Atomistry » Sodium » PDB 1qtk-1s3x » 1rs0
Atomistry »
  Sodium »
    PDB 1qtk-1s3x »
      1rs0 »

Sodium in PDB 1rs0: Crystal Structure Analysis of the Bb Segment of Factor B Complexed with Di-Isopropyl-Phosphate (Dip)

Enzymatic activity of Crystal Structure Analysis of the Bb Segment of Factor B Complexed with Di-Isopropyl-Phosphate (Dip)

All present enzymatic activity of Crystal Structure Analysis of the Bb Segment of Factor B Complexed with Di-Isopropyl-Phosphate (Dip):
3.4.21.47;

Protein crystallography data

The structure of Crystal Structure Analysis of the Bb Segment of Factor B Complexed with Di-Isopropyl-Phosphate (Dip), PDB code: 1rs0 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) 19.82 / 2.60
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 98.449, 98.449, 125.678, 90.00, 90.00, 120.00
R / Rfree (%) 21.2 / 25.1

Other elements in 1rs0:

The structure of Crystal Structure Analysis of the Bb Segment of Factor B Complexed with Di-Isopropyl-Phosphate (Dip) 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 Di-Isopropyl-Phosphate (Dip) (pdb code 1rs0). 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 Di-Isopropyl-Phosphate (Dip), PDB code: 1rs0:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in 1rs0

Go back to Sodium Binding Sites List in 1rs0
Sodium binding site 1 out of 7 in the Crystal Structure Analysis of the Bb Segment of Factor B Complexed with Di-Isopropyl-Phosphate (Dip)


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 Di-Isopropyl-Phosphate (Dip) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na742

b:16.1
occ:1.00
 O A:HOH933 3.6 36.9 1.0
O A:HOH841 4.0 25.9 1.0
O A:HOH927 4.3 40.1 1.0

Sodium binding site 2 out of 7 in 1rs0

Go back to Sodium Binding Sites List in 1rs0
Sodium binding site 2 out of 7 in the Crystal Structure Analysis of the Bb Segment of Factor B Complexed with Di-Isopropyl-Phosphate (Dip)


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 Di-Isopropyl-Phosphate (Dip) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na743

b:16.4
occ:1.00
 CA A:TRP309 3.8 33.1 1.0
N A:TRP309 3.9 30.3 1.0
C A:ASP308 4.1 29.1 1.0
CB A:TRP309 4.2 34.1 1.0
O A:ASP308 4.3 27.9 1.0
CD1 A:TRP309 4.3 37.1 1.0
CD A:LYS312 4.3 41.9 1.0
CB A:ASP308 4.4 32.2 1.0
CG A:TRP309 4.7 37.5 1.0
CB A:LYS312 4.9 33.0 1.0
CA A:ASP308 5.0 31.4 1.0

Sodium binding site 3 out of 7 in 1rs0

Go back to Sodium Binding Sites List in 1rs0
Sodium binding site 3 out of 7 in the Crystal Structure Analysis of the Bb Segment of Factor B Complexed with Di-Isopropyl-Phosphate (Dip)


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 Di-Isopropyl-Phosphate (Dip) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na744

b:19.4
occ:1.00
 N A:SER447 3.7 40.1 1.0
CB A:GLU446 4.0 42.0 1.0
CA A:SER447 4.0 40.7 1.0
CB A:SER447 4.1 40.5 1.0
CD1 A:LEU450 4.1 38.2 1.0
OE1 A:GLN565 4.2 41.1 1.0
O A:HOH941 4.4 41.4 1.0
C A:GLU446 4.4 40.4 1.0
NE2 A:GLN565 4.7 43.7 1.0
CA A:GLU446 4.8 40.2 1.0
CD A:GLN565 4.9 40.4 1.0
CG A:LEU450 4.9 39.8 1.0

Sodium binding site 4 out of 7 in 1rs0

Go back to Sodium Binding Sites List in 1rs0
Sodium binding site 4 out of 7 in the Crystal Structure Analysis of the Bb Segment of Factor B Complexed with Di-Isopropyl-Phosphate (Dip)


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 Di-Isopropyl-Phosphate (Dip) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na745

b:19.3
occ:1.00
 CD A:LYS594 3.1 46.9 1.0
NE2 A:GLN722 3.5 39.6 1.0
ND2 A:ASN719 3.8 37.4 1.0
CG A:LYS594 3.9 43.4 1.0
CB A:PHE721 4.1 31.8 1.0
CE A:LYS594 4.3 48.8 1.0
NZ A:LYS594 4.3 48.9 1.0
OD1 A:ASN719 4.4 34.6 1.0
CG A:ASN719 4.5 34.4 1.0
CG A:PHE721 4.5 31.8 1.0
CD1 A:LEU598 4.7 33.2 1.0
CD A:GLN722 4.7 38.8 1.0
CD1 A:PHE721 4.9 31.8 1.0

Sodium binding site 5 out of 7 in 1rs0

Go back to Sodium Binding Sites List in 1rs0
Sodium binding site 5 out of 7 in the Crystal Structure Analysis of the Bb Segment of Factor B Complexed with Di-Isopropyl-Phosphate (Dip)


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 Di-Isopropyl-Phosphate (Dip) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na746

b:20.8
occ:1.00
 NH1 A:ARG580 3.3 53.2 1.0
CA A:PRO586 3.9 38.0 1.0
CB A:PRO586 4.0 38.1 1.0
CB A:GLU576 4.1 41.5 1.0
OE2 A:GLU576 4.1 55.7 1.0
CG2 A:THR579 4.2 35.3 1.0
CG A:GLU576 4.2 48.4 1.0
CG A:ARG580 4.2 36.9 1.0
O A:GLU576 4.3 37.6 1.0
CD A:GLU576 4.4 51.9 1.0
CB A:THR579 4.4 35.3 1.0
CA A:GLU576 4.5 38.5 1.0
CZ A:ARG580 4.6 51.2 1.0
CD A:ARG580 4.7 40.2 1.0
N A:PRO586 4.8 39.6 1.0
C A:GLU576 4.9 37.9 1.0
C A:PRO586 4.9 40.2 1.0
O A:PRO586 4.9 41.9 1.0

Sodium binding site 6 out of 7 in 1rs0

Go back to Sodium Binding Sites List in 1rs0
Sodium binding site 6 out of 7 in the Crystal Structure Analysis of the Bb Segment of Factor B Complexed with Di-Isopropyl-Phosphate (Dip)


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 Di-Isopropyl-Phosphate (Dip) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na747

b:42.6
occ:1.00
 C A:GLY387 3.8 45.6 1.0
O A:GLY387 3.8 46.3 1.0
CA A:GLY387 4.0 43.6 1.0
CA A:ARG390 4.0 42.2 1.0
O A:LYS388 4.1 49.0 1.0
CB A:ARG390 4.2 42.0 1.0
N A:ARG390 4.2 43.6 1.0
O A:ASP389 4.3 46.2 1.0
C A:ASP389 4.4 45.7 1.0
CG A:PRO393 4.4 45.2 1.0
N A:LYS388 4.4 46.6 1.0
C A:LYS388 4.5 47.5 1.0
CB A:PRO393 4.6 44.5 1.0
CA A:PRO393 4.8 43.6 1.0
CA A:LYS388 5.0 46.7 1.0

Sodium binding site 7 out of 7 in 1rs0

Go back to Sodium Binding Sites List in 1rs0
Sodium binding site 7 out of 7 in the Crystal Structure Analysis of the Bb Segment of Factor B Complexed with Di-Isopropyl-Phosphate (Dip)


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 Di-Isopropyl-Phosphate (Dip) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na748

b:41.0
occ:1.00
 I A:IOD741 3.4 41.8 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: Tue Dec 15 05:35:13 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy