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Sodium in PDB 4eif: Crystal Structure of Cytochrome C6C L50Q Mutant From Synechococcus Sp. Pcc 7002

Protein crystallography data

The structure of Crystal Structure of Cytochrome C6C L50Q Mutant From Synechococcus Sp. Pcc 7002, PDB code: 4eif was solved by S.Krzywda, W.Bialek, P.Zatwarnicki, M.Jaskolski, A.Szczepaniak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.18 / 1.04
Space group P 4 21 2
Cell size a, b, c (Å), α, β, γ (°) 56.380, 56.380, 50.050, 90.00, 90.00, 90.00
R / Rfree (%) 11.9 / 14.5

Other elements in 4eif:

The structure of Crystal Structure of Cytochrome C6C L50Q Mutant From Synechococcus Sp. Pcc 7002 also contains other interesting chemical elements:

Iron (Fe) 1 atom
Chlorine (Cl) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Cytochrome C6C L50Q Mutant From Synechococcus Sp. Pcc 7002 (pdb code 4eif). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of Cytochrome C6C L50Q Mutant From Synechococcus Sp. Pcc 7002, PDB code: 4eif:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 4eif

Go back to Sodium Binding Sites List in 4eif
Sodium binding site 1 out of 3 in the Crystal Structure of Cytochrome C6C L50Q Mutant From Synechococcus Sp. Pcc 7002


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 Cytochrome C6C L50Q Mutant From Synechococcus Sp. Pcc 7002 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na102

b:15.3
occ:0.71
O A:HOH291 2.3 17.1 0.3
OE1 A:GLU11 2.4 15.3 0.8
OE1 A:GLN8 2.4 16.2 0.8
O A:HOH222 2.5 15.2 1.0
O A:HOH292 2.5 17.1 0.5
CD A:GLN8 3.3 15.3 0.8
CD A:GLU11 3.6 13.6 0.8
NE2 A:GLN8 3.7 19.6 0.8
CB A:GLU11 4.0 9.4 1.0
CG A:GLU11 4.4 11.7 1.0
OE2 A:GLU11 4.5 16.6 0.8
CA A:GLN8 4.5 9.2 1.0
O A:HOH240 4.5 21.2 1.0
CG A:GLN8 4.6 12.6 1.0
CB A:GLN8 4.6 10.9 1.0
O A:GLN8 4.6 8.9 1.0

Sodium binding site 2 out of 3 in 4eif

Go back to Sodium Binding Sites List in 4eif
Sodium binding site 2 out of 3 in the Crystal Structure of Cytochrome C6C L50Q Mutant From Synechococcus Sp. Pcc 7002


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 Cytochrome C6C L50Q Mutant From Synechococcus Sp. Pcc 7002 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na103

b:14.1
occ:0.91
O A:HOH267 2.3 24.1 1.0
O A:VAL25 2.4 9.3 1.0
O A:HOH249 2.4 27.0 1.0
O A:HOH320 2.5 22.4 1.0
C A:VAL25 3.4 7.0 0.5
C A:VAL25 3.5 7.1 0.6
N A:ARG26 4.2 6.2 0.5
O A:ILE24 4.2 7.1 1.0
CA A:VAL25 4.2 6.6 1.0
CA A:ARG26 4.3 6.6 0.5
O A:HOH340 4.3 24.2 0.4
N A:ARG26 4.4 6.1 0.6
N A:ARG27 4.5 6.8 0.5
O A:HOH295 4.6 21.4 1.0
N A:ARG27 4.6 7.1 0.6
CA A:ARG26 4.6 6.0 0.6
C A:ILE24 4.9 5.9 1.0
C A:ARG26 5.0 6.6 0.5
N A:VAL25 5.0 5.7 1.0

Sodium binding site 3 out of 3 in 4eif

Go back to Sodium Binding Sites List in 4eif
Sodium binding site 3 out of 3 in the Crystal Structure of Cytochrome C6C L50Q Mutant From Synechococcus Sp. Pcc 7002


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 Cytochrome C6C L50Q Mutant From Synechococcus Sp. Pcc 7002 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na104

b:14.1
occ:1.00
O A:ASP63 2.3 10.3 1.0
O A:HOH242 2.4 20.6 1.0
O A:HOH235 2.5 18.2 1.0
O A:HOH239 2.6 16.0 1.0
C A:ASP63 3.5 9.0 1.0
CB A:ASP63 4.2 9.3 0.5
CB A:ASP63 4.3 10.3 0.5
CA A:ASP63 4.3 8.6 0.5
CA A:ASP63 4.3 8.6 0.5
CG A:ASP63 4.4 11.8 0.5
N A:LYS64 4.6 9.2 1.0
OD2 A:ASP63 4.6 16.7 0.5
CA A:LYS64 4.8 10.7 1.0
O A:HOH250 4.8 23.0 1.0

Reference:

W.Bialek, S.Krzywda, P.Zatwarnicki, M.Jaskolski, A.Szczepaniak. Cytochrome C6 and C6C From Synechococcus Sp. Pcc 7002 - Structure and Function. To Be Published.
Page generated: Tue Dec 15 06:38:56 2020

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