Atomistry » Sodium » PDB 1qtk-1s3x » 1rtk
Atomistry »
  Sodium »
    PDB 1qtk-1s3x »
      1rtk »

Sodium in PDB 1rtk: Crystal Structure Analysis of the Bb Segment of Factor B Complexed with 4-Guanidinobenzoic Acid

Enzymatic activity of Crystal Structure Analysis of the Bb Segment of Factor B Complexed with 4-Guanidinobenzoic Acid

All present enzymatic activity of Crystal Structure Analysis of the Bb Segment of Factor B Complexed with 4-Guanidinobenzoic Acid:
3.4.21.47;

Protein crystallography data

The structure of Crystal Structure Analysis of the Bb Segment of Factor B Complexed with 4-Guanidinobenzoic Acid, PDB code: 1rtk was solved by K.Ponnuraj, Y.Xu, K.Macon, D.Moore, J.E.Volanakis, S.V.Narayana, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.81 / 2.30
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 98.355, 98.355, 125.657, 90.00, 90.00, 120.00
R / Rfree (%) 20.8 / 24.5

Other elements in 1rtk:

The structure of Crystal Structure Analysis of the Bb Segment of Factor B Complexed with 4-Guanidinobenzoic Acid also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Iodine (I) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure Analysis of the Bb Segment of Factor B Complexed with 4-Guanidinobenzoic Acid (pdb code 1rtk). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the Crystal Structure Analysis of the Bb Segment of Factor B Complexed with 4-Guanidinobenzoic Acid, PDB code: 1rtk:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in 1rtk

Go back to Sodium Binding Sites List in 1rtk
Sodium binding site 1 out of 7 in the Crystal Structure Analysis of the Bb Segment of Factor B Complexed with 4-Guanidinobenzoic Acid


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure Analysis of the Bb Segment of Factor B Complexed with 4-Guanidinobenzoic Acid within 5.0Å range:

Sodium binding site 2 out of 7 in 1rtk

Go back to Sodium Binding Sites List in 1rtk
Sodium binding site 2 out of 7 in the Crystal Structure Analysis of the Bb Segment of Factor B Complexed with 4-Guanidinobenzoic Acid


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure Analysis of the Bb Segment of Factor B Complexed with 4-Guanidinobenzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na743

b:4.8
occ:1.00
 CA A:TRP309 3.8 28.9 1.0
N A:TRP309 3.9 26.8 1.0
C A:ASP308 4.1 27.1 1.0
CD A:LYS312 4.1 38.2 1.0
O A:ASP308 4.2 26.2 1.0
CB A:TRP309 4.2 32.2 1.0
CB A:ASP308 4.3 28.1 1.0
CD1 A:TRP309 4.4 36.6 1.0
CG A:TRP309 4.8 36.4 1.0
CB A:LYS312 4.8 27.2 1.0
CA A:ASP308 4.9 27.9 1.0
O A:HOH809 4.9 32.6 1.0
NZ A:LYS312 4.9 45.1 1.0

Sodium binding site 3 out of 7 in 1rtk

Go back to Sodium Binding Sites List in 1rtk
Sodium binding site 3 out of 7 in the Crystal Structure Analysis of the Bb Segment of Factor B Complexed with 4-Guanidinobenzoic Acid


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure Analysis of the Bb Segment of Factor B Complexed with 4-Guanidinobenzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na744

b:14.5
occ:1.00
 N A:SER447 3.8 39.3 1.0
OE1 A:GLN565 3.9 35.2 1.0
CA A:SER447 4.0 40.1 1.0
CB A:GLU446 4.1 42.9 1.0
CB A:SER447 4.1 40.1 1.0
CD1 A:LEU450 4.3 33.6 1.0
C A:GLU446 4.4 40.4 1.0
CD A:GLN565 4.8 30.5 1.0
CA A:GLU446 4.8 40.8 1.0
CD2 A:LEU450 4.8 35.5 1.0
CG A:LEU450 4.8 36.5 1.0
NE2 A:GLN565 4.9 33.3 1.0

Sodium binding site 4 out of 7 in 1rtk

Go back to Sodium Binding Sites List in 1rtk
Sodium binding site 4 out of 7 in the Crystal Structure Analysis of the Bb Segment of Factor B Complexed with 4-Guanidinobenzoic Acid


