Haloalkane Dehalogenase HALOTAG7 at the Resolution 1.5A, Northeast Structural Genomics Consortium (Nesg) Target OR151

Enzymatic activity of Crystal Structure of Haloalkane Dehalogenase HALOTAG7 at the Resolution 1.5A, Northeast Structural Genomics Consortium (Nesg) Target OR151

All present enzymatic activity of Crystal Structure of Haloalkane Dehalogenase HALOTAG7 at the Resolution 1.5A, Northeast Structural Genomics Consortium (Nesg) Target OR151:
3.8.1.5;

Protein crystallography data

The structure of Crystal Structure of Haloalkane Dehalogenase HALOTAG7 at the Resolution 1.5A, Northeast Structural Genomics Consortium (Nesg) Target OR151, PDB code: 4kaf was solved by A.P.Kuzin, S.Lew, T.K.Neklesa, D.Noblin, J.Seetharaman, M.Maglaqui, R.Xiao, E.Kohan, H.Wang, J.K.Everett, T.B.Acton, G.Kornhaber, G.T.Montelione, C.Crews, L.Tong, Northeast Structural Genomics Consortium (Nesg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.40 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 68.930, 94.800, 100.502, 90.00, 90.00, 90.00
R / Rfree (%) 14.8 / 16.5

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Haloalkane Dehalogenase HALOTAG7 at the Resolution 1.5A, Northeast Structural Genomics Consortium (Nesg) Target OR151 (pdb code 4kaf). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Crystal Structure of Haloalkane Dehalogenase HALOTAG7 at the Resolution 1.5A, Northeast Structural Genomics Consortium (Nesg) Target OR151, PDB code: 4kaf:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 4kaf

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Sodium binding site 1 out of 6 in the Crystal Structure of Haloalkane Dehalogenase HALOTAG7 at the Resolution 1.5A, Northeast Structural Genomics Consortium (Nesg) Target OR151


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Haloalkane Dehalogenase HALOTAG7 at the Resolution 1.5A, Northeast Structural Genomics Consortium (Nesg) Target OR151 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:24.3
occ:1.00
 H A:ALA226 2.1 10.6 1.0
OE2 A:GLU224 2.2 36.3 1.0
O B:HOH581 2.8 17.0 1.0
O A:HOH715 2.8 29.8 1.0
N A:ALA226 2.9 8.8 1.0
HA A:PRO225 3.0 10.9 1.0
HB3 A:ALA226 3.2 13.0 1.0
CD A:GLU224 3.2 31.5 1.0
O A:HOH536 3.2 12.7 1.0
HB2 A:ALA226 3.2 13.0 1.0
CB A:ALA226 3.5 10.8 1.0
OE1 A:GLU224 3.5 36.2 1.0
CA A:PRO225 3.8 9.1 1.0
HA A:GLU224 3.8 14.5 1.0
C A:PRO225 3.8 10.7 1.0
CA A:ALA226 3.8 9.2 1.0
HB3 A:PRO225 4.1 13.9 1.0
HB3 A:GLU224 4.3 20.2 1.0
H A:ASN227 4.3 10.0 1.0
O B:HOH517 4.3 8.9 1.0
O B:HOH601 4.4 19.6 1.0
O B:HOH543 4.4 13.5 1.0
HA A:ALA226 4.4 11.0 1.0
HB1 A:ALA226 4.5 13.0 1.0
CG A:GLU224 4.5 18.0 1.0
CB A:PRO225 4.5 11.6 1.0
O A:HOH796 4.5 33.2 1.0
O A:HOH694 4.5 26.9 1.0
CA A:GLU224 4.6 12.1 1.0
CB A:GLU224 4.7 16.9 1.0
O A:HOH708 4.7 28.5 1.0
O A:GLY223 4.7 14.5 1.0
HB2 A:PRO225 4.9 13.9 1.0
N A:ASN227 4.9 8.4 1.0
C A:ALA226 4.9 9.2 1.0
N A:PRO225 5.0 9.3 1.0
HG3 A:GLU224 5.0 21.6 1.0

