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Sodium in PDB 1m5q: Crystal Structure of A Novel Sm-Like Archaeal Protein From Pyrobaculum Aerophilum

Protein crystallography data

The structure of Crystal Structure of A Novel Sm-Like Archaeal Protein From Pyrobaculum Aerophilum, PDB code: 1m5q was solved by C.Mura, M.Phillips, A.Kozhukhovsky, D.Eisenberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.97 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 83.322, 172.427, 148.108, 90.00, 90.00, 90.00
R / Rfree (%) 19.1 / 23.6

Other elements in 1m5q:

The structure of Crystal Structure of A Novel Sm-Like Archaeal Protein From Pyrobaculum Aerophilum also contains other interesting chemical elements:

Cadmium (Cd) 28 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of A Novel Sm-Like Archaeal Protein From Pyrobaculum Aerophilum (pdb code 1m5q). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Crystal Structure of A Novel Sm-Like Archaeal Protein From Pyrobaculum Aerophilum, PDB code: 1m5q:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 1m5q

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Sodium binding site 1 out of 5 in the Crystal Structure of A Novel Sm-Like Archaeal Protein From Pyrobaculum Aerophilum


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 A Novel Sm-Like Archaeal Protein From Pyrobaculum Aerophilum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na3004

b:65.3
occ:1.23
CG2 A:VAL27 3.7 20.4 1.0
OE1 G:GLU32 3.8 30.1 1.0
OE1 A:GLN25 3.9 31.4 1.0
OE1 G:GLU58 4.0 41.9 1.0
CG2 A:VAL33 4.1 25.5 1.0
OH G:TYR34 4.3 27.9 1.0
CD G:GLU32 4.6 26.4 1.0
CD A:GLN25 4.6 32.9 1.0
CG1 A:VAL33 4.7 27.4 1.0
ND2 G:ASN54 4.7 27.8 1.0
CG1 A:VAL27 4.8 20.9 1.0
OE2 G:GLU32 4.9 26.7 1.0
NE2 A:HIS72 4.9 24.6 1.0
CD G:GLU58 4.9 39.6 1.0
CB A:VAL27 4.9 21.4 1.0
OE2 G:GLU58 5.0 40.4 1.0

Sodium binding site 2 out of 5 in 1m5q

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Sodium binding site 2 out of 5 in the Crystal Structure of A Novel Sm-Like Archaeal Protein From Pyrobaculum Aerophilum


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 A Novel Sm-Like Archaeal Protein From Pyrobaculum Aerophilum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na3001

b:76.2
occ:1.99
NZ C:LYS55 3.6 46.8 1.0
OE2 B:GLU58 3.6 42.9 1.0
OE1 C:GLN25 4.3 31.8 1.0
CG2 C:VAL33 4.3 27.8 1.0
OE1 B:GLU32 4.3 29.4 1.0
CE C:LYS55 4.5 47.5 1.0
CG2 C:VAL27 4.6 24.2 1.0
CD B:GLU58 4.6 43.4 1.0
OH B:TYR34 4.8 27.7 1.0
CG1 C:VAL33 4.8 26.5 1.0
ND2 B:ASN54 4.9 26.4 1.0
OE1 B:GLU58 4.9 44.2 1.0

Sodium binding site 3 out of 5 in 1m5q

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Sodium binding site 3 out of 5 in the Crystal Structure of A Novel Sm-Like Archaeal Protein From Pyrobaculum Aerophilum


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 A Novel Sm-Like Archaeal Protein From Pyrobaculum Aerophilum within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Na3005

b:83.0
occ:1.95
O Q:HOH2076 2.5 46.8 1.0
OE1 Q:GLU58 3.8 49.0 1.0
CG2 R:VAL33 4.1 27.5 1.0
OE1 R:GLN25 4.3 36.7 1.0
OE2 Q:GLU58 4.4 52.5 1.0
CG2 R:VAL27 4.5 28.0 1.0
CD Q:GLU58 4.6 48.7 1.0
CG1 R:VAL33 4.6 26.9 1.0
OE1 Q:GLU32 4.6 37.6 1.0
CD R:GLN25 4.9 36.3 1.0
CB R:VAL33 4.9 29.1 1.0
ND2 Q:ASN54 5.0 36.1 1.0
CE R:LYS55 5.0 47.2 1.0

Sodium binding site 4 out of 5 in 1m5q

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Sodium binding site 4 out of 5 in the Crystal Structure of A Novel Sm-Like Archaeal Protein From Pyrobaculum Aerophilum


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 A Novel Sm-Like Archaeal Protein From Pyrobaculum Aerophilum within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Na3002

b:59.6
occ:1.61
O R:HOH4056 2.4 46.4 1.0
OE1 R:GLU58 3.8 46.9 1.0
NE2 S:GLN25 4.1 34.8 1.0
CG2 S:VAL33 4.2 30.5 1.0
NZ S:LYS55 4.2 42.9 1.0
OE2 R:GLU58 4.2 51.1 1.0
CD R:GLU58 4.4 47.3 1.0
CG1 S:VAL33 4.6 31.2 1.0
CD S:GLN25 4.7 34.6 1.0
OE1 R:GLU32 4.7 37.5 1.0
OE1 S:GLN25 4.8 36.2 1.0
CG2 S:VAL27 4.8 23.7 1.0
CB S:VAL33 5.0 30.7 1.0

Sodium binding site 5 out of 5 in 1m5q

Go back to Sodium Binding Sites List in 1m5q
Sodium binding site 5 out of 5 in the Crystal Structure of A Novel Sm-Like Archaeal Protein From Pyrobaculum Aerophilum


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 A Novel Sm-Like Archaeal Protein From Pyrobaculum Aerophilum within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Na3003

b:67.7
occ:1.67
O V:HOH5062 2.3 32.6 1.0
O V:HOH5089 2.5 37.1 1.0
OE2 V:GLU58 3.8 36.6 1.0
OE1 V:GLU32 3.8 23.2 1.0
O W:HOH5064 4.1 40.0 1.0
OE1 W:GLN25 4.3 26.7 1.0
CG2 W:VAL27 4.3 14.4 1.0
OH V:TYR34 4.4 19.7 1.0
CG2 W:VAL33 4.4 19.1 1.0
O V:HOH5053 4.5 29.1 1.0
CD V:GLU32 4.5 24.2 1.0
ND2 V:ASN54 4.7 21.3 1.0
OE2 V:GLU32 4.7 24.8 1.0
CD V:GLU58 4.8 38.1 1.0
NZ W:LYS55 4.9 40.8 1.0
CD W:GLN25 4.9 24.8 1.0
OE1 V:GLU58 5.0 41.8 1.0

Reference:

C.Mura, M.Phillips, A.Kozhukhovsky, D.Eisenberg. Structure and Assembly of An Augmented Sm-Like Archaeal Protein 14-Mer Proc.Natl.Acad.Sci.Usa V. 100 4539 2003.
ISSN: ISSN 0027-8424
PubMed: 12668760
DOI: 10.1073/PNAS.0538042100
Page generated: Tue Dec 15 05:29:46 2020

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