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Sodium in PDB 4ryf: CLPP1/2 Heterocomplex From Listeria Monocytogenes

Enzymatic activity of CLPP1/2 Heterocomplex From Listeria Monocytogenes

All present enzymatic activity of CLPP1/2 Heterocomplex From Listeria Monocytogenes:
3.4.21.92;

Protein crystallography data

The structure of CLPP1/2 Heterocomplex From Listeria Monocytogenes, PDB code: 4ryf was solved by M.Dahmen, M.-T.Vielberg, M.Groll, S.A.Sieber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 97.230, 127.150, 265.500, 90.00, 90.00, 90.00
R / Rfree (%) 18 / 21.6

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Sodium atom in the CLPP1/2 Heterocomplex From Listeria Monocytogenes (pdb code 4ryf). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 14 binding sites of Sodium where determined in the CLPP1/2 Heterocomplex From Listeria Monocytogenes, PDB code: 4ryf:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 14 in 4ryf

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Sodium binding site 1 out of 14 in the CLPP1/2 Heterocomplex From Listeria Monocytogenes


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of CLPP1/2 Heterocomplex From Listeria Monocytogenes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na301

b:51.6
occ:1.00
 O A:HOH402 2.4 31.3 1.0
O A:ILE84 3.1 54.4 1.0
O A:LYS82 3.1 53.4 1.0
ND2 B:ASN192 3.7 70.9 1.0
C A:LYS82 4.0 50.1 1.0
O A:LYS85 4.1 53.9 1.0
C A:ILE84 4.3 55.2 1.0
CA A:LYS82 4.3 47.5 1.0
O A:ILE81 4.4 45.1 1.0
O A:PRO86 4.5 49.1 1.0
C A:LYS85 4.6 56.6 1.0
CA A:LYS85 4.8 60.4 1.0
CG B:ASN192 5.0 72.5 1.0
N A:LYS85 5.0 57.4 1.0

Sodium binding site 2 out of 14 in 4ryf

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Sodium binding site 2 out of 14 in the CLPP1/2 Heterocomplex From Listeria Monocytogenes


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of CLPP1/2 Heterocomplex From Listeria Monocytogenes within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na301

b:51.2
occ:1.00
 O B:LYS82 2.9 52.9 1.0
O B:ILE84 3.0 59.9 1.0
C B:LYS82 3.7 51.4 1.0
ND2 C:ASN192 3.8 67.7 1.0
CA B:LYS82 4.1 50.8 1.0
O B:ILE81 4.1 50.6 1.0
C B:ILE84 4.2 58.9 1.0
O B:LYS85 4.2 55.0 1.0
O B:PRO86 4.4 52.6 1.0
C B:LYS85 4.7 59.0 1.0
N B:PHE83 4.8 50.5 1.0
CA B:LYS85 4.9 62.8 1.0
N B:ILE84 5.0 51.6 1.0
C B:PHE83 5.0 53.6 1.0
C B:ILE81 5.0 50.4 1.0

Sodium binding site 3 out of 14 in 4ryf

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Sodium binding site 3 out of 14 in the CLPP1/2 Heterocomplex From Listeria Monocytogenes


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of CLPP1/2 Heterocomplex From Listeria Monocytogenes within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na301

b:46.9
occ:1.00
 O C:ILE81 3.0 49.1 1.0
O C:PRO86 3.1 55.6 1.0
O C:ILE84 3.8 55.5 1.0
N C:VAL88 4.0 54.0 1.0
C C:ILE81 4.1 46.9 1.0
C C:PRO86 4.1 57.1 1.0
CA C:THR87 4.2 56.6 1.0
CG2 C:VAL88 4.2 50.8 1.0
CA C:LYS82 4.2 47.8 1.0
O C:LYS82 4.3 55.2 1.0
C C:THR87 4.5 55.7 1.0
C C:LYS82 4.5 48.8 1.0
CB C:VAL88 4.5 52.1 1.0
N C:THR87 4.6 56.1 1.0
N C:LYS82 4.6 46.8 1.0
O C:LYS85 4.7 65.5 1.0
CG2 C:ILE81 4.8 45.6 1.0
CA C:VAL88 4.9 53.0 1.0
C C:ILE84 4.9 59.3 1.0
CG1 C:ILE84 4.9 52.4 1.0

Sodium binding site 4 out of 14 in 4ryf

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Sodium binding site 4 out of 14 in the CLPP1/2 Heterocomplex From Listeria Monocytogenes


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of CLPP1/2 Heterocomplex From Listeria Monocytogenes within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na301

b:46.1
occ:1.00
 O D:ILE81 2.9 45.8 1.0
O D:PRO86 3.0 52.5 1.0
O D:ILE84 3.4 48.3 1.0
C D:ILE81 4.0 46.1 1.0
C D:PRO86 4.0 55.1 1.0
O D:LYS82 4.1 48.1 1.0
CA D:LYS82 4.1 46.0 1.0
N D:VAL88 4.2 48.5 1.0
CA D:THR87 4.3 52.7 1.0
CG2 D:VAL88 4.3 40.7 1.0
C D:LYS82 4.3 46.0 1.0
O D:LYS85 4.4 61.1 1.0
C D:ILE84 4.5 50.7 1.0
N D:LYS82 4.5 45.5 1.0
N D:THR87 4.6 54.8 1.0
C D:THR87 4.6 51.2 1.0
CG1 D:ILE84 4.7 46.4 1.0
CB D:VAL88 4.7 44.1 1.0
C D:LYS85 4.7 58.5 1.0
CG2 D:ILE81 5.0 43.4 1.0

Sodium binding site 5 out of 14 in 4ryf

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Sodium binding site 5 out of 14 in the CLPP1/2 Heterocomplex From Listeria Monocytogenes


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of CLPP1/2 Heterocomplex From Listeria Monocytogenes within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na301

b:34.6
occ:1.00
 O E:ILE84 2.6 41.0 1.0
O E:LYS82 3.2 38.6 1.0
O E:PRO86 3.6 44.7 1.0
O E:ILE81 3.6 37.7 1.0
C E:ILE84 3.8 43.0 1.0
O E:LYS85 3.8 47.4 1.0
C E:LYS82 3.9 38.3 1.0
CA E:LYS82 4.1 36.7 1.0
C E:LYS85 4.2 46.2 1.0
C E:PRO86 4.5 42.6 1.0
CA E:LYS85 4.5 48.5 1.0
N E:LYS85 4.6 45.1 1.0
C E:ILE81 4.6 36.7 1.0
N E:ILE84 4.7 40.4 1.0
ND2 F:ASN192 4.7 62.3 1.0
CA E:ILE84 4.8 41.4 1.0
N E:PHE83 4.8 39.4 1.0
C E:PHE83 4.9 39.7 1.0
N E:LYS82 4.9 35.3 1.0
CG1 E:ILE84 4.9 41.1 1.0
N E:PRO86 4.9 43.5 1.0

Sodium binding site 6 out of 14 in 4ryf

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Sodium binding site 6 out of 14 in the CLPP1/2 Heterocomplex From Listeria Monocytogenes


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of CLPP1/2 Heterocomplex From Listeria Monocytogenes within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na301

b:57.4
occ:1.00
 O F:ILE84 2.6 43.3 1.0
O F:HOH409 2.7 38.5 1.0
O F:LYS82 3.0 37.7 1.0
C F:LYS82 3.8 34.9 1.0
C F:ILE84 3.9 41.3 1.0
O F:LYS85 3.9 48.3 1.0
O F:ILE81 3.9 39.8 1.0
O F:PRO86 4.0 47.3 1.0
CA F:LYS82 4.2 34.7 1.0
ND2 G:ASN192 4.2 65.1 1.0
C F:LYS85 4.3 47.4 1.0
CA F:LYS85 4.5 48.7 1.0
N F:LYS85 4.7 44.5 1.0
N F:ILE84 4.7 35.7 1.0
C F:PHE83 4.8 36.0 1.0
N F:PHE83 4.8 33.5 1.0
C F:PRO86 4.8 46.3 1.0
CA F:ILE84 4.9 38.1 1.0
C F:ILE81 4.9 37.1 1.0
O F:PHE83 5.0 37.2 1.0

Sodium binding site 7 out of 14 in 4ryf

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Sodium binding site 7 out of 14 in the CLPP1/2 Heterocomplex From Listeria Monocytogenes


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of CLPP1/2 Heterocomplex From Listeria Monocytogenes within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na301

b:44.6
occ:1.00
 O G:ILE84 2.7 39.5 1.0
O G:ILE81 3.0 35.1 1.0
O G:PRO86 3.1 33.9 1.0
O G:LYS82 3.5 35.0 1.0
C G:ILE84 3.9 38.3 1.0
C G:LYS82 3.9 33.8 1.0
O G:LYS85 4.0 41.2 1.0
CA G:LYS82 4.0 32.1 1.0
C G:PRO86 4.1 36.7 1.0
C G:ILE81 4.1 33.8 1.0
C G:LYS85 4.3 40.1 1.0
CG1 G:ILE84 4.4 31.6 1.0
N G:LYS82 4.6 32.3 1.0
N G:ILE84 4.6 35.7 1.0
CA G:THR87 4.7 36.8 1.0
CA G:ILE84 4.7 36.3 1.0
N G:LYS85 4.8 40.3 1.0
N G:THR87 4.8 38.5 1.0
CA G:LYS85 4.8 42.4 1.0
N G:PRO86 4.8 37.2 1.0
N G:PHE83 4.8 33.5 1.0
CG2 G:VAL88 4.8 31.4 1.0
N G:VAL88 4.9 35.5 1.0

Sodium binding site 8 out of 14 in 4ryf

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Sodium binding site 8 out of 14 in the CLPP1/2 Heterocomplex From Listeria Monocytogenes


