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Sodium in PDB 4f4r: Crystal Structure of D-Mannonate Dehydratase Homolog From Chromohalobacter Salexigens (Target Efi-502114), with Bound Na, Ordered Loop

Enzymatic activity of Crystal Structure of D-Mannonate Dehydratase Homolog From Chromohalobacter Salexigens (Target Efi-502114), with Bound Na, Ordered Loop

All present enzymatic activity of Crystal Structure of D-Mannonate Dehydratase Homolog From Chromohalobacter Salexigens (Target Efi-502114), with Bound Na, Ordered Loop:
4.2.1.8;

Protein crystallography data

The structure of Crystal Structure of D-Mannonate Dehydratase Homolog From Chromohalobacter Salexigens (Target Efi-502114), with Bound Na, Ordered Loop, PDB code: 4f4r was solved by M.W.Vetting, R.Toro, R.Bhosle, N.F.Al Obaidi, L.L.Morisco, S.R.Wasserman, S.Sojitra, E.Washington, A.Scott Glenn, S.Chowdhury, B.Evans, J.Hammonds, B.Hillerich, J.Love, R.D.Seidel, H.J.Imker, 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) 30.89 / 1.80
Space group P 4 2 2
Cell size a, b, c (Å), α, β, γ (°) 111.389, 111.389, 84.576, 90.00, 90.00, 90.00
R / Rfree (%) 14.5 / 17.1

Other elements in 4f4r:

The structure of Crystal Structure of D-Mannonate Dehydratase Homolog From Chromohalobacter Salexigens (Target Efi-502114), with Bound Na, Ordered Loop also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of D-Mannonate Dehydratase Homolog From Chromohalobacter Salexigens (Target Efi-502114), with Bound Na, Ordered Loop (pdb code 4f4r). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of D-Mannonate Dehydratase Homolog From Chromohalobacter Salexigens (Target Efi-502114), with Bound Na, Ordered Loop, PDB code: 4f4r:

Sodium binding site 1 out of 1 in 4f4r

Go back to Sodium Binding Sites List in 4f4r
Sodium binding site 1 out of 1 in the Crystal Structure of D-Mannonate Dehydratase Homolog From Chromohalobacter Salexigens (Target Efi-502114), with Bound Na, Ordered Loop


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 D-Mannonate Dehydratase Homolog From Chromohalobacter Salexigens (Target Efi-502114), with Bound Na, Ordered Loop within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na501

b:32.8
occ:1.00
 OE1 A:GLU237 2.3 26.4 1.0
OD2 A:ASP211 2.3 21.9 1.0
OE1 A:GLU263 2.5 20.1 1.0
OD2 A:ASP238 2.5 23.2 1.0
OD1 A:ASP211 2.6 17.8 1.0
CG A:ASP211 2.8 22.6 1.0
CD A:GLU237 3.1 23.1 1.0
CD A:GLU263 3.2 25.2 1.0
O A:HOH766 3.2 32.0 1.0
CG A:ASP238 3.3 19.8 1.0
CG A:GLU237 3.5 24.7 1.0
OE2 A:GLU263 3.7 22.7 1.0
CD2 A:HIS213 3.7 25.3 1.0
O A:HOH642 3.8 18.0 1.0
O A:HOH747 3.9 30.7 1.0
CB A:ASP238 3.9 18.9 1.0
OE2 A:GLU237 4.0 21.5 1.0
CG A:GLU263 4.2 19.6 1.0
CB A:ASP211 4.2 21.8 1.0
OD1 A:ASP238 4.2 21.2 1.0
NE2 A:HIS213 4.4 22.6 1.0
NH2 A:ARG284 4.4 20.3 1.0
CG A:HIS213 4.7 21.6 1.0
CB A:GLU237 4.7 22.1 1.0
O A:HOH640 4.8 23.6 1.0
NE2 A:HIS214 4.8 19.9 1.0
CA A:HIS213 4.9 19.5 1.0

Reference:

M.W.Vetting, R.Toro, R.Bhosle, N.F.Al Obaidi, L.L.Morisco, S.R.Wasserman, S.Sojitra, E.Washington, A.Scott Glenn, S.Chowdhury, B.Evans, J.Hammonds, B.Hillerich, J.Love, R.D.Seidel, H.J.Imker, J.A.Gerlt, S.C.Almo, Enzyme Function Initiative (Efi). Crystal Structure of D-Mannonate Dehydratase Homolog From Chromohalobacter Salexigens (Target Efi-502114), with Bound Na, Ordered Loop To Be Published.
Page generated: Mon Oct 7 15:15:02 2024

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