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Yttrium in PDB 3v3c: Crystal Structure of Chloroplast Atp Synthase C-Ring From Pisum Sativum

Protein crystallography data

The structure of Crystal Structure of Chloroplast Atp Synthase C-Ring From Pisum Sativum, PDB code: 3v3c was solved by S.Saroussi, N.Nelson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.89 / 3.40
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 139.130, 102.380, 122.430, 90.00, 101.22, 90.00
R / Rfree (%) 29.9 / 32.2

Other elements in 3v3c:

The structure of Crystal Structure of Chloroplast Atp Synthase C-Ring From Pisum Sativum also contains other interesting chemical elements:

Sodium (Na) 14 atoms

Yttrium Binding Sites:

The binding sites of Yttrium atom in the Crystal Structure of Chloroplast Atp Synthase C-Ring From Pisum Sativum (pdb code 3v3c). This binding sites where shown within 5.0 Angstroms radius around Yttrium atom.
In total 10 binding sites of Yttrium where determined in the Crystal Structure of Chloroplast Atp Synthase C-Ring From Pisum Sativum, PDB code: 3v3c:
Jump to Yttrium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Yttrium binding site 1 out of 10 in 3v3c

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Yttrium binding site 1 out of 10 in the Crystal Structure of Chloroplast Atp Synthase C-Ring From Pisum Sativum


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Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 1 of Crystal Structure of Chloroplast Atp Synthase C-Ring From Pisum Sativum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Y103

b:0.5
occ:1.00
 CG A:GLN42 3.6 90.3 1.0
CB A:GLN42 4.4 60.7 1.0
CA A:GLN42 4.7 61.3 1.0
O A:ARG41 4.8 46.0 1.0

Yttrium binding site 2 out of 10 in 3v3c

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Yttrium binding site 2 out of 10 in the Crystal Structure of Chloroplast Atp Synthase C-Ring From Pisum Sativum


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 2 of Crystal Structure of Chloroplast Atp Synthase C-Ring From Pisum Sativum within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Y104

b:80.7
occ:1.00
 O N:ARG41 4.3 42.0 1.0
CA N:GLN42 4.7 53.8 1.0
CB N:GLN42 4.8 47.9 1.0

Yttrium binding site 3 out of 10 in 3v3c

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Yttrium binding site 3 out of 10 in the Crystal Structure of Chloroplast Atp Synthase C-Ring From Pisum Sativum


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 3 of Crystal Structure of Chloroplast Atp Synthase C-Ring From Pisum Sativum within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Y105

b:66.7
occ:0.50
 O E:ARG41 4.6 45.2 1.0
CB E:GLN42 4.8 53.6 1.0
CA E:GLN42 4.9 50.9 1.0

Yttrium binding site 4 out of 10 in 3v3c

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Yttrium binding site 4 out of 10 in the Crystal Structure of Chloroplast Atp Synthase C-Ring From Pisum Sativum


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 4 of Crystal Structure of Chloroplast Atp Synthase C-Ring From Pisum Sativum within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Y106

b:0.4
occ:1.00
 O F:ARG41 4.5 47.2 1.0
CA F:GLN42 4.9 55.2 1.0

Yttrium binding site 5 out of 10 in 3v3c

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Yttrium binding site 5 out of 10 in the Crystal Structure of Chloroplast Atp Synthase C-Ring From Pisum Sativum


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 5 of Crystal Structure of Chloroplast Atp Synthase C-Ring From Pisum Sativum within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Y107

b:72.7
occ:1.00
 CB G:GLN42 4.6 32.0 1.0
CA G:GLN42 5.0 46.7 1.0

Yttrium binding site 6 out of 10 in 3v3c

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Yttrium binding site 6 out of 10 in the Crystal Structure of Chloroplast Atp Synthase C-Ring From Pisum Sativum


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 6 of Crystal Structure of Chloroplast Atp Synthase C-Ring From Pisum Sativum within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Y108

b:73.3
occ:1.00
 OE2 H:GLU44 3.0 0.7 1.0
CD H:GLU44 3.7 0.8 1.0
CG H:GLU44 3.9 0.2 1.0
O H:ARG41 4.3 37.8 1.0
CA H:GLN42 4.3 55.0 1.0
CB H:GLN42 4.5 46.7 1.0
OE1 H:GLU44 4.7 0.7 1.0
CD H:PRO43 4.8 51.1 1.0

Yttrium binding site 7 out of 10 in 3v3c

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Yttrium binding site 7 out of 10 in the Crystal Structure of Chloroplast Atp Synthase C-Ring From Pisum Sativum


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 7 of Crystal Structure of Chloroplast Atp Synthase C-Ring From Pisum Sativum within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Y110

b:87.1
occ:0.50
 O L:ARG41 4.7 57.1 1.0
CB L:GLN42 4.8 54.6 1.0
CA L:GLN42 4.9 53.6 1.0

Yttrium binding site 8 out of 10 in 3v3c

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Yttrium binding site 8 out of 10 in the Crystal Structure of Chloroplast Atp Synthase C-Ring From Pisum Sativum


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 8 of Crystal Structure of Chloroplast Atp Synthase C-Ring From Pisum Sativum within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Y111

b:89.7
occ:1.00
 NE2 K:GLN42 3.2 0.9 1.0
OE1 K:GLU44 3.5 1.0 1.0
CD K:GLN42 3.6 0.9 1.0
OE1 K:GLN42 3.6 0.5 1.0
O K:ARG41 4.1 30.7 1.0
CD K:GLU44 4.4 0.0 1.0
CG K:GLU44 4.7 0.6 1.0
CG K:GLN42 4.7 0.8 1.0
CA K:GLN42 4.7 56.6 1.0
CD K:PRO43 4.9 54.5 1.0

Yttrium binding site 9 out of 10 in 3v3c

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Yttrium binding site 9 out of 10 in the Crystal Structure of Chloroplast Atp Synthase C-Ring From Pisum Sativum


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 9 of Crystal Structure of Chloroplast Atp Synthase C-Ring From Pisum Sativum within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Y112

b:0.3
occ:1.00
 O C:VAL81 3.1 0.1 1.0
C C:VAL81 3.3 0.5 1.0
CA C:VAL81 4.0 0.5 1.0
N C:VAL81 4.9 0.1 1.0

Yttrium binding site 10 out of 10 in 3v3c

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Yttrium binding site 10 out of 10 in the Crystal Structure of Chloroplast Atp Synthase C-Ring From Pisum Sativum


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 10 of Crystal Structure of Chloroplast Atp Synthase C-Ring From Pisum Sativum within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Y113

b:0.1
occ:1.00
 O D:VAL81 3.2 0.1 1.0
C D:VAL81 3.2 0.6 1.0
CA D:VAL81 4.0 0.0 1.0
CG2 D:VAL81 4.8 0.6 1.0
CB D:VAL81 4.8 0.9 1.0

Reference:

S.Saroussi, M.Schushan, N.Ben-Tal, W.Junge, N.Nelson. Structure and Flexibility of the C-Ring in the Electromotor of Rotary F(O)F(1)-Atpase of Pea Chloroplasts. Plos One V. 7 43045 2012.
ISSN: ESSN 1932-6203
PubMed: 23049735
DOI: 10.1371/JOURNAL.PONE.0043045
Page generated: Sat Oct 12 20:40:10 2024

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