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Sodium in PDB 4ys6: Crystal Structure of An Abc Transporter Solute Binding Protein (IPR025997) From Clostridium Phytofermentans (CPHY_1585, Target Efi- 511156) with Bound Beta-D-Glucose

Protein crystallography data

The structure of Crystal Structure of An Abc Transporter Solute Binding Protein (IPR025997) From Clostridium Phytofermentans (CPHY_1585, Target Efi- 511156) with Bound Beta-D-Glucose, PDB code: 4ys6 was solved by M.W.Vetting, Y.Patskovsky, N.F.Al Obaidi, R.Toro, L.L.Morisco, J.Benach, J.Koss, 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), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 23.94 / 1.70
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 80.686, 80.686, 170.004, 90.00, 90.00, 120.00
R / Rfree (%) 15 / 18.3

Other elements in 4ys6:

The structure of Crystal Structure of An Abc Transporter Solute Binding Protein (IPR025997) From Clostridium Phytofermentans (CPHY_1585, Target Efi- 511156) with Bound Beta-D-Glucose also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of An Abc Transporter Solute Binding Protein (IPR025997) From Clostridium Phytofermentans (CPHY_1585, Target Efi- 511156) with Bound Beta-D-Glucose (pdb code 4ys6). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Crystal Structure of An Abc Transporter Solute Binding Protein (IPR025997) From Clostridium Phytofermentans (CPHY_1585, Target Efi- 511156) with Bound Beta-D-Glucose, PDB code: 4ys6:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 4ys6

Go back to Sodium Binding Sites List in 4ys6
Sodium binding site 1 out of 5 in the Crystal Structure of An Abc Transporter Solute Binding Protein (IPR025997) From Clostridium Phytofermentans (CPHY_1585, Target Efi- 511156) with Bound Beta-D-Glucose


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 An Abc Transporter Solute Binding Protein (IPR025997) From Clostridium Phytofermentans (CPHY_1585, Target Efi- 511156) with Bound Beta-D-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:18.9
occ:1.00
O A:HOH662 2.3 24.1 1.0
O A:GLY291 2.3 18.4 1.0
O A:ALA286 2.4 16.7 1.0
H A:GLY291 2.9 20.8 1.0
C A:ALA286 3.2 16.3 1.0
HA A:ILE287 3.3 19.5 1.0
N A:GLY291 3.4 17.3 1.0
C A:GLY291 3.4 17.3 1.0
HA2 A:GLY290 3.4 22.2 1.0
HB1 A:ALA286 3.5 21.7 1.0
N A:ILE287 3.9 16.1 1.0
CA A:GLY291 3.9 17.1 1.0
CA A:ILE287 4.0 16.2 1.0
C A:GLY290 4.1 21.4 1.0
CA A:ALA286 4.1 16.1 1.0
HA A:ALA286 4.1 19.4 1.0
CA A:GLY290 4.2 18.5 1.0
CB A:ALA286 4.2 18.1 1.0
H A:GLY290 4.4 25.0 1.0
HB3 A:ALA286 4.5 21.7 1.0
O A:HOH610 4.5 23.2 1.0
HA A:GLU292 4.6 18.7 1.0
HA3 A:GLY291 4.6 20.5 1.0
N A:GLU292 4.6 17.1 1.0
HA2 A:GLY291 4.6 20.5 1.0
C A:ILE287 4.7 16.9 1.0
H A:ILE287 4.7 19.3 1.0
O A:ILE287 4.7 17.9 1.0
N A:GLY290 4.8 20.9 1.0
H A:ALA293 4.8 20.4 1.0
HG13 A:ILE287 4.8 20.6 1.0
HA3 A:GLY290 4.9 22.2 1.0
HG12 A:ILE287 5.0 20.6 1.0

Sodium binding site 2 out of 5 in 4ys6

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Sodium binding site 2 out of 5 in the Crystal Structure of An Abc Transporter Solute Binding Protein (IPR025997) From Clostridium Phytofermentans (CPHY_1585, Target Efi- 511156) with Bound Beta-D-Glucose