Sodium binding site 2 out of 6 in 4kaf

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Sodium binding site 2 out of 6 in the Crystal Structure of Haloalkane Dehalogenase HALOTAG7 at the Resolution 1.5A, Northeast Structural Genomics Consortium (Nesg) Target OR151


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Haloalkane Dehalogenase HALOTAG7 at the Resolution 1.5A, Northeast Structural Genomics Consortium (Nesg) Target OR151 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:19.3
occ:1.00
 O A:PRO184 2.7 13.2 1.0
O A:ARG189 2.8 8.1 1.0
HA A:PRO190 2.8 10.2 1.0
HB A:VAL187 2.9 8.9 1.0
H A:LEU191 2.9 12.6 1.0
O A:VAL187 3.1 8.2 1.0
HB2 A:PRO184 3.6 17.8 1.0
C A:PRO184 3.6 9.5 1.0
HA A:PRO184 3.6 11.6 1.0
N A:LEU191 3.7 10.5 1.0
CA A:PRO190 3.7 8.5 1.0
C A:ARG189 3.8 8.3 1.0
CB A:VAL187 3.8 7.5 1.0
HG A:LEU191 3.9 12.4 1.0
CA A:PRO184 3.9 9.7 1.0
HB3 A:PRO184 3.9 17.8 1.0
CB A:PRO184 4.0 14.8 1.0
C A:VAL187 4.0 7.8 1.0
H A:VAL187 4.0 8.9 1.0
HG12 A:VAL187 4.1 12.1 1.0
C A:PRO190 4.2 9.7 1.0
N A:PRO190 4.2 8.5 1.0
CA A:VAL187 4.4 7.5 1.0
HB2 A:LEU191 4.4 14.8 1.0
CG1 A:VAL187 4.4 10.1 1.0
HG11 A:VAL187 4.5 12.1 1.0
HA A:MSE185 4.6 16.5 0.4
O A:VAL188 4.6 8.7 1.0
N A:VAL187 4.6 7.4 1.0
CG A:LEU191 4.7 10.4 1.0
HB3 A:PRO190 4.7 10.9 1.0
N A:MSE185 4.7 8.8 0.4
N A:MSE185 4.8 8.7 0.6
C A:VAL188 4.8 8.7 1.0
CG2 A:VAL187 4.8 7.4 1.0
HG23 A:VAL187 4.8 8.9 1.0
CB A:LEU191 4.9 12.3 1.0
CB A:PRO190 4.9 9.1 1.0
CA A:LEU191 4.9 11.4 1.0
HG21 A:VAL187 4.9 8.9 1.0
HD12 A:LEU191 5.0 12.8 1.0

Sodium binding site 3 out of 6 in 4kaf

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Sodium binding site 3 out of 6 in the Crystal Structure of Haloalkane Dehalogenase HALOTAG7 at the Resolution 1.5A, Northeast Structural Genomics Consortium (Nesg) Target OR151


