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Sodium in PDB 2e84: Crystal Structure of High-Molecular Weight Cytochrome C From Desulfovibrio Vulgaris (Miyazaki F) in the Presence of Zinc Ion

Protein crystallography data

The structure of Crystal Structure of High-Molecular Weight Cytochrome C From Desulfovibrio Vulgaris (Miyazaki F) in the Presence of Zinc Ion, PDB code: 2e84 was solved by N.Shibata, K.Suto, M.Sato, Y.Morimoto, M.Kitamura, Y.Higuchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.20 / 2.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.090, 84.070, 142.670, 90.00, 90.00, 90.00
R / Rfree (%) 20.4 / 25.9

Other elements in 2e84:

The structure of Crystal Structure of High-Molecular Weight Cytochrome C From Desulfovibrio Vulgaris (Miyazaki F) in the Presence of Zinc Ion also contains other interesting chemical elements:

Iron (Fe) 16 atoms
Zinc (Zn) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of High-Molecular Weight Cytochrome C From Desulfovibrio Vulgaris (Miyazaki F) in the Presence of Zinc Ion (pdb code 2e84). 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 High-Molecular Weight Cytochrome C From Desulfovibrio Vulgaris (Miyazaki F) in the Presence of Zinc Ion, PDB code: 2e84:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 2e84

Go back to Sodium Binding Sites List in 2e84
Sodium binding site 1 out of 4 in the Crystal Structure of High-Molecular Weight Cytochrome C From Desulfovibrio Vulgaris (Miyazaki F) in the Presence of Zinc Ion


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 High-Molecular Weight Cytochrome C From Desulfovibrio Vulgaris (Miyazaki F) in the Presence of Zinc Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na561

b:29.9
occ:1.00
ND1 A:HIS527 2.9 29.9 1.0
CE A:LYS523 3.4 51.3 1.0
NZ A:LYS523 3.6 52.3 1.0
CE1 A:HIS527 3.8 31.6 1.0
CG A:HIS527 3.8 27.1 1.0
CB A:HIS527 4.0 22.1 1.0
CG A:LYS523 4.3 40.1 1.0
CD A:LYS523 4.4 46.1 1.0
CA A:ALA524 4.6 31.9 1.0
O A:HOH1468 4.8 49.1 1.0
O A:LYS523 4.9 32.8 1.0
N A:ALA524 4.9 32.4 1.0
CB A:ALA524 4.9 31.2 1.0
NE2 A:HIS527 4.9 19.6 1.0
CD2 A:HIS527 5.0 22.6 1.0

Sodium binding site 2 out of 4 in 2e84

Go back to Sodium Binding Sites List in 2e84
Sodium binding site 2 out of 4 in the Crystal Structure of High-Molecular Weight Cytochrome C From Desulfovibrio Vulgaris (Miyazaki F) in the Presence of Zinc Ion


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 High-Molecular Weight Cytochrome C From Desulfovibrio Vulgaris (Miyazaki F) in the Presence of Zinc Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na562

b:60.0
occ:1.00
OE1 A:GLU124 2.2 65.2 1.0
CD A:GLU124 3.2 65.2 1.0
OE2 A:GLU124 3.7 71.8 1.0
CG A:GLU124 4.5 59.4 1.0

Sodium binding site 3 out of 4 in 2e84

Go back to Sodium Binding Sites List in 2e84
Sodium binding site 3 out of 4 in the Crystal Structure of High-Molecular Weight Cytochrome C From Desulfovibrio Vulgaris (Miyazaki F) in the Presence of Zinc Ion


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 High-Molecular Weight Cytochrome C From Desulfovibrio Vulgaris (Miyazaki F) in the Presence of Zinc Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na563

b:42.3
occ:1.00
OD2 A:ASP136 2.0 63.2 1.0
CG A:ASP136 2.8 62.9 1.0
OD1 A:ASP136 3.0 61.7 1.0
O A:HOH1513 3.1 43.0 1.0
O A:HOH1509 3.4 52.8 1.0
O A:HOH1508 3.8 56.9 1.0
CB A:ASP136 4.1 57.0 1.0
CBB A:HEM1303 4.2 61.2 1.0
O A:ASP136 4.2 58.6 1.0
C A:ASP136 4.6 57.2 1.0
CA A:ASP136 4.8 56.4 1.0

Sodium binding site 4 out of 4 in 2e84

Go back to Sodium Binding Sites List in 2e84
Sodium binding site 4 out of 4 in the Crystal Structure of High-Molecular Weight Cytochrome C From Desulfovibrio Vulgaris (Miyazaki F) in the Presence of Zinc Ion


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 High-Molecular Weight Cytochrome C From Desulfovibrio Vulgaris (Miyazaki F) in the Presence of Zinc Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na564

b:22.6
occ:1.00
O A:MET279 2.3 24.1 1.0
O A:HOH1319 2.8 34.2 1.0
O2D A:HEM1308 3.3 48.4 1.0
O A:HOH1320 3.3 69.3 1.0
C A:MET279 3.4 25.6 1.0
O A:HOH1318 3.7 38.6 1.0
N A:MET279 3.9 21.7 1.0
O A:HOH1343 4.1 41.9 1.0
CA A:MET279 4.1 23.2 1.0
NH1 A:ARG417 4.2 69.9 1.0
N A:VAL280 4.4 24.0 1.0
CGD A:HEM1308 4.4 46.2 1.0
CB A:ALA278 4.5 13.0 1.0
NZ A:LYS414 4.5 74.3 1.0
CB A:MET279 4.6 23.3 1.0
CA A:VAL280 4.6 23.2 1.0
CD A:ARG417 4.6 50.9 1.0
C A:ALA278 4.7 19.6 1.0
CA A:ALA278 4.9 15.5 1.0

Reference:

H.Osuka, K.Suto, M.Sato, N.Shibata, M.Kitamura, Y.Morimoto, K.Ozawa, H.Akutsu, Y.Higuchi, N.Yasuoka. Structure of High-Molecular Weight Cytochrome C From Desulfovibrio Vulgaris (Miyazaki F) To Be Published.
Page generated: Tue Dec 15 05:47:53 2020

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