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 An Abc Transporter Solute Binding Protein (IPR025997) From Clostridium Phytofermentans (CPHY_1585, Target Efi- 511156) with Bound Beta-D-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na405

b:36.8
occ:1.00
O A:GLU133 2.4 14.4 1.0
O A:HOH667 2.4 56.1 1.0
OD1 A:ASN136 2.4 25.0 1.0
O A:HOH680 3.0 41.3 1.0
OE1 A:GLU133 3.2 61.7 1.0
O A:HOH677 3.3 62.5 1.0
HA A:ASN136 3.3 17.8 1.0
C A:GLU133 3.4 16.4 1.0
HA A:GLU133 3.5 18.6 1.0
CG A:ASN136 3.5 22.9 1.0
O A:HOH657 3.7 23.6 1.0
H A:ASN136 3.7 17.0 1.0
CA A:GLU133 4.0 15.5 1.0
HB3 A:GLU133 4.0 22.4 1.0
CA A:ASN136 4.0 14.8 1.0
HA A:LYS134 4.2 16.0 1.0
N A:ASN136 4.2 14.1 1.0
CD A:GLU133 4.3 62.4 1.0
CB A:ASN136 4.3 16.1 1.0
N A:LYS134 4.5 13.8 1.0
CB A:GLU133 4.5 18.6 1.0
O A:HOH621 4.5 26.3 1.0
ND2 A:ASN136 4.5 27.3 1.0
HD21 A:ASN136 4.5 32.7 1.0
HB3 A:ASN136 4.6 19.3 1.0
CA A:LYS134 4.7 13.3 1.0
C A:LYS134 5.0 13.3 1.0

Sodium binding site 3 out of 5 in 4ys6

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Sodium binding site 3 out of 5 in the Crystal Structure of An Abc Transporter Solute Binding Protein (IPR025997) From Clostridium Phytofermentans (CPHY_1585, Target Efi- 511156) with Bound Beta-D-Glucose


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 An Abc Transporter Solute Binding Protein (IPR025997) From Clostridium Phytofermentans (CPHY_1585, Target Efi- 511156) with Bound Beta-D-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na406

b:32.4
occ:1.00
O A:HOH655 2.2 41.5 1.0
O A:HOH513 2.4 33.6 1.0
O A:SER54 2.4 17.8 0.4
O A:SER54 2.4 17.4 0.6
OD1 A:ASP56 2.5 23.3 1.0
O A:HOH528 2.5 27.9 1.0
CG A:ASP56 3.2 28.4 1.0
HG A:SER54 3.2 35.6 0.6
OD2 A:ASP56 3.5 23.5 1.0
O A:HOH507 3.6 34.8 1.0
C A:SER54 3.6 18.7 0.4
C A:SER54 3.6 19.1 0.6
HB3 A:ASN55 3.6 20.4 1.0
O A:HOH570 3.8 25.2 1.0
HB2 A:ASN55 3.8 20.4 1.0
C A:ASN55 3.8 15.2 1.0
O A:ASN55 3.9 17.5 1.0
HB3 A:SER54 3.9 26.9 0.4
OG A:SER54 4.0 29.6 0.6
CB A:ASN55 4.1 17.0 1.0
N A:ASP56 4.1 15.5 1.0
HB3 A:SER54 4.1 27.1 0.6
O A:HOH537 4.2 30.2 1.0
CA A:ASN55 4.3 14.9 1.0
HA A:ASP56 4.3 19.5 1.0
HB2 A:SER54 4.3 26.9 0.4
CB A:ASP56 4.3 17.6 1.0
H A:ASP56 4.4 18.6 1.0
N A:ASN55 4.4 16.9 1.0
CB A:SER54 4.5 22.4 0.4
CA A:ASP56 4.5 16.3 1.0
CB A:SER54 4.5 22.6 0.6
CA A:SER54 4.7 17.8 0.4
HB2 A:ASP56 4.7 21.1 1.0
CA A:SER54 4.7 17.1 0.6
O A:HOH681 4.7 38.9 1.0

Sodium binding site 4 out of 5 in 4ys6

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Sodium binding site 4 out of 5 in the Crystal Structure of An Abc Transporter Solute Binding Protein (IPR025997) From Clostridium Phytofermentans (CPHY_1585, Target Efi- 511156) with Bound Beta-D-Glucose


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 An Abc Transporter Solute Binding Protein (IPR025997) From Clostridium Phytofermentans (CPHY_1585, Target Efi- 511156) with Bound Beta-D-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na407

b:37.0
occ:1.00
O A:HOH651 2.3 24.3 1.0
O A:HOH671 2.3 36.6 1.0
O A:VAL295 2.4 16.5 1.0
O A:HOH674 2.7 51.5 1.0
H A:VAL295 3.0 19.5 1.0
C A:VAL295 3.6 13.8 1.0
N A:VAL295 3.8 16.3 1.0
HG22 A:VAL295 4.0 32.8 1.0
O A:HOH501 4.0 35.7 1.0
HA A:PRO294 4.1 22.5 1.0
HG23 A:VAL295 4.1 32.8 1.0
HA A:ASN296 4.1 17.4 1.0
CA A:VAL295 4.3 14.6 1.0
CG2 A:VAL295 4.5 27.4 1.0
N A:ASN296 4.6 14.1 1.0
HB3 A:ASN296 4.6 20.8 1.0
C A:PRO294 4.7 18.3 1.0
CA A:ASN296 4.8 14.5 1.0
CA A:PRO294 4.8 18.7 1.0
HB3 A:PRO294 4.9 30.3 1.0

Sodium binding site 5 out of 5 in 4ys6

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Sodium binding site 5 out of 5 in the Crystal Structure of An Abc Transporter Solute Binding Protein (IPR025997) From Clostridium Phytofermentans (CPHY_1585, Target Efi- 511156) with Bound Beta-D-Glucose


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 An Abc Transporter Solute Binding Protein (IPR025997) From Clostridium Phytofermentans (CPHY_1585, Target Efi- 511156) with Bound Beta-D-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na408

b:58.7
occ:1.00
OG A:SER35 2.3 34.1 1.0
O A:HOH685 2.4 48.0 1.0
O A:HOH629 2.4 48.3 1.0
O A:HOH607 2.5 40.4 1.0
O A:ASN31 2.9 17.1 1.0
HB3 A:ASN31 3.2 17.8 1.0
O A:HOH648 3.5 39.8 1.0
CB A:SER35 3.6 22.9 1.0
HA A:ASN31 3.6 19.5 1.0
C A:ASN31 3.7 16.1 1.0
HB2 A:SER35 3.7 27.5 1.0
CA A:ASN31 4.0 16.2 1.0
H A:SER35 4.0 17.7 1.0
CB A:ASN31 4.0 14.8 1.0
HB3 A:SER35 4.2 27.5 1.0
OH A:TYR52 4.4 20.5 1.0
N A:SER35 4.5 14.7 1.0
CA A:SER35 4.5 15.4 1.0
OD1 A:ASN31 4.5 21.4 1.0
HA A:SER35 4.5 18.5 1.0
HH A:TYR52 4.6 24.6 1.0
HB2 A:ASN31 4.7 17.8 1.0
HA A:GLN32 4.7 17.6 1.0
N A:GLN32 4.8 13.9 1.0
CG A:ASN31 4.8 18.3 1.0

Reference:

M.W.Vetting, Y.Patskovsky, N.F.Al Obaidi, R.Toro, L.L.Morisco, J.Benach, J.Koss, 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 An Abc Transporter Solute Binding Protein (IPR025997) From Clostridium Phytofermentans (CPHY_1585, Target Efi-511156) with Bound Beta-D-Glucose To Be Published.
Page generated: Tue Dec 15 10:04:25 2020

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