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Sodium in PDB 1rrk: Crystal Structure Analysis of the Bb Segment of Factor B

Enzymatic activity of Crystal Structure Analysis of the Bb Segment of Factor B

All present enzymatic activity of Crystal Structure Analysis of the Bb Segment of Factor B:
3.4.21.47;

Protein crystallography data

The structure of Crystal Structure Analysis of the Bb Segment of Factor B, PDB code: 1rrk 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) 19.67 / 2.00
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 98.980, 98.980, 126.428, 90.00, 90.00, 120.00
R / Rfree (%) 22 / 24.5

Other elements in 1rrk:

The structure of Crystal Structure Analysis of the Bb Segment of Factor B also contains other interesting chemical elements:

Cobalt (Co) 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 (pdb code 1rrk). 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, PDB code: 1rrk:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in 1rrk

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Sodium binding site 1 out of 7 in the Crystal Structure Analysis of the Bb Segment of Factor B


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 within 5.0Å range:

Sodium binding site 2 out of 7 in 1rrk

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Sodium binding site 2 out of 7 in the Crystal Structure Analysis of the Bb Segment of Factor B


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na743

b:18.8
occ:1.00
 CA A:TRP309 3.8 32.5 1.0
N A:TRP309 3.9 31.7 1.0
C A:ASP308 4.1 30.4 1.0
CB A:TRP309 4.1 37.6 1.0
O A:ASP308 4.1 31.3 1.0
CD A:LYS312 4.2 41.9 1.0
CB A:ASP308 4.3 32.3 1.0
CD1 A:TRP309 4.4 46.2 1.0
CG A:TRP309 4.7 44.2 1.0
CB A:LYS312 4.8 31.4 1.0
CA A:ASP308 4.9 32.2 1.0

Sodium binding site 3 out of 7 in 1rrk

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Sodium binding site 3 out of 7 in the Crystal Structure Analysis of the Bb Segment of Factor B


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na744

b:21.6
occ:1.00
 O A:HOH959 3.5 32.0 1.0
N A:SER447 3.9 40.2 1.0
CB A:GLU446 4.0 45.0 1.0
OE1 A:GLN565 4.1 44.1 1.0
CA A:SER447 4.1 39.3 1.0
CB A:SER447 4.2 37.8 1.0
CD1 A:LEU450 4.3 42.6 1.0
O A:HOH991 4.4 33.7 1.0
C A:GLU446 4.4 41.4 1.0
NE2 A:GLN565 4.5 41.2 1.0
CD A:GLN565 4.7 40.6 1.0
CA A:GLU446 4.8 42.2 1.0
CG A:LEU450 4.8 42.3 1.0
O A:GLU446 5.0 39.6 1.0

Sodium binding site 4 out of 7 in 1rrk

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Sodium binding site 4 out of 7 in the Crystal Structure Analysis of the Bb Segment of Factor B


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na745

b:25.8
occ:1.00
 CD A:LYS594 3.1 47.5 1.0
NE2 A:GLN722 3.6 43.3 1.0
ND2 A:ASN719 3.6 28.4 1.0
CG A:LYS594 3.7 43.6 1.0
CB A:PHE721 4.1 28.7 1.0
CE A:LYS594 4.2 49.6 1.0
CD1 A:LEU598 4.4 34.5 1.0
NZ A:LYS594 4.4 52.5 1.0
CG A:ASN719 4.5 28.5 1.0
CG A:PHE721 4.6 29.2 1.0
OD1 A:ASN719 4.6 30.3 1.0
CD A:GLN722 4.8 41.1 1.0
CD1 A:PHE721 5.0 29.8 1.0

Sodium binding site 5 out of 7 in 1rrk

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Sodium binding site 5 out of 7 in the Crystal Structure Analysis of the Bb Segment of Factor B


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na746

b:27.8
occ:1.00
 NH2 A:ARG580 3.2 57.8 1.0
CZ A:ARG580 3.5 56.5 1.0
O A:HOH951 3.6 39.3 1.0
NE A:ARG580 3.6 53.9 1.0
CA A:PRO586 3.8 44.2 1.0
CB A:PRO586 4.0 44.4 1.0
CB A:GLU576 4.1 41.5 1.0
CG2 A:THR579 4.3 34.1 1.0
NH1 A:ARG580 4.3 59.0 1.0
O A:GLU576 4.4 32.1 1.0
OE2 A:GLU576 4.4 60.4 1.0
CG A:GLU576 4.4 51.3 1.0
CG A:ARG580 4.5 42.9 1.0
CB A:THR579 4.5 33.4 1.0
CA A:GLU576 4.5 36.8 1.0
CD A:GLU576 4.6 56.2 1.0
N A:PRO586 4.7 43.1 1.0
O A:HOH930 4.7 37.5 1.0
CD A:ARG580 4.7 46.9 1.0
O A:PRO586 4.7 44.4 1.0
C A:PRO586 4.8 44.3 1.0
C A:GLU576 4.9 35.4 1.0

Sodium binding site 6 out of 7 in 1rrk

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Sodium binding site 6 out of 7 in the Crystal Structure Analysis of the Bb Segment of Factor B


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na747

b:38.1
occ:1.00
 CB A:ARG390 3.9 34.4 1.0
CA A:GLY387 3.9 38.9 1.0
C A:ASP389 4.0 36.9 1.0
O A:ASP389 4.0 38.1 1.0
C A:GLY387 4.0 39.5 1.0
N A:ARG390 4.0 36.7 1.0
CG A:PRO393 4.0 41.5 1.0
CA A:ARG390 4.0 36.5 1.0
CB A:PRO393 4.1 41.9 1.0
CA A:PRO393 4.2 41.1 1.0
O A:GLY387 4.3 38.4 1.0
N A:LYS388 4.3 35.8 1.0
N A:ASP389 4.4 38.7 1.0
CA A:ASP389 4.7 37.2 1.0
C A:LYS388 4.7 38.3 1.0
N A:GLY387 4.9 38.6 1.0
N A:PRO393 4.9 37.8 1.0

Sodium binding site 7 out of 7 in 1rrk

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Sodium binding site 7 out of 7 in the Crystal Structure Analysis of the Bb Segment of Factor B


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na748

b:41.4
occ:1.00
 I A:IOD741 3.3 34.9 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 22:01:03 2024

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