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Haloalkane Dehalogenase HALOTAG7 at the Resolution 1.5A, Northeast Structural Genomics Consortium (Nesg) Target OR151 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:28.5
occ:1.00
 HE2 A:HIS23 1.9 12.7 1.0
OD2 A:ASP21 2.2 36.1 0.7
OD1 A:ASP21 2.3 26.2 0.7
CG A:ASP21 2.6 20.1 0.7
HB2 A:ASP21 2.6 21.9 0.3
NE2 A:HIS23 2.7 10.6 1.0
O A:ASP36 2.8 11.0 1.0
O A:HOH523 3.0 10.3 1.0
HG12 A:VAL37 3.3 13.4 1.0
HD2 A:HIS23 3.4 10.0 1.0
CD2 A:HIS23 3.4 8.3 1.0
CB A:ASP21 3.5 18.3 0.3
HB3 A:ASP21 3.6 21.9 0.3
HG13 A:VAL37 3.8 13.4 1.0
CE1 A:HIS23 3.8 9.7 1.0
H A:ASP21 3.8 16.5 0.3
H A:ASP21 3.9 16.9 0.7
C A:ASP36 3.9 10.0 1.0
H A:ASP36 3.9 10.8 1.0
CG1 A:VAL37 4.0 11.2 1.0
CB A:ASP21 4.0 12.8 0.7
HE1 A:HIS23 4.0 11.6 1.0
O A:ASP21 4.1 12.1 0.7
OD1 A:ASP21 4.1 18.0 0.3
HA A:VAL37 4.1 11.2 1.0
HB3 A:ASP36 4.3 11.3 1.0
CG A:ASP21 4.3 22.5 0.3
N A:ASP21 4.4 13.8 0.3
HB2 A:ASP21 4.4 15.4 0.7
CA A:ASP21 4.5 15.3 0.3
N A:ASP21 4.5 14.1 0.7
HB3 A:ASP21 4.6 15.4 0.7
HG11 A:VAL37 4.6 13.4 1.0
O A:ASP21 4.6 10.3 0.3
CA A:ASP21 4.7 14.4 0.7
N A:ASP36 4.7 9.0 1.0
CG A:HIS23 4.7 7.8 1.0
C A:ASP21 4.7 12.3 0.7
N A:VAL37 4.8 8.1 1.0
CA A:VAL37 4.8 9.3 1.0
CA A:ASP36 4.8 9.1 1.0
ND1 A:HIS23 4.8 8.1 1.0
C A:ASP21 4.8 14.1 0.3

Sodium binding site 4 out of 6 in 4kaf

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Sodium binding site 4 out of 6 in the Crystal Structure of Haloalkane Dehalogenase HALOTAG7 at the Resolution 1.5A, Northeast Structural Genomics Consortium (Nesg) Target OR151


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Haloalkane Dehalogenase HALOTAG7 at the Resolution 1.5A, Northeast Structural Genomics Consortium (Nesg) Target OR151 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na405

b:60.6
occ:1.00
 HG3 A:MSE185 2.6 31.6 0.6
HG2 A:MSE185 2.8 31.6 0.6
SE A:MSE185 2.8 18.2 0.4
HB3 A:MSE185 2.9 17.6 0.4
CG A:MSE185 3.1 26.3 0.6
HG2 A:MSE185 3.3 9.5 0.4
CG A:MSE185 3.4 7.9 0.4
CB A:MSE185 3.6 14.7 0.4
HB2 A:MSE185 3.9 24.0 0.6
HB2 A:MSE185 4.0 17.6 0.4
CB A:MSE185 4.1 20.0 0.6
HB2 A:PHE154 4.2 26.7 1.0
HE1 A:MSE185 4.2 8.9 0.6
HA A:MSE185 4.3 15.3 0.6
HG3 A:MSE185 4.4 9.5 0.4
SE A:MSE185 4.5 72.1 0.6
CE A:MSE185 4.6 27.1 0.4
HD2 A:PHE154 4.7 33.3 1.0
O A:PHE154 4.7 25.7 1.0
HA A:MSE185 4.7 16.5 0.4
CA A:MSE185 4.8 12.8 0.6
CE A:MSE185 4.8 7.4 0.6
CA A:MSE185 4.8 13.7 0.4
HB3 A:MSE185 4.9 24.0 0.6
HE2 A:MSE185 4.9 32.6 0.4
HE1 A:MSE185 4.9 32.6 0.4

Sodium binding site 5 out of 6 in 4kaf

Go back to Sodium Binding Sites List in 4kaf
Sodium binding site 5 out of 6 in the Crystal Structure of Haloalkane Dehalogenase HALOTAG7 at the Resolution 1.5A, Northeast Structural Genomics Consortium (Nesg) Target OR151


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of Haloalkane Dehalogenase HALOTAG7 at the Resolution 1.5A, Northeast Structural Genomics Consortium (Nesg) Target OR151 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na402

b:28.2
occ:1.00
 H B:ALA226 2.2 10.9 1.0
OE2 B:GLU224 2.2 35.9 1.0
O A:HOH592 2.7 18.4 1.0
O B:HOH736 2.9 27.9 1.0
HA B:PRO225 3.0 10.8 1.0
N B:ALA226 3.0 9.1 1.0
O B:HOH540 3.2 13.5 1.0
HB3 B:ALA226 3.3 12.7 1.0
HB2 B:ALA226 3.3 12.7 1.0
CD B:GLU224 3.3 30.1 1.0
CB B:ALA226 3.6 10.6 1.0
CA B:PRO225 3.8 9.0 1.0
OE1 B:GLU224 3.8 34.5 1.0
C B:PRO225 3.9 9.5 1.0
CA B:ALA226 3.9 8.6 1.0
HA B:GLU224 3.9 11.3 1.0
HB3 B:PRO225 4.0 13.3 1.0
HB3 B:GLU224 4.2 17.0 1.0
H B:ASN227 4.3 9.8 1.0
O A:HOH759 4.4 32.1 1.0
O A:HOH521 4.4 10.5 1.0
O A:HOH554 4.4 15.2 1.0
O A:HOH647 4.4 23.8 1.0
O B:HOH813 4.4 36.0 1.0
CB B:PRO225 4.4 11.1 1.0
HA B:ALA226 4.5 10.3 1.0
HB1 B:ALA226 4.6 12.7 1.0
CG B:GLU224 4.6 19.1 1.0
O B:HOH784 4.7 31.7 1.0
CB B:GLU224 4.7 14.2 1.0
CA B:GLU224 4.7 9.4 1.0
HB2 B:PRO225 4.8 13.3 1.0
N B:ASN227 4.9 8.2 1.0
C B:ALA226 5.0 7.8 1.0
O B:GLY223 5.0 12.2 1.0
N B:PRO225 5.0 7.8 1.0

Sodium binding site 6 out of 6 in 4kaf

Go back to Sodium Binding Sites List in 4kaf
Sodium binding site 6 out of 6 in the Crystal Structure of Haloalkane Dehalogenase HALOTAG7 at the Resolution 1.5A, Northeast Structural Genomics Consortium (Nesg) Target OR151


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of Haloalkane Dehalogenase HALOTAG7 at the Resolution 1.5A, Northeast Structural Genomics Consortium (Nesg) Target OR151 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na403

b:33.9
occ:1.00
 O B:HOH590 2.7 18.0 1.0
O B:HOH792 2.8 34.2 1.0
HA B:PRO19 3.1 12.0 1.0
H B:PHE18 3.6 12.1 1.0
O B:PHE18 3.8 9.4 1.0
HB3 B:PRO19 3.9 12.5 1.0
CA B:PRO19 3.9 10.0 1.0
C B:PHE18 4.0 9.6 1.0
N B:PRO19 4.2 10.2 1.0
N B:PHE18 4.3 10.1 1.0
O B:HOH787 4.3 32.2 1.0
O B:HOH788 4.4 32.4 1.0
CB B:PRO19 4.5 10.4 1.0
HA3 B:GLY17 4.6 12.9 1.0
CA B:PHE18 4.8 8.8 1.0
O B:HOH693 4.8 17.5 0.7
HD3 B:PRO19 4.9 13.1 1.0
HA2 B:GLY17 4.9 12.9 1.0
HB3 B:PHE18 5.0 9.3 1.0

Reference:

A.P.Kuzin, S.Lew, T.K.Neklesa, D.Noblin, J.Seetharaman, M.Maglaqui, R.Xiao, E.Kohan, H.Wang, J.K.Everett, T.B.Acton, G.Kornhaber, G.T.Montelione, C.Crews, L.Tong. Northeast Structural Genomics Consortium Target OR151 To Be Published.
Page generated: Mon Oct 7 16:27:34 2024

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