Atomistry » Sodium » PDB 6ytt-6z6u » 6z1y
Atomistry »
  Sodium »
    PDB 6ytt-6z6u »
      6z1y »

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

Go back to Sodium Binding Sites List in 6z1y
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

Go back to Sodium Binding Sites List in 6z1y
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

Go back to Sodium Binding Sites List in 6z1y
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

Go back to Sodium Binding Sites List in 6z1y
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

Go back to Sodium Binding Sites List in 6z1y
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

Go back to Sodium Binding Sites List in 6z1y
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 Oct 8 15:18:10 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy