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Sodium in PDB 1m64: Crystal Structure of Q363F Mutant Flavocytochrome C3

Enzymatic activity of Crystal Structure of Q363F Mutant Flavocytochrome C3

All present enzymatic activity of Crystal Structure of Q363F Mutant Flavocytochrome C3:
1.3.99.1;

Protein crystallography data

The structure of Crystal Structure of Q363F Mutant Flavocytochrome C3, PDB code: 1m64 was solved by C.G.Mowat, K.L.Pankhurst, C.S.Miles, D.Leys, M.D.Walkinshaw, G.A.Reid, S.K.Chapman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 78.520, 88.886, 91.194, 90.00, 104.42, 90.00
R / Rfree (%) 16.3 / 22.4

Other elements in 1m64:

The structure of Crystal Structure of Q363F Mutant Flavocytochrome C3 also contains other interesting chemical elements:

Iron (Fe) 8 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Q363F Mutant Flavocytochrome C3 (pdb code 1m64). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Q363F Mutant Flavocytochrome C3, PDB code: 1m64:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 1m64

Go back to Sodium Binding Sites List in 1m64
Sodium binding site 1 out of 2 in the Crystal Structure of Q363F Mutant Flavocytochrome C3


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 Q363F Mutant Flavocytochrome C3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na3002

b:9.8
occ:1.00
O A:HOH3009 2.5 9.5 1.0
O A:THR536 2.5 8.7 1.0
O A:GLU534 2.5 7.3 1.0
O A:THR506 2.5 6.7 1.0
O A:GLY508 2.6 7.6 1.0
O A:MET507 3.1 9.7 1.0
C A:MET507 3.3 10.1 1.0
C A:GLY508 3.5 9.3 1.0
C A:GLU534 3.5 8.3 1.0
O A:HOH3019 3.6 10.4 1.0
C A:THR506 3.7 9.0 1.0
C A:THR536 3.7 10.3 1.0
CA A:MET507 3.7 9.1 1.0
N A:GLY508 3.7 9.4 1.0
CA A:GLU534 4.0 7.3 1.0
CG A:GLU534 4.0 7.5 1.0
O A:HOH3033 4.1 9.9 1.0
CA A:GLY508 4.1 9.7 1.0
N A:MET507 4.1 9.1 1.0
N A:THR536 4.2 9.6 1.0
O A:HOH3054 4.4 11.8 1.0
C A:VAL535 4.4 9.7 1.0
N A:GLY509 4.5 8.6 1.0
N A:GLY537 4.5 9.2 1.0
CA A:THR536 4.5 9.5 1.0
N A:VAL535 4.5 8.8 1.0
CA A:GLY537 4.6 11.0 1.0
CB A:GLU534 4.6 7.9 1.0
NE2 A:HIS505 4.7 9.1 1.0
CA A:GLY509 4.7 8.9 1.0
CA A:VAL535 4.8 9.5 1.0
O A:VAL535 4.8 8.6 1.0
OG1 A:THR506 4.8 6.2 1.0
O A:GLY533 4.8 8.0 1.0
CA A:THR506 4.9 7.6 1.0

Sodium binding site 2 out of 2 in 1m64

Go back to Sodium Binding Sites List in 1m64
Sodium binding site 2 out of 2 in the Crystal Structure of Q363F Mutant Flavocytochrome C3


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 Q363F Mutant Flavocytochrome C3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na4002

b:10.1
occ:1.00
O B:HOH4016 2.5 8.7 1.0
O B:GLU534 2.5 7.6 1.0
O B:THR506 2.5 7.9 1.0
O B:THR536 2.5 9.1 1.0
O B:GLY508 2.6 8.4 1.0
O B:MET507 3.1 8.9 1.0
C B:MET507 3.3 9.5 1.0
C B:GLU534 3.5 7.7 1.0
C B:GLY508 3.5 11.0 1.0
O B:HOH4034 3.5 10.1 1.0
C B:THR536 3.6 10.3 1.0
C B:THR506 3.7 7.1 1.0
CA B:MET507 3.7 7.7 1.0
N B:GLY508 3.7 9.6 1.0
CA B:GLU534 4.0 7.5 1.0
CG B:GLU534 4.0 7.0 1.0
O B:HOH4060 4.1 9.4 1.0
CA B:GLY508 4.1 9.6 1.0
N B:MET507 4.1 7.3 1.0
N B:THR536 4.2 8.0 1.0
O B:HOH4041 4.3 11.0 1.0
C B:VAL535 4.4 7.0 1.0
N B:GLY509 4.5 8.9 1.0
N B:GLY537 4.5 9.6 1.0
CA B:THR536 4.5 7.8 1.0
N B:VAL535 4.5 8.1 1.0
CA B:GLY537 4.6 9.8 1.0
CB B:GLU534 4.6 6.8 1.0
CA B:GLY509 4.7 10.3 1.0
NE2 B:HIS505 4.8 8.4 1.0
O B:GLY533 4.8 7.5 1.0
OG1 B:THR506 4.8 6.7 1.0
CA B:VAL535 4.8 6.9 1.0
O B:VAL535 4.8 7.0 1.0
CA B:THR506 4.9 8.1 1.0

Reference:

C.G.Mowat, K.L.Pankhurst, C.S.Miles, D.Leys, M.D.Walkinshaw, G.A.Reid, S.K.Chapman. Engineering Water to Act As An Active Site Acid Catalyst in A Soluble Fumarate Reductase Biochemistry V. 41 11990 2002.
ISSN: ISSN 0006-2960
PubMed: 12356299
DOI: 10.1021/BI0203177
Page generated: Tue Dec 15 05:29:44 2020

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