Atomistry » Sodium » PDB 3bjp-3c7h » 3bpx
Atomistry »
  Sodium »
    PDB 3bjp-3c7h »
      3bpx »

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

Go back to Sodium Binding Sites List in 3bpx
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

Go back to Sodium Binding Sites List in 3bpx
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

Go back to Sodium Binding Sites List in 3bpx
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

Go back to Sodium Binding Sites List in 3bpx
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

Go back to Sodium Binding Sites List in 3bpx
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

Go back to Sodium Binding Sites List in 3bpx
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: Sun Aug 17 12:52:37 2025

Last articles

Mn in 9LJU
Mn in 9LJW
Mn in 9LJS
Mn in 9LJR
Mn in 9LJT
Mn in 9LJV
Mg in 9UA2
Mg in 9R96
Mg in 9VM1
Mg in 9P01
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy