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Sodium in PDB 3bpx: Crystal Structure of Marr

Protein crystallography data

The structure of Crystal Structure of Marr, PDB code: 3bpx was solved by V.Saridakis, D.Shahinas, X.Xu, D.Christendat, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.29 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 40.109, 51.527, 139.243, 90.00, 90.00, 90.00
R / Rfree (%) 22.2 / 28.4

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Marr (pdb code 3bpx). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Crystal Structure of Marr, PDB code: 3bpx:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 3bpx

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Sodium binding site 1 out of 6 in the Crystal Structure of Marr


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Marr within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na146

b:25.8
occ:1.00
 OG1 A:THR32 2.7 20.7 1.0
NE2 A:GLN35 3.4 21.9 1.0
CG A:GLN35 3.5 21.4 1.0
CB A:THR32 3.6 21.4 1.0
CG2 A:THR32 3.7 21.2 1.0
NH1 A:ARG70 3.9 50.8 1.0
CD A:GLN35 3.9 22.6 1.0
CD A:ARG70 4.0 41.2 1.0
CG2 A:THR67 4.3 22.2 1.0
OG1 A:THR67 4.3 22.6 1.0
CZ A:ARG70 4.3 48.1 1.0
NE A:ARG70 4.3 45.7 1.0
CB A:ALA34 4.5 19.6 1.0
N A:GLN35 4.5 19.7 1.0
CB A:GLN35 4.5 20.7 1.0
CB A:THR67 4.7 20.5 1.0
CA A:THR67 4.7 21.2 1.0
CA A:THR32 5.0 20.5 1.0
CA A:GLN35 5.0 20.4 1.0

Sodium binding site 2 out of 6 in 3bpx

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Sodium binding site 2 out of 6 in the Crystal Structure of Marr


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Marr within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na147

b:25.1
occ:1.00
 O A:HOH264 2.9 20.8 1.0
O A:ILE42 2.9 17.2 1.0
N A:VAL93 3.0 17.0 1.0
CB A:PRO46 3.2 18.7 1.0
CA A:PRO46 3.3 18.2 1.0
CG2 A:VAL93 3.5 14.9 1.0
C A:ILE42 3.7 19.2 1.0
CB A:VAL93 3.7 19.1 1.0
N A:PRO46 3.8 19.4 1.0
CA A:GLU92 3.8 17.9 1.0
CG2 A:ILE42 3.8 21.7 1.0
C A:GLU92 3.9 18.0 1.0
CA A:HIS43 3.9 19.8 1.0
CA A:VAL93 3.9 18.3 1.0
CD A:PRO46 4.0 18.9 1.0
CG A:GLU92 4.1 22.7 1.0
N A:HIS43 4.1 19.0 1.0
CG A:PRO46 4.1 18.8 1.0
O A:HIS43 4.2 22.4 1.0
C A:HIS43 4.4 22.3 1.0
O A:VAL93 4.4 21.6 1.0
CB A:GLU92 4.4 20.3 1.0
C A:GLU45 4.6 20.2 1.0
C A:VAL93 4.7 20.3 1.0
C A:PRO46 4.7 18.8 1.0
OE2 A:GLU98 4.8 20.5 1.0
CA A:ILE42 4.8 19.2 1.0
CB A:ILE42 4.8 16.1 1.0
O A:LEU91 4.8 21.3 1.0
N A:GLU92 4.9 18.0 1.0
O A:GLU45 4.9 19.0 1.0

Sodium binding site 3 out of 6 in 3bpx

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Sodium binding site 3 out of 6 in the Crystal Structure of Marr


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Marr within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na148

b:26.1
occ:1.00
 O A:HOH326 2.5 32.7 1.0
N A:ARG95 2.9 21.2 1.0
CB A:THR94 3.4 19.0 1.0
CA A:THR94 3.5 17.7 1.0
O A:HOH268 3.5 22.3 1.0
C A:THR94 3.6 21.4 1.0
CB A:ARG95 3.7 23.0 1.0
CA A:ARG95 3.9 21.7 1.0
O A:HOH372 4.0 57.5 1.0
CG2 A:THR94 4.1 12.9 1.0
OE1 A:GLU78 4.5 40.2 1.0
OG1 A:THR94 4.6 19.0 1.0
OE1 A:GLU92 4.7 28.7 1.0
NH1 A:ARG95 4.8 39.8 1.0
O A:THR94 4.8 18.8 1.0
N A:THR94 4.9 19.7 1.0
N A:ARG96 5.0 19.5 0.5
N A:ARG96 5.0 19.2 0.5

Sodium binding site 4 out of 6 in 3bpx

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Sodium binding site 4 out of 6 in the Crystal Structure of Marr


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Marr within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na149

b:25.0
occ:1.00
 O A:HOH306 2.7 46.5 1.0
OD1 A:ASP51 2.7 26.0 1.0
N A:TYR89 2.8 22.0 1.0
N A:ASP51 3.2 21.8 1.0
CA A:ARG88 3.2 22.6 1.0
C A:ARG88 3.5 23.6 1.0
CB A:ARG88 3.5 22.9 1.0
CG A:ASP51 3.6 24.7 1.0
N A:GLN50 3.7 21.1 1.0
CB A:GLN50 3.7 20.7 1.0
CB A:ASP51 3.7 24.1 1.0
O A:TYR89 3.8 21.0 1.0
CA A:TYR89 3.9 22.6 1.0
CA A:GLN50 4.0 21.9 1.0
CG A:ARG88 4.0 22.7 1.0
CA A:ASP51 4.0 23.2 1.0
C A:GLN50 4.0 22.0 1.0
CB A:TYR89 4.2 26.9 1.0
CB A:LYS49 4.3 24.3 1.0
C A:TYR89 4.3 21.8 1.0
O A:ARG87 4.4 26.1 1.0
O A:HOH368 4.4 58.0 1.0
C A:LYS49 4.5 21.2 1.0
CG A:GLN50 4.5 21.8 1.0
CG A:LYS49 4.5 29.1 1.0
NE A:ARG88 4.5 25.2 1.0
N A:ARG88 4.5 22.8 1.0
O A:ARG88 4.7 23.2 1.0
OD2 A:ASP51 4.8 27.9 1.0
CA A:LYS49 4.8 22.4 1.0
CD2 A:TYR89 4.8 32.9 1.0
CD A:ARG88 4.9 26.8 1.0
O A:HOH376 4.9 19.6 1.0
C A:ARG87 4.9 24.4 1.0
CG A:TYR89 5.0 27.0 1.0

Sodium binding site 5 out of 6 in 3bpx

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Sodium binding site 5 out of 6 in the Crystal Structure of Marr


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of Marr within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na146

b:28.9
occ:1.00
 OE2 A:GLU112 2.8 31.0 1.0
OE1 A:GLU108 2.8 24.6 1.0
N B:LYS8 2.8 22.8 1.0
N B:LEU7 3.2 28.1 1.0
CB B:LYS8 3.4 22.0 1.0
CZ3 A:TRP111 3.5 23.6 1.0
CD A:GLU112 3.5 31.2 1.0
CE3 A:TRP111 3.5 25.6 1.0
CG A:GLU112 3.6 31.5 1.0
CB B:LEU7 3.6 27.4 1.0
CB B:PRO6 3.6 33.9 1.0
CA B:LEU7 3.7 26.8 1.0
CA B:LYS8 3.7 20.9 1.0
C B:LEU7 3.7 25.1 1.0
C B:PRO6 3.8 29.3 1.0
CD A:GLU108 3.9 25.8 1.0
CA B:PRO6 4.1 31.8 1.0
CB A:GLU108 4.2 22.9 1.0
O A:GLU108 4.3 23.7 1.0
CG A:GLU108 4.5 25.0 1.0
CD2 A:HIS18 4.5 19.8 1.0
NE2 A:HIS18 4.6 17.1 1.0
O B:PRO6 4.6 25.9 1.0
CA A:GLU108 4.7 23.6 1.0
OE1 A:GLU112 4.7 31.5 1.0
CH2 A:TRP111 4.8 24.0 1.0
CD2 A:TRP111 4.8 25.7 1.0
CG B:LEU7 4.8 30.1 1.0
OE2 A:GLU108 4.8 26.7 1.0
CG B:LYS8 4.8 19.0 1.0
C A:GLU108 4.8 25.2 1.0
O B:LEU7 4.9 25.0 1.0
C B:LYS8 4.9 18.4 1.0

Sodium binding site 6 out of 6 in 3bpx

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Sodium binding site 6 out of 6 in the Crystal Structure of Marr


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of Marr within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na147

b:28.5
occ:1.00
 O B:HOH365 2.7 38.1 1.0
O B:HOH312 2.7 43.5 1.0
OG1 B:THR32 2.8 20.7 1.0
NE2 B:GLN35 3.3 20.0 1.0
CG2 B:THR32 3.7 23.0 1.0
CB B:THR32 3.8 22.2 1.0
CG B:GLN35 3.8 20.2 1.0
CD B:GLN35 4.0 18.6 1.0
CG B:ARG70 4.2 27.0 1.0
O B:HOH283 4.3 35.4 1.0
CB B:ALA34 4.4 20.9 1.0
OG1 B:THR67 4.5 17.9 1.0
N B:GLN35 4.7 17.1 1.0
CG2 B:THR67 4.7 19.2 1.0
CA B:THR67 4.7 18.3 1.0
CB B:ARG70 4.8 21.4 1.0
CB B:GLN35 4.9 15.9 1.0
CB B:THR67 4.9 20.1 1.0

Reference:

V.Saridakis, D.Shahinas, X.Xu, D.Christendat. Structural Insight on the Mechanism of Regulation of the Marr Family of Proteins: High-Resolution Crystal Structure of A Transcriptional Repressor From Methanobacterium Thermoautotrophicum. J.Mol.Biol. V. 377 655 2008.
ISSN: ISSN 0022-2836
PubMed: 18272181
DOI: 10.1016/J.JMB.2008.01.001
Page generated: Mon Oct 7 06:06:06 2024

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