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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

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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

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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

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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

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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

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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

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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

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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: Sun Oct 6 22:01:32 2024

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