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Sodium in PDB 2ovl: Crystal Structure of A Racemase From Streptomyces Coelicolor A3(2)

Protein crystallography data

The structure of Crystal Structure of A Racemase From Streptomyces Coelicolor A3(2), PDB code: 2ovl was solved by K.N.Rao, S.K.Burley, S.Swaminathan, New York Sgx Researchcenter For Structural Genomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.05 / 2.13
Space group P 4 21 2
Cell size a, b, c (Å), α, β, γ (°) 177.603, 177.603, 111.812, 90.00, 90.00, 90.00
R / Rfree (%) 21.5 / 24.3

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of A Racemase From Streptomyces Coelicolor A3(2) (pdb code 2ovl). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of A Racemase From Streptomyces Coelicolor A3(2), PDB code: 2ovl:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 2ovl

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Sodium binding site 1 out of 4 in the Crystal Structure of A Racemase From Streptomyces Coelicolor A3(2)


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 A Racemase From Streptomyces Coelicolor A3(2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na400

b:48.3
occ:1.00
OE2 A:GLU224 2.5 34.1 1.0
OE1 A:GLU249 2.7 37.0 1.0
OD1 A:ASP197 2.7 20.5 1.0
OE2 A:GLU223 2.9 27.6 1.0
OD2 A:ASP197 3.1 26.6 1.0
CD A:GLU249 3.2 34.6 1.0
OD1 A:ASN199 3.2 29.1 1.0
CG A:ASP197 3.3 22.1 1.0
CD A:GLU224 3.3 35.2 1.0
OE2 A:GLU249 3.5 35.7 1.0
CD A:GLU223 3.5 23.6 1.0
CG A:GLU224 3.6 29.3 1.0
CG A:GLU223 3.6 21.4 1.0
CB A:GLU224 3.7 24.2 1.0
O A:HOH451 3.7 30.0 1.0
CG A:ASN199 3.9 24.8 1.0
CA A:ASN199 4.1 21.9 1.0
CG A:GLU249 4.1 30.9 1.0
OE1 A:GLU224 4.3 36.9 1.0
N A:ASN199 4.4 21.3 1.0
CB A:GLU223 4.6 19.1 1.0
CB A:ASN199 4.6 23.3 1.0
OE1 A:GLU223 4.6 25.5 1.0
ND2 A:ASN199 4.7 22.4 1.0
CB A:ASP197 4.7 20.7 1.0
N A:GLU224 4.8 18.6 1.0
C A:GLU223 4.8 19.1 1.0
O A:GLU223 4.9 15.6 1.0
CA A:GLU224 4.9 22.1 1.0

Sodium binding site 2 out of 4 in 2ovl

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Sodium binding site 2 out of 4 in the Crystal Structure of A Racemase From Streptomyces Coelicolor A3(2)


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 A Racemase From Streptomyces Coelicolor A3(2) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na400

b:37.9
occ:1.00
OE2 B:GLU224 2.3 31.9 1.0
OD2 B:ASP197 2.6 25.4 1.0
OE1 B:GLU249 2.6 38.7 1.0
OD1 B:ASP197 2.7 22.3 1.0
OE2 B:GLU223 2.9 28.9 1.0
CG B:ASP197 3.0 22.8 1.0
CD B:GLU249 3.1 34.9 1.0
OD1 B:ASN199 3.2 24.9 1.0
CD B:GLU224 3.3 32.0 1.0
OE2 B:GLU249 3.5 38.0 1.0
O B:HOH493 3.5 42.0 1.0
CD B:GLU223 3.7 29.8 1.0
CG B:GLU223 3.7 26.9 1.0
CG B:GLU224 3.8 26.9 1.0
O B:HOH448 3.8 34.4 1.0
CG B:ASN199 3.9 24.3 1.0
O B:HOH426 4.0 30.2 1.0
CB B:GLU224 4.0 23.9 1.0
CG B:GLU249 4.1 31.1 1.0
CA B:ASN199 4.2 23.2 1.0
OE1 B:GLU224 4.4 30.8 1.0
N B:ASN199 4.5 21.7 1.0
CB B:ASP197 4.5 22.7 1.0
CB B:GLU223 4.6 24.7 1.0
ND2 B:ASN199 4.6 23.1 1.0
CB B:ASN199 4.7 22.7 1.0
OE1 B:GLU223 4.8 29.3 1.0
NZ B:LYS168 4.9 29.7 1.0
C B:GLU223 5.0 23.1 1.0

