Atomistry » Sodium » PDB 3epz-3f9l » 3f72
Atomistry »
  Sodium »
    PDB 3epz-3f9l »
      3f72 »

Sodium in PDB 3f72: Crystal Structure of the Staphylococcus Aureus PI258 Cadc Metal Binding Site 2 Mutant

Protein crystallography data

The structure of Crystal Structure of the Staphylococcus Aureus PI258 Cadc Metal Binding Site 2 Mutant, PDB code: 3f72 was solved by A.Kandegedara, S.Thiyagarajan, K.C.Kondapalli, T.L.Stemmler, B.P.Rosen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.30 / 2.31
Space group P 43
Cell size a, b, c (Å), α, β, γ (°) 89.471, 89.471, 148.536, 90.00, 90.00, 90.00
R / Rfree (%) 23.7 / 28.8

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the Staphylococcus Aureus PI258 Cadc Metal Binding Site 2 Mutant (pdb code 3f72). 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 the Staphylococcus Aureus PI258 Cadc Metal Binding Site 2 Mutant, PDB code: 3f72:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 3f72

Go back to Sodium Binding Sites List in 3f72
Sodium binding site 1 out of 5 in the Crystal Structure of the Staphylococcus Aureus PI258 Cadc Metal Binding Site 2 Mutant


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 the Staphylococcus Aureus PI258 Cadc Metal Binding Site 2 Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na123

b:41.2
occ:1.00
OD1 A:ASN64 2.5 33.1 1.0
CG A:ASN64 3.5 40.1 1.0
CA A:ASN64 3.7 40.1 1.0
O A:ASN64 4.0 40.0 1.0
CA A:GLY67 4.1 37.1 1.0
CB A:ASN64 4.2 39.5 1.0
O A:ALA63 4.3 41.3 1.0
C A:ASN64 4.4 39.7 1.0
N A:ASN64 4.6 40.2 1.0
ND2 A:ASN64 4.7 29.8 1.0
C A:GLY67 4.7 37.8 1.0
N A:GLY67 4.8 39.6 1.0
C A:ALA63 4.8 40.0 1.0
N A:VAL68 5.0 37.6 1.0

Sodium binding site 2 out of 5 in 3f72

Go back to Sodium Binding Sites List in 3f72
Sodium binding site 2 out of 5 in the Crystal Structure of the Staphylococcus Aureus PI258 Cadc Metal Binding Site 2 Mutant


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 the Staphylococcus Aureus PI258 Cadc Metal Binding Site 2 Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na124

b:58.2
occ:1.00
CE1 A:HIS75 3.6 67.2 1.0
NH1 A:ARG44 3.6 42.9 1.0
NH2 A:ARG44 3.9 35.0 1.0
NE2 A:HIS75 4.0 70.4 1.0
CZ A:ARG44 4.2 42.9 1.0
O A:HOH145 4.5 64.2 1.0
ND1 A:HIS75 4.9 65.6 1.0

Sodium binding site 3 out of 5 in 3f72

Go back to Sodium Binding Sites List in 3f72
Sodium binding site 3 out of 5 in the Crystal Structure of the Staphylococcus Aureus PI258 Cadc Metal Binding Site 2 Mutant


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 the Staphylococcus Aureus PI258 Cadc Metal Binding Site 2 Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na123

b:55.5
occ:1.00
O B:HOH138 2.3 53.6 1.0
N B:GLU102 3.3 38.8 1.0
N B:ALA103 3.5 35.8 1.0
CA B:GLY101 3.7 38.5 1.0
C B:GLY101 3.8 38.8 1.0
CB B:ALA103 3.9 34.0 1.0
CA B:GLU102 4.1 39.9 1.0
CB B:GLU102 4.2 42.6 1.0
C B:GLU102 4.3 36.8 1.0
CA B:ALA103 4.3 35.3 1.0
ND1 A:HIS114 4.5 61.0 1.0
O B:GLY101 4.9 37.8 1.0
O A:HOH141 5.0 51.2 1.0

Sodium binding site 4 out of 5 in 3f72

Go back to Sodium Binding Sites List in 3f72
Sodium binding site 4 out of 5 in the Crystal Structure of the Staphylococcus Aureus PI258 Cadc Metal Binding Site 2 Mutant


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 the Staphylococcus Aureus PI258 Cadc Metal Binding Site 2 Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na124

b:55.1
occ:1.00
ND1 B:HIS76 3.3 43.8 1.0
CD2 B:HIS75 3.4 34.4 0.5
OG1 B:THR79 3.6 38.5 1.0
NH2 B:ARG44 3.6 44.6 1.0
NE B:ARG44 3.8 51.7 1.0
NE2 B:HIS75 3.8 36.7 0.5
CE1 B:HIS76 3.9 44.5 1.0
CA B:HIS76 4.1 35.4 1.0
CZ B:ARG44 4.2 47.4 1.0
CG B:HIS76 4.3 37.9 1.0
O B:HIS75 4.3 33.1 1.0
CB B:THR79 4.4 37.1 1.0
CG B:HIS75 4.5 34.1 0.5
N B:HIS76 4.5 35.9 1.0
C B:HIS75 4.5 35.5 1.0
CB B:HIS76 4.6 35.5 1.0
CG2 B:THR79 4.7 33.6 1.0
CD B:ARG44 4.9 39.3 1.0
NE2 B:HIS76 4.9 42.1 1.0
CE1 B:HIS75 5.0 32.0 0.5

Sodium binding site 5 out of 5 in 3f72

Go back to Sodium Binding Sites List in 3f72
Sodium binding site 5 out of 5 in the Crystal Structure of the Staphylococcus Aureus PI258 Cadc Metal Binding Site 2 Mutant


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 the Staphylococcus Aureus PI258 Cadc Metal Binding Site 2 Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na123

b:70.0
occ:1.00
CD2 F:HIS76 3.4 71.5 1.0
NH2 F:ARG44 3.5 79.0 1.0
ND1 F:HIS75 3.6 77.7 1.0
NE2 F:HIS76 3.8 72.7 1.0
CE1 F:HIS75 4.0 75.8 1.0
NE F:ARG44 4.1 71.7 1.0
OG1 F:THR79 4.3 65.0 1.0
CZ F:ARG44 4.3 76.3 1.0
CG F:HIS76 4.4 68.6 1.0
CB F:THR79 4.6 66.6 1.0
CA F:HIS76 4.7 67.3 1.0
CG2 F:THR79 4.7 63.1 1.0
N F:HIS76 4.8 67.0 1.0
CG F:HIS75 4.8 74.5 1.0
CE1 F:HIS76 4.8 71.0 1.0
O F:HIS75 5.0 67.8 1.0
C F:HIS75 5.0 68.2 1.0

Reference:

A.Kandegedara, S.Thiyagarajan, K.C.Kondapalli, T.L.Stemmler, B.P.Rosen. Role of Bound Zn(II) in the Cadc Cd(II)/Pb(II)/Zn(II)-Responsive Repressor. J.Biol.Chem. V. 284 14958 2009.
ISSN: ISSN 0021-9258
PubMed: 19286656
DOI: 10.1074/JBC.M809179200
Page generated: Tue Dec 15 06:10:25 2020

Last articles

Zn in 7L0B
Zn in 7KZZ
Zn in 7KZL
Zn in 7L3O
Zn in 7L52
Zn in 7L6T
Zn in 7KZ7
Zn in 7L6R
Zn in 7KKM
Zn in 7KKQ
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy