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Sodium in PDB 2j5w: Ceruloplasmin Revisited: Structural and Functional Roles of Various Metal Cation Binding Sites

Enzymatic activity of Ceruloplasmin Revisited: Structural and Functional Roles of Various Metal Cation Binding Sites

All present enzymatic activity of Ceruloplasmin Revisited: Structural and Functional Roles of Various Metal Cation Binding Sites:
1.16.3.1;

Protein crystallography data

The structure of Ceruloplasmin Revisited: Structural and Functional Roles of Various Metal Cation Binding Sites, PDB code: 2j5w was solved by I.Bento, C.Peixoto, V.N.Zaitsev, P.F.Lindley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 68.52 / 2.80
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 209.140, 209.139, 82.752, 90.00, 90.00, 120.00
R / Rfree (%) 17.5 / 22.6

Other elements in 2j5w:

The structure of Ceruloplasmin Revisited: Structural and Functional Roles of Various Metal Cation Binding Sites also contains other interesting chemical elements:

Copper (Cu) 7 atoms
Calcium (Ca) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Ceruloplasmin Revisited: Structural and Functional Roles of Various Metal Cation Binding Sites (pdb code 2j5w). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Ceruloplasmin Revisited: Structural and Functional Roles of Various Metal Cation Binding Sites, PDB code: 2j5w:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 2j5w

Go back to Sodium Binding Sites List in 2j5w
Sodium binding site 1 out of 3 in the Ceruloplasmin Revisited: Structural and Functional Roles of Various Metal Cation Binding Sites


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Ceruloplasmin Revisited: Structural and Functional Roles of Various Metal Cation Binding Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na3043

b:55.2
occ:1.00
 O A:SER237 2.4 54.2 1.0
OH A:TYR48 2.4 49.0 1.0
O A:GLY45 2.5 57.9 1.0
O A:TYR36 2.5 65.4 1.0
C A:GLY45 3.5 57.9 1.0
CZ A:TYR48 3.5 48.5 1.0
N A:GLY45 3.5 59.0 1.0
C A:SER237 3.5 53.9 1.0
C A:TYR36 3.6 65.6 1.0
CE1 A:TYR48 3.8 49.2 1.0
CA A:GLY45 3.8 58.5 1.0
SD A:MET240 3.9 50.3 1.0
OD1 A:ASN238 3.9 48.9 1.0
O A:HOH2064 3.9 44.5 1.0
CA A:ASN238 4.2 52.2 1.0
CE A:MET240 4.2 46.8 1.0
CA A:TYR36 4.2 65.6 1.0
N A:ASN238 4.3 52.9 1.0
CA A:SER237 4.6 54.6 1.0
CB A:SER237 4.6 54.7 1.0
N A:ARG46 4.7 57.2 1.0
CB A:ILE44 4.7 60.3 1.0
C A:ILE44 4.7 59.9 1.0
N A:LEU37 4.7 65.7 1.0
CG A:ASN238 4.7 51.7 1.0
CE2 A:TYR48 4.7 48.9 1.0
CB A:TYR36 4.9 65.1 1.0
N A:ILE44 4.9 61.3 1.0
OG A:SER237 5.0 55.6 1.0

Sodium binding site 2 out of 3 in 2j5w

Go back to Sodium Binding Sites List in 2j5w
Sodium binding site 2 out of 3 in the Ceruloplasmin Revisited: Structural and Functional Roles of Various Metal Cation Binding Sites


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Ceruloplasmin Revisited: Structural and Functional Roles of Various Metal Cation Binding Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na3044

b:56.0
occ:1.00
 OH A:TYR401 2.3 54.5 1.0
O A:SER598 2.3 51.6 1.0
O A:GLY398 2.4 54.7 1.0
O A:HOH2101 2.4 36.7 1.0
O A:PHE389 2.6 52.6 1.0
CZ A:TYR401 3.4 56.1 1.0
SD A:MET601 3.4 48.9 1.0
C A:SER598 3.5 51.8 1.0
C A:GLY398 3.5 54.7 1.0
CE1 A:TYR401 3.6 56.7 1.0
C A:PHE389 3.7 53.2 1.0
N A:GLY398 3.9 55.0 1.0
CE A:MET601 4.0 47.3 1.0
CA A:GLY398 4.1 55.0 1.0
OD1 A:ASN599 4.1 50.7 1.0
CA A:PHE389 4.1 53.0 1.0
CA A:ASN599 4.2 49.9 1.0
O A:HOH2146 4.2 46.0 1.0
N A:ASN599 4.2 50.7 1.0
O A:HOH2098 4.3 32.1 1.0
CA A:SER598 4.5 52.6 1.0
N A:GLY399 4.6 54.5 1.0
CB A:SER598 4.6 53.0 1.0
CE2 A:TYR401 4.6 56.0 1.0
CG A:MET601 4.6 46.2 1.0
CB A:PHE389 4.7 53.0 1.0
N A:PHE390 4.8 54.1 1.0
CA A:GLY399 4.9 54.7 1.0
OG A:SER598 4.9 53.6 1.0
CB A:ILE397 4.9 55.0 1.0
CD1 A:TYR401 5.0 56.7 1.0
C A:ILE397 5.0 55.1 1.0

Sodium binding site 3 out of 3 in 2j5w

Go back to Sodium Binding Sites List in 2j5w
Sodium binding site 3 out of 3 in the Ceruloplasmin Revisited: Structural and Functional Roles of Various Metal Cation Binding Sites


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Ceruloplasmin Revisited: Structural and Functional Roles of Various Metal Cation Binding Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na3045

b:43.8
occ:1.00
 O A:PHE748 2.3 44.7 1.0
O A:SER936 2.3 40.1 1.0
O A:HOH2217 2.4 38.7 1.0
OH A:TYR760 2.5 31.7 1.0
O A:GLY757 2.5 42.1 1.0
SD A:MET939 3.4 33.9 1.0
C A:PHE748 3.4 45.4 1.0
C A:SER936 3.5 40.8 1.0
C A:GLY757 3.6 42.6 1.0
CZ A:TYR760 3.6 30.9 1.0
CE A:MET939 3.8 31.2 1.0
CE1 A:TYR760 3.8 31.5 1.0
N A:GLY757 3.9 44.8 1.0
CA A:PHE748 4.0 45.1 1.0
OD1 A:ASN937 4.0 37.4 1.0
CA A:GLY757 4.0 43.8 1.0
O A:HOH2211 4.1 36.8 1.0
O A:HOH2297 4.2 29.7 1.0
CA A:ASN937 4.2 39.2 1.0
N A:ASN937 4.3 39.8 1.0
CA A:SER936 4.5 42.1 1.0
N A:LEU749 4.6 45.8 1.0
CB A:PHE748 4.6 44.4 1.0
N A:SER758 4.7 41.3 1.0
CB A:SER936 4.7 42.4 1.0
CE2 A:TYR760 4.8 29.8 1.0
CG A:MET939 4.9 34.9 1.0
CA A:LEU749 4.9 46.0 1.0
CG A:ASN937 4.9 39.7 1.0

Reference:

I.Bento, C.Peixoto, V.N.Zaitsev, P.F.Lindley. Ceruloplasmin Revisited: Structural and Functional Roles of Various Metal Cation-Binding Sites. Acta Crystallogr.,Sect.D V. 63 240 2007.
ISSN: ISSN 0907-4449
PubMed: 17242517
DOI: 10.1107/S090744490604947X
Page generated: Tue Dec 15 05:51:33 2020

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