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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

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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 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

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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 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

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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 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

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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 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

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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 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

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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 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

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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 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: Tue Dec 15 05:35:13 2020

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