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of CLPP1/2 Heterocomplex From Listeria Monocytogenes within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na302

b:38.5
occ:1.00
 O H:MET81 2.7 54.3 1.0
O H:ALA86 2.7 64.7 1.0
O H:VAL84 2.9 61.0 1.0
C H:ALA86 3.8 63.5 1.0
C H:MET81 3.9 50.9 1.0
C H:VAL84 4.0 59.8 1.0
CG2 H:VAL84 4.1 48.8 1.0
O H:ASN82 4.1 54.9 1.0
O H:LYS85 4.2 65.9 1.0
CA H:ASN82 4.2 49.9 1.0
C H:ASN82 4.3 51.2 1.0
CA H:ASP87 4.3 60.8 1.0
C H:LYS85 4.4 65.5 1.0
N H:VAL88 4.5 56.2 1.0
N H:ASP87 4.5 62.6 1.0
N H:ASN82 4.5 47.8 1.0
CG2 H:VAL88 4.7 43.8 1.0
N H:ALA86 4.7 63.4 1.0
OD2 H:ASP87 4.8 59.4 1.0
N H:VAL84 4.8 55.5 1.0
CA H:VAL84 4.8 57.1 1.0
C H:ASP87 4.8 57.9 1.0
N H:LYS85 4.9 62.2 1.0
CA H:ALA86 4.9 63.0 1.0
CA H:LYS85 4.9 66.3 1.0

Sodium binding site 9 out of 14 in 4ryf

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Sodium binding site 9 out of 14 in the CLPP1/2 Heterocomplex From Listeria Monocytogenes


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of CLPP1/2 Heterocomplex From Listeria Monocytogenes within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Na302

b:25.1
occ:1.00
 O I:ALA86 2.7 46.0 1.0
O I:MET81 2.7 36.3 1.0
O I:VAL84 2.9 44.7 1.0
C I:ALA86 3.7 44.5 1.0
C I:MET81 3.9 36.2 1.0
CG2 I:VAL84 4.0 41.5 1.0
C I:VAL84 4.0 46.4 1.0
O I:ASN82 4.2 41.9 1.0
O I:LYS85 4.2 49.3 1.0
CA I:ASP87 4.2 43.1 1.0
CA I:ASN82 4.3 38.8 1.0
N I:VAL88 4.3 40.6 1.0
C I:ASN82 4.4 40.8 1.0
N I:ASP87 4.4 42.7 1.0
C I:LYS85 4.4 49.5 1.0
N I:ASN82 4.6 35.8 1.0
CG2 I:VAL88 4.6 36.1 1.0
C I:ASP87 4.7 41.0 1.0
N I:ALA86 4.7 47.0 1.0
OD2 I:ASP87 4.7 45.6 1.0
N I:VAL84 4.8 44.3 1.0
CA I:VAL84 4.8 45.0 1.0
CA I:ALA86 4.9 44.6 1.0
N I:LYS85 4.9 49.6 1.0
CA I:LYS85 5.0 52.4 1.0
CB I:VAL84 5.0 43.2 1.0

Sodium binding site 10 out of 14 in 4ryf

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Sodium binding site 10 out of 14 in the CLPP1/2 Heterocomplex From Listeria Monocytogenes


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of CLPP1/2 Heterocomplex From Listeria Monocytogenes within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Na302

b:24.4
occ:1.00
 O J:VAL84 2.7 36.0 1.0
O J:MET81 2.7 32.3 1.0
O J:ALA86 2.8 33.1 1.0
C J:VAL84 3.8 36.2 1.0
C J:ALA86 3.9 33.6 1.0
C J:MET81 3.9 31.9 1.0
O J:ASN82 4.0 39.0 1.0
CG2 J:VAL84 4.0 33.6 1.0
CA J:ASN82 4.2 32.9 1.0
C J:ASN82 4.2 35.1 1.0
O J:LYS85 4.2 35.2 1.0
C J:LYS85 4.3 35.8 1.0
CA J:ASP87 4.5 32.8 1.0
N J:ASN82 4.5 31.9 1.0
N J:ASP87 4.6 33.2 1.0
N J:VAL84 4.6 33.8 1.0
N J:VAL88 4.6 31.8 1.0
CA J:VAL84 4.7 34.7 1.0
N J:ALA86 4.7 34.1 1.0
N J:LYS85 4.8 37.0 1.0
CG2 J:VAL88 4.8 28.9 1.0
CA J:LYS85 4.8 38.2 1.0
OD2 J:ASP87 4.9 37.0 1.0
CA J:ALA86 4.9 34.2 1.0
CB J:VAL84 4.9 34.7 1.0
C J:ASP87 5.0 32.7 1.0
N J:PHE83 5.0 35.0 1.0

Reference:

M.Dahmen, M.-T.Vielberg, M.Groll, S.A.Sieber. CLPP12 Heterocomplex From Listeria Monocytogenes To Be Published.
Page generated: Sun Aug 17 21:43:50 2025

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