Sodium binding site 3 out of 4 in 2ovl

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Sodium binding site 3 out of 4 in the Crystal Structure of A Racemase From Streptomyces Coelicolor A3(2)


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 A Racemase From Streptomyces Coelicolor A3(2) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na400

b:48.2
occ:1.00
CD2 C:HIS299 2.6 41.1 1.0
NZ C:LYS166 2.9 29.4 1.0
OE1 C:GLU249 2.9 45.6 1.0
OE2 C:GLU319 2.9 43.5 1.0
OE2 C:GLU223 3.0 34.1 1.0
NE2 C:HIS299 3.2 42.5 1.0
OD2 C:ASP197 3.2 32.5 1.0
CG C:HIS299 3.9 38.9 1.0
CD C:GLU249 3.9 42.3 1.0
NZ C:LYS168 4.0 35.2 1.0
O C:HOH427 4.0 44.4 1.0
CD C:GLU319 4.0 42.0 1.0
CE C:LYS166 4.0 28.0 1.0
OE2 C:GLU249 4.1 43.6 1.0
OE2 C:GLU270 4.1 38.9 1.0
CD C:GLU223 4.1 32.2 1.0
OE1 C:GLU319 4.4 44.4 1.0
CE1 C:HIS299 4.4 41.7 1.0
CG C:ASP197 4.4 26.4 1.0
OE1 C:GLU223 4.5 29.8 1.0
CB C:HIS299 4.6 35.9 1.0
ND1 C:HIS299 4.8 40.0 1.0

Sodium binding site 4 out of 4 in 2ovl

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Sodium binding site 4 out of 4 in the Crystal Structure of A Racemase From Streptomyces Coelicolor A3(2)


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 A Racemase From Streptomyces Coelicolor A3(2) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na400

b:46.5
occ:1.00
OE2 D:GLU224 2.6 37.5 1.0
OD1 D:ASP197 2.7 31.1 1.0
OD2 D:ASP197 2.8 32.9 1.0
OE1 D:GLU249 2.9 40.8 1.0
OE2 D:GLU223 3.1 34.8 1.0
CG D:ASP197 3.1 30.5 1.0
OD1 D:ASN199 3.1 36.7 1.0
CD D:GLU249 3.2 38.6 1.0
OE2 D:GLU249 3.4 39.2 1.0
O D:HOH457 3.4 40.6 1.0
CD D:GLU224 3.5 36.3 1.0
CB D:GLU224 3.8 29.8 1.0
CD D:GLU223 3.8 34.4 1.0
CG D:GLU223 3.8 30.8 1.0
CG D:ASN199 3.9 33.4 1.0
CG D:GLU224 4.0 33.3 1.0
CA D:ASN199 4.0 29.8 1.0
N D:ASN199 4.2 28.8 1.0
CG D:GLU249 4.3 35.5 1.0
O D:HOH425 4.4 29.6 1.0
OE1 D:GLU224 4.5 38.6 1.0
CB D:ASN199 4.5 32.6 1.0
CB D:ASP197 4.6 30.1 1.0
ND2 D:ASN199 4.6 34.7 1.0
CB D:GLU223 4.7 29.0 1.0
O D:GLU223 4.8 24.6 1.0
C D:GLU223 4.9 25.8 1.0
N D:GLU224 5.0 24.5 1.0
OE1 D:GLU223 5.0 35.0 1.0

Reference:

K.N.Rao, S.K.Burley, S.Swaminathan. Crystal Structure of A Racemase From Streptomyces Coelicolor A3(2) To Be Published.
Page generated: Tue Dec 15 05:53:02 2020

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