Sodium in PDB 6z1y: Crystal Structure of Type-I Ribosome-Inactivating Protein Trichobakin (Tbk)

Protein crystallography data

The structure of Crystal Structure of Type-I Ribosome-Inactivating Protein Trichobakin (Tbk), PDB code: 6z1y was solved by K.M.Boyko, A.Y.Nikolaeva, V.V.Britikov, E.V.Bocharov, E.V.Britikova, T.B.T.Le, C.V.Phan, V.O.Popov, S.A.Usanov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.41 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 71.720, 73.730, 88.070, 90.00, 96.85, 90.00
R / Rfree (%) 17.2 / 22.7

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Type-I Ribosome-Inactivating Protein Trichobakin (Tbk) (pdb code 6z1y). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Crystal Structure of Type-I Ribosome-Inactivating Protein Trichobakin (Tbk), PDB code: 6z1y:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 6z1y

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Sodium binding site 1 out of 6 in the Crystal Structure of Type-I Ribosome-Inactivating Protein Trichobakin (Tbk)


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 Type-I Ribosome-Inactivating Protein Trichobakin (Tbk) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na301

b:0.9
occ:1.00
 O A:ASN145 2.7 8.7 1.0
O A:HOH459 2.9 10.1 1.0
O A:ALA118 3.0 9.8 1.0
O A:HOH544 3.3 4.2 1.0
O A:HOH507 3.4 9.0 1.0
C A:ALA118 3.9 9.7 1.0
C A:ASN145 3.9 10.5 1.0
O A:HOH479 4.0 4.2 1.0
CA A:ALA118 4.2 9.2 1.0
O A:HOH473 4.6 5.5 1.0
CA A:ASN145 4.7 12.0 1.0
O A:ALA117 4.7 9.4 1.0
N A:SER146 4.9 10.3 1.0
CB A:ALA118 5.0 9.9 1.0
CB A:ASN145 5.0 12.6 1.0
CA A:SER146 5.0 9.5 1.0

Sodium binding site 2 out of 6 in 6z1y

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Sodium binding site 2 out of 6 in the Crystal Structure of Type-I Ribosome-Inactivating Protein Trichobakin (Tbk)


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 Type-I Ribosome-Inactivating Protein Trichobakin (Tbk) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na301

b:4.2
occ:1.00
 O B:ASP176 2.8 17.7 1.0
C B:ASP176 3.5 17.3 1.0
CG B:PRO130 4.0 9.1 1.0
CA B:ASP176 4.2 18.8 1.0
CB B:PRO130 4.3 8.9 1.0
N B:LYS177 4.3 15.2 1.0
CA B:LYS177 4.5 13.7 1.0
CB B:ASP176 4.6 20.7 1.0

Sodium binding site 3 out of 6 in 6z1y

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Sodium binding site 3 out of 6 in the Crystal Structure of Type-I Ribosome-Inactivating Protein Trichobakin (Tbk)


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 Type-I Ribosome-Inactivating Protein Trichobakin (Tbk) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na302

b:4.2
occ:1.00
 O B:HOH551 2.7 8.6 0.5
OG C:SER12 2.8 8.8 1.0
O B:HOH443 2.8 7.9 1.0
O B:ASN145 2.8 9.5 1.0
O B:ALA118 3.0 8.2 1.0
O B:HOH550 3.2 5.7 1.0
O B:HOH490 3.4 9.0 1.0
CB C:SER12 3.6 7.8 1.0
O B:HOH543 3.8 7.5 0.5
C B:ALA118 3.9 9.3 1.0
O B:HOH456 4.0 9.1 1.0
C B:ASN145 4.0 11.6 1.0
CA B:ALA118 4.2 9.7 1.0
O C:HOH519 4.2 27.6 1.0
O B:HOH485 4.6 7.5 1.0
O B:ALA117 4.7 9.1 1.0
CA B:ASN145 4.9 12.3 1.0
CB B:ALA118 4.9 9.2 1.0
CA B:SER146 5.0 10.8 1.0
N B:SER146 5.0 11.0 1.0

Sodium binding site 4 out of 6 in 6z1y

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Sodium binding site 4 out of 6 in the Crystal Structure of Type-I Ribosome-Inactivating Protein Trichobakin (Tbk)


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 Type-I Ribosome-Inactivating Protein Trichobakin (Tbk) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na301

b:10.9
occ:1.00
 O D:HOH418 2.3 26.0 1.0
O D:MET246 2.5 26.7 1.0
O C:ASN244 2.6 16.2 1.0
ND2 C:ASN245 2.7 14.6 1.0
O D:ARG243 2.7 18.4 1.0
O C:HOH517 2.8 33.0 1.0
O D:HOH445 3.3 21.7 1.0
C C:ASN244 3.7 15.5 1.0
CA C:ASN245 3.8 17.5 1.0
C D:MET246 3.8 25.9 1.0
CG C:ASN245 3.8 15.9 1.0
O C:HOH424 3.8 17.9 1.0
C D:ARG243 3.9 17.5 1.0
N C:ASN245 4.2 16.3 1.0
CB C:ASN245 4.3 17.3 1.0
CA D:ASN244 4.5 18.1 1.0
N D:MET246 4.6 18.2 1.0
N D:ASN244 4.6 17.4 1.0
OXT D:ALA247 4.6 31.9 1.0
C D:ALA247 4.7 35.2 1.0
N D:ALA247 4.7 26.4 1.0
CA D:MET246 4.8 22.9 1.0
CA D:ARG243 4.8 18.3 1.0
C D:ASN244 4.8 18.0 1.0
OD1 C:ASN245 4.8 20.7 1.0
CB D:ARG243 4.9 18.6 1.0
C C:ASN245 4.9 21.5 1.0
CA C:ASN244 4.9 15.0 1.0
CA D:ALA247 4.9 32.2 1.0
CG D:MET246 5.0 25.2 1.0

Sodium binding site 5 out of 6 in 6z1y

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Sodium binding site 5 out of 6 in the Crystal Structure of Type-I Ribosome-Inactivating Protein Trichobakin (Tbk)


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 Type-I Ribosome-Inactivating Protein Trichobakin (Tbk) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na302

b:4.6
occ:1.00
 O C:VAL214 2.6 11.6 1.0
O C:HOH529 2.7 15.3 1.0
OG C:SER191 2.8 9.2 1.0
O C:HOH532 2.9 32.4 1.0
O C:HOH470 2.9 14.8 1.0
O C:HOH546 3.0 25.8 1.0
O C:HOH539 3.2 14.4 1.0
C C:VAL214 3.9 10.4 1.0
O C:HOH538 3.9 31.9 1.0
CB C:SER191 3.9 9.0 1.0
N C:VAL214 4.3 11.3 1.0
CG1 C:VAL213 4.3 13.8 1.0
CA C:VAL214 4.5 11.8 1.0
O C:HOH554 4.6 14.3 1.0
CD2 C:LEU215 4.6 16.1 1.0
CA C:SER191 4.7 8.9 1.0
CB C:VAL214 4.8 12.0 1.0
N C:LEU215 4.9 10.6 1.0

Sodium binding site 6 out of 6 in 6z1y

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Sodium binding site 6 out of 6 in the Crystal Structure of Type-I Ribosome-Inactivating Protein Trichobakin (Tbk)


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 Type-I Ribosome-Inactivating Protein Trichobakin (Tbk) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na303

b:5.1
occ:1.00
 O D:ASN244 2.6 14.4 1.0
O C:ARG243 2.7 15.2 1.0
O C:MET246 2.7 17.7 1.0
ND2 D:ASN245 2.7 11.6 1.0
O C:HOH527 3.0 30.1 1.0
O D:HOH448 3.1 38.2 1.0
O C:HOH457 3.3 30.1 1.0
O C:HOH523 3.5 11.9 1.0
O D:HOH382 3.5 28.3 1.0
C D:ASN244 3.7 18.0 1.0
C C:ARG243 3.7 16.2 1.0
CA D:ASN245 3.8 17.5 1.0
CG D:ASN245 3.9 17.1 1.0
C C:MET246 3.9 22.4 1.0
O D:HOH329 4.0 8.4 1.0
N D:ASN245 4.2 17.4 1.0
CB D:ASN245 4.3 16.1 1.0
CA C:ASN244 4.4 15.0 1.0
N C:ASN244 4.5 15.3 1.0
N C:MET246 4.5 19.9 1.0
CB C:ARG243 4.6 26.0 1.0
CA C:MET246 4.6 23.2 1.0
CA C:ARG243 4.7 21.2 1.0
CB C:MET246 4.8 25.4 1.0
C C:ASN244 4.8 15.5 1.0
C D:ASN245 4.9 16.2 1.0
O C:ALA247 4.9 25.5 1.0
C C:ALA247 4.9 28.9 1.0
CA D:ASN244 4.9 18.1 1.0
OD1 D:ASN245 4.9 17.2 1.0
N C:ALA247 5.0 20.6 1.0

Reference:

V.V.Britikov, E.V.Britikova, E.V.Bocharov, T.B.T.Le, C.V.Phan, A.Y.Nikolaeva, K.M.Boyko, A.S.Arseniev, S.A.Usanov. Crystal Structure of Type-I Ribosome-Inactivating Protein Trichobakin (Tbk) To Be Published.
Page generated: Tue Dec 15 16:46:07 2020

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