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure Analysis of the Bb Segment of Factor B Complexed with 4-Guanidinobenzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na745

b:7.5
occ:1.00
 CD A:LYS594 3.2 45.1 1.0
NE2 A:GLN722 3.5 36.0 1.0
ND2 A:ASN719 3.7 22.5 1.0
CG A:LYS594 3.8 40.7 1.0
CB A:PHE721 4.1 24.5 1.0
CE A:LYS594 4.3 47.0 1.0
CD1 A:LEU598 4.4 28.9 1.0
NZ A:LYS594 4.5 49.2 1.0
CG A:ASN719 4.6 24.8 1.0
CG A:PHE721 4.6 25.1 1.0
OD1 A:ASN719 4.7 26.9 1.0
CD A:GLN722 4.7 35.2 1.0

Sodium binding site 5 out of 7 in 1rtk

Go back to Sodium Binding Sites List in 1rtk
Sodium binding site 5 out of 7 in the Crystal Structure Analysis of the Bb Segment of Factor B Complexed with 4-Guanidinobenzoic Acid


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure Analysis of the Bb Segment of Factor B Complexed with 4-Guanidinobenzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na746

b:16.9
occ:1.00
 O A:HOH940 3.3 35.2 1.0
NH1 A:ARG580 3.4 54.5 1.0
O A:HOH922 3.7 46.5 1.0
CA A:PRO586 4.0 40.1 1.0
CB A:PRO586 4.0 39.8 1.0
CB A:GLU576 4.1 35.7 1.0
CG A:ARG580 4.2 35.5 1.0
CG2 A:THR579 4.3 27.0 1.0
O A:GLU576 4.4 28.5 1.0
CG A:GLU576 4.5 44.8 1.0
OE2 A:GLU576 4.5 52.1 1.0
CB A:THR579 4.6 26.2 1.0
CA A:GLU576 4.6 32.0 1.0
CD A:GLU576 4.6 48.4 1.0
CZ A:ARG580 4.6 51.4 1.0
CD A:ARG580 4.7 41.0 1.0
N A:PRO586 4.8 39.3 1.0
C A:GLU576 4.9 30.3 1.0
O A:PRO586 4.9 42.3 1.0
C A:PRO586 5.0 40.4 1.0

Sodium binding site 6 out of 7 in 1rtk

Go back to Sodium Binding Sites List in 1rtk
Sodium binding site 6 out of 7 in the Crystal Structure Analysis of the Bb Segment of Factor B Complexed with 4-Guanidinobenzoic Acid


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure Analysis of the Bb Segment of Factor B Complexed with 4-Guanidinobenzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na747

b:38.8
occ:1.00
 CA A:GLY387 3.9 39.9 1.0
CB A:PRO393 3.9 41.1 1.0
C A:GLY387 4.0 40.9 1.0
CG A:PRO393 4.1 39.8 1.0
C A:ASP389 4.2 42.6 1.0
N A:ARG390 4.3 41.5 1.0
N A:LYS388 4.3 42.4 1.0
N A:ASP389 4.3 42.8 1.0
O A:GLY387 4.4 41.6 1.0
O A:ASP389 4.4 43.3 1.0
CA A:PRO393 4.4 40.9 1.0
CA A:ARG390 4.5 41.7 1.0
CA A:ASP389 4.7 41.9 1.0
C A:LYS388 4.7 43.1 1.0
N A:GLY387 5.0 37.9 1.0
CA A:LYS388 5.0 42.1 1.0

Sodium binding site 7 out of 7 in 1rtk

Go back to Sodium Binding Sites List in 1rtk
Sodium binding site 7 out of 7 in the Crystal Structure Analysis of the Bb Segment of Factor B Complexed with 4-Guanidinobenzoic Acid


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure Analysis of the Bb Segment of Factor B Complexed with 4-Guanidinobenzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na748

b:32.0
occ:1.00
 I A:IOD741 3.4 29.2 1.0
O A:HOH1010 4.6 25.9 1.0

Reference:

K.Ponnuraj, Y.Xu, K.Macon, D.Moore, J.E.Volanakis, S.V.Narayana. Structural Analysis of Engineered Bb Fragment of Complement Factor B: Insights Into the Activation Mechanism of the Alternative Pathway C3-Convertase. Mol.Cell V. 14 17 2004.
ISSN: ISSN 1097-2765
PubMed: 15068800
DOI: 10.1016/S1097-2765(04)00160-1
Page generated: Sun Oct 6 22:01:38 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