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Sodium in PDB 7ynx: Crystal Structure of PIRH2 Bound to Poly-Ala Peptide

Enzymatic activity of Crystal Structure of PIRH2 Bound to Poly-Ala Peptide

All present enzymatic activity of Crystal Structure of PIRH2 Bound to Poly-Ala Peptide:
2.3.2.27;

Protein crystallography data

The structure of Crystal Structure of PIRH2 Bound to Poly-Ala Peptide, PDB code: 7ynx was solved by C.Dong, X.Yan, Y.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.52 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 69.47, 80.27, 84.87, 90, 90, 90
R / Rfree (%) 21.6 / 26.4

Other elements in 7ynx:

The structure of Crystal Structure of PIRH2 Bound to Poly-Ala Peptide also contains other interesting chemical elements:

Zinc (Zn) 16 atoms

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Sodium atom in the Crystal Structure of PIRH2 Bound to Poly-Ala Peptide (pdb code 7ynx). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 12 binding sites of Sodium where determined in the Crystal Structure of PIRH2 Bound to Poly-Ala Peptide, PDB code: 7ynx:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 12 in 7ynx

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Sodium binding site 1 out of 12 in the Crystal Structure of PIRH2 Bound to Poly-Ala Peptide


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 PIRH2 Bound to Poly-Ala Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na311

b:34.9
occ:1.00
 N A:GLY19 3.4 35.1 1.0
O A:GLY19 3.5 32.9 1.0
CD A:ARG18 3.8 27.6 1.0
CA A:ARG18 3.9 28.0 1.0
CD1 A:ILE63 4.0 35.0 1.0
NH1 A:ARG18 4.2 34.0 1.0
C A:ARG18 4.2 28.9 1.0
O A:GLN17 4.3 44.2 1.0
CG2 A:ILE63 4.3 30.0 1.0
CA A:GLY19 4.4 35.0 1.0
C A:GLY19 4.4 33.5 1.0
CB A:ARG18 4.5 28.6 1.0
NE A:ARG18 4.7 28.4 1.0
CG A:ARG18 4.8 31.3 1.0
O A:HOH460 4.8 51.8 1.0
CZ A:ARG18 4.9 34.6 1.0
N A:ARG18 5.0 34.2 1.0

Sodium binding site 2 out of 12 in 7ynx

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Sodium binding site 2 out of 12 in the Crystal Structure of PIRH2 Bound to Poly-Ala Peptide


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 PIRH2 Bound to Poly-Ala Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na312

b:13.8
occ:1.00
 O A:HOH427 3.0 25.0 1.0
NH1 A:ARG41 3.1 23.4 1.0
NH2 A:ARG25 3.2 22.2 1.0
NH1 A:ARG25 3.3 23.3 1.0
N A:ARG41 3.4 27.2 1.0
CZ A:ARG25 3.7 29.2 1.0
CB A:CYS40 3.7 25.0 1.0
CD1 A:LEU29 3.8 26.3 1.0
CG A:ARG41 3.9 27.0 1.0
CB A:ARG41 3.9 30.9 1.0
CD A:ARG41 3.9 26.0 1.0
CA A:CYS40 4.0 31.0 1.0
C A:CYS40 4.2 27.7 1.0
CE2 A:TYR23 4.2 28.2 1.0
CZ A:ARG41 4.3 32.2 1.0
CA A:ARG41 4.3 27.9 1.0
O A:HIS91 4.4 20.9 1.0
NE A:ARG41 4.6 25.2 1.0
SG A:CYS40 4.6 29.5 1.0
CZ A:TYR23 4.7 28.1 1.0
CD2 A:TYR23 4.7 25.6 1.0
CA A:LEU92 4.7 26.3 1.0
OH A:TYR23 4.9 20.8 1.0
NH2 A:ARG54 4.9 24.7 1.0
CG A:LEU92 5.0 29.4 1.0
NE A:ARG25 5.0 24.5 1.0

Sodium binding site 3 out of 12 in 7ynx

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Sodium binding site 3 out of 12 in the Crystal Structure of PIRH2 Bound to Poly-Ala Peptide


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 PIRH2 Bound to Poly-Ala Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na313

b:48.7
occ:1.00
 O A:HOH465 2.9 40.8 1.0
O A:CYS105 3.9 30.7 1.0
NH1 A:ARG142 4.4 24.6 1.0
CE2 A:PHE55 4.7 33.0 1.0
CZ A:PHE55 4.7 33.2 1.0
CG2 A:ILE107 4.8 27.1 1.0
CA A:GLY106 4.8 30.1 1.0
CD2 A:HIS153 4.8 25.9 1.0
O A:GLY106 4.8 36.6 1.0
NE2 A:HIS153 4.9 25.2 1.0
C A:GLY106 4.9 35.0 1.0

Sodium binding site 4 out of 12 in 7ynx

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Sodium binding site 4 out of 12 in the Crystal Structure of PIRH2 Bound to Poly-Ala Peptide


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 PIRH2 Bound to Poly-Ala Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na314

b:53.4
occ:1.00
 N A:HIS118 3.4 25.9 1.0
O A:HOH461 3.6 44.9 1.0
NZ A:LYS113 3.7 65.3 1.0
CA A:PHE117 4.0 29.9 1.0
CB A:HIS118 4.1 25.6 1.0
C A:PHE117 4.2 25.1 1.0
CA A:HIS118 4.3 27.1 1.0
CB A:PHE117 4.5 31.0 1.0
O A:HIS118 4.7 30.5 1.0
CE A:LYS113 4.8 64.5 1.0

Sodium binding site 5 out of 12 in 7ynx

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Sodium binding site 5 out of 12 in the Crystal Structure of PIRH2 Bound to Poly-Ala Peptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of PIRH2 Bound to Poly-Ala Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na315

b:42.5
occ:1.00
 CG2 A:VAL158 3.9 27.5 1.0
CG2 A:ILE110 4.0 27.7 1.0
CB A:ALA200 4.1 24.9 1.0
CB A:ILE110 4.5 26.3 1.0
CG1 A:ILE110 4.8 29.2 1.0

Sodium binding site 6 out of 12 in 7ynx

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Sodium binding site 6 out of 12 in the Crystal Structure of PIRH2 Bound to Poly-Ala Peptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of PIRH2 Bound to Poly-Ala Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na316

b:43.6
occ:1.00
 ND2 A:ASN123 3.4 32.8 1.0
O A:HOH416 3.5 45.9 1.0
CG A:ASN123 4.4 37.2 1.0
OD1 A:ASN123 4.5 32.7 1.0
NH2 A:ARG142 5.0 31.8 1.0

Sodium binding site 7 out of 12 in 7ynx

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Sodium binding site 7 out of 12 in the Crystal Structure of PIRH2 Bound to Poly-Ala Peptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of PIRH2 Bound to Poly-Ala Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na317

b:48.7
occ:1.00
 O A:HOH404 2.3 33.1 1.0
ND1 A:HIS169 3.5 29.8 1.0
O A:HOH441 3.7 34.3 1.0
CE1 A:HIS169 3.9 30.9 1.0
CG A:HIS169 4.1 27.0 1.0
SG A:CYS148 4.1 35.2 1.0
ZN A:ZN307 4.2 45.7 1.0
OG1 A:THR171 4.3 27.0 1.0
SG A:CYS172 4.3 29.3 1.0
OE2 A:GLU150 4.5 57.7 1.0
CB A:HIS169 4.5 27.8 1.0
NE2 A:HIS169 4.7 29.8 1.0
CB A:CYS148 4.8 34.4 1.0
CD2 A:HIS169 4.8 31.1 1.0
CG2 A:VAL157 4.9 23.6 1.0

Sodium binding site 8 out of 12 in 7ynx

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Sodium binding site 8 out of 12 in the Crystal Structure of PIRH2 Bound to Poly-Ala Peptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of PIRH2 Bound to Poly-Ala Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na312

b:14.9
occ:1.00
 NH1 B:ARG41 3.2 20.3 1.0
O B:HOH421 3.2 22.6 1.0
N B:ARG41 3.3 25.6 1.0
NH2 B:ARG25 3.3 19.7 1.0
NH1 B:ARG25 3.4 21.6 1.0
CB B:CYS40 3.5 25.5 1.0
CG B:ARG41 3.8 21.6 1.0
CZ B:ARG25 3.8 24.3 1.0
CD1 B:LEU29 3.8 20.7 1.0
CA B:CYS40 3.9 29.1 1.0
CB B:ARG41 3.9 24.6 1.0
CD B:ARG41 3.9 24.4 1.0
C B:CYS40 4.1 26.2 1.0
CE2 B:TYR23 4.1 22.0 1.0
CA B:ARG41 4.2 23.5 1.0
CZ B:ARG41 4.3 25.3 1.0
O B:HIS91 4.4 23.8 1.0
NE B:ARG41 4.6 19.0 1.0
CZ B:TYR23 4.6 26.6 1.0
CD2 B:TYR23 4.6 22.3 1.0
SG B:CYS40 4.6 25.1 1.0
OH B:TYR23 4.8 22.5 1.0
CA B:LEU92 4.8 25.1 1.0
NH2 B:ARG54 4.9 30.1 1.0
CG B:LEU29 4.9 25.5 1.0

Sodium binding site 9 out of 12 in 7ynx

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Sodium binding site 9 out of 12 in the Crystal Structure of PIRH2 Bound to Poly-Ala Peptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Crystal Structure of PIRH2 Bound to Poly-Ala Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na313

b:41.4
occ:1.00
 N B:HIS101 3.1 33.1 1.0
CA B:TYR100 3.7 23.6 1.0
C B:TYR100 3.9 31.8 1.0
CB B:TYR100 4.0 25.4 1.0
CB B:HIS101 4.1 31.4 1.0
CA B:HIS101 4.1 34.2 1.0
O B:HIS101 4.1 40.1 1.0
OH B:TYR85 4.3 29.0 1.0
C B:HIS101 4.6 30.6 1.0
N B:TYR100 5.0 24.5 1.0

Sodium binding site 10 out of 12 in 7ynx

Go back to Sodium Binding Sites List in 7ynx
Sodium binding site 10 out of 12 in the Crystal Structure of PIRH2 Bound to Poly-Ala Peptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Crystal Structure of PIRH2 Bound to Poly-Ala Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na314

b:53.4
occ:1.00
 ND2 B:ASN123 3.3 37.1 1.0
CG B:ASN123 4.4 41.0 1.0
OD1 B:ASN123 4.7 36.4 1.0

Reference:

C.Dong, X.Yan, Y.Li. Crystal Structure of PIRH2 Bound to Poly-Ala Peptide To Be Published.
Page generated: Wed Oct 9 09:56:46